key: cord- - hrx w r authors: destache, christopher j. title: optimizing economic outcomes in acute exacerbations of chronic bronchitis date: - - journal: pharmacotherapy doi: . /phco. . . s. sha: doc_id: cord_uid: hrx w r the treatment of community‐acquired respiratory tract infections, such as acute exacerbations of chronic bronchitis (aecb), constitutes a huge socioeconomic burden. in most cases, an antimicrobial agent is advocated to lessen morbidity and prevent serious clinical sequelae. use of antimicrobial agents for aecb, however, is controversial, as it is difficult to distinguish between bacterial and nonbacterial aecb, and only marginal benefits have been reported. antimicrobial agents, however, have reduced relapse rates, prolonged the time between exacerbations, shortened the duration of symptoms, and reduced the need for hospitalization. microbiologic resistance and individual patient characteristics play important roles in determining the most appropriate antimicrobial agent for patients with aecb. more research on the effect of resistant bacteria on antimicrobial response rates will enable physicians to prescribe economically rational antimicrobial therapy for this common infection. the treatment of community-acquired respiratory tract infections (rtis), such as acute exacerbations of chronic bronchitis (aecb), constitutes a huge socioeconomic burden. in most instances, use of an appropriate antibiotic is advocated to lessen morbidity and prevent serious clinical sequelae. use of antibiotics for aecb is controversial, however, due to the difficulty of distinguishing between bacterial and nonbacterial aecb and the marginal benefits of antibiotics reported in early studies. cost is another factor. however, it is necessary to look beyond the initial antibiotic cost to the larger overall management costs when evaluating the economic rationale for antibiotic use in aecb. indeed, antibiotic treatment is associated with lower relapse rates, longer periods between exacerbations, shorter duration of symptoms, and reduced hospitalizations. community-acquired rtis are among the most prevalent of infectious diseases and represent a considerable global burden. lower rtis, including aecb and pneumonia, represent a serious clinical challenge, particularly in the face of increasing global antimicrobial resistance. they account for nearly half of all communityacquired infections and are the leading cause of death from infectious diseases in the united states. worldwide, lower rtis were responsible for . million deaths in . several strategies show promise for optimizing the clinical and economic outcomes associated with lower rtis, particularly aecb. the term aecb has no precise definition but is typically bacterial in origin. it presents as a worsening of symptoms associated with the persistent inflammation and irritation of the bronchial tree that occurs in chronic bronchitis. characteristic symptoms of aecb include change in sputum color, consistency, or amount, accompanied by an increase in cough, dyspnea, and chest tightness. exacerbations occur more commonly in smokers and in patients aged years and older. if left untreated, aecb can result in inflammatory damage, which may contribute further to the progressive deterioration in respiratory function associated with chronic bronchitis. antibiotic treatment therefore is initiated with the objective of limiting this progression, providing relief from symptoms, and reducing disability. as well as causing significant morbidity, aecb is also associated with high socioeconomic cost. in the u.s. alone, for example, over million cases of chronic bronchitis are reported annually, with each patient experiencing an average of one acute exacerbation/year. chronic obstructive pulmonary disease (copd), the fourth leading cause of death in the u.s., frequently develops alongside chronic bronchitis and accounts for million office visits and , hospitalizations/ year. annual costs associated with treatment of aecb exceed $ billion. table shows the pathogens most commonly implicated in aecb. the most frequent bacterial causes are nontypeable haemophilus influenzae, moraxella catarrhalis, and streptococcus pneumoniae, which together account for approximately % of all episodes of aecb. in recent years, so-called atypical respiratory pathogens, such as chlamydia pneumoniae and mycoplasma pneumoniae, have emerged as important pathogens in aecb; these pathogens are thought to precipitate up to % of exacerbations. up to % of aecb episodes are thought to be viral in etiology, the most common viral cause being the rhinovirus. in most cases, the microbial etiology of a particular aecb episode is not identified at the time of treatment and antibiotics therefore are administered empirically, at least in the initial phase of treatment. this approach requires agents that have a spectrum of activity encompassing each of the key bacterial pathogens likely to be encountered. traditionally, amoxicillin (or ampicillin), sulfamethoxazole-trimethoprim (smx-tmp), tetracyclines, and erythromycin have been considered first-line agents for treatment of aecb. however, the clinical utility of these agents is likely to be hampered by the increasing global spread of drug-resistant pathogens. indeed, ␤-lactamase production in up to % of h. influenzae and more than % of m. catarrhalis isolates renders these strains resistant to penicillins and cephalosporins. , furthermore, resistance to penicillin and macrolides has spread at an alarming rate through s. pneumoniae. the increasing resistance to existing antibiotics among key respiratory pathogens is one of the factors driving the search for novel classes of antimicrobials. new options for treating aecb include the cephalosporins, second-generation macrolides, and newer fluoroquinolones with enhanced antipneumococcal activity. in addition, the ketolides are a new class of antibiotics designed specifically to combat communityacquired rtis, particularly those caused by resistant organisms. telithromycin (hmr ) is the first member of this class to reach clinical development. numerous in vitro studies confirm the potent activity of telithromycin against pathogens commonly implicated in communityacquired rtis, irrespective of their ␤-lactam or macrolide susceptibility. the use of antibiotics in the treatment of aecb has been under considerable debate since the early s. arguments against the routine prescribing of antibiotics for aecb include the difficulties in distinguishing between aecb of bacterial and nonbacterial etiology and the marginal benefits reported from antibiotic interventions. some placebo-controlled trials showed no benefit with antibiotic therapy. it also has been suggested that such intervention might delay diagnosis of serious underlying disease. in addition, the cost of antibiotics (particularly of the newer agents) has been used as justification for frugal prescribing in some instances. however, when evaluating the economic rationale for antibiotic use in aecb, it is necessary to look beyond the initial antibiotic acquisition cost to the larger overall costs of managing aecb, including physician visits, hospitalizations, and lost productivity due to work absenteeism. a landmark study published in provided the first definitive evidence of the place of antibiotics in the treatment of aecb. in this study, patients with aecb and copd were randomized to receive either antibiotic therapy or placebo. patients who experienced subsequent exacerbations were crossed over to the other arm of the study. the antibiotics used in this trial were smx-tmp, amoxicillin, and doxycycline in standard dosages. patients were stratified by severity of exacerbation, based on subjective criteria. overall, the study demonstrated that the success rate for antibiotic-treated exacerbations was . times higher than for the placebotreated arm ( % vs %). of importance from an outcome standpoint, % of placebo-treated patients deteriorated, compared with % in the antibiotic-treated arm. this difference was most marked for patients with the severest disease, where deterioration was more than -fold greater in the placebo arm compared with the antibiotic arm. in relation to previously published aecb trial results, - the authors identified a number of consequences of not treating aecb episodes with antibiotics. these included a higher failure rate (and thus shorter periods between acute infections), longer duration of symptoms, and theoretically increased hospital admissions. the rationale for using antibiotics for aecb is further supported by studies showing that vaccination against h. influenzae reduces the number of aecb episodes. furthermore, in selected patient groups, prophylactic use of antibiotics has been found to reduce aecb and accelerate recovery by slowing the deterioration of respiratory status. finally, a meta-analysis of nine randomized, placebo-controlled trials demonstrated a small but statistically significant clinical benefit of using antibiotics in the treatment of aecb. a number of factors affect the clinical and economic outcomes of antibiotic therapy for aecb, including patient profiles, choice of antibiotic, and local resistance patterns. however, studies of antibiotic therapy for aecb have failed to either account for differences among patients or examine the effect of increasing rates of antimicrobial resistance on clinical and economic outcomes. to determine whether the antibiotic prescribed by the pulmonologist affected the relative efficacy and costs of treating aecb, a retrospective review of patients with copd and aecb was performed. the medical records of patients with these conditions who visited the pulmonary department of the creighton university school of medicine over a -year period were studied. chronic bronchitis was defined as meeting two or more of the following criteria: increased cough and sputum production, change in color or tenacity of sputum, decreased breath sounds or increased wheezing, increased dyspnea, and fever above . ºf (in patients not receiving oral steroids). the chosen antibiotic, length of therapy, antibiotic failure or hospitalization (within weeks of initial therapy), length of time between aecb episodes, and costs (antibiotic costs and total costs of aecb treatment) were recorded. based on the opinion of pulmonologists, antibiotics were categorized as first line (amoxicillin, smx-tmp, tetracycline, erythromycin), second line (cephradine, cefuroxime, cefaclor, cefprozil), and third line (amoxicillinclavulanate, azithromycin, ciprofloxacin). of the patient medical records reviewed, patients met the eligibility criteria and were included in the analysis. this included aecb episodes requiring antibiotic treatment, with an average of . episodes/patient. of these aecb episodes, were treated with first-line agents (predominantly amoxicillin and smx-tmp), with second-line agents (predominantly cefaclor and cefuroxime), and with third-line antibiotics. ninety-five percent of patients received a first-line antibiotic at their first office visit; % received a second-or third-line antibiotic at their second office visit; and % of patients who received second-line antibiotics also received a third-line agent at a third office visit. in of the episodes ( . %), therapy failed within weeks. both treatment failure and hospitalizations were significantly more frequent in patients receiving first-line antibiotics than in those receiving third-line therapy (figure ). although the pharmacy costs for treating each aecb episode were lower with first-line agents, there was a trend toward lower total cost for managing patients with second-and third-line agents ( table ) . it was concluded that this study found that in patients with copd experiencing an aecb, the use of third-line antibiotics significantly reduced treatment failure rates and the need for hospitalization, while prolonging the time between aecb episodes. this study is the first to show the effect of antibiotic selection on both clinical and economic outcomes in aecb. its findings are supported by a recent study demonstrating that administration of antibiotics significantly reduced relapse rates in outpatients with acute exacerbations of copd. furthermore, of the patients treated with antibiotics, relapse was highest among those who had received amoxicillin. further prospective studies are warranted to help identify which patients would benefit most from the more expensive antibiotics, thus helping to reduce the total cost of managing patients with aecb episodes. a review of the treatment of aecb presented evidence that treatment outcome might reflect a number of patient-specific variables, in particular the presence of cardiopulmonary disease, such as heart failure, and the number of exacerbations/year. indeed, patients with four or more exacerbations/year may be at risk of antibiotic failure and may require a third-line antibiotic (e.g., azithromycin, amoxicillinclavulanate, or ciprofloxacin). , a number of other risk factors also were identified that place a patient at increased risk of hospitalization during an acute exacerbation. these include age of years or older, compromised lung function, and severe pulmonary and nonpulmonary dysfunction. however, no studies to date have documented whether the risk of hospitalization might be linked to the prevalence of resistant pathogens. these data need to be determined, as they will have a major impact on the utility of prescribing more potent antibiotics for patients at risk, such as the elderly and those with severe lung dysfunction. the effect of antibiotics on long-term outcomes in aecb has been studied. a double-blind, randomized trial-the gemifloxacin long-term outcome in bronchitis evaluation (globe) study-compared gemifloxacin (an investigational quinolone) with clarithromycin in patients with aecb for weeks. over this period, patients who received gemifloxacin had significantly fewer aecb relapses compared with those receiving clarithromycin ( % success compared with %, p< . ). moreover, hospitalization was required for only of ( . %) patients receiving gemifloxacin, compared with of ( . %) patients who received clarithromycin (p= . ). another research group determined antibiotic treatment intervals in a community-based program. in this study, patients with aecb were categorized according to their antibiotic therapy: ␤-lactams ( patients), macrolides ( ), and quinolones ( ). overall, the mean time interval between antibiotic courses for patients experiencing an aecb relapse (as determined by the prescribing physician) was significantly longer for patients treated with quinolones ( . days, p= . ) than for those treated with either macrolides or ␤-lactams ( . and days, respectively). regular reevaluation of antibiotic treatment approaches for aecb is warranted, with the aim of minimizing treatment failures and subsequent hospitalizations, thereby reducing costs, while containing the spread of antimicrobial resistance. guidelines for treatment of aecb are still evolving. nevertheless, it is clear that clinical risk stratification (taking into account disease severity and comorbidity) and studies of health outcomes are helping to provide the necessary rationale for clinically and economically effective use of antimicrobials for aecb. the infectionfree interval might be an appropriate outcome measure with which to compare differences between antibiotics in patients with aecb. in addition, resistant organisms should be cultured from patients with aecb to determine whether resistance is a factor in the outcome of aecb. communityacquired pneumonia in adults: guidelines for management the global burden of disease: a comprehensive assessment of mortality and disability from diseases, injuries and risk factors in and projected to standards for the diagnosis and care of patients with chronic obstructive pulmonary disease morbidity and mortality: chartbook on cardiovascular, lung, and blood diseases. publication no. - acute exacerbation of copd: factors associated with poor treatment outcome infectious exacerbations of chronic bronchitis: diagnosis and management epidemiology and treatment of chronic bronchitis and its exacerbations chlamydia pneumoniae, strain twar, infection in patients with chronic obstructive pulmonary disease the alexander project - : latest susceptibility data from this international study of bacterial pathogens from community-acquired lower respiratory tract infections respiratory tract infections: epidemiology and surveillance antibiotic therapy in exacerbations of chronic obstructive pulmonary disease prophylactic use of oxytetracycline for exacerbations of chronic bronchitis exacerbations of chronic bronchitis: treatment with oxytetracycline value of ampicillin in the hospital treatment of exacerbations of chronic bronchitis a controlled study of the effect of treatment on chronic bronchitis: an evaluation using pulmonary function tests antibiotic regimens in severe and acute purulent exacerbations of chronic bronchitis antibiotic regimens in moderately ill patients with purulent exacerbations of chronic bronchitis role of infection in chronic bronchitis a controlled trial of a killed haemophilus influenzae vaccine for prevention of acute exacerbation of chronic bronchitis prophylactic treatment of chronic bronchitis antibiotics in chronic obstructive pulmonary disease exacerbations: a meta-analysis clinical and economic considerations in acute exacerbations of chronic bronchitis antibiotics are associated with lower relapse rates in outpatients with acute exacerbations of copd guidelines for the treatment of acute exacerbations of chronic bronchitis recommendations on the management of chronic bronchitis clinical studies in chronic bronchitis: a need for better definition and classification of severity gemifloxacin long-term outcomes in bronchitis exacerbations (globe) study: an assessment of health outcome benefits in aecb patients following days' gemifloxacin therapy [abstr antibiotic use and antibiotic treatment intervals (ati) in patients with exacerbations of chronic bronchitis [abstr the infection-free interval: its use in evaluating antimicrobial treatment of acute exacerbation of chronic bronchitis key: cord- - zua mji authors: leriger, michelle m.; phipps, amber r.; norton, bridget m.; spitznagel, rachel a. title: improving the compliance of intraoperative antibiotic redosing: a quality improvement initiative date: - - journal: pediatr qual saf doi: . /pq . sha: doc_id: cord_uid: zua mji introduction: at children’s hospital and medical center in omaha, nebraska, the intraoperative antibiotic redosing guidelines and the time frame considered compliant for redosing were unclear. this lack of clarity plus an ill-defined process for ensuring intraoperative antibiotic redosing resulted in a compliance rate of %. the organization’s surgical site infection (ssi) rate was . %, above the national benchmark of . %. the primary project goal was to increase intraoperative antibiotic redosing compliance. the secondary project goal was to decrease ssis. methods: with recommendations from the infectious disease society of america, we developed new organizational redosing guidelines, as well as a new antibiotic-specific reminder alert in the electronic medical record. implementation of the new guidelines and processes occurred after providing education to the anesthesiologists, surgeons, and circulating nurses. monthly evaluation of data allowed for quick recognition of oversights followed by the initiation of process updates. results: data showed that the initial compliance rate for the intraoperative redosing of antibiotics was %. following interventions, compliance has reached and sustained an average of %. survey results show that provider knowledge of the guidelines and process has improved. though not directly related, the national surgical quality improvement program observed that the ssi rate decreased from . % in to . % in . conclusions: this project demonstrates that comprehensive education along with antibiotic-specific electronic medical record alerts significantly increased the compliance of intraoperative antibiotic redosing at children’s hospital & medical center. continuous education and monthly updates sustained results for over months. surgical site infections (ssis) are infections of the incision or organ space that occur after surgery. , ssis are reported in approximately %− % of surgical procedures and are associated with increased morbidity and mortality. [ ] [ ] [ ] the cost of treating ssis in the united states is increasing. solutions for patient safety (sps) estimates an average cost of $ , per ssi, with a range of $ , to $ , . [ ] [ ] [ ] the cost can exceed $ , per ssi when an antimicrobial-resistant organism is involved. annually, the estimated cost to the u.s. health system is between . and . billion dollars. it is often difficult to determine the cost of an individual ssi, and this is true at children's hospital & medical center because direct cost accounting is not used. approximately % to % of ssis are preventable. correctly administered perioperative prophylactic antibiotics decrease the rate of ssis. , clinical practice guidelines for antimicrobial prophylaxis published in the american journal of health-system pharmacy recommend intraoperative antibiotic dosing intervals during surgical procedures based on the pharmacokinetics of each drug. , in the cardiac surgical patient population, correct intraoperative antibiotic redosing has decreased ssi rates. at the children's hospital & medical center in omaha, nebraska, the ssi rate was higher than the abstract introduction: at children's hospital and medical center in omaha, nebraska, the intraoperative antibiotic redosing guidelines and the time frame considered compliant for redosing were unclear. this lack of clarity plus an ill-defined process for ensuring intraoperative antibiotic redosing resulted in a compliance rate of %. the organization's surgical site infection (ssi) rate was . %, above the national benchmark of . %. the primary project goal was to increase intraoperative antibiotic redosing compliance. the secondary project goal was to decrease ssis. methods: with recommendations from the infectious disease society of america, we developed new organizational redosing guidelines, as well as a new antibiotic-specific reminder alert in the electronic medical record. implementation of the new guidelines and processes occurred after providing education to the anesthesiologists, surgeons, and circulating nurses. monthly evaluation of data allowed for quick recognition of oversights followed by the initiation of process updates. results: data showed that the initial compliance rate for the intraoperative redosing of antibiotics was %. following interventions, compliance has reached and sustained an average of %. survey results show that provider knowledge of the guidelines and process has improved. though not directly related, the national surgical quality improvement program observed that the ssi rate decreased from . % in to . % in . conclusions: this project demonstrates that comprehensive education along with antibiotic-specific electronic medical record alerts significantly increased the compliance of intraoperative antibiotic redosing at children's hospital & medical center. continuous education and monthly updates sustained results for over months. (pediatr qual saf ; :e ; doi: . /pq . ; published online april , .) national benchmark based on data from the national surgical quality improvement program (nsqip) database. nsqip uses a systematic sampling process to ensure a representative sample of surgical cases. it excludes cardiac, ophthalmology, interventional radiology, dental procedures, and endoscopies. the hospital contributes to the nsqip database entering % of cases annually. in , children's ssi rate for all cases was . %, whereas the benchmark was . %. the nsqip database identified ssis. therefore, based on the hospital's total surgical volume, approximately ssis occurred in . our hospital created an ssi workgroup to implement policies based on sps recommendations to decrease ssis. sps is a network of over children's hospitals with the shared goal of harm reduction by designing and advising on the implementation of evidence-based bundles to reduce the harm caused by hospital-acquired conditions and serious safety events. ssis are the fourth largest contributor to harm reported across the sps network. sps designed a bundle to reduce harm from ssis to hospitalized children. bundle elements include preoperative baths, no razor use, appropriate preoperative antibiotic timing, appropriate skin antisepsis, and appropriate antibiotic redosing (table ) . the primary goal of this quality improvement (qi) project was to increase intraoperative antibiotic redosing compliance from . % to % for qualifying cases. as referenced, the time frame for this project aligned with our hospital's focus on improving patient safety and decreasing hospital-acquired conditions. therefore, a secondary project goal was to decrease ssis. we identified a need to establish consistent intraoperative antibiotic redosing guidelines and define the exact time frame, in minutes, considered compliant for intraoperative antibiotic redosing. additionally, a well-defined process for ordering intraoperative antibiotics was necessary. qi projects are exempt from institutional review board application and approval. this project utilized the plan do check act (pdca) methodology (table ) , thorough data analysis, and on-going education. our project team consisted of anesthesiologists, a surgeon, an operating room (or) nurse, a pharmacist, and an information technology (it) specialist. in may , we gathered baseline data. concurrently, monthly meetings were held with the ssi workgroup to review current processes. the ssi workgroup consisted of a surgeon from each subspecialty, a pharmacist from the antimicrobial stewardship program, members from the performance improvement department, an it specialist, or nursing managers, and anesthesiologists. at these meetings, research into existing intraoperative antibiotic redosing guidelines and policies took place. most committee members, including the anesthesiologists, surgeons, and or nurses, were unaware of formal antibiotic redosing guidelines. however, we discovered that hospital guidelines did exist via a paper ordering sheet. in june , members of the project team worked with members of the hospital's antimicrobial stewardship program to establish perioperative antimicrobial guidelines utilizing information from the infectious disease society of america and information compiled from hospitals that are part of the children's hospital association network (table ) . , , this work outlined procedures and drug-specific timeframes for intraoperative antibiotic redosing. to be deemed compliant with the redosing, antibiotics needed to be administered minutes before or after the electronic medical record (emr) redosing due time, determined by the antibiotic administration start time. if a procedure was longer than half-lives, the drug was to be readministered. renal function did not play a specific role in the creation of the guidelines; however, the pharmacy looks at the creatinine clearance if available on each patient before fulfilling a requested redose. with new guidelines established, the project team collected baseline data from all qualifying intraoperative cases. this analysis excluded antibiotics given outside of the or. initial data analysis was calculated using the antibiotic-specific redosing time frames from the preexisting guidelines. these guidelines required antibiotic redoses to be given within a -minute window on either side of the due time. if a case required more than redose, all required redoses needed to be administered correctly, or the case was considered noncompliant. as stated, most physicians were unaware of these guidelines. in june , we assessed surgeon and anesthesia provider knowledge using a survey. of the who received the survey, responded for a response rate of . %. only % of responders felt that they had a clear understanding of the redosing guidelines. the lack of clarity is evident by the average compliance rate of . % (fig. ) . following the development of guidelines and the collection of data, the project team worked with it analysts to create intraoperative antibiotic reminder alerts for anesthesia providers. an antibiotic-specific redosing reminder was created in the federally qualified emr by august . the alert appears on the left side of the anesthesia record, flashing yellow minutes before the antibiotic is due. it changes to red when the antibiotic becomes due. the project team created laminated cards with the new guidelines and posted them at every anesthesia workstation. education on the new guidelines, the time frame considered compliant for redosing, and the new emr alert was provided at department meetings in august and sent via email to all anesthesiologists and surgeons. the process for ordering the antibiotics consisted of the or circulating nurse calling the pharmacy to request a redose. all education was provided before the project go-live date of august , . newly hired anesthesiologists received the information regarding the guidelines and processes in their orientation. following the project initiation, monthly evaluation of emr data occurred. the performance improvement department conducted an initial data review with potential cases of noncompliance sent to the anesthesiologists on the project team. the review of these noncompliant cases involved peer-to-peer conversations and revisions in the process followed by further education if required ( table ). anesthesiologists often notated in the record as to why the antibiotic redose was late or missed. this notation was crucial as sometimes the peer-to-peer conversations would take place weeks after surgery, making recall difficult. by analyzing noncompliance, we identified oversights in the process, recurring issues with providers, and issues at specific locations or times of day (table ) . anesthesia providers received monthly updates on compliance rates. in october , the anesthesia resident involved in a missed antibiotic redose was unaware of the hospital's new guidelines and thought the emr alert was incorrect and therefore ignored it. education sessions or emails about the process and guidelines *initial preoperative dose should occur within min of incision for all antibiotics, except vancomycin and fluoroquinolones which should be given within min of incision. †redosing: time should be measured from the start of administration of the preoperative dose not from the beginning of the procedure; occurs if the duration of the procedure exceeds drug half-lives or excessive blood loss; and if patient has moderate to severe renal dysfunction contact pharmacy for dosing assistance. ‡severe penicillin allergy: ige-mediated reaction (eg, anaphylaxis, urticaria, bronchospasm) or exfoliative dermatitis (stevens-johnson syndrome, toxic epidermal necrolysis),or a life-threatening hypersensitivity reaction. §initial preoperative dose should occur within min of incision for all antibiotics, except vancomycin and fluoroquinolones which should be given within min of incision. time should be measured from the start of administration of the preoperative dose not from the beginning of the procedure. ¶antimicrobial stewardship program committee approval excluded anesthesia residents as identified by the missed antibiotic dose. anesthesia residents rotate through the ors monthly and play an important role in direct patient care. to address this oversight, we included the perioperative antimicrobial guidelines and education on the emr alerts in the resident orientation. this oversight also highlighted the problem that redosing was strictly reliant on the anesthesia team. therefore, the time-out process was updated to include a discussion on antibiotic redosing. the circulating nurse writes the redosing time on the surgical whiteboard for all members of the or team to see, adding a layer of protection in the process. in november , a provider recognized that the new guidelines did not address redosing in neonates. team leaders discussed this with the team pharmacist, who created separate neonatal guidelines for those less than days of age with normal renal function. in november , during data analysis and with input from anesthesiologists, it was determined that misses or near misses were occurring off hours (after pm and on the weekends) and in non-or locations (such as the fetal care center). to account for this, we updated the emr antibiotic reminder to alert minutes before the time due, allowing staff more time to order and physically receive the antibiotics. project leaders discussed these obstacles at group meetings and encouraged anesthesia providers to order the antibiotics early in these circumstances. the pharmacy representative on the team was also made aware of this problem to provide education to the pharmacy staff. providers received updates when new pdca cycles or updates in the process occurred. the framework for the composition of this article utilized the standards for quality improvement reporting excellence (squire) guidelines. following project implementation, compliance with intraoperative antibiotic redosing increased from the average of . % to % within the first month. analysis of august data started on the implementation date of august . at the end of the second month, compliance rates had increased to % (fig. ) . data evaluation continues monthly, with compliance averaging . % over the last months. the team implemented updates, focused on education of changes, and stressed the importance of communication when they discovered potential gaps in the process (table ) . although not all of those changes increased compliance rates, the changes needed to occur to prevent future errors. in april , anesthesia providers were resurveyed using the same set of questions. seventy-five percent of anesthesia providers who responded had a clear understanding of the frequency at which commonly used antibiotics should be redosed intraoperatively according to the hospital guidelines, a % improvement. based on new survey results, anesthesia provider knowledge regarding the correct redosing timeframe considered complaint was also %, an improvement of % from project initiation. the antibiotic redosing team and hospital's ssi workgroup worked well together. the ssi workgroup's goal was to institute the bundle modeled off of the sps bundle to decrease the rate of ssis (table ). in january , we implemented the final element of the bundle. as mentioned, one part of this bundle was appropriate antibiotic redosing. specific data on the compliance rates of other portions of the bundle were not available due to inconsistent record keeping. at project initiation, our hospital's ssi rate was . % for , when the overall rate in the nsqip database was . %. our hospital's ssi rate has decreased to . % as of january , which correlated to the observed rate of ssis for the entire nsqip database. this qi initiative defined evidence-based intraoperative antibiotic redosing guidelines and the timeframe considered compliant for antibiotic redosing. it utilized an antibiotic-specific emr alert to remind anesthesia providers when an antibiotic was due. throughout the project, monthly evaluation of data allowed for quick recognition of oversights or problems followed by the initiation of process updates. although not all pdca cycles or revisions resulted in noticeable change, they did ensure that high compliance rates were sustained. the use of emr alerts as part of single or multifaceted improvement initiatives has been reported in other studies. , , one university-associated hospital incorporated emr reminders as part of a multifaceted approach to improving intraoperative antibiotic redosing. their compliance rates improved by % to approximately %. another study looking only at the use of emr alerts to improve the administration of the second antibiotic dose found an absolute improvement of . %, with approximately % compliance rate. this study showed sustained compliance rates months later. our compliance rates increased the first month significantly (fig. ) and have remained high for over months, averaging . %. we believe that our compliance rates rose so significantly because our institution's previous guidelines were unclear and that our compliance rates are higher than those reported by other institutions because of the multilayered approach of our study. we utilized preimplementation education, and to sustain momentum, we sent reports of monthly audits and project updates to anesthesia providers via email and communicated at department meetings. additionally, providers involved in noncompliance would get an individual email as a reminder to maintain vigilance. by evaluating all possible cases of noncompliance for accuracy and any notes made by the anesthesia providers, we were able to implement changes to ensure sustainability. combining extensive education with the emr antibiotic-specific reminders highlights the strengths of this project. although timely notification in the emr is likely the most important factor in achieving compliance, several other factors likely contributed. the new guidelines were widely disseminated and accessible, whereas the previous guidelines were not. additionally, the new guidelines were updated to reflect the definition of compliance used throughout the rest of the institution, which states that redoses should be administered within a -minute window on either side of the due time. analysis of baseline data using the preexisting guidelines required a stricter -minute redosing window to be compliant. one limitation of the project is that antibiotic ordering still requires diligence on the part of the or team and, ultimately, the anesthesia providers. upon initial development of the reordering process, the project team wanted the emr to alert the or pharmacy when an antibiotic redose was near due; however, limitations in the emr made this impossible, and we were unable to identify an alternative solution for pharmacy involvement in the reordering process. per hospital policy, physicians order all antibiotics from the pharmacy to ensure administration of the correct dose, which can take additional time. and, as with any qi project, communication is imperative. some providers remained unaware of the changes implemented with this project. the education initially excluded residents and new providers, as we identified with monthly audits. an additional limitation is that or nurses do not always write the antibiotic redosing time on the whiteboard despite this being part of the time-out process. we have not initiated any pdca cycles to improve this, but it is something we could consider in the future. finally, we did not have a control group without intervention because the project included all cases meeting requirements for redosing by nature of the qi initiative. due to the shortened redosing interval of some antibiotics, there is a concern for acute kidney injury, so in september , the team worked on updating the guidelines to address renal dosing. to our knowledge, there have not been any cases of acute kidney injury reported. improved compliance with intraoperative antibiotic redosing was one component of the bundle initiative instituted by the hospital's ssi workgroup. we cannot delineate the impact of the correct antibiotic redosing on the overall decrease in the ssis. although the antibiotic redosing portion of the ssi bundle has remained consistent, data on the compliance rate of all portions of the bundle are not available due to inconsistent record keeping. although we cannot draw a clear correlation between the ssi rate and our improved intraoperative compliance redosing, correct intraoperative antibiotic redosing has been shown to decrease ssis, and this qi project demonstrates that comprehensive education along with antibiotic-specific emr alerts significantly increased the compliance of intraoperative antibiotic redosing. through effort by many individuals, the changes have now become standard practice. utilizing continual education and monthly updates, we have sustained results for over months. the authors have no financial interest to declare in relation to the content of this article. healthcare infection control practices advisory committee. centers for disease control and prevention guideline for the prevention of surgical site infection implementation of a multifaceted program to sustainably improve appropriate intraoperative antibiotic redosing improving timely surgical antibiotic prophylaxis redosing administration using computerized record prompts financial impact of failing to prevent surgical site infections. qual manag health care agency for healthcare research and quality estimating the proportion of healthcare-associated infections that are reasonably preventable and the related mortality and costs electronic medical record interventions and recurrent perioperative antibiotic administration: a before-and-after study surgical infection society; society for healthcare epidemiology of america. clinical practice guidelines for antimicrobial prophylaxis in surgery children's hospitals' solutions for patient safety. every patient. every day the quality toolbox diagnosis and management of complicated intra-abdominal infection in adults and children: guidelines by the surgical infection society and the infectious diseases society of america the authors would like to acknowledge the children's hospital & medical center performance improvement department, it department, pharmacy, and antimicrobial stewardship program for their contributions and assistance throughout the project. key: cord- -fyqc bat authors: gleckman, richard; gantz, nelson m. title: cost‐effective antibiotic prescribing date: - - journal: pharmacotherapy doi: . /j. - . .tb .x sha: doc_id: cord_uid: fyqc bat antibiotics are often misused, resulting in a high frequency of adverse effects, emergence of drug‐resistant organisms, and excessive costs. the high cost of antibiotics is currently receiving the greatest attention. considerable cost savings can be achieved by appropriate prescribing of antibiotics for patients receiving these drugs prophylactically as well as for those with established infections. this article cites specific examples of how cost‐effective antibiotic prescribing practices can realize substantial cost savings without any diminished quality in patient care. therapy of established disease appropriate indications use of "therapeutic equivalents" single agent therapy oral versus parenteral route treatment duration hidden costs self or family administration no class of drugs in the hospital formulary is currently receiving closer scrutiny than the antibiotics. these agents are being subjected to intensive examination because of increased pharmaceutical lobbying efforts, concern over the emergence of drugresistant organisms, and the continuous introduction of new compounds. undoubtedly, however, the keen interest in antibiotics primarily stems from the fact that, as a class of drugs, they account for the single largest component of the pharmacy budget. in this age of cost-containment antibiotics will continue to remain in the limelight, particularly for those pharmacists and hospital administrators dedicated to holding the fiscal line. we shall identify antibiotic prescribing practices, both prophylactic and therapeutic, that can be changed to permit cost reductions. we will also describe innovative approaches that are being implemented to counteract the spiraling costs of health delivery. it is often unappreciated that between one-fourth and one-half of all antibiotics prescribed within a hospital are dispensed for prophylaxis. most of these agents are administered to surgical patients to prevent postoperative infections. it thus becomes apparent that if guidelines for perioperative antibiotic use are complied with, significant cost savings can be realized. postoperative wound infections are not only unsightly, but they contribute to morbidity and, most importantly, constitute a threat to the patient's life. these postoperative infections can cause extensive focal infection, bacteremia, hematogenous dissemination, septic shock and multiple organ failure. in addition, postoperative wound infections significantly increase the expense of hospitalization. ' prophylactic antibiotics are indicated exclusively for selective clean and clean-contaminated surgical procedures. clean procedures are those in which neither the respiratory, alimentary, genitourinary, or oropharyngeal cavities are entered and there is no break in technique. clean-contaminated procedures are those in which these cavities are entered without unusual contamination. antibiotic prophylaxis is indicated for a "clean" procedure when a prosthesis is being implanted, or the risk exists for a catastrophic infection. antibiotic prophylaxis is indicated for a "clean-contaminated" procedure when the incidence and consequences of infection are great, and the responsible organisms are predictable and susceptible to antibiotics. infections that are associated with frankly contaminated and dirty procedures merit antibiotics, but here the indication is not prophylaxis but definitive therapy of an established infection. a number of factors have been identified that contribute to postoperative wound infections. surgical factors have included the duration of the operation, the extent of local contamination, and the presence of hematomas, debris and foreign bodies.* host factors that predispose to wound infections include age greater than years, malnutrition, obesity, diabetes mellitus, malignant diseases and the presence of remote infe~tion.~ concerns about prophylactic antibiotics have focused on four issues: drug expense, adverse drug reactions, alterations in the patient's indigenous microflora with the risk for superinfection, and the emergence of drug-resistant organisms that pose a threat to other patients exposed to the hospital flora. these concerns can only be allayed by the intelligent use of perioperative antibiotics in well defined indications. preferred prophylactic antibiotics should be nontoxic, inexpensive, and possess activity against the major pathogens likely to be encountered in the operative area. however, the antibiotics need not be active against every bacterial species present in the operative area. a very limited role exists for the second generation agent cefoxitin, and no indication exists for the third generation cephalosporins cefotaxime, moxalactam, and cefoperazone for perioperative pro phyla xi^.^ these more expensive agents have not been found to be more effective than less expensive agents, and their unrestrained use could encourage the emergence of drug-resistant organisms. effective antibiotic prophylaxis requires attainment of significant tissue concentrations during the "critical period", the period of the early inflammatory response to bacterial contamination. as a general rule adequate tissue concentrations of an antibiotic during the critical period can be obtained by a single dose of the drug administered shortly before the operation, and additional doses dispensed either earlier or later are usually unnecessary. the most common error in surgical prophylaxis appears to be excessive duration of admini~tration.~ no study indicates value to extending prophylaxis beyond hours. limiting perioperative antibiotic prescribing to the first hours would reduce drug-related adverse reactions, the rate of emergence of resistance microorganisms, and the cost of medications. table , , and outline those clean and cleancontaminated surgical procedures that merit perioperative prophylactic antibiotics. the tables describe the indication for prophylaxis and also provide a recommended antibiotic program. among the first generation cephalosporins cefazolin is probably the preferred agent for prophylaxis. this drug produces the highest and most sustained serum concentrations, can be given as infrequently as every hours, and when administered according to a three times daily schedule, is the least expensive cephalosporin. when cefaxolin is prescribed for prophylaxis gram of the drug should be administered i.m. on call to the operating room or i.v. at anesthesia induction. prophylactic antibiotics are also indicated for patients with congenital valvular disease, acquired valvular heart disease or prosthetic valves who are to be subjected to dental, urinary tract, biliary tract or lower intestinal tract instrumentation or surgery. the prophylaxis is designed to prevent bacterial endocarditis. detailed recommendations have been previously published to assist the physician in managing these patients the suggestion has also been made that patients with orthopedic implants be considered candidates for prophylactic antibiotics when they are exposed to procedures that could result in bacteremia. the implant could serve as a locus minoris resistentiae, and a deep wound infection would ensue. this suggestion has, however, neither been confirmed nor refuted by properly executed prospective controlled studies. table lists those operative procedures where prophylactic antibiotic administration has been a common practice despite the lack of controlled studies and scientific justification. we feel that perioperative antibiotics should not be routinely prescribed for these procedures until properly performed clinical studies document their value. major cost savings and a reduction of adverse effects can be attained by appropriate antibiotic usage. a number of investigations have confirmed that at least to % of prescribed antibiotics are not indicated. approximately one quarter to one half billion dollars could be saved annually in the united gleckman and gantz one day is clamped ahigh risk patients for cesarean section prophylaxis include women from the lower socioeconomic status, obese women and patients who have internal fetal monitoring. some experts also recommend prophylaxis for those women with prolonged labor, membranes ruptured more than hours or women subjected to multiple vaginal examinations. states, without compromising patient care by more appropriate antibiotic pre~cribing.'-~ one example of the problem of antibiotic misuse is the practice of prescribing antibiotics for those disorders in which studies have failed to demonstrate any benefit from drug therapy. no justification exists to treat nonpregnant women or elderly chronically catheterized patients with asymptomatic bacteriuria.'o similarly, antibiotics appear to be of no proven value when administered to patients with acute symptomatic bronchitis or acute symptomatic exacerbations of chronic bronchitis. acute bronchitis, an inflammatory disorder of the trachea and bronchi, occurs predominantly in the winter and is often preceded by an upper respiratory infection. invariably a self-limited disease, acute bronchitis is caused most frequently by viruses. antibiotic treatment is not indicated for this inflammatory process. acute exacerbations of chronic bronchitis, consisting of a change in the color, consistency and amount of sputum as well as increasing cough and dyspnea, have been ascribed to viruses (rhinovirus, coronavi rus, influenza) , mycoplasma pneumoniae and bacteria, including haemophilis influenzae, streptococcus pneumoniae, gram-negative bacilli and "normal respiratory flora." antibiotics have been prescribed to shorten the duration of the exacerbation, prevent respiratory failure or forestall progressive pulmonary deterioration that often occurs in patients with chronic bronchitis. no evidence has emerged that antibiotics can accomplish any of these desired goals. in fact, nicotra and associates could not document any beneficial effect by the addition of antibiotics to the conventional modes of therapy in patients with acute exacerbations of chronic bronchitis requiring hospitalization.'* it has become ritual to prescribe antibiotics to noncompromised patients with localized cutaneous abscesses. for patients with normal host defenses drainage is adequate therapy, and antibiotics are not indicated. i in addition to the problem of prescribing antibiotics for disorders in which no benefit has been established, physicians often equate "best" treatment with the newest, invariably more expensive, antibiotic. penicillin g remains the drug of choice for pneumococcal pneumonia, community-acquired aspiration pneumonia, dental infections, streptococcal pharyngitis and syphilis. although the more expensive cephalosporins possess an expanded spectrum of activity, cure rates are not improved by prescribing these antibiotics instead of penicillin. only when controlled studies show enhanced efficacy or reduced toxicity should the newer, more expensive agent be prescribed. similarly, the inexpensive sulfonamides remain highly effective agents to treat communityacquired symptomatic bacterial cystitis in women. in the absence of a history of an allergic reaction to sulfonamide, there is no reason to prescribe the more expensive compounds, such as cefaclor, cephalexin, cefadroxil, nitrofuratoin or trimethoprimsulfame-thoxazole, when treating a woman with symptomatic, community-associated bacterial cystitis. generic gentamicin is available at a cost that is approximately one-third that of the other aminoglycosides tobramycin, netilmicin, or amikacin. for hospitals, particularly community hospitals, where gentamicin-resistant gram negative bacilli are uncommon pathogens, generic gentamicin can be selected as the preferred aminoglycoside. in other hospitals, generic gentamicin can be substituted for the other aminoglycosides as soon as results of antibiotic susceptibility tests permit. for patients with suspected or established infections caused by pseudornonas aeruginosa, tobramycin should be selected while awaiting the results of antibiotic susceptibility tests. tobramycin is also preferred by some experts for treating patients with renal insufficiency who have infections requiring an aminoglycoside; the rationale is based on a lower frequency of nephrotoxicity, as measured by serum creatinine values. amikacin should be selected to treat infections caused by proteus vulgaris or providencia stuarfii while awaiting susceptibility reports. for patients with nosocomial gram negative infections requiring an aminoglycoside, tobramycin or amikacin should be selected initially if gentamicin resistant strains are prevalent in the hospital. as soon as the results of antibiotic susceptibility tests are available, gentamicin can be substituted for tobramycin or amikacin. with the above exceptions, gentamicin can be selected initially or after the results of susceptibility tests are known; this strategy will result in considerable cost savings to patients. cephalosporins account for up to one third of total pharmacy drug expenditures. the first generation cephalosporins cephalothin, cephapirin and cefazolin have essentially the same spectrum of activity. pharmacokinetically, cephalothin and cephapirin are interchangeable, but use of cephapirin can result in substantial savings. because of its more favorable pharmacokinetic profile, cefazolin can be given in doses that are one third those of cephalothin or cephapirin, with comparable effectiveness. cefazotin also requires less frequent dosing per day than cephalothin (four versus six times). since cefazolin can be given intramuscularly, intravenous administration costs are saved. cefazolin also is subject to competitive pricing since it is sold by two drug companies. with desirable pharmacokinetic properties as well as the ability to purchase the drug on bid, cefazolin is probably the first generation cephalosporin of choice. a common error in antibiotic prescribing is the failure to modify therapy when the results of antimicrobial susceptibility tests are available. an example of this error is the severely ill patient presenting with high fever, sweats, chills, hypotension and no obvious source of infection. broad spectrum therapy with two antibiotics is usually prescribed pending the results of cultures and antimicrobial susceptibility tests. initial therapy should not dictate later therapy, however. when the infecting organism is known and the susceptibility report is available, it is often possible to discontinue the initial broad spectrum combination drugs and prescribe a single, less expensive and potentially less toxic agent. while multiple drugs may be preferred therapy to treat selected infections such as fneumocysfis carinii pneumonia, malaria, toxoplasmosis, tuberculosis, enterococcal endocarditis, infection caused by psuedomonas aeruginosa or gram negative bacteremia in an immunosuppressed host, a single pathogen usually requires therapy with only one antibiotic. prescribing more than one drug to the patient is not only more expensive, but this practice often entails greater risk for untoward events. the use of a combination of antibiotics has been the conventional initial therapy for patients with intraabdominal and pelvic sepsis. until the results of cultures and susceptibility tests are available, usually an aminoglycoside with clindamycin, metronidazole, chloramphenicol or one of the extended spectrum pencillins (carbenicillin or ticarcillin) is prescribed to assure activity for the anaerobic components, particularly bacferoides fragilis, as well as the facultative gram-negative rods contributing to these infections. recently, cefoxitin therapy has been compared with the combination of clindamycin plus amikacin for the treatment of mixed aerobicianaerobic infections." a prospective randomized trial of patients given these therapies revealed no difference in therapeutic efficacy or incidence of toxicity. however, the cost of cefoxitin therapy was significantly less than the cost of the drug omb bin at ion.'^ these results were confirmed in a subsequent study of patients given either cefoxitin or a combination of clindamycin and an aminoglycoside for the treatment of polymicrobial pelvic and abdominal infections. therefore, it appears that cefoxitin alone may well be as safe and therapeutically effective as the standard combination treatments when it is administered to selected patients with community-acquired mixed anaerobidaerobic infections that result from appendicitis, diverticulitis, bowel trauma, pelvic inflammatory disease or endometritis. however, it would be preferable to add an aminoglycoside to cefoxitin for those patients with intraabdominal or pelvic infections who have received antibiotics within the preceding weeks or who have experienced a nosocomial abdominal or pelvic infection. considerable cost savings can be achieved by changing from parenteral to oral antibiotic administration and by replacing hospitalization with carefully supervised home treatments. oral therapy eliminates the cost of intravenous solutions and sets and the personnel time involved in preparation and infusion. recent studies have confirmed the efficacy and reduced expense of oral antibiotics prescribed for selected children with osteomyelitis and septic arthritis. " in , it was reported that favorable results ensued when oral antibiotic therapy was prescribed for hospitalized patients with serious infectionsz fourteen patients with osteomyelitis were treated successfully with oral cephalexin after they had received a short course of parenteral cephaloridine. however, it was not until when tetzlaff and associates reported on children with osteomyelitis and septic arthritis, who had been treated with a brief initial course of intravenous therapy followed by oral antibiotics, that major attention was directed to this novel cost saving approach. the children with acute osteomyelitis and septic arthritis were hospitalized for the entire course of therapy. parenteral therapy was given initially for about one week, and volume , number , july~august then oral antibiotics were administered for a mean of approximately weeks. drug absorption was monitored by measuring serum antibiotic concentrations and by determining serum bacterial activity. the oral antibiotics were well tolerated and all infections except one responded in , prober and associates reported on their experience treating children with serious staphylococcal infections (predominantly osteomyelitis). the children were treated with a short course of parenteral therapy followed by oral administration of antibiotic~.~~ once the children became asymptomatic they were discharged from the hospital for supervised oral therapy at home. the children were seen once or twice weekly in an outpatient setting; serum bactericidal levels of the antibiotics were monitored. this report and subsequent studies appear to indicate that with careful monitoring oral antibiotic therapy can be as effective as the standard prolonged intravenous therapy for specific skeletal infections in oral therapy is cost effective, particularly when given at home, and this form of treatment is not associated with the inherent risks of intravenous infusion, namely, chemical phlebitis and bacteremia. home oral therapy permits increased patient comfort for the child. however, oral therapy necessitates careful sequential clinical monitoring; demonstration of therapeutic serum bactericidal antibiotic concentrations is since follow-up evaluations beyond years on children who have received oral therapy have not been reported, prolonged vigilance will be required to detect recrudescent disease; relapses have been detected more than years after the first attack of osteomyelitis. hospitalization and parenteral antibiotic therapy has been considered the conventional treatment program for women with acute symptomatic community-acquired bacterial pyelonephritis. however, this infection can be treated in an outpatient setting when diagnosis is secure, the patient does not appear "toxic", the patient can tolerate oral medication, clinical and laboratory "follow-up" can be obtained, and the patient has not recently received antibiotics or been subjected to instrumentation. trimethoprimsulfamethoxazole possesses a spectrum of activity that encompasses most organisms that cause community-oriented bacterial pyelonephritis in women, and this drug has been successfully used for the outpatient treatment of symptomatic pyelonephri-ti^.^^ metronidazole administered orally is well absorbed even in the presence of food. consequently, the serum concentrations of metronidazole that are achieved are similar after either oral or intravenous administration of the drug. patients who are responding to parenteral metronidazole therapy can be successfully switched to oral metronidazole when the clinical situation dictates, and this results in substantial savings. if a patient is unable to swallow tablets, the drug can be given as a liquid preparation that can be formulated by the hospital pharmacist. duration of drug therapy contributes to antibiotic costs. virtually all recommendations as to how long drug therapy should continue are empiric, even for common disorders such as pneumococcal pneumonia and streptococcal c e l l~l i t i s .~~~ since limited information is available on the precise duration of drug therapy, patients are probably treated for unnecessarily long periods. as new data emerge, however, we learn that antibiotic therapy can often be shortened, thereby resulting in cost savings and diminished toxicity. single dose therapy has emerged as the preferred treatment tactic for acute, symptomatic bacterial cystitis in young women.i when compared to the conventional - day course of treatment single dose therapy is less expensive, safer, equally effective, and associated with better compliance. single dose treatment of women with bacterial cystitis has not resulted in bacteremias, hospitalization or death. ' single dose treatment should be limited to women who are not pregnant, have neither renal insufficiency nor structural abnormalities of the urinary tract, and are able to provide post-treatment cultures. the following antimicrobial agents are safe and effective single dose therapy: sulfisoxazole g; trimethoprim mg; trimethoprim-sulfamethoxazole regularstrength tablets and amoxicillin g." no explanation exists for why cephalosporins have consistently failed as single dose therapy.i a single oral dose of grams of metronidazole (eight mg or four mg tablets) is less expensive, as effective, and as well tolerated as the conventional - day course of therapy to treat vaginitis caused by trichomonas ~a g i n a l i s .~~ studies have also documented the efficacy of shorter treatment courses employing regimens of ampicillin, tetracycline or erythromycin to treat disseminated gonococcal i n f e~t i o n .~~ formerly, disseminated gonococcal infections were treated for a minimum of weeks by the intravenous route exclusively. adults with disseminated gonococcal infection can be effectively treated with a one week program consisting initially of million units of penicillin g administered every hours followed by oral ampicillin or amoxicillin prescribed as mg four times daily. , hospitalization is usually recommended to establish the diagnosis of disseminated gonococcal disease since misdiagnosis occurs not infrequently with this disorder. selected patients can complete the oral regimens in an outpatient setting or, alternatively, they can be treated entirely without ho~pitalization.~~ acceptable oral regimens consist of giving amoxicillin ( mg four times daily), tetracycline ( mg four times daily), or erythromycin ( mg four times daily) for at least days. the following requirements should be met before home treatment is recommended: the diagnosis should be well established; the patient should be considered compliant; complications, such as purulent joint effusions, must be cost-effective anti b iotlc prescribing gleckman and ganfz absent; and the patient must be able to return for follow-up observations. the standard treatment for pulmonary tuberculosis consists of the combination of isoniazid (inh)ethambutol, inh-rifampin, or rifampin-ethambutol prescribed for - months. prolonged chemotherapy is expensive and is associated with compliance and toxicity problems. studies have confirmed that specific regimens given for to months to adults with uncomplicated pulmonary tuberculosis are as effective as more prolonged therapy and have the advantage of being less expensive and well tolerated. s short course treatment regimens for adults consist of administering inh ( mg) and rifampin ( mg) daily for to months. if the patient has had previous antituberculosis therapy or has emigrated from an area such as asia or africa, where high levels of initial drug resistance exist, then the inh-rifampin should be supplemented with streptomycin ( - mg/kg), pyrazinamide ( mg/kg), or ethambutol ( mg/kg) daily for the first months, pending the results of susceptibility tests. if resistance to inh or rifampin is found by susceptibility tests, then short course chemotherapy is not indicated. a regimen should be selected using two or three drugs to which the organisms are susceptible, and it should be given for a period of to months. for the abbreviated treatment to be successful, patient compliance is critical. patients should be seen monthly, pill counts should be performed, urines should be tested for the presence of inh and rifampin, and bacteriologic examinations of sputum must be done. treatment should be continued until at least months have elapsed from the time of conversion of the sputum culture from positive to negative. for most patients, the total duration of therapy will be months. patients should be followed closely for year after completing the short course regimen in order to detect relapse. for noncompliant patients, after an initial phase of daily inhrifampin treatment administered for to months, therapy can be continued twice-weekly with inh ( mg/kg) and rifampin ( mg) for to months. the medications must be administered under supervision, and patients who receive intermittent rifampin should be monitored for the development of thrombocytopenia and a "flu syndrome." these abbreviated treatments cannot be recommended for children, for patients harboring drug-resistant organisms, for patients with extra-pulmonary tuberculosis, for patients with unique predisposing concomitant disease, such as silicosis or diabetes, or patients who have experienced previous drug failure or microbiological relapse. conventional therapy for endocarditis caused by penicillin-susceptible streptococci, defined as those strains with a minimum inhibitory concentration of d . pg/ml, consist of either million units of penicillin per day administered intravenously alone for four weeks or million units of parenteral penicillin for four weeks and concomitant streptomycin ( g/day) during the initial two weeks. a regimen consisting of penicillin and streptomycin prescribed for only two weeks appears to be as safe and as effective as these four week regimen^.^^.^^ no data are available showing that the relapse rate after the two week treatment course exceeds that of the conventional - week treatment program. the patients are treated in the hospital and receive procaine penicillin ( . million units every six hours) and streptomycin ( mg every hours) intramuscularly for weeks. short term therapy is not, however, recommended for patients who have had symptoms that exceed three months or have infection involving a prosthetic valve. preexisting vestibular disease, the presence of complications, (mycotic aneurysm, shock, cerebritis), abnormal renal function, or the identification of streptococcal endocarditis caused by resistant (mic > . pg/ml) or nutritionally dependent strains precludes short course therapy. the principal disadvantages of the two week regimen are the frequent intramuscular injections required and the risk of streptomycin-induced otoxicity. the total cost of antibiotic therapy consists of a number of components, only one of which is the drug price. "hidden" costsadministration sets and supplies, tests for laboratory monitoring, pharmacy preparation time and nursing timeare usually omitted in cost analyses. these ancillary costs can account for approximately one-half of the total expense of antibiotic the rap^.^' potentially less toxic antibiotics that require minimal laboratory monitoring for evidence of adverse reactions can decrease drug costs. for example, laboratory monitoring of renal function and aminoglycoside serum concentrations can contribute as much as one-third of the total antibiotic costs when aminoglycoside antibiotics are pre-s~ribed.~' an antibiotic such as cefazolin that possesses desirable pharmacokinetic properties (i.e., infrequent dosing, reduced dosage and diminished nephrotoxicity when compared with other first generation cephalosporins) and can be prescribed by the intramuscular route can decrease these "hidden" costs considerably. for example, by substituting intramuscular cefazolin for an intravenous betalactam resistant penicillin, a savings of $ per day could occur. when studies demonstrate that different antibiotics provide equivalent therapeutic eff icacy and safety, these "hidden" costs should be considered when antibiotic recommendations are being offered. prolonged administration of intravenous antibiotics, i.e., therapy that exceeds weeks in duration, has emerged as the preferred treatment course for patients with osteomyelitis, infective endocarditis and systemic fungal infections. traditionally, these patients have remained in the hospital for the dura- pharmacotherapy volume , number , july/august tion of treatment even though one to two weeks after the onset of therapy many patients feel well and are anxious to return home to complete their treatment. one innovative approach to the treatment of these serious infections has focused on the use of selfadministration of intravenous antibiotics in the the cost of home parenteral antibiotic therapy is about one-fourth to one-third of the inhospital the concept of home intravenous therapy is not new. successful home intravenous programs have included patients with hemophilia who receive clotting factors, patients with parenteral alimentation, and patients sustained by chronic hemodialysis. in , rucker and harrison were the first investigators to report on the use of intravenously administered antibiotics given in the home. sixty-two children with cystic fibrosis were treated at home with either intravenous gentamicin or colistimethate for the management of pseudomonas-related pulmonary infections. in that study, infectious episodes were treated at home, resulting in a % reduction in the need for hospitalization. the patients were seen once weekly, and no major complications were noted. subsequent reports on parenteral administration of antibiotics at home appeared in , (table ) and to date patients have been treated at five centers in the united states and almost half of the patients ( ) were treated at home in a program developed at the fairfax hospital, a large community-teaching hospital in the washington, d.c. area. patients selected for home treatment are considered to have responded satisfactorily to the intravenous program initiated in the hospital and require only a more extended course of intravenous antibiotics. home intravenous programs are coordinated by a team consisting of infectious disease specialists, pharmacists and nurses skilled in performing intravenous infusion. one to two days prior to discharge the patients and a family member are taught the techniques necessary to care for an i.v. cannula. the cannula is changed twice a week at home by a visiting nurse or in the hospital's outpatient department. the duration of home i.v. therapy averaged two to three weeks. in each of the published series, patients with osteomyelitis and septic arthritis have predominated, but patients with other infections have also been successfully managed (table ) . a vast array of antibiotics have been used, and the solutions, which have been prepared in the hospital pharmacy, are kept refrigerated at home. antibiotics with long half-lives, such as cefazolin, are preferred since they permit dosing every six or eight hours. patients may be given a four or five day supply of antibiotic, depending on the stability of the drug, and they are instructed to return to the outpatient department once or twice weekly to have their progress evaluated. all studies have monitored patients for cornplications of the initial infection, compliance, adverse effects, including antibiotic toxicities and i.v. compli-cations, and superinfection. to date, all programs have confirmed the safety and efficacy of this form of therapy. long-term follow-up is not available in all of the studies, but short term efficacy data parallel the experience of in-hospital care. patients have been able to return to work and to school. home antibiotic programs require compliant patients, appropriate close monitoring, and the houra-day availability of a hospital team consisting of a pharmacist, i.v. nurse and physician. successful programs also require that insurance carriers reimburse patients for these out-of-hospital extended charges. to date, medicare has not paid for outpatient antibiotic therapy, and some insurance carriers will reimburse policy holders for only % of the charges. it appears that for selected patients substantial cost savings can be realized with this novel approach to prolonged antibiotic the rap^.^' success of home intravenous antibiotic programs mandates careful selection of patients. those selected must be well enough to go home (except for the need for intravenous therapy), be compliant, and be proficient or have a family member trained in the administration and aseptic care of an i.v. cannula. various strategies have been advocated to reduce antibiotic misuse. approaches have included physician education, omission from formulary, restriction of selected antibiotics by pharmacists or infectious disease specialists, peer audits of prescribing practices, and surveillance of drug use by clinical pharm a c i s t~.~~ an additional strategy for improving antibiotic prescribing practices consists of providing more readily accessible information on antibiotics to clinic i a n~.~~ unfortunately, these efforts have often had limited success. in a study by jones et al, hospital staff did not improve their usage of antibiotics after an intensive educational program. a greater impact on unjustified antibiotic usage has been reported in studies employing direct control measures. substantial savings resulted when usage of selected antibiotics required either an infectious disease consultation or written justification by the mcgowan and finland demonstrated that by removing an antibiotic from the restricted list, there was a marked increase in usage of that agent ' in a study by durbin and associates, physicians were required to indicate the rationale for antibiotic usage. depending on the category selected, drugs were discontinued after days for prophylaxis, after days for empirical therapy, and after days for a therapeutic indication. a new prescription form had to be completed for the drug to be reordered. this program resulted in a % reduction in the mean duration of antibiotic prophylaxis. there was, however, little impact on antimicrobial use on the medical service with the prescription system. another approach that could reduce indiscriminate antibiotic usage is for hospitals to develop their own antibiotic guidelines similar to those developed the guidelines should be developed by a multidisciplinary committee composed of physicians who prescribe antibiotics as well as representatives from infectious diseases, pharmacy, and hospital administration. there should be agreements as to what constitutes appropriate and unacceptable antibiotic usage. once antimicrobial surveillance data to monitor compliance are accumulated, corrective action will require peer pressure from chiefs of services and strong administrative support. postoperative wound infection: a controlled study of the increased duration of hospital stay and direct costs of hospitalization postoperative wound infections: the influence of ultraviolet irradiation on the operating room and of various other factors surgical wound infection occurrence in clean operations the third-generation cephalosporins: a plea for restraint use of antimicrobial drugs in general hospitals: patterns of prophylaxis prevention of bacterial endocarditis use of antibiotics: a brief exposition of the problem and some tentative solutions this is medical progress? trends and consequences of antibiotic use in the united states a study of antimicrobial misuse in a university hospital the controversy of treatment of asymptomatic bacteriuria in nonpregnant women-resolved role of infection in chronic bronchitis antibiotic therapy of acute exacerbations of chronic bronchitis. a controlled study using tetracycline cutaneous abscesses clinical management of urinary tract infection antibiotic combinations: the clinical relevance of synergy and antagonism prospective, randomized, comparative study of clindamycin, chloramphenicol, and ticarcillin, each in combination with gentamicin, in therapy for intraabdominal and female genital tract sepsis cost comparison of two antimicrobial regimens for treating mixed aerobic-anaerobic infections a prospective randomized controlled trial of cefoxitin versus clindamycin-aminoglycoside in mixed anaerobic-aerobic infections clindamycin treatment of osteomyelitis and septic arthritis in children oral antibiotic therapy for skeletal infections of children. ii. therapy of osteomyelitis and suppurative arthritis high-dose dicloxacillin treatment of acute staphylococcal osteomyelitis in children long-term follow-up of ambulatory management of osteomyelitis success with cephalordine-cephalexin therapy use of the serum bactericidal titer to assess the adequacy of oral antibiotic therapy in the treatment of acute hematogenous osteomyelitis marks mi et at. oral antibiotic therapy of skeletal infections in children oral antibiotic therapy for bone and joint infections oral versus parenteral therapy of pyelonephritis metronidazole: an update on its expanding role in clinical medicine for how long should antimicrobial therapy continue (editorial) current practices in antimicrobial dosing efficacy of single-dose and conventional amoxicillin in urinary-tract infections localized by the antibody coated bacteria technique treatment of trichomonas vaginalis infections treatment of disseminated gonococcal infections gonococcal tenosynovitis-dermatitis and septic arthritis sexually transmitted diseases treatment guidelines short-course chemotherapy for tuberculosis with largely twice-weekly isoniazid-rifampin british thoracic association. a controlled trial of six months chemotherapy in pulmonary tuberculosis. second report: results during the months after the end of chemotherapy guidelines for short-course tuberculosis chemotherapy antimicrobial therapy for penicillin-sensitive streptococcal infective endocarditis: two-week regimens outpatient intravenous medications in the management of cystic fibrosis intravenous antibiotic therapy in an outpatient setting intravenous antibiotic therapy at home feasibility of outpatient self-administration of parenteral antibiotics outpatient intravenous antibiotics experience with patients intravenous antibiotic therapy at home training patients to administer intravenous antibiotics at home self-administration of intravenous antibiotics: an efficient, cost-effective home care program. cma j . frame pt. outpatient intravenous antibiotic therapy (editorial) evaluation of antibiotic usage: a comprehensive look at alternative approaches antimicrobial misuse, antibiotic policies and information resources the effect of an educational program upon hospital antibiotic use the antibiotic utilization committee: an effective tool in the implementation of drug utilization review that monitors the medical justification and cost of antibiotic use infection and antibiotic usage at boston city hospital: changes in prevalence during the decade - usage of antibiotics in a general hospital: effect of requiring justification improved antibiotic usage following introduction of a novel prescription system successful two-week treatment schedule for penicillin-susceptible streptococcus viridans endocarditis guidelines for peer review, veterans administration ad hoc interdisciplinary advisory committee on antimicrobial use, audits of antimicrobial usage the influence of dose frequency - key: cord- - nvrakbs authors: patel, zara m.; hwang, peter h. title: acute bacterial rhinosinusitis date: - - journal: infections of the ears, nose, throat, and sinuses doi: . / - - - - _ sha: doc_id: cord_uid: nvrakbs acute bacterial rhinosinusitis (abrs) is a highly prevalent disease associated with significant direct and indirect costs. it is paramount that a practitioner can distinguish between acute viral rhinosinusitis and abrs to avoid unnecessary antibiotic usage. it is also important to understand that establishing a diagnosis of abrs does not necessitate the prescribing of antibiotics, unless the abrs patient presents with severe or worsening symptoms or an abrs complication. complications include extension of infection to the orbit and central nervous system. injudicious use of antibiotics imparts societal costs in terms of financial expense as well as contributing to higher levels of bacterial resistance. this chapter reviews the epidemiology, clinical features, diagnosis, and treatment of abrs. acute sinusitis, also known as acute rhinosinusitis, is an inflammation of the nasal cavity and paranasal sinuses that lasts up to weeks [ , ] . we preferentially use the term rhinosinusitis in place of sinusitis to acknowledge that the inflammation seen in sinusitis involves the nasal cavity as well. although many patients present with rhinosinusitis that has lasted longer than weeks, these more protracted forms of sinusitis-subacute and chronic rhinosinusitis-are discussed in chap. . the definitions for the various types of rhinosinusitis are summarized in table . . it is estimated that % of the u.s. population is affected by acute and chronic rhinosinusitis [ ] . women appear to be affected more than men, and the most commonly affected age group among adults is mid- s to mid- s [ ] . older age, smoking, air travel, exposure to changes in atmospheric pressure as with flying or diving, swimming in chlorinated pools, asthma and allergies, dental disease, and immunodeficiency are all considered risk factors for the development of ars [ ] . direct costs from managing acute and chronic sinusitis are estimated at $ billion dol-lars per year in the u.s., not accounting for significant indirect costs attributable to lost work productivity and reduced job effectiveness [ , ] . acute rhinosinusitis is the fifth most common diagnosis for which antibiotics are prescribed; thus correct diagnosis of ars and judicious treatment with antibiotics are particularly important in an age of growing bacterial resistance [ ] . most patients suffering with sinus symptoms will have a viral etiology of their inflammation [ ] . it can be quite difficult for a primary care physician to distinguish between simple upper respiratory infections (uri), episodes of acute viral rhinosinusitis (avrs), and episodes of true bacterial rhinosinusitis (abrs). almost % of patients with viral uris have evidence of avrs [ ] . the most common viruses that cause vrs are rhinovirus, influenza virus, and coronavirus; others include parainfluenza virus, adenovirus, respiratory syncytial virus, and metapneumovirus [ ] . patients with avrs typically develop symptoms - days after infection. viruses attach to the nasal epithelium and can spread from the nasal cavity to the paranasal sinuses. once within the paranasal sinuses, viruses may exert direct toxic effects on mucociliary clearance, and may induce epithelial permeability and hypersecretion from inflammatory cytokines. these alterations lead to the mucosal edema, thickened secretions, and ostial obstruction characteristic of acute rhinosinusitis. acute bacterial rhinosinusitis most commonly occurs as a complication of viral infection, complicating . - . % of cases of the common cold [ ] , however, other factors may also predispose to abrs, such as allergy, immune dysfunction, impaired ciliary function, anatomic narrowing of the sinuses, or poor dentition [ ] . the most common bacteria associated with abrs are streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis. microaerophilic streptococci and anaerobic bacteria are commonly identified if the abrs originates from an odontogenic source. when a sinus culture is positive in a patient with abrs, a single pathogen is usually found in high concentration, although in approximately % of the patients, two pathogens can be found in high concentration [ ] . the usefulness and validity of sinus cultures have recently been reconsidered as more is understood about the complex commensal bacterial community comprising the sinus microbiome. however, cultures are still helpful in some clinical situations such as complicated or nosocomial abrs. nosocomial bacterial sinusitis may develop in patients on transplant services or in the intensive care unit, particularly in those who have had prolonged intubation or who have nasogastric tubes or feeding tubes. in contrast to communityacquired sinusitis, nosocomial sinusitis is more likely to involve resistant bacteria, including staphylococcus aureus and gram-negative bacilli such as pseudomonas [ , ] . patients with acute rhinosinusitis typically complain of nasal congestion and obstruction, purulent nasal discharge, and facial pain or pressure that is worse when bending forward. maxillary tooth discomfort may be present if the maxillary sinus is involved. other less specific symptoms can include fever, fatigue, cough, hyposmia, ear pressure, headache, and halitosis. these symptoms apply to both avrs and abrs. therefore, it is not possible for patients nor clinicians to discern a viral from bacterial infection based on symptoms alone. another diagnostic fallacy is that if nasal drainage is colored it must be from a bacterial infection [ ] . to discern avrs from abrs, the clinician should focus on the duration and course of the symptoms. acute viral rhinosinusitis will typically have partial or complete resolution of symptoms by days, with a peak at - days [ ] . if symptoms persist beyond days, or if symptoms improve but worsen again within days ("double-worsening"), there is a higher likelihood that the patient has abrs [ ] . on physical examination, findings may include purulent drainage in the nose or posterior pharynx and nasal speech. although many physicians have been taught to percuss the sinuses to evaluate for pain, this has not been shown to be useful [ ] . similarly, transillumination of the sinuses to detect an air-fluid level is an insensitive test and not recommended [ ] . examination of the nasal cavity with either anterior rhinoscopy (performed with a handheld otoscope or nasal speculum) or nasal endoscopy (using a flexible or rigid endoscope) may show diffuse mucosal edema, narrowing of the middle meatus, inferior turbinate hypertrophy, and purulence. a complete head and neck examination is important to both confirm the suspected diagnosis of acute rhinosinusitis as well as rule out any other possible diagnoses and evaluate for any possible complications. complications from abrs, less commonly seen in adults than children, are rare but can be potentially serious, even life-threatening. bacterial sinusitis can spread beyond the paranasal sinuses and nasal cavity to the orbit or surrounding tissues directly, or to the central nervous system (cns) either directly or hematogenously. chapter discusses complications of abrs in children. orbital complications include preseptal cellulitis, orbital cellulitis, subperiosteal abscess, orbital abscess, and cavernous sinus thrombophlebitis. the chandler classification, the most common method of characterizing orbital complications, organizes orbital complications in terms of progressive severity (see fig. . ) [ ] . infection in preseptal cellulitis involves the eyelid skin in front of the orbital septum and tarsal plates of the eyelids, while infection in orbital cellulitis, subperiosteal abscess, and orbital abscess involves the orbit. in orbital cellulitis, there is diffuse inflammation of the orbital fat and extraocular muscles. in subperiosteal abscess, there is a collection of pus in the space between the orbital bony wall and periorbita, and in orbital abscess, there is a collection of pus in the orbital fat. it is important to distinguish preseptal cellulitis from orbital infection (cellulitis or abscess), because preseptal infections do not threaten vision while orbital infections do. patients with preseptal cellulitis will present with lid swelling and redness of the periorbital region but will not have involvement of the orbit (postseptal compartment) so will not have any of the three "orbital signs": impaired extraocular motility, decrease in vision, or proptosis. patients with orbital cellulitis or abscess will present with similar lid changes, but in addition will have one or more orbital signs as a result inflammation of the extraocular muscles and fat within the orbit. patients with orbital cellulitis or abscess may also have chemosis (edema of the conjunctiva), pain with eye movement, and/or diplopia. in general, patients with subperiosteal or orbital abscess have more pronounced orbital signs than those with orbital cellulitis. because most sinogenic orbital abscesses arise from the ethmoid or medial frontal sinuses, the inflammation in the orbit is often most pronounced medially and/or superomedially, and the eye may be displaced inferolaterally. patients with chronic sinus obstruction with nasal polyps may develop a frontal sinus mucocele that silently erodes the frontal sinus floor (orbital roof); an acute superinfection may cause orbital cellulitis or abscess ( fig. . ). cavernous sinus thrombophlebitis can sometimes be insidious, but advanced cases will be marked by cranial nerve palsies involving iii, iv, vi (sometimes also v and v ), fever, photophobia, visual loss, and signs of contralateral orbital involvement. acute bacterial rhinosinusitis may also lead to cns infections, including meningitis, epidural abscess, subdural empyema, or brain abscess. symptoms of meningitis include fever, headache, photophobia, nuchal rigidity, and mental status changes. symptoms of epidural and brain abscesses may include headache, mental status changes, lethargy, and nausea and vomiting. there may or may not be papilledema or unilateral neurological findings on examination. osteomyelitis of the paranasal sinus bones can occur as a consequence of abrs but is a rare complication. patients usually complain of dull pain at the involved site and have localized tenderness, warmth, erythema, and swelling; fever may be present. chronic frontal sinusitis may lead to osteomyelitis of the anterior table of the frontal sinus with frontal "bossing"-i.e., swell- patients with any of the signs or symptoms suggesting a complication of abrs should be urgently referred to an emergency department for evaluation and management. while preseptal cellulitis alone may respond to oral antibiotics, patients with any other orbital or any cns complication require intravenous antibiotics, close inpatient monitoring, and may require emergency surgery to drain an abscess if one is present. an ophthalmologist should be consulted for patients with orbital complications, and consultation with a neurologist or neurosurgeon is usually indicated for patients with cns complications. orbital cellulitis or abscess may lead to permanent loss of vision if not appropriately and promptly treated. neurologic complications may progress rapidly and lead to permanent disability or death if not recognized and treated promptly. adequate clinical suspicion as well as prompt recognition and treatment of extrasinus complications are essential. imaging is not indicated in uncomplicated abrs. a practitioner should consider ordering an imaging study only to rule out a complication of abrs or to establish an alternative diagnosis. it is important to remember that "abnormal" findings involving the sinuses do not necessarily confirm a diagnosis of acute rhinosinusitis, as % of normal individuals may demonstrate some form of abnormal mucosal thickening of the sinuses on ct [ ] . equally important, imaging cannot distinguish between viral and bacterial rhinosinusitis [ ] . when there is sufficient indication, ct with contrast or magnetic resonance imaging (mri) are the studies of choice. computed tomography better delineates bony detail, while mri provides superior delineation of soft tissue detail. when a complication is suspected, contrast-enhanced imaging is indicated to demarcate areas of extrasinus infection. plain films are no longer indicated in evaluating adult sinusitis [ ] . no role has been established for routine cultures in uncomplicated abrs. cultures may be considered when there is concern for a complication of sinusitis, antimicrobial resistance, or an unusual organism-the last might be suspected in the case of an immunocompromised host. nasal cavity cultures from blindly obtained swabs are not reliable indicators of true pathogens in the sinuses and are therefore not useful in the diagnosis of abrs [ ] . the gold standard in the diagnosis of abrs is a maxillary sinus antral puncture and aspiration via an inferior meatal or canine fossa approach. however, sinus aspiration is invasive and not available to most primary care physicians. endoscopic culture of the middle meatus is minimally invasive alternative and has been shown to correlate well with maxillary sinus cultures obtained by antral puncture [ ]. there are many conditions that can cause symptoms of rhinorrhea, facial pain, or dental pain, mimicking the presentation of abrs. the common cold, allergic and nonallergic rhinitis, and primary dental pathology are the most typical. temporomandibular joint disorders, neuralgias, and other causes of atypical facial pain should also be considered, as well as primary headache disorders such as migraine, tension headache, and cluster headache. importantly, in immunosuppressed patients, acute invasive fungal sinusitis must also be considered (see chap. ). acute bacterial rhinosinusitis is generally a selflimited disease and can resolve on its own without antibiotics. systematic reviews and meta-analyses have found that the majority of patients with abrs will resolve their symptoms without antibiotic therapy within weeks [ ] . therefore, contrary to conventional wisdom, the successful distinction of abrs from avrs does not equate with an automatic indication to prescribe antibiotics. in the first days of symptoms, supportive therapy alone is indicated for uncomplicated abrs in adults regardless of whether a diagnosis of avrs or abrs has been made, except for cases of "double worsening" or severe symptoms persisting for at least days. severe symptoms are defined as high fever (temperature °f or higher) and purulent nasal drainage [ , ] . "double worsening" refers to worsening of symptoms after initial improvement. this is suggestive of an initial viral infection followed by a bacterial superinfection. guidelines regarding treatment of abrs have been published for adults by the american academy of otolaryngology -head and neck surgery (aao-hns) [ ] , for both adults and children by the infectious disease society of america (idsa) [ ] , and for children by the american academy of pediatrics (aap) [ ] . the idsa and aap guidelines are similar, but these differ from the aao-hns guidelines in that the latter offers the option of "watchful waiting" rather than antibiotics for up to days beyond abrs diagnosis for adults whose followup is assured. the aap also offers the option of "watchful waiting" in children diagnosed with non-severe "persistent" uncomplicated abrs but only up to days. figure . shows the aao-hns decision tree, table . compares aao-hns and idsa guidelines for adults with abrs, and table . summarizes the aap guidelines for children with abrs. the antibiotic options for children are further discussed in the aap guidelines [ ] . it is important to note that daytime cough is a symptom of abrs for children, unlike adults, and the aap recommends a clinical diagnosis of abrs in children who have ( ) nasal drainage or daytime cough persisting for more than days without improvement, ( ) worsening or new onset of nasal discharge, daytime cough, or fever after initial improvement, or ( ) severe onset, which is defined as fever ≥ °c ( . °f) plus concurrent nasal discharge for at least days. part of the risk-benefit analysis of treating abrs with antibiotics involves an appreciation for potential complications of antibiotic therapy. a cochrane review in found that although using antibiotics can help shorten the course of abrs, the number of adults needed to treat to see that benefit is greater than the number needed to see adverse effects [ ] . metaanalyses of randomized controlled trials have found that, compared with placebo, adults with abrs may benefit from antibiotics at the cost of increased adverse events. estimates of the number needed to treat to benefit range from to patients, while the number needed to harm is approximately eight patients [ ] . the clinician should consider that results of these metaanalyses may be influenced by inclusion and exclusion criteria. the cochrane review analyzed ten trials that randomized antibiotics versus placebo to treat adults with clinically diagnosed abrs [ ] , but many of these trials did not meet current criteria for abrs so probably included avrs as well as abrs. for example, some trials included patients with only or even days of symptoms [ ] . exclusion criteria also may have influenced results, and common exclusion criteria in the ten trials were recent antibiotic use ( % of the trials), severe symptoms ( %), prior ear-nose-throat disease ( %), previous sinus surgery ( %), immune deficiency ( %), and comorbidities such as diabetes, heart failure, or pulmonary disease ( %) [ ] . of course, exceptions to clinical guidelines always exist, especially in immunocompromised patients and any patient in whom a complication is suspected. the individual clinical situation should dictate therapy above all and may warrant immediate antibiotic treatment and referral to a specialist. the clinician should decide if the risk of watchful waiting in the individual patient outweighs the benefit. this was illustrated by a complication that occurred in a patient randomized to the placebo arm of one trial of amoxicillinclavulinate; the patient had persistent symptoms despite weeks of placebo followed by week of antibiotic and was found to have a brain abscess (the abscess pathogen was susceptible to the antibiotic) [ ] . as cultures are not indicated in abrs, the initial choice of antibiotic treatment is empiric and is based on the most common pathogens (as outlined above). therefore, first-line therapy for adults would be oral amoxicillin or amoxicillinclavulanate ( / three times daily or / mg twice daily), depending on the resistance patterns within the community. in communities with a higher prevalence of beta-lactam resistance among haemophilus influenzae and moraxella catarrhalis isolates, amoxicillinclavulanate is preferred [ , ] . macrolides and trimethoprim-sulfamethoxazole are not recommended due to high rates of s. pneumoniae resistance (and for trimethoprim-sulfamethoxazole, also h. influenzae resistance) [ , ] . all doses given are for patients with normal renal function. in adults with specific risk factors for antibiotic resistance, high dose amoxicillin with clavulanate ( g/ mg twice daily) would be indicated. examples of risk factors for resistance include living in communities where the prevalence of penicillin-non-susceptible s. pneumoniae exceeds %; age > years; hospitalization in the last days; antibiotic use in the previous month; immunocompromise; multiple comorbidities; or severe infection with evidence of systemic toxicity and threat of suppurative complications [ , ] . for adults with penicillin allergy, oral doxycycline ( mg twice daily or mg daily) is a table . adult acute bacterial rhinosinusitis (abrs): recommendations for evaluation and treatment by the american academy of otolaryngology-head and neck surgery (aao-hns) [ ] and the infectious disease society of america (idsa) [ ] recommendation aao-hns idsa clinical diagnosis of acute bacterial rhinosinusitis (abrs) symptoms of acute rhinosinusitis that: ( ) persist ≥ days or ( ) worsen after initial improvement ("double worsening") same as ( ) and ( ) the aao-hns states that "watchful waiting" in adults "should be offered only when there is assurance of follow-up such that antibiotic therapy is started if the patient's condition fails to improve by days after abrs diagnosis or if it worsens at any time" [ ] . b first-line therapy with amoxicillin-clavulanate rather than amoxicillin is generally recommended by the aao-hns for the following: older age (age > years), immunocompromise, comorbid conditions (chronic cardiac, hepatic, or renal disease), history of recurrent abrs, moderate to severe symptoms, or risk factors for resistant organisms such as antibiotics within the past month, contact with health care environment, contact with child in daycare, high prevalence of resistant bacteria in the community. the aao-hns recommends high-dose amoxicillin (idsa recommends high dose amoxicillin-clavulanate) for adults at increased risk for infection with amoxicillin-resistant organisms c both aao-hns and idsa recommended either doxycycline or a respiratory fluoroquinolone such as levofloxacin in penicillin-allergic patients, but the food and drug administration subsequently recommended against use of fluoroquinolones for abrs unless no alternatives exist (see the text). reasonable alternative, as is a combination of clindamycin plus a third-generation cephalosporin such as cefixime or cefpodoxime [ ] . fluoroquinolones have traditionally been another alternative, but are now highly cautioned against due to an increasing recognition of serious side effects, including tendinitis, tendon rupture, and peripheral neuropathy. the food and drug administration has advised that fluoroquinolones should be used for abrs only when no alternative options exist [ ] . for children with abrs, the first-line treatment recommended by the aap is amoxicillin at standard pediatric dosing ( mg/kg per day in divided doses) for children aged and older with uncomplicated abrs of mild to moderate severity and who do not have risk factors for antimicrobial resistance (no antibiotics within weeks and no day care), or high-dose amoxicillin ( - mg/kg per day in divided doses, up to a maximum of g per dose) in communities with high prevalence of resistant bacteria (i.e., penicillin non-susceptible s. pneumoniae) [ ] . for children presenting with moderate to severe abrs, as well as children under age years, attending day care, or who have recently received an antibiotic, the aap recommends high dose amoxicillin-clavulinate. a single mg/kg dose of intravenous of intramuscular ceftriaxone may be given to children who are vomiting, unable to tolerate oral medications, or are unlikely to be adherent to initial doses of antibiotics [ ] . oral antibiotics may be started h after this parenteral dose, to complete the course of therapy. for additional details regarding treatment of children with abrs, including treatment in patients with penicillin allergies, the reader is referred to the aap guidelines [ ] . note that these guidelines do not apply to children younger than age . the recommended duration of antibiotic treatment is - days in adults (longer in children), provided the patient is improving. longer courses ( ) persistent nasal drainage or daytime cough or both for > days ("persistent illness") or ( ) worsening course (see text) or ( ) severe onset of symptoms (t °f plus nasal drainage) lasting ≥ days cough is not included as a symptom of abrs in adults (see table . ) use of radiologic imaging (ct with contrast) only for suspected complication involving orbit or central nervous system similar recommendations for adults initial therapy of abrs antibiotics for worsening course or severe onset (" " or " " above), but antibiotics or watchful waiting (for up to days) for "persistent illness" (" " above) if a patient does not improve or in fact worsens with first-line therapy, a change in therapy is indicated. there is not good evidence to guide the choice of second-line therapy, but one may consider either increasing the dose or changing class of antibiotics. options in adults include high dose amoxicillin ( g twice daily) with clavulanate, doxycycline, levofloxacin, and moxifloxacin. the latter quinolone options should again be prescribed with caution, with regard for potential adverse effects of fluoroquinolone use [ ] . if patients with abrs have failed to respond to both first-line and second-line therapies, or if at any time a potential complication is suspected, they should be referred for further evaluation to a specialist and possibly undergo radiologic imaging. the use of over-the-counter antipyretics and analgesics can help to treat fever and pain in abrs [ ] . saline irrigations offer the opportunity for symptomatic relief with a favorably low side effect profile (minor nasal burning and irritation) [ ] . however, there are no randomized controlled trials of the use of saline irrigations in abrs [ ] , so their benefit is unknown. in addition, patients cannot obtain sterile solutions for nasal irrigations so whether or not there is risk with nasal irrigations with non-sterile solutions is unknown. intranasal glucocorticoid sprays can be helpful in abrs. a meta-analysis of three studies has shown a minor benefit in adding nasal steroid sprays to the treatment regimen of patients with abrs [ ] . other therapies that are sometimes used in supportive treatment of abrs include oral and topical decongestants, antihistamines, and mucolytics. however, none of these therapies has good evidence to support its use; some may actually cause harmful side effects, such as raising blood pressure (associated with oral decongestants), and irritating or overdrying the nasal lining (associated with antihistamines) [ ] . acute bacterial rhinosinusitis is one of the most common infections treated by primary care providers. the distinction between abrs and viral upper respiratory tract infections is usually made based on duration and time course of compatible symptoms, with abrs characterized by either persistence of symptoms for at least days, worsening of symptoms (or double worsening), or severe onset of symptoms including high fever for days. radiologic imaging and sinus cultures are not indicated for uncomplicated abrs. adults with non-severe, uncomplicated abrs and whose follow-up is assured may be observed without antibiotics (watchful waiting) or treated with antibiotics. patients with orbital or cns complications require aggressive treatment with intravenous antibiotics and possibly surgery. rhinosinusitis: establishing definitions for clinical research and patient care clinical practice guideline (update): adult sinusitis summary health statistics for u.s. adults: national health interview survey in the clinic. acute sinusitis antimicrobial treatment guidelines for acute bacterial rhinosinusitis productivity costs in patients with refractory chronic rhinosinusitis medical management and diagnosis of chronic rhinosinusitis: a survey of treatment patterns by united states otolaryngologists clinial practice. acute sinusitis in adults acute community-acquired sinusitis mandell, douglas, and bennett's principles and practice of infectious diseases european position paper on rhinosinusitis and nasal polyps . a summary for otorhinolaryngologists sinusitis of the maxillary antrum nosocomial sinusitis in patients in the medical intensive care unit: a prospective epidemiological study nosocomial sinusitis rhinovirus infections in an industrial population characteristics of illness and antibody response adult acute rhinosinusitis a practical guide for the diagnosis and treatment of acute sinusitis the pathogenesis of orbital complications in acute sinusitis endoscopically directed middle meatal cultures versus maxillary sinus taps in acute bacterial maxillary rhinosinusitis: a meta-analysis a -year-old woman with acute onset of facial pressure, rhinorrhea, and tooth pain: review of acute rhinosinusitis clinical practice guideline for the diagnosis and management of acute bacterial sinusitis in children, aged to years antibiotics for clinically diagnosed acute rhinosinusitis in adults predicting prognosis and effect of antibiotic treatment in rhinosinusitis effect of amoxicillin-clavulinate in clinically diagnosed acute rhinosinusitis. a placebo-controlled, double-blind, randomized trial in general practice fda drug safety communication: fda advises restricting fluoroquinolone antibiotic use for certain uncomplicated infections; warns about disabling side effects that can occur together saline nasal irrigation for acute upper respiratory tract infections intranasal steroids for acute sinusitis key: cord- -fm rm authors: leja, mārcis; dumpis, uga title: what would the screen-and-treat strategy for helicobacter pylori mean in terms of antibiotic consumption? date: - - journal: dig dis sci doi: . /s - - -z sha: doc_id: cord_uid: fm rm several guidelines recommend the screen-and-treat strategy, i.e. active search for the presence of helicobacter pylori infection and its eradication to prevent the possibility of gastric cancer. it is thought that a relatively short duration antibiotic regimen given once in a lifetime would not significantly increase overall antibiotic consumption. however, this would mean offering antibiotic treatment to the majority of the population in countries with the biggest burden of gastric cancer who would, therefore, have the greatest benefit from such a strategy. so far, no country has implemented an eradication strategy. with an example based on the current situation in latvia, we have estimated the increase in antibiotic consumption if the screen-and-treat strategy was applied. depending on the scenario that might be chosen, clarithromycin consumption would increase up to sixfold, and amoxicillin consumption would double if the recommendations of the current guideline in the local circumstances was applied. it appears that an increase in commonly used antibiotic consumption cannot be justified from the viewpoint of antibiotic stewardship policies. solutions to this problem could be the use of antibiotics that are not required for treating life-threatening diseases or more narrow selection of the target group, e.g. young people before family planning to avoid transmission to offspring. additional costs related to the increase in resistome should be considered for future cost-effectiveness modelling of the screen-and-treat strategy. although declining in incidence, gastric cancer will remain an important healthcare issue for the foreseeable future due to aging and the increase in global population. the group of experts gathered by the international agency for research on cancer (iarc) has suggested implementation of gastric cancer prevention by helicobacter pylori (h. pylori) eradication in well-controlled research settings (ml was part of the working group) [ ] . the annual total number of new cases accounts for ~ one million, responsible for > % of global cancer-related deaths each year [ ] . this number is estimated to remain stable for at least the next years if no prevention measures are implemented [ ] . infection with h. pylori is the key risk factor for this type of cancer, responsible for ~ % of the distal (non-cardia) cancer cases [ , ] . several prevention strategies, including primary and secondary prevention are suggested to decrease the mortality caused by gastric cancer. only about - % of individuals infected with h. pylori are likely to develop gastric cancer in their lifetime [ , ] . ideally, only the bacteria potentially leading to cancer or other diseases should be eradicated; however, risk stratification attempts based on h. pylori virulence factor identification or host susceptibility, e.g. by detecting the relevant polymorphisms of proinflammatory cytokines, have not led to a strategy that could be recommended for routine practice [ ] . vaccine development still does not provide encouraging results suggesting that it is close to a routine practice [ ] . eradication of h. pylori in adults hosting the infection appears to be the most effective prevention strategy. the only reliable approach to eliminate the infection is simultaneous use of at least two different antibiotics in combination with potent acid suppression using a proton pump inhibitor or a potassium-competitive acid blocker (pcab) [ ] . a screen-and-treat strategy would mean active testing for presence of h. pylori in the (mostly healthy) general population, and offering eradication to those testing positive [ ] . it is expected that h. pylori eradication would reduce the risk of gastric cancer in the population for ~ % [ ] . such a strategy should comply with the principles of good governance and organization, and the benefits should be well-balanced against the risks that any potential intervention could create [ ] . several risks have been suggested for population-based h. pylori eradication; however, the possible adverse effects related to increased antibiotic consumption probably are the most significant. resistant h. pylori strains are emerging due to high antibiotic consumption [ ] . however, the most significant risks will probably be related to induction of resistance in other clinically relevant bacteria than h. pylori and increase the pool of resistant genes in the gut and upper respiratory system [ ] [ ] [ ] . the currently recommended choice of antibiotics depends on the local resistance pattern of h. pylori, unless susceptibility-based individual therapy is prescribed [ , ] . clarithromycin and amoxicillin are the most widely prescribed antibiotics, frequently used in both low and high clarithromycin-resistant regions. according to the guidelines, the clarithromycin-containing regimen is the choice where h. pylori is clearly sensitive to clarithromycin (for individualized treatment) or if h. pylori resistance to clarithromycin does not exceed % in the reference population [ ] . although the resistance of h. pylori to clarithromycin correlates to the overall use of this antibiotic in a particular population, the choice of treatment solely depends on h. pylori resistance. furthermore, no differences in the eradication regimen are currently recommended, depending on whether the treatment is given for a clinically evident disease, e.g. for complicated ulcer disease or malt lymphoma from prevention strategies in population-based settings. the author viewpoint is that negative effects upon the gut microbiome would not be a significant concern in the case of treating patients with a clinically significant disease, yet should be considered in preventive interventions. the european maastricht v/florence consensus (ml was part of the working group) recommended the screenand-treat strategy in communities at high risk of gastric cancer and consideration of this approach in communities with intermediate to low risk of gastric cancer [ ] . kyoto global consensus has for the first time categorized h. pylori gastritis as an infectious disease, irrespective of symptoms and complications [ ] , which has been reinforced by the maastricht v [ ] and brazilian consensus [ ] . all h. pylori infected subjects are recommended to undergo eradication therapy according to the kyoto consensus unless there are competing considerations, such as comorbidities, re-infection rates in their communities, competing health priorities of society or financial issues [ ] . the recent guidelines of asean (association southeast asian nations) countries support eradication to prevent gastric cancer by considering this strategy as costeffective, depending on the disease burden in the relevant community [ ] . a similar opinion was formed in the second asia-pacific consensus guidelines for h. pylori infection a decade ago for communities with high incidence of gastric cancer [ ] . at the same time, some of the guidelines and expert group recommendations are less enthusiastic regarding population-based eradication. the american college of gastroenterology does not recommend active search of h. pylori in an asymptomatic population [ ] . an expert group hosted by iarc has suggested the need for interventional strategies to decrease the burden of gastric cancer [ , ] ; however, experts recommended that this be done by the means of well-designed clinical studies evaluating the feasibility, acceptance, costs, effectiveness and adverse consequences. a european expert group (ml was part of the working group) within the eu joint action in cancer control (cancon) has been even more critical-they concluded that, as of today, there is no screening method that can be readily recommended for implementation in the eu member states, although there seems to be a need for one [ ] . this also included the screen-and-treat strategy for h. pylori. there is common agreement [ , , ] that the optimal timing for eradicating h. pylori must come before the development of precancerous lesions, since a proportion of the subjects could be progressing to gastric cancer if eradicated at the stage that precancerous lesions (atrophy, intestinal metaplasia, dysplasia) become evident. in japan, currently eradication therapy is reimbursed for all the individuals with h. pylori infection and active gastritis (in addition to the ongoing screening activities for gastric cancer), which means that endoscopy is required to confirm the condition. thereafter, significant increase in eradication therapies has occurred [ ] , yet this cannot be considered an organized screening strategy. in korea, a high gastric cancer incidence country with a gastric cancer screening program [ ] , h. pylori management guidelines do not address the search for the presence of the bacteria in general population [ ] . the country probably closest to the real implementation of screen-and-treat strategy in an organized way is slovenia, where the professional society has issued guidelines for such a strategy [ ] ; it must be mentioned that this country has considerable experience in implementing other types of cancer screening in an organized manner, including screening for colorectal cancer. fourteen-day duration of eradication therapies, including for bismuth-containing therapies, is currently recommended by maastricht v, unless shorter duration therapies ( days) are proven effective locally [ ] . similarly, the toronto consensus recommends a -day treatment [ ] . it is noteworthy that the recommended duration of treatment has extended with the time to achieve higher effectiveness of these therapies. in , the maastricht iii consensus considered days as a valid duration for treatment [ ] . maastricht iv in extended treatment to - days giving a gain of ~ % in the success rates [ ] . the general who principles for screening have been set more than half a century ago by wilson and jungner [ ] , and they are still used as of today although updated in the new genomic era [ ] . furthermore, principles of good screening organization and governance have been consistently emphasized by the expert groups [ ] . the above principles include implementation of the program only when sufficient scientific evidence (with proven effects on the mortality as the end-point) is available and following thorough cost effectiveness analysis, precise definition of the target population as well as invitation strategy, piloting of a screening system, setting up a robust quality assurance system before the system is launched in full operation. h. pylori infection is highly prevalent, affecting about half of the global population [ ] ; the prevalence of precancerous lesions in the general population is also considerable [ ] . therefore, population-based efforts such as the screen-and-treat strategy should follow the general rules of screening. it must be mentioned that the current h. pylori management guidelines so far are lacking this approach. adverse events related to h. pylori eradication therapy are common, but usually they are mild and of short-term duration; the most common symptoms are diarrhea, nausea and/or vomiting, epigastric pain, and altered taste [ ] . a large systemic review performed in demonstrated adverse effects in % of the subjects receiving eradication therapy for peptic ulcer compared to % in patients on a proton pump inhibitor (ppi) or no treatment (rr . ; % ci: . to . ) [ ] . treatment with oral and parenteral antibiotics results in a rapid and significant alteration of the intestinal microbiota. the most obvious outcome of disruption of normal gut microbiome is clostridium difficile infection (cdi). cdi is a major threat to both outpatients and those hospitalized. although any antimicrobium can predispose a patient to cdi, the risk is especially great when using broad-spectrum antimicrobials, which disrupt normal enteric flora [ ] . prolonged treatment with antimicrobial agents is also associated with an increased risk of cdi by extending the time disruption of normal enteric flora [ ] . although not being a typical adverse event, a number of cases have been published on cdi after eradication therapy of h. pylori [ ] . awareness of the complication is particularly important when both duration and indications for h. pylori eradication therapy have been extended. significant perturbation of the gut microbiome might follow the use of antibiotics; however, in the majority of cases the gut microflora would be expected to return to its initial state within a few months [ , ] . resistome is defined as a collection of all antibiotic resistance genes and their precursors in both pathogenetic and non-pathogenic bacteria [ ] . the gut microbiota is a large reservoir of antibiotic-resistance genes [ ] ; an average number of such genes per sample has been reported [ ] . many earlier and more recent studies have suggested long-lasting persistence of resistant pharyngeal and/or gut bacteria following the use of traditional antibiotics used to eradicate h. pylori. one-week treatment of healthy volunteers with macrolides (azithromycin or clarithromycin) has been associated to a significantly increased proportion of macrolide-resistant streptococci in the pharynx compared to a placebo-treated group; resistant streptococci were present for up to days following treatment [ ] . similar data on macrolide-resistant streptococci persistence in the pharynx for more than year in patients receiving clarithromycin-containing h. pylori eradication regimens have been reported by others [ ] . another study has addressed the presence of resistant staphylococcus, streptococcus, enterococcus and bacteroides spp. in samples from nostrils, throat and feces before, weeks and year following triple h. pylori eradication therapy (clarithromycin, metronidazole and omeprazole for days) in a group with peptic ulcer disease, as well as a control group not receiving this treatment [ ] . resistant isolates, in particular of staphylococci and streptococci were higher after year, but not in the control group. another study based on the same patient data demonstrated that this treatment facilitated the selection of highly resistant enterococci present, even years after treatment [ ] . the same group has also addressed erm(b) gene levels (one of the mechanisms for macrolide resistance) both in throat and fecal samples. these levels increased dramatically by - orders of magnitude immediately after antibiotic treatment. in a proportion of the subjects, erm(b) remained elevated years after treatment [ ] . however, the small sample of subjects in this study should be noted. more recently, larger studies applying s rrna gene and metagenomic sequencing have been reported by yap et al. [ ] who investigated stool samples in -year-old volunteers from malaysia before h. pylori eradication, and at , , months thereafter. despite microbial diversity was similar pre-and post-h. pylori eradication with no significant differences in richness and evenness of bacterial species, changes in the bacterial communities at the phylum and genus levels were noted, e.g., the relative abundance of bacterioidetes decreased and firmicutes increased. an important study primarily addressing metabolic effects of h. pylori eradication in general population in taiwan was recently published [ ] . significant perturbation of gut microbiota in short-term was revealed, and it was significantly greater for concomitant and bismuth quadruple therapies than for a standard triple. bismuth quadruple therapy, on the other hand, was not associated with an increase in resistance in e. coli. the authors also demonstrated that for other therapies the resistance rates of e. coli and k. pneumoniae to certain antibiotics were restored at week and year after therapy [ ] . however, this study focussed only on gut microbiome and effect on resistance rates in gram-negative bacteria. widespread use of amoxicillin and clarithromycin causes concern about resistance rates in gram-positive bacteria such as str. pneumoniae and s. aureus [ , ] . current evolution of sequencing methods will provide significant evidence related to the potential perturbation of microbiota following antibiotic treatment, including h. pylori eradication. several studies comparing the effect of different h. pylori eradication regimens on the gut microbiome or resistome are in progress in different countries, including taiwan, spain and latvia. in most of them, the diversity of microbiota is addressed by means of s rrna gene sequencing, whereas others apply metagenome sequencing. the use of antibiotics is the primary driver for the development of resistance and also leads to other adverse effects ranging from allergic reactions to cdi [ ] . the term "antimicrobial stewardship" is encountered in a growing number and increasingly diverse range of contexts, from antimicrobial stewardship programmes in hospitals and the community [ ] , to veterinary antimicrobial stewardship [ ] , one health antimicrobial stewardship [ ] and the who global stewardship framework [ ] . because of the rapidly increasing use of the term without a sole clear definition, it has evolved differently in different settings, influenced by local interpretations [ ] . in general, antimicrobial stewardship programs have a direct responsibility to ensure prudent antibiotic prescribing. reducing antibiotic exposure should minimize the duration and extent of disruption of the microbiome, thereby reducing collateral damage and improving patient outcomes. prolonged courses of antibiotics also increase the risk of colonization with multidrug resistant organisms. therefore, the chain of transmission increases the risk of horizontally infecting more than one patient. interrupting this chain is as important as preventing the development of resistance. data from developed nations suggest that % or more of antibiotic prescriptions are for outpatients [ ] . therefore, limiting their use of antibiotics is essential in reducing both resistance and adverse events. over the last years, several developed countries introduced nationwide initiatives aimed at reduced antibiotic consumption, achieved a drop of > %. in sweden between and , the number of prescriptions per inhabitants per year in outpatient care, including primary health care, decreased by % from to , whereas among children aged - years it decreased by % from to [ ] . between and , a statistically significant decreasing trend in antibiotic use was also seen in finland, luxembourg and norway [ ] . in march , the white house released the national action plan for combating antibiotic-resistant bacteria, which set a target of reducing inappropriate antibiotic use in the outpatient setting by % by [ ] . in light of these trends, any suggestion for mass treatment of infections that would lead to an increase in antibiotic consumption will be carefully scrutinized by national authorities and experts. amoxicillin and clarithromycin, drugs of choice for treatment of h. pylori infections suggested by current guidelines, have wide application for the treatment of several community-acquired infections and account for large proportion of ambulatory antibiotic prescriptions in many countries. they are part of the suggested first or second line treatment regimens for community acquired pneumonia [ ] [ ] [ ] [ ] . amoxicillin or amoxicillin/clavulanate is often suggested as first-line treatment for otitis media, bacterial rhinosinusitis, dental infection and urinary tract infections. macrolides are often recommended as replacement treatment for patients with penicillin allergy. use of azithromycin has been suggested for mass treatment for chlamydia trachomatis eye infections in developing countries. this has already provoked significant concern on its potential adverse events, even though the prevalence of chlamydia is significantly lower than h. pylori. monitoring of the resistance in multiple organisms has been suggested on this indication [ ] . we conducted an exercise by estimating the expected increase in clarithromycin and amoxicillin consumption in latvia if an h. pylori eradication program would be implemented. latvia is a small country (population ~ two million) in northern europe with a relatively low consumption of antibiotics and relatively high incidence of gastric cancerthe incidence per , inhabitants in both genders is . (asr, world population) [ ] . we used data on the clarithromycin (j fa ), amoxicillin (j cr ), and amoxicillin beta-lactam combination (j cr ) consumption in the country provided by the state agency of medicines and expressed in defined daily doses (ddd) per inhabitants in latvia within the period - . mathematical projection for the next years was made, and population distribution per relevant age groups from the official statistics was used. according to the guidelines [ ] , a -day eradication regimen with g per day amoxicillin and g per day clarithromycin was used in the estimates, considering that latvia still belongs to low h. pylori resistance areas to clarithromycin, and therefore, clarithromycin-based triple therapy could be considered the first choice. the prevalence of the infection was considered %, based on our previous studies [ ] . three different scenarios for a screen-and-treat strategy were evaluated: ( ) eradication is limited every year just to persons reaching adulthood- years of age; for the estimates we considered a % adherence rate, since it was expected that the campaign would result in additional therapies outside the target group; ( ) within a -year period, screen-and-treat would be offered to the risk-group defined as - -year-old individuals; one third of the target group would be covered per year with the % compliance as an assumption; ( ) within a -year period, screen-and-treat would be offered to all adult individuals assuming a similar % compliance rate. for scenarios and , additional eradication of the group reaching adulthood was considered starting from year . the results are given in fig. . scenario would lead to a moderate increase in clarithromycin and amoxicillin consumption, scenario to ~ threefold increase, but scenario to more than a sixfold increase of clarithromycin, with a slightly lower (twofold) increase in amoxicillin consumption. such an increase in antibiotic consumption would move latvia from a group of countries with low antibiotic consumption to a group with average antibiotic consumption (see fig. ; data on antibiotic consumption vaccine (either preventive or therapeutic) would be potentially the best solution of the problem [ , ] ; however, current developments have not been promising. non-antibiotic h. pylori eradication regimens have gained significant clinical interest. the use of natural products, including various plant (even mushroom) and fruit extracts, natural oils, chinese herbs, garlic, ginger, green tea, curcumin, cranberries and pistacia gum have been studied, predominantly under laboratory conditions [ ] [ ] [ ] [ ] . some of these compounds had activity against h. pylori, but the results of clinical evaluations in monotherapies have been less promising; also, the quality of these trials has been criticized [ ] . probiotics as a single agent have been also used without major success [ ] . laboratory and animal experiments show the effectiveness of several non-antibiotic treatment modalities against h. pylori. antimicrobial polypeptides (ph-sensitive, helix-coil conformation transitionable agent with a bactericidal activity) have been developed to target and selectively eradicate h. pylori as a single therapeutic agent, without significant effects on commensal bacteria [ ] . another group developed docosahexaenoic acid-loaded lipid nanoparticles with bactericidal activity against h. pylori [ ] . this bactericidal in latvia compared to other countries in the european union/european economic area, with the hypothetical scenarios of an h. pylori screenand-treat strategy expressed as ddd per inhabitants per day. note: the bars in blue indicate the current consumption of antibacterials (including latvia). the bars in red are consumption of antibacterials in latvia with various scenarios during the first year of a screenand-treat strategy implementation. scenario : eradication limited to anybody reaching years of age. scenario : the age group - years invited for screen-and-treat within a -year period; % compliance. scenario : all adults invited for screen-and-treat within a -year period; % compliance agent could also eradicate h. pylori without affecting the other bacteria (lactobacillus, e. coli, s. epidermidis and s. aureus) [ ] . since the abovementioned approaches are still far from clinical practice, regimens that are expected to interfere less with the microbiota and less likely to be responsible for gut (and other location) resistome development are more attractive for clinical applications in the near future. single antibiotic regimens, in particular those not containing macrolides, could attract interest in this respect. use of high-dose amoxicillin is one case, although more frequent dosing is required due to the pharmacokinetics of this drug. high-dose amoxicillin-based dual therapy for first-line h. pylori eradication has so far been evaluated predominantly in asia [ , ] , although a pilot study has been reported in europe [ ] . more profound reduction of the gastric acidity also could contribute to a higher effectiveness of the therapy. sugimoto and yamaoka [ ] have recently reviewed the effectiveness of pcab in h. pylori eradication therapies compared to the traditional ppi containing therapies, and demonstrated significant advantages of the pcab. therefore, one directions for future therapies could be pcab and high-dose (multiple dose) amoxicillin in combination. another approach would be the use of antimicrobial agents that are not typically used in managing life-threatening disease, as well as those causing less induction of the pool resistant genes. bismuth-based therapies are mainly used to overcome the resistance of h. pylori to commonly used antibiotics in clinical settings [ , , ] . an additional gain with these therapies is avoiding the use of clarithromycin and amoxicillin. however, bismuth is not available in many countries. the concern with bismuth-related adverse events is predominantly related to the fact that in the s, use of high-dose bismuth salts for long periods was associated with neurotoxicity; however, systemic review and meta-analysis on bismuth use for h. pylori eradication did not reveal serious adverse events for such therapy [ ] . a recent meta-analysis by ko et al. [ ] has suggested the superiority of bismuth-containing therapies over nonbismuth regimens; furthermore, adding bismuth to conventional standard eradication regimens provides additional gain in the efficacy of the therapies. another meta-analysis on a single capsule -day bismuth-containing quadruple therapy has suggested ~ % eradication success both in first-and second-line therapy [ ] . short-term dysbiosis restoration to baseline levels within an -week period following -day bismuth quadruple therapy has been reported from taiwan; s rrna gene sequencing of the v -v region and sampling before the treatment, as well as , , and weeks thereafter, was used [ ] . therefore, bismuth-containing quadruple therapy is also related to dysbiosis; other antibacterial agents contained in this treatment, in particular metronidazole, could be responsible for perturbations in the microbiota. there are still insufficient data on the potency of bismuth-based therapies to induce and cause persistent resistome. an alternative to the empiric eradication regimen is a h. pylori susceptibility-based individual therapy. this allows avoiding unnecessary use of antibiotics and increasing the effectiveness of the treatment [ ] . however, this is considering only h. pylori resistance patterns, not the effects upon the other gut microbiome. usually, even after h. pylori resistance testing, several options for eradication therapies are remaining, and lower negative effects upon the gut microbiome should ideally considered to be the choice. finally, narrowing the target group for h. pylori eradication, e.g. by targeting young adults before family planning and, therefore, before the potential transmission of the infection to offspring, could be another approach in decreasing the misuse of antibiotics. in spite of the failures mentioned above, individual risk stratification based on gender, lifestyle factors, host and h. pylori genetics continue to be of interest in risk stratification. several meta-analyses have suggested convincing cost-effectiveness of population-wide h. pylori eradication [ ] [ ] [ ] . the benefit is likely to be highest in communities with a high risk of gastric cancer; in developed countries, such an approach could be either cost-effective or cost-neutral if considered on the positive side in reducing the cost of dyspepsia treatment [ ] . few other cost-effectiveness studies have since been published. in denmark, a low h. pylori prevalence country, a -year follow-up of a randomized study population ( , individuals aged - years at enrollment) failed to achieve either quality-of-life or cost-effectiveness [ ] , whereas a modelling exercise in china proved cost-effective in a population-based screen-and-treat strategy related to gastric cancer, peptic ulcer disease and dyspepsia reduction. furthermore, the highest effectiveness was in the age group of years [ ] . screen-and-treat has also been estimated as cost-effective for employees in japan [ ] . however, these studies have not considered the potential costs associated to the increase in the pool of resistant bacteria. the real costs behind the resistome are difficult to estimate; at least two major issues must be considered: ) cost of the resistance and ) cost-effectiveness of interventions to reduce it [ ] . there is also a huge range in the estimates of additional cost, varying from < $ to > $ , per patient episode [ ] . however, generally the current costings could be an underestimated, and therefore, interventions in using antibiotics on a wide-scale could reflect as highly cost-saving benefit. the hidden costs of antibiotic resistance in the united states have recently been estimated by michaelidis et al. [ ] who considered: ( ) hospitalization costs; ( ) secondline inpatient antibiotic costs; ( ) second-line out-patient antibiotic costs, and ( ) antibiotic stewardship costs. the authors estimated that the total hidden cost attributable to each ambulatory antibiotic prescription was $ (range: $ - ), and each ambulatory antibiotic prescription would increase antibiotic costs by % (range: - %), if the cost of the resistance was incorporated into antibiotic costs paid by patients or payers [ ] . applying this estimate to the cost-effectiveness estimates of h. pylori eradication and modelling the costs of resistome for other countries globally probably would change the very beneficial cost-effectiveness picture of screen-and-treat strategy. the cost-effectiveness estimates should also incorporate those of organizing the activities and governance of the process, exactly as in traditional cancer screening program settings [ ] . finally, compliance rates of the target population, equal participation of both genders and coverage of the lower socioeconomic class members is critical for the success for any preventive strategy, and should be considered in cost-effectiveness modelling. because of the necessity of antibiotic use and potential adverse events, participation rates could be lower for an h. pylori screen-and-treat strategy than for traditional screening approaches. this has been suggested by the participation results in the danish community h. pylori screening trial [ ] and is currently being addressed in the gistar cohort in latvia [ ] . the screen-and-treat strategy clearly increases the consumption of antibiotics on a population level. in avoiding the problems of treating life-threatening diseases due to increased resistome, antibiotics with high potential for resistome induction, and use for treating life-threatening diseases (such as macrolides) should be avoided in populationbased h. pylori eradication regimens for otherwise healthy people. narrowing of the target groups for the screen-andtreat strategy is desirable, e.g. for young people before family planning and potential transmission of h. pylori to their offspring. finally, in implementing any screen-and-treat strategy, this should be done under thorough surveillance corresponding to the general principles of screening governance, including surveillance of the incidence of serious infections and all-cause mortality. fr/book-and-repor t-serie s/iarc-worki ng-group -repor ts/-em-helic obact er-pylor i-em-eradi catio n-as-a-strat egy-for-preve nting -gastr ic-cance r- global cancer statistics : globocan estimates of incidence and mortality worldwide for cancers in countries fr/book-and-repor t-serie s/iarc-worki ng-group -repor ts/-em-helic obact er-pylor i-em-eradi catio n-as-a-strat egy-for-preve nting -gastr ic-cance r- global burden of cancers attributable to infections in : a synthetic analysis global burden of gastric cancer attributable to helicobacter pylori review article: 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cancer: theoretical and practical considerations effects of community screening for helicobacter pylori: -year follow-up evaluation of a randomized controlled trial multicentric randomised study of helicobacter pylori eradication and pepsinogen testing for prevention of gastric cancer mortality: the gistar study acknowledgments the work was supported by erdf (european regional development fund) in latvia, project id. nr. . . . / /a/ 'optimisation of h. pylori eradication therapy for population-based gastric cancer prevention'. conflict of interest the authors declare that they have no conflict of interest. key: cord- - rqc cg authors: opal, s. m. title: the challenge of emerging infections and progressive antibiotic resistance date: journal: intensive care medicine in years doi: . / - - - _ sha: doc_id: cord_uid: rqc cg nan our collective vulnerability to the threat of emerging microbial pathogens remains disturbingly evident as we enter the twenty-fi rst century. despite two centuries of knowledge about the germ theory of disease, breaking the genetic code, and sequencing the genomes of virtually every major bacterial and viral pathogen capable of causing disease in humankind, we still fi nd ourselves susceptible to infectious diseases. densely concentrated cities with interconnected human societies linked by international aviation put us at continued risk from future epidemics that will inevitably occur [ ] . the ever expanding population growth of our species will force environmental change as we venture into sparsely inhabited rainforests, populate remote ecosystems and cultivate natural habitats to support our voracious human appetite for goods and services. global warming, environmental degradation and land development along with human upheavals and natural calamities will create new outbreaks with novel pathogens and renew the spread of ancient scourges like cholera [ ] and plague [ ] . numerous examples of intercontinental spread of microbial pathogens within the last fi ve years alone give notice of the susceptibility of human populations to emerging infectious diseases (table ) [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . this is perhaps best exemplifi ed by the tragic events set into motion in late when a previously unidentifi ed, obscure, animal coronavirus (now known as severe acute respiratory syndrome [sars]-cov) was fi rst introduced into an unsuspecting human population in southern china [ ] . current molecular evidence indicates that a food handler in an exotic food 'wet market' in guangdong province probably fi rst became infected by an animal coronavirus from a civet cat. this newly derived animal virus was adapt at infecting humans and was effi ciently spread person-to-person by infected aerosol [ ] . an ill chinese physician from the affected region traveled to hong kong to attend a wedding. while spending a single night in amoy garden hotel in the city, this infected individual appeared to spread the virus to at least other hotel guests. over the next several days these people returned to their homes in fi ve different countries incubating the sars-cov pathogen in their respiratory secretions. over the next - months, this newly acquired coronavirus spread to over countries worldwide and caused over cases of sars resulting in nearly deaths in early [ ] . through a global effort from a large number of very diligent public health offi cials and laboratory scientists, the outbreak ended within a year and has yet to be seen again, except for occasional laboratory-acquired accidents [ ] . a diverse array of pathogens has produced recent outbreaks and concerns for our vulnerability to pathogens within the global village we occupy and share with other fl ora, fauna and microorganisms ( table ). the spread of mosquito- avian infl uenza [ ] [ ] [ ] [ ] infl uenza a (h n ) risk of pandemic infl uenza; sporadic human cases of avian fl u in asia -mortality rates> % severe acute sars associated coronavirus risk of spread of zoonotic respiratory syndrome viruses; outbreak from a (sars) [ ] [ ] [ ] southern china to worldwide epidemic in - cases and deaths monkey pox [ ] orthopox virus risk of exotic pet trade; outbreak in wild rodents and humans in mid-western usa from sale of gambian giant rats from africa west nile virus mosquito-borne fl avivirus risk of international spread; (wnv) [ , ] wnv from africa to new york in , thousands of cases and hundreds of deaths in north america over next years inhalational anthrax intentional release of vulnerability to [ , ] bacillus anthracis spores bioterrorism; cases, in usa mail system [ ] [ ] [ ] [ ] oseltamivir-resistant infl uenza genes -community azole-resistant outbreaks now occur candida spp. borne west nile virus in north america [ , ] , prion-related food-borne variant creutzfeldt-jakob disease [ ] , and hemorrhagic fever viruses [ ] are a constant reminder of our susceptibility to pathogens that naturally reside in other animal species. the omnipresent fear of the next pandemic of infl uenza has been heightened by recent evolutionary changes in virulence and transmissibility of avian fl u viruses [ ] . standard chemotherapeutic regimens for infectious diseases may not reliably rescue persons with severe infections in the new millennium. community and nosocomial outbreaks of multidrug resistant pathogens as evidenced by methicillin and vancomycin resistance [ ] in staphylococcus aureus and resistance to the new anti-viral neuraminidase inhibitors [ , ] by recent infl uenza isolates are cause for real concern. the care of hospitalized, critically ill patients is likely to fundamentally change if current trends in the progressive emergence of antimicrobial resistance to commonly prescribed antibiotics are not signifi cantly altered in the near future. regrettably, there is little evidence that the situation is likely to change unless concerted efforts are taken on several fronts to reverse the current trajectory of increasing antibiotic resistance [ , ] . the fi tness of a microorganism is dependent upon its capacity to genetically adapt to rapidly changing environmental conditions. antimicrobial agents exert strong selective pressures on microbial populations, favoring those organisms that are capable of resisting them. genetic variability may occur by a variety of mechanisms. point mutations may occur in a nucleotide base pair, which is referred to as micro-evolutionary change [ ] . these mutations may alter the target site of an antimicrobial agent, altering with its inhibitory capacity. point mutations inside or adjacent to the active sites of existing beta-lactamase genes (e.g., genes for tem- , shv- ) have generated a remarkable array of newly recognized extended-spectrum beta-lactamases [ ] . beta-lactam antibiotics have been known for almost years and their widespread use has created selection pressures on bacterial pathogens to resist their inhibitory actions. at least different bacterial enzymes have now been characterized that hydrolyze beta-lactam antibiotics [ ] . the hydrolyzing enzymes exist in four basic molecular classes and are classifi ed as listed in table . the enzymes are either serine hydrolases (class a, c, and d) or zinc containing metalloenzymes with a zinc-binding thiol group its active site (class b enzymes). the microevolutionary events that account for the differential activities of this array of beta-lactamases have been carefully studied, and these bacterial enzymes now even have their own internet website devoted specifi cally to their molecular properties (http:// www.lahey.org/studies/webt.htm). beta-lactamase activity has become so ubiquitous among bacterial populations that it has prompted the development of specifi c beta-lactamase inhibitor compounds (clavulanate, tazobactam and sulbactam) in an effort to combat this common bacterial resistance mechanism. this has been countered by the generation of inhibitors of these beta-lactamase inhibitors by multidrug-resistant bacteria [ ] in the ongoing confl ict between pathogens and chemotherapeutic strategies to eradicate these microorganisms. recently it has been demonstrated that at least some bacterial populations have the capacity to increase their mutation rates during times of environmental stress such as exposure to an antibiotic. this stress response is known as the 'sos' response or transient hypermutation [ ] . it is highly advantageous for the organism to increase the rate of genetic variation at times of unfavorable environmental conditions. it is possible for bacteria to upregulate the pace of evolution in an attempt to develop a clone that can resist the action of an antibiotic. the dna polymerase in such organisms has reduced fi delity of replication and subsequently an increased rate in the mutational occurrences as a result of excess nucleotide mispairing. the recombination system of bacteria (the reca system) becomes less restrictive in the degree homology between dna sequences before a crossover event is permitted to occur. a fl urry of mutational events occur in stressed bacteria in a fi nal attempt to generate a resistant subpopulation of bacteria in the presence of an environmental challenge such as the presence of a new antibiotic. this process has even been phenotypically linked with alterations in growth rate and biofi lm formation in some strains of pseudomonas aeruginosa [ ] . a second level of genomic variability in bacteria is referred to as a macro-evolutionary change and results in whole-scale rearrangements of large segments of dna as a single event. such rearrangements may include inversions, duplica- tions, insertions, deletions, or transposition of large sequences of dna from one location of a bacterial chromosome or plasmid to another. these whole-scale rearrangements of large segments of the bacterial genome are frequently created by specialized genetic elements known as transposons or insertion sequences, which have the capacity to move independently as a unit from the rest of the bacterial genome [ ] . acquisition of foreign dna sequences from the extracellular environment may be taken up by naturally competent bacteria (e.g., some streptococci and neisserial organisms) by transformation. these sequences can then become integrated into the host genome into homologous sequences by the generalized recombination and dna repair system bacteria. inheritance of these foreign dna elements further contributes to the organism's ability to cope with selection pressures imposed upon them by antimicrobial agents [ ] . a third level of genetic variability in bacteria is created by the acquisition of foreign dna carried by plasmids and bacteriophages. these extrachromosomal dna elements provide ready access to disposable yet potentially highly advantageous genes including antibiotic resistance genes from plasmids or phage particles. these elements are autonomously self-replicating, and they can remain unattached in the cytoplasm of bacterial cells or integrate directly into the chromosome of the bacterial host. they have the capacity to replicate and move independently from the chromosome adding further variability to the entire bacterial genomic dna. evidence from whole genome sequencing projects indicates that these genomic rearrangements, bacteriophage sequences and insertion sequences are commonplace in bacterial chromosomes [ ] . these genetic variations provide bacteria with the seemingly limitless system to alter their genomes, rapidly evolve and develop resistance to virtually any antimicrobial agent. recent examples of vancomycin-resistance in enterococci [ ] , s. aureus [ ] , and extended spectrum beta-lactamases [ ] , carbapenemase production [ ] and transferable quinolone resistance in p. aeruginosa and enterobacteria [ ] attest to the capacity of microorganisms to adapt to environmental stresses induced by antibiotic exposure. viruses [ ] and fungi [ ] are also quite capable of rapid antimicrobial resistance development and these resistance capacities pose additional threats in the management of icu patients with serious infections from a variety of potential pathogens [ ] . antibiotic resistance genes probably arose from detoxifying enzymes or synthetic enzymes with altered substrate specifi city by critical mutations or recombination events resulting in the formation of mosaic genes with entirely new functions [ ] . altered penicillin binding proteins that mediate beta-lactam resistance in multiple bacterial genera (e.g., methicillin-resistant s. aureus [mrsa], penicillin-resistant streptococci and pneumococci, chromosomal resistance in gonococci) may have evolved from gene fusions for penicillin binding proteins involved in bacterial cell wall synthesis [ ] . another common resistance strategy is a change in the regulation of metabolic activity of an enzyme system that is affected by the antibiotic. increasing the rate of folate precursor synthesis, for example, can overcome the inhibitor effects of sulfa drugs and trimethoprim [ ] . many common antibiotic resistance genes were accidentally acquired ('stolen') from antibiotic producing bacteria. streptomyces and related soil bacteria are the source of many standard antimicrobial agents in use in clinical medicine today. these bacteria have co-evolved the capacity to synthesize antibiotics along with the necessary resistance genes to protect their own metabolic machinery from the very antibiotic they produce. the resistance genes from these antibiotic producing bacteria provide a ready genetic blueprint to resist the target antibiotic if susceptible bacteria can acquire these resistance genes. recent evidence confi rming that this does indeed occur was found by yokoyama and colleagues in japan during an investigation of a sudden outbreak of p. aeruginosa with high-level resistance to essentially all the clinically available aminoglycosides [ ] . these investigators discovered that the resistant strain had acquired a new methylase gene that blocked the binding site for inhibition by aminoglycosides on a specifi c sequence on s ribosomal rna. this identical mechanism and highly homologous gene is found in aminoglycoside-producing strains of streptomyces and related bacteria. at least seven distinctive mechanisms of antibiotic resistance have been described in bacteria and are summarized on table . detoxifying enzymes are used to degrade beta-lactams [ ] , and modify aminoglycosides so they no longer enter bacterial membranes and attach to their ribosomal target. there are over such enzymes identifi ed that can inhibit aminoglycosides by one of three general reactions: n-acetylation, o-nucleotidylation, and o-phosphorylation [ ] . detoxifying enzymes are also one of the resistance mechanisms against chloramphenicol, and are rarely utilized by certain bacterial strains to inactivate macrolides, lincosamides, tetracyclines and streptogramins. it was recognized early in the history of antibiotic development that penicillin is effective against gram-positive bacteria but not against gram-negative bacteria [ ] . this difference in susceptibility to penicillin is due in large part to the outer membrane, a lipid bilayer that acts as a barrier to the penetration of antibiotics into the cell. situated outside the peptidoglycan cell wall of gramnegative bacteria, this outer membrane is absent in gram-positive bacteria. the outer portion of this lipid bilayer is composed principally of lipopolysaccharide (lps) made up of tightly bound hydrocarbon molecules that impede the entry of hydrophobic antibiotics, such as penicillins or macrolides. the passage of hydrophilic antibiotics through this outer membrane is facilitated by the presence of porins, proteins that are arranged so as to form water-fi lled diffusion channels through which antibiotics may traverse [ ] . bacteria usually produce a large number of porins with differing physiochemical properties, permeability characteristics and size; approximately porin molecules/ cell for escherichia coli. bacteria are able to regulate the relative number of different porins in response to the osmolarity of their microenvironment. in hyperosmolar conditions, e. coli represses the synthesis of larger porins (ompf) while continuing to express smaller ones (ompc) [ ] . mutations resulting in the loss of specifi c porins can occur in clinical isolates and determine increased resistance to beta-lactam antibiotics. resistance to aminoglycosides and carbapenems emerging during therapy has also been associated with a lack of production of outer membrane proteins. in p. aeruginosa, resistance to imipenem appears to be due to an interaction between chromosomal beta-lactamase activity and a loss of a specifi c entry channel, the d porin [ ] . the rate of entry of aminoglycoside molecules into bacterial cells is a function of their binding to a usually non-saturable anionic transporter, whereupon they retain their positive charge and are subsequently 'pulled' across the cytoplasmic membrane by the internal negative charge of the cell. this process requires energy and a threshold level of internal negative charge before signifi cant transport occurs (proton motive force) [ ] . these aminoglycoside-resistant isolates with altered proton motive force may occur during long-term aminoglycoside therapy. these isolates usually have a 'small colony' phenotype due to their reduced rate of growth. im- gram-neg: gram-negative bacteria; tmp: trimethoprim; tcn: tetracycline; +++: most common mechanism; ++: common; +: less common, -: not reported (see reference [ ] ) active effl ux of antimicrobial agents is increasingly utilized by bacteria and fungi as a mechanism of antibiotic resistance. some strains of e. coli, shigella, and other enteric organisms express a membrane transporter system that leads to multidrug resistance by drug effl ux [ ] . specifi c effl ux pumps also exist that promote the egress of single classes of antimicrobial agents. effl ux mechanisms are the major mechanism of resistance to tetracyclines in gram-negative bacteria. some strains of s. pneumoniae, s. pyogenes, s. aureus, and s. epidermidis, use an active effl ux mechanism to resist macrolides, streptogramins, and azalides [ ] . this effl ux mechanism is mediated by the mef (for macrolide effl ux) genes in streptococci and msr (for macrolide streptogramin resistance) genes in staphylococci. a similar effl ux system, encoded by a gene referred to as mrea (for macrolide resistance effl ux), has been described in group b streptococci. this mechanism of resistance may be more prevalent in community-acquired infections than was generally appreciated. dissemination of these resistance genes among important bacterial pathogens constitutes a major threat to the continued usefulness of macrolide antibiotics [ ] . active effl ux mechanisms may also contribute to the full expression of betalactam resistance in p. aeruginosa. multidrug effl ux pumps in the inner and outer membrane of p. aeruginosa may combine with periplasmic beta-lactamases and membrane permeability components for full expression of antibiotic resistance [ ] . active effl ux of fl uoroquinolones by specifi c quinolone pumps or multidrug transporter pumps has also been detected in enteric bacteria and staphylococci [ ] . resistance to a wide variety of antimicrobial agents, including tetracyclines, macrolides, lincosamides, streptogramins and the aminoglycosides, may result from alteration of ribosomal binding sites. the mls b -determinant has the genes that produce enzymes to dimethylate adenine residues on the -s ribosomal rna of the -s subunit of the prokaryotic ribosome, disrupting the binding of these drugs to the ribosome. resistance to aminoglycosides may also be mediated at the ribosomal level. mutations of the s protein of the -s subunit have been shown to interfere with binding streptomycin to the ribosome. ribosomal resistance to streptomycin may be a signifi cant cause of streptomycin resistance among enterococcal isolates. ribosomal resistance to the -deoxystreptamine aminoglycosides (gentamicin, tobramycin, amikacin) appears to be uncommon and may require multiple mutations in that these aminoglycosides bind at several sites on both the s and s subunits of the ribosome [ ] . vancomycin and other glycopeptide antibiotics such as teicoplanin bind to dalanine-d-alanine, which is present at the termini of peptidoglycan precursors. the large glycopeptide molecules prevent the incorporation of the precursors into the cell wall. resistance of enterococci to vancomycin has been classifi ed as a-g based upon the genotype, type of target site modifi cation and level of resistance to vancomycin and teicoplanin [ ] . strains of e. faecium and e. faecalis with high-level resistance to both vancomycin and teicoplanin have class a resistance. class a resistance is mediated by the vana gene cluster found on an r plasmid. this protein synthesizes peptidoglycan precursors that have a depsipeptide terminus (d-alanine-d-lactate) instead of the usual d-alanine-d-alanine. the modified peptidoglycan binds glycopeptide antibiotics with reduced affi nity, thus conferring resistance to vancomycin and teicoplanin. the other classes of vancomycin resistance genes vary in level of resistance, species distribution and specifi c cell wall alterations [ , ] . vancomycin-intermediate strains of resistant s. aureus (visa) have been isolated with heterogeneous resistance patterns. visa strains express unusually thick peptidoglycan cell walls that are less completely cross-linked together. the cell wall in some strains of visa contains non-amidated glutamine precursors that provide an increased number of false binding sites to vancomycin [ ] . the vancomycin molecules are absorbed to these excess binding sites thereby reducing vancomycin concentrations at the growth point of peptidoglycan synthesis along the inner surface of the cell wall. the arrival of high level vancomycin resistance from vana expressing s. aureus [ ] has created a renewed sense of urgency in the need to develop novel strategies to combat multi-drug resistant bacterial pathogens. beta-lactam antibiotics inhibit bacteria by binding covalently to penicillinbinding proteins (pbps) in the cytoplasmic membrane. these target proteins catalyze the synthesis of the peptidoglycan that forms the cell wall of bacteria. in gram-positive bacteria, resistance to beta-lactam antibiotics may occur by a decrease in the affi nity of the pbp for the antibiotic or with a change in the amount of pbp produced by the bacterium [ ] . these low affi nity binding pbps may be inducible where their production is stimulated by exposure of the microorganism to the beta-lactam drug [ ] . the structural gene (meca) that determines the low-affi nity pbp of mrsa shares extensive sequence homology with a pbp of e. coli, and the genes that regulate the production of the low-affi nity pbp have considerable sequence homology with the genes that regulate the production of staphylococcal penicillinase [ ] . the pbps of beta-lactamase-negative penicillin-resistant strains of n. gonorrhoeae, n. meningitidis, and haemophilus infl uenzae have shown reduced penicillin-binding affi nity [ ] . their pbps appear to be encoded by hybrid genes containing segments of dna scavenged from resistant strains of related species, similar to penicillin-resistant pneumococci [ ] . dna gyrase (also known as bacterial topoisomerase ii) is necessary for the supercoiling of chromosomal dna in bacteria in order to have effi cient cell division [ ] . another related enzyme, topoisomerase iv is also required for segregation of bacterial genomes into two daughter cells during cell division. these enzymes consist of two a subunits encoded by the gyra gene and two b subunits encoded by the gyrb gene (or parc and pare for topoisomerase iv. although spontaneous mutation ot the a-subunit of the gyra locus is the most common cause of resistance to multiple fl uoroquinolones in enteric bacteria, b-subunit alterations may also affect resistance to these drugs. dna gyrase (topoisomerase ii) is the primary site of action in gram-negative bacteria whereas topoisomerase iv is the principal target of quinolones in gram-positive bacteria. mutations in a variety of chromosomal loci have been described that resulted in altered dna gyrases resistant to nalidixic acid and the newer fl uoroquinolones in enterobacteriaceae and p. aeruginosa. many of these mutations involve the substitution of single amino acids at key enzymatic sites (located between amino acids - in the gyrase a subunit) that are involved in the generation of the dna gyrase-bacterial dna complex [ ] . there are two common genes that mediate resistance to sulfa drugs in a wide variety of pathogenic bacteria. these are known as sul and sul . these genes give rise to altered forms of the target enzyme for sulfonamide, dihydropteroate synthase (dhps) [ ] . the altered dhps enzymes mediated by the sulfonamide resistance genes no longer bind to sulfa yet continue to synthesize dihydropteroate from para-aminobenzoic acid substrate. trimethoprim is a potent inhibitor of bacterial dihydrofolate reductase (dhfr). a large number of altered dhfr enzymes with loss of inhibition by trimethoprim have been described from genes found primarily on r plasmids. these altered dhfr genes are widespread in gram-negative bacteria and are also found in staphylococci (the dfra gene) [ ] . tetracycline resistance may be mediated by a mechanism that interferes with the ability of tetracycline to bind to the ribosome. the ubiquitous tetm resistance gene and related tetracycline resistance determinants protect the ribosome from tetracycline action. the tetm gene generates protein with elongation factor-like activity that may stabilize ribosomal transfer rna interactions in the presence of tetracycline molecules [ ] . sulfonamides compete with para-aminobenzoic acid to bind the enzyme dihydropteroate synthase, and thereby block folic acid synthesis necessary for nucleic acid synthesis. sulfonamide resistance may be mediated in some bacteria by the over production of the synthetic enzyme dihydropteroate synthase. the gene responsible for dhps is felp and strains of bacteria that produce excess dhps can overwhelm sulfa inhibition [ ] . trimethoprim resistance may also occur in a similar fashion, by making excess amounts of dihydrofolate reductase from the bacterial chromosomal gene fola [ ] . an unusual mechanism of resistance to specifi c antibiotics is by the development of auxotrophs, which have specifi c growth factor requirements not seen in wild-type strains. these mutants require substrates that normally are synthesized by the target enzymes, and thus if the substrates are present in the environment, the organisms are able to grow despite inhibition of the synthetic enzyme by an antibiotic. bacteria that lose the enzyme thymidylate synthetase are 'thymine dependent'. if they can acquire exogenous supplies of thymidine to synthesize thymidylate via salvage pathways from the host, they are highly resistant to sulfa drugs and trimethoprim [ ] . once an antibiotic resistance gene evolves, the resistance determinant can disseminate among bacterial populations by transformation, transduction, conjugation, or transposition. favored clones of bacteria then proliferate in the fl ora of patients who receive antibiotics. antibiotic-resistance genes were found among bacteria even in the pre-antibiotic therapy era [ ] . however, selection pressures placed upon microbial populations by a highly lethal antimicrobial compound create an environment in which individual clones that resist the antibiotic are markedly favored. these resistant populations then proliferate and rapidly replace other susceptible strains of bacteria. while some antibiotic resistance genes place a metabolic 'cost' on bacteria, many microorganisms have evolved strategies to limit this cost by limiting expression, alternate gene products or phase variation. these mechanisms allow favorable but sometimes 'costly' genes that mediate antibiotic resistance to persist in the absence of continued antibiotic selection pressure and yet be rapidly expressed upon re-exposure to antibiotics [ ] . plasmids are particularly well adapted to serve as agents of genetic evolution and r-gene dissemination. plasmids are extrachromosomal genetic elements that are made of circular double-stranded dna molecules that range from less than to greater than kilobase pairs and are extremely common in clinical isolates of bacterial pathogens. although multiple copies of a specifi c plasmid or multiple different plasmids, or both, may be found in a single bacterial cell, closely related plasmids often cannot coexist in the same cell. this observation has led to a classifi cation scheme of plasmids based upon incompatibility groups [ ] . plasmids may determine a wide range of functions besides antibiotic resistance, including virulence and metabolic capacities. plasmids are autonomous, self-replicating genetic elements that possess an origin for replication and genes that facilitate its stable maintenance in host bacteria. conjugative plasmids require additional genes that can initiate self-transfer. the transfer of plasmid dna between bacterial species is a complex process, and thus conjugative plasmids tend to be larger than non-conjugative ones. some small plasmids may be able to utilize the conjugation apparatus of a coresident conjugative plasmid. many plasmid-encoded functions enable bacterial strains to persist in the environment by resisting noxious agents, such as heavy metals. mercury released from dental fi llings may increase the number of antibiotic-resistant bacteria in the oral fl ora. hexachlorophene and other topical bacteriostatic agents in the environment may actually promote plasmid-mediated resistance to these agents and other antimicrobial agents [ ] . transposons are specialized sequences of dna that are mobile and can translocate as a unit from one area of the bacterial chromosome to another. they can also move back and forth between the chromosome and plasmid or bacteriophage dna. transposable genetic elements possess a specialized system of recombination that is independent of the generalized recombination system that permits recombination of largely homologous sequences of dna by crossover events (the reca system of bacteria). the reca-independent recombination system ('transposase') of transposable elements usually occurs in a random fashion between non-homologous dna sequences and results in whole-scale modifi cations of large sequences of dna as a single event [ ] . there are two types of transposable genetic elements, transposons and insertion sequences. these mobile sequences probably play an important physiologic role in genetic variation and evolution in prokaryotic organisms. transposons differ from insertion sequences in that they mediate a recognizable phenotypic marker such as an antibiotic-resistance trait. either element can translocate as an independent unit. both elements are fl anked on either end by short identical sequences of dna in reverse order (inverted repeats). these inverted-repeat dna termini are essential to the transposition process. transposons and insertion sequences must be physically integrated with chromosome, bacteriophage, or plasmid dna in order to be replicated and maintained in a bacterial population. some transposons have the capability to move from one bacterium to another without being transferred within a plasmid or bacteriophage. these conjugative transposons are found primarily in aerobic and anaerobic gram-positive organisms and can rapidly and effi ciently spread antibiotic resistance genes [ , ] . transposition, like point mutation, is a continuous and ongoing process in bacterial populations. transposons are also essential in the evolution of r plasmids that contain multiple antibiotic-resistance determinants [ ] . high-level vancomycin resistance (vana) in enterococci is mediated by a composite transposon that encodes a series of genes needed to express vancomycin resistance [ ] . single transposons may encode multiple antibiotic-resistance determinants within their inverted-repeat termini as well [ ] . genetic exchange of antibiotic-resistance genes occurs between bacteria of widely disparate species and different genera. identical aminoglycoside-resistance genes can spread between gram-negative and gram-positive bacteria and between aerobic and anaerobic bacteria [ ] . given the highly variable environmental selection pressures created by a wide variety of antibiotics and the plasticity of bacterial genomes, the ongoing evolution of multi-drug resistant bacterial organisms is probably inevitable [ ] . the structural genes that mediate antibiotic resistance are often closely linked and may exist in tandem along the bacterial chromosome or plasmid. genetic analysis of sequences of dna adjacent to resistance genes has identifi ed unique integration units near promoter sites [ ] . these integration regions are known as integrons, and they function as convenient recombinational 'hot spots' for site-specifi c recombination events between largely non-homologous sequences of dna. the integron provides its own integrase function [ ] with a common attachment and integration site for acquisition of foreign dna sequences. integrons are widespread in bacterial populations and provide a convenient site for insertion of multiple different resistance genes from foreign dna sources. there are four classes of integrons with type i integrons being the most common in pathogenic microorganisms [ ] . integrons also serve as effi cient expression cassettes for resistance genes. integrons possess a promoter site in close proximity to the 'end of the newly inserted dna sequence. numerous clusters of different resistance genes have been linked into integrons through specifi c insertion sites. integrons may have as many as fi ve resistance genes linked in sequence and fl anked between specifi c base-pair spacer units [ , ] . integron-mediated multiple resistance gene cassettes have been fl anked by transposons, mobilized to plasmids, and then transferred between bacterial species by conjugation. by these systems of genetic exchange, widespread dissemination of multiple antibiotic resistance genes is accomplished in a rapid and frighteningly effi cient manner [ ] . for some time concerned scientists have been warning about the possibility of widespread antibiotic resistance leading to the loss of effectiveness of antibiotics in clinical medicine [ ] [ ] [ ] [ ] . these warnings have largely been ignored as it was assumed that this human need and the profi t motive of free enterprise would stimulate pharmaceutical companies to continuously develop new antibiotics. if we could discover new targets for future antimicrobial drugs it may be possible to keep pace or even exceed the rate of antibiotic resistance gene development by microbial pathogens. for a number of disconcerting reasons, humans may be losing ground rather than gaining on pathogens in the st century. a recent survey of new pharmaceutical products in found only fi ve new antibiotics out of the new molecular entities in the research and development pipeline [ ] . the pace of new antibiotic discovery is turning into a trickle and drying up compared to what it was even years ago [ ] . the market reality is regrettably set against the development of new antibiotics in favor of more lucrative options with greater market profi t from drugs for chronic illnesses with less risk and longer revenue streams [ ] [ ] [ ] . the reimbursement and return on investments are unfavorable for antibiotics and the market system is not meeting the needs of society with respect to new antibiotic development. some far reaching and bold initiatives are desperately needed if a crisis in loss of antibi-otic effectiveness is to be avoided [ , ] . the disincentives for new antibiotic development and some proposed solutions are listed in table . bacterial strains contain complex aggregations of genes that may be linked together to combat the inhibitory effects of antibiotics. since prokaryotic organisms all contribute to a common 'gene pool', favorable genes mediating antibiotic resistance may disseminate among bacterial diverse microbial genera and species. increasing evidence of multiple antibiotic resistance mechanisms within the same bacterium against a single type of antibiotic, and cooperation between bacterial populations within biofi lms attest to the remarkably ingenuity and fl exibility of bacterial populations [ , , ] . thus the use of one antibiotic may select for the emergence of resistance to another. mobile genetic elements and rapidly evolving integron cassettes with multiple antibiotic resistance genes endow bacteria with a remarkable capacity to resist antibiotics [ ] . although the development of antibiotic resistance may be inevitable, the rate at which it develops can be reduced by the rational use of antibiotics. use of th century diagnostic methods employ real-time pcr, genomics, (culture and susceptibility tests) to treat proteomics to identify pathogens, and st century diseases encourages empiric resistance genes; target and treat specifi c broad-spectrum antibiotic drug use infections with narrow spectrum drugs pcr: polymerase chain reaction the wider accessibility to molecular techniques and computer technology to rapidly identify the specifi c microorganisms, their resistance potential, and track their spread between patients within the hospital and or the community will be of considerable benefi t in the control of antibiotic resistance. the need to utilize empiric, broad-spectrum antibiotics for days and even weeks while samples are being sent for culture and susceptibility testing needs to stop. we need specifi c information in real time to assure patients with specifi c infections are being treated with effective, narrow-spectrum drugs [ ] . the use of antibiotics for non-medical uses should be entirely banned. up to % of antibiotic use today is for non-medical use in agriculture, food preparation, and other industrial uses [ ] . this adds to environmental contamination with low levels of antibiotics. sub-inhibitory concentrations of antibiotics foster the development of resistant clones of bacteria that can cause infections in humans. the use of non-antibiotic approaches to the management of infectious diseases needs to be supported and developed. the use of plasma-based antibody therapies and anti-bacterial, anti-viral and anti-fungal vaccines should be encouraged in the future [ ] [ ] [ ] . the management of common invasive pathogens such as staphylococcal infections has become very complicated given the rapid spread of simultaneous beta-lactam, aminoglycoside, and quinolone-resistant isolates [ ] . recent reports of vancomycin-resistant s. aureus in japan and the united states suggest that common, invasive, microbial pathogens may become refractory to any chemotherapeutic agent in the future [ , , ] . new drug discoveries have allowed us to be one step ahead of the bacterial pathogens for the latter half of the twentieth century. it is unlikely we will continue this record of remarkable success against microbial pathogens in the new millennium. the rapid evolution of resistance has limited the duration of the effectiveness of antibiotics against certain pathogens. the best hope for the future is the continued development of new antibiotic strategies [ ] . in order to retain the antimicrobial activity of existing and new antibiotics, clinicians can assist through careful antibiotic stewardship and tightened infection control measures. antimicrobial agents have had a substantial impact in decreasing human morbidity and mortality rates and have served us well over the antimicrobial era. it behooves us to improve our diagnostic and surveillance efforts and to exercise caution in administering antibiotics if we are to maintain their continued effi cacy. forecast and control of epidemics in a globalized world multidrug resistance in yersinia pestis mediated by a transferable plasmid h n infl uenza: a protean pandemic threat induction of proinfl ammatory cytokines in human macrophages by infl uenza a (h n ) wiruses: a mechanism for the unusual severity of human disease enhanced virulence of infl uenza a viruses with the haemagglutinin of the pandemic virus the structure and receptor binding properties of the infl uenza hemagglutinin viral shedding patterns of coronavirus in patients with probable severe acute respiratory syndrome planning for epidemics -the lessons of sars public 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antibiotic resistance a functional classifi cation scheme for βlactamases and its correlation with molecular structure error-prone polymerase, dna polymerase iv, is responsible for transient hypermutation during adaptive mutation in escherichia coli pseudomonas biofi lm formation and antibiotic resistance are linked to phenotypic variation infection with vancomycin-resistant staphylococcus aureus containing the vana resistance gene multifocal outbreaks of metallo-βlactamase-producing pseudomonas aeruginosa resistant to broad-spectrum β-lactams, including carbapenems antimicrobial resistance in intensive care units the origins and molecular basis of antibiotic resistance acquisition of s rrna methylase gene in pseudomonas aeruginosa interactions of outer membrane proteins - and - with peptidoglycan sacculus of escherichia coli k- interplay of impermeability and chromosomal beta-lactamase activity in imipenem-resistant pseudomonas aeruginosa membrane potential and gentamicin uptake in staphylococcus aureus drug effl ux as a mechanism of resistance active effl ux, a common mechanism for biocide and antibiotic resistance inner membrane effl ux components are responsible for β-lactam specifi city of multidrug effl ux pumps in pseudomonas aeruginosa genetic characterization of vang, a novel vancomycin resistance locus for enterococcus faecalis contribution of a thickened cell wall and its glutamine nonamidated component to the vancomycin resistance expressed by staphylococcus aureus m transition from resistance to hypersusceptibility to beta-lactam antibiotics associated with loss of a low-affi nity penicillin-binding protein in a streptococcus faecium mutant highly resistant to penicillin penicillin-binding proteins and ampicillin resistance in haemophilus infl uenzae activity of quinolones against gram-positive cocci: mechanisms of drug action and bacterial resistance sulfonamide resistance in haemophilus infl uenzae mediated by acquisition of sul or a short insertion in chromosomal folp trimethoprim resistance high-level tetracycline resistance in neisseria gonorrhoeae is result of acquisition of streptococcal tetm determinant phenotypic switching of antibiotic resistance circumvents permanent costs in staphylococcus aureus plasmid-determined resistance to antimicrobial drugs and toxic metal ions in bacteria conjugative transfer of staphylococcal antibiotic resistance markers in the absence of detectable plasmid dna dispersal in campylobacter spp. of apha- , a kanamycin resistance determinant from gram-positive cocci origins of the mobile gene cassettes found in integrons multidrug resistance among enterobacteriaceae is strongly associated with the presence of integrons and is independent of species or isolate origin trends in antimicrobial drug development antibiotics at the crossroads safety and antigenicity of non-adjuvanted and mf -adjuvanted infl uenza a/duck/singapore/ (h n ) vaccine; a randomized trial of two potential vaccines against h n infl uenza antibody concentration and clinical protection after hib conjugate vaccination in the united kingdom immunogenicity and impact on nasopharyngeal carriage of a nonavalent pneumococcal conjugate vaccine antimicrobial resistance: the example of staphylococcus aureus key: cord- -t vukbwp authors: liang, zhongjie; li, lianchun; wang, yuanyuan; chen, limin; kong, xiangqian; hong, yao; lan, lefu; zheng, mingyue; guang-yang, cai; liu, hong; shen, xu; luo, cheng; li, keqin kathy; chen, kaixian; jiang, hualiang title: molecular basis of ndm- , a new antibiotic resistance determinant date: - - journal: plos one doi: . /journal.pone. sha: doc_id: cord_uid: t vukbwp the new delhi metallo-β-lactamase (ndm- ) was first reported in in a swedish patient. a recent study reported that klebsiella pneumonia ndm- positive strain or escherichia coli ndm- positive strain was highly resistant to all antibiotics tested except tigecycline and colistin. these can no longer be relied on to treat infections and therefore, ndm- now becomes potentially a major global health threat. in this study, we performed modeling studies to obtain its d structure and ndm- /antibiotics complex. it revealed that the hydrolytic mechanisms are highly conserved. in addition, the detailed analysis indicates that the more flexible and hydrophobic loop , together with the evolution of more positive-charged loop leads to ndm- positive strain more potent and extensive in antibiotics resistance compared with other mbls. furthermore, through biological experiments, we revealed the molecular basis for antibiotics catalysis of ndm- on the enzymatic level. we found that ndm- enzyme was highly potent to degrade carbapenem antibiotics, while mostly susceptible to tigecycline, which had the ability to slow down the hydrolysis velocity of meropenem by ndm- . meanwhile, the mutagenesis experiments, including d a, c a, k a and k e, which displayed down-regulation on meropenem catalysis, proved the accuracy of our model. at present, there are no effective antibiotics against ndm- positive pathogen. our study will provide clues to investigate the molecular basis of extended antibiotics resistance of ndm- and then accelerate the search for new antibiotics against ndm- positive strain in clinical studies. the new delhi metallo-b-lactamase (ndm- ) was first reported in in a swedish patient, who travelled to new delhi and acquired a urinary tract infection caused by klebsiella pneumonia [ ] . a recent study reported that klebsiella pneumonia ndm- positive strain or escherichia coli ndm- positive strain was highly resistant to all antibiotics tested except tigecycline and colistin [ ] . since august , the spreading and dissemination of ndm- positive strain has occurred, with cases being globally reported by medias from countries including united states, canada, sweden, united kingdom, austria, belgium, france, netherlands, germany, africa, oman, australia, japan and china [ ] . although ndm- -positive cases are not currently prevalent in the worldwide, it can spread through renal or bone marrow transplantation, dialysis, cerebral infarction, chronic obstructive pulmonary disease, pregnancy, burns, road traffic accidents, and cosmetic surgery. in addition, ndm- positive strain can destroy carbapenem antibiotics such as meropenem, imipenem, doripenem and ertapenem by breaking down the carbapenem groups of antibiotics, which have been serving as the basis for the treatment of antibiotic-resistant bacterial infections and now can no longer be relied on for this purpose due to the emergence of nmd- positive strain. therefore, the spread of the pathogenic microorganisms carrying ndm- gene (also been called ''super bugs'') now becomes potentially a major global health threat. ndm- belongs to the metallo-b-lactamase (mbl, class b) family containing zn + and other divalent cations as cofactors. it inactivates almost all classes of b-lactams antibiotics including carbapenems by catalyzing the hydrolytic cleavage of the substrate amide bond. on the basis of the protein sequence similarities, three different lineages, named as subclass b , b and b have been characterized. a number of experimental and theoretical studies have also been devoted to understanding structural and mechanistic properties of mbls [ , , , ] . however, since this novel mbl-ndm- is likely more potent and extensive than known mbls in inactivating b-lactams antibiotics, it is urgent for us to address the ligand binding properties and catalytic mechanism of ndm- in order to light up the road for the development of novel antibiotics to combat emerging ndm- positive pathogen. to explore the molecular basis for antibiotics hydrolysis by ndm- , homology modeling method was performed to obtain the d structure. then molecular docking method was applied to obtain the binding modes with antibiotics and the comparison of ndm- with other mbls complexes was also investigated. in addition, ndm- catalyzed hydrolysis of various antibiotics substrates was monitored by following the absorbance variations resulting from the opening of the b-lactam ring, which suggested that ndm- displays different resistant abilities to different kinds of antibiotics. based on the modeling results, four point mutants, including d a, c a, k a and k e, were made and their enzymatic activities were measured comparing with the wildtype. the significantly decreased activity of mutants validated the accuracy of our model. on the other hand, it shed light on the catalytic mechanism of the novel ndm- from the molecular basis for the first time. furthermore, enzymatic activities toward different antibiotics tested in our study would provide clues to accelerate the new antibiotics design against ndm- positive strain in further studies. overall structure of ndm- from homology modeling as the multiple sequences alignment shown in figure a , among vim- (b subclass), cpha (b subclass) and fez- (b subclasses), ndm- is highly homologous to the b subclass (vim- , sequence identity is %). in addition, sequence alignment indicates that ndm- contains the identical coordinating residues (his-his-his) in the zn + (i)-binding site and (asp-cys-his) in the zn + (ii)-binding site of the b subclass, which implies that ndm- belongs to the b subclass of mbls. accordingly, the crystal structure of vim- (pdb id: whg) was used as the template in homology modeling [ ] . as shown in figure b , the overall structure of ndm- shares the common characteristic folding of ab/ba sandwich, which resembles the architectural features in other b subclass. the active site of ndm- is highly homologous to that of vim- . in the active site (figure a ), zn + (i) is coordinated with three conserved histidine residues , and , while zn + (ii) is coordinated with the conserved residues asp , cys and his , which is exactly consistent with the x-ray crystal structures [ , ] . a water molecule bridging both zinc ions acts as the nucleophile during the b-lactam hydrolysis. two mobile loops in the active site shown in figure b are crucial for substrate recognition, binding and catalysis in mbls [ , ] . in ndm- , the loop , also called the flapping loop, is composed of amino acids ldmpgfgava (residues - ). compared with the loop (qsfdgavyp) in vim- and vim- , the size of the active site cavity is enlarged with less bulky amino acids, suggesting a broader substrate profile. besides it is worth noting that it is more hydrophobic than others [ ] . there is only one benzene ring of phe in the middle of the loop of ndm- , and the side-chains of asp and met pointed to the solvent, the less bulky amino acids, especially for the glycines, are proposed to make the loop more flexible for substrate binding. in the crystal structure of ndm- in complex with hydrolyzed ampicillin (pdb id: q x) [ ] , the loop represents a more open state compared with our model, while in the crystal structure of apo ndm- (pdb id: s z) [ ] , the loop displays a semi-closed state. consequently, it is proposed to undergo significant conformational changes during the substrate binding, in different states with or without substrate. regarding the loop , arg and asn in vim- was proved to play important roles for substrate binding, catalysis and inhibition through h-bond interactions [ , ] . while in ndm- , the arginine is mutated to ala , which also enlarges the size of active site cavity. moreover, lys instead of tyr in vim- , probably plays the similar role of arg in vim- by forming electrostatic interaction with the carboxyl of substrate. the detailed comparison of the two loops in ndm- and vim- is shown in figure b . furthermore, two residues, lys and tyr , were pointed to play crucial roles in stabilizing the conformation of the active site, through h-bond network (with residues asn , asp , thr , his and ser ) and hydrophobic interactions (with residues leu , leu , leu and leu ) [ ] . besides the unique residues in the two loops, the n terminus of ndm- is longer than other analogues. even without modeled in our structure, it is speculated to assist in loop packing so as to affect the hydrolytic catalysis. ndm- also contains an additional insert between residues and , which is not present in other mbls. since the insert is in the opposite side of the active site, with a distance of around Å , its role in the hydrolysis reaction is still unknown. in summary, the unique structural characteristics probably contributes to the more potent hydrolysis and broader substrate range of the novel mbl-ndm- , especially for those bulkier antibiotics, which are not degraded by other mbls. after the d structure of ndm- was modeled, molecular docking study was performed. two reported effective antibiotics (tigecycline and colistin) against ndm- positive strains [ ] and other well-known antibiotics including carbapenem, which were reported to be destroyed by ndm- positive pathogen, were docked into the active site of ndm- . the molecular docking data indicates that the latter antibiotics fit the active site of ndm- quite well. taking two typical antibiotics, imipenem and carbapenem as example, the docked complex structures revealed that although the antibiotics adopted diverse conformations in the active site, the lactam motifs were positioned in the same orientation by coordinating with zinc ions tightly ( figure c ), which suggested that the catalytic mechanisms were highly conserved among b subclass enzymes, as shown in figure . substrate-binding polarizes the lactam bond due to coordination of the carbonyl oxygen with zn + (i) and the lactam nitrogen with zn + (ii). attack of the water oxygen leads to oxyanion stabilized by zn + (i), which is followed by subsequent cleavage of the c-n bond. then, the lactam nitrogen is expelled as an anion and stabilized by coordination with zn + (ii) acting as a general acid. the last step is the protonation of the nitrogen, which is considered as the rate-limiting and the most controversial step to date [ ] . compare to other known b subclass enzymes such as vim- and vim- , the loop of ndm- harbors a lysine-rich positive-charged region, which is more favorable for protonation, probably accounting for its potent catalytic activity at least in part. notably, colistin, the reported antibiotic susceptible for ndm- positive pathogens, was not able to fit the active site well probably due to its bulky volume. comparison the complex structure of ndm- / meropenem with vim- /meropenem and fez- / meropenem to gain the structural insight into the mechanism of the potent hydrolysis of ndm- , the intermolecular interactions of three models of ndm- , vim- and fez- in complex with antibiotics meropenem were compared and analyzed in details ( figure a -c). in ndm- complex structure, the lactam oxygen and the carboxyl oxygen atoms coordinate with zn + (i) and zn + (ii) with distances of . Å and . Å respectively. in addition, the h-bond between the atom n d of asn and the lactam oxygen atom with distance of . Å also contributes to the polarization of the lactam bond. meanwhile, the water molecule, which bridges with the two zinc ions with distances of . Å and . Å respectively, can serve as the nucleophile to attack the atom c of b-lactam. the carbonyl methyl of meropenem forms h-bonds with the atom n e of gln . together with the fact that the relatively bulky active site cavity caused by the residue variations in the flexible loop , ndm- is potent to hydrolyze bulkier antibiotics. different with ndm- /meropenem, the vim- / meropenem has a strong h-bond between the carboxyl of meropenem and arg in the loop . moreover, phe and try in the loop form hydrophobic interactions with meropenem, and dramatically reduce the size of the active site cavity. structurally, the hydrophobic interactions make the lactam ring rotate to the loop and elongate the distance between the lactam oxygen and zn + (i) to . Å . (figure b ) consequently, the shallow active site makes the lactam more difficult to be positioned in a proper orientation for catalysis, which probably explains its weaker activity to catalyze antibiotics compared with ndm- . in contrast, fez- shares little structural similarity with ndm- and vim- , especially for that the flapping loop is not conserved in fez- , which leads to a flat active site cleft [ ] . obviously,meropenem mediates no other interactions with fez- except for the lactam motif ( figure c ), suggesting the low binding affinity for substrates. and the fez- /meropenem flexible characteristic makes the antibiotic little access to proper orientation for hydrolysis. in agreement with our intermolecular interaction models of enzymes with antibiotics, the reported minimal inhibitory concentrations of meropenem for vim- and fez- positive e.coli strains are both . mg/ml, while for ndm- positive e.coli strain, it is mg/ml [ , ] , suggesting that ndm- is probably more potent in antibiotics hydrolysis. besides, the binding modes of hydrolyzed antibiotics were also investigated. taking the hydrolyzed meropenem for example ( figure ) , it is noticed that the original carboxyl formed electrostatic interactions with lys . the hydrophobic residues such as leu , val and ala in the loop formed stable hydrophobic interactions with the dimethylamino group. it appears that the conformations of antibiotics undergo slight exchange during the catalysis. to validate the results extracted from the in silico study, we went ahead to perform ''wet'' experiments to further explore the detailed molecular basis for the catalytic mechanism of ndm- . firstly, we constructed a his and sumo (small ubiquitin-related modifier) tagged ndm- expression plasmid and overexpressed sumo-ndm- in e.coli bl (de ) strain; then we purified fusion protein by ni-column affinity chromatography, the ndm- protein was released from fusion protein by ulp- (ubiquitin-like protein-specific protease ) protease cleavage. more than % pure ndm- protein was obtained by final gel filtration chromatography ( figure a, b and c) . secondly, the ndm- catalyzed hydrolysis of various antibiotics substrates was monitored by following the absorbance variations resulting from the opening of the b-lactam ring. the susceptibilities of seven typical antibiotics were assessed. the chemical structures of these antibiotics are displayed in figure . as shown in figure a , ndm- rapidly hydrolyzes the carbapenem antibiotics including meropenem and imipenem, and it harbored moderate catalytic hydrolysis ability against cephalosporin antibiotics, including ceftazidime, cefotaxime and cefpirome. in contrast, ndm- is susceptible to tigecycline and monobactam-aztreonam, which is similar with the catalytic ability of vim- and ndm- -positive enterobacteriaceae [ , ] . to explore the detailed mechanism for the susceptibility of the two antibiotics against ndm- positive strain, mm meropenem was used as ndm- substrate, then mm and mm tigecycline or aztreonam were mixed with the reaction system as the inhibitors. surprisingly, tigecycline probably displayed a certain degree of inhibition against ndm- . the hydrolysis velocity of meropenem by ndm- is partially slowed down when different concentrations of tigecycline were added into the reaction system ( figure b ). for another ndm- positive strain susceptive antibiotic aztreonam, we didn't see any inhibitory effects on ndm- favorite substrate (data now shown). in short, our data revealed the molecular basis of the novel mbl-ndm- , of which ndm- positive strain possessed potent resistance to carbapenems. on the other hand, we identified a weak inhibitortigecycline, which was previously reported to inhibit the growth of ndm- harbored klebsiella pneumonia [ ] . our work may pave the road in designing inhibitors and new antibiotics susceptible against ndm- . meanwhile, based on our d model, we designed the following point mutants, including, d a, c a, k a and k e. then the activity of the mutants for meropenem was measured and the result is shown in figure c . it is obvious that the mutants almost completely lose their activity in antibiotics hydrolysis. this result in turn verified the accuracy of our d model in which the zn + (ii) is coordinated with the conserved residues asp and cys , in spite that it is still intriguing whether the effect is structural or functional. however, the decreased catalytic activity implied the mechanism should be zn + (ii) assisted, supporting the proposal that zn + (ii) ion is crucial for stabilizing the development of a negative charge on the b-lactam nitrogen atom(as show in figure ). regarding k a and k e mutants, the significantly decreased hydrolysis activity indicated that the electrostatic interaction between the original carboxyl group of hydrolyzed antibiotics and positive-charged side-chain of k probably afford one of the driving force for the catalysis. while with respect to loop (ldmpgfgava), we did the loop displacement with qsfdga-vyp in vim- and vim- . different with the point mutants, the hydrolytic catalysis didn't decrease compared with the wild-type, which means only the loop change wouldn't affect the hydrolytic catalysis very much. moreover, it was reported that a f, q d and a f/q d mutants strongly weakened the imipenem hydrolysis activity of ndm- , proving the crucial roles of the unique ha( )hq( )d motif compared with hfhdd motif in other mbls [ ] . furthermore, since loop and loop are critical for substrate binding and catalysis, more attention would be paid on the glycines in loop and lysines in loop . nowadays, the antibiotics resistance in gram-negative bacteria has already been a great risk to the public health. the newly emergent ndm- , called ''superbug'', possesses more potent hydrolysis ability toward almost all antibiotics and hence becomes a new threat in clinical surgery. this is one typical example of the remarkable ability of bacteria to adapt and eventually become resistant to new antibiotics. it is made much easier by the existence of plasmids, which can transmit easily from bacterium to bacterium. in this study, the structural models of ndm- / antibiotics complex were obtained from homology modeling and molecular docking methods. the detailed analysis indicates that the loop of more flexibility and hydrophobic, together with the loop of more positive-charged, leads to ndm- more potent in antibiotics hydrolysis compared with other mbls. meanwhile, the experiments proved that ndm- was highly resistant to carbapenems and cephalosporins and susceptible to aztreoname and tigecycline, which was firstly implied to slow down the hydrolysis velocity of meropenem by ndm- in our study. moreover, the mutant results displayed the molecular basis for the catalytic mechanism. at present, there are no effective antibiotics against ndm- positive pathogen. an appreciated strategy is to identify drug candidates from the existing antibiotics, such as tigecycline, based on the d model of ndm- by using structurebased virtual screening (e.g., molecular docking and ligand-based, receptor-based and pharmacophore-based drug design) in conjunction with bioassay. this strategy has been used successfully in the discovery of the compound cinanserin against sars (severe acute respiratory syndrome) [ ] . taken together, our study provided clues to investigate the molecular basis of extended antibiotics resistance of ndm- and shed light upon the discovery of new antibiotics against ndm- positive strains in clinical studies. the protein sequence of ndm- from enterococcus faecium (hq ) was retrieved from ncbi (http://www.ncbi.nlm.nih. gov) protein database. blastp program was then performed to search for its homologues from the rcsb protein databank [ ] . accordingly, the crystal structure of vim- (pdb id: whg) was selected as the template [ ] , whose sequence identity with ndm- is %. to analyze the sequence conservation, sequences alignment of ndm- , vim- , cpha and fez- was performed and gaps were inserted into the sequences to find an optimal alignment as shown in figure . the d structure of ndm- was then modeled by using the insightii software (accelrys inc., san diego, ca, usa) and optimized by energy minimization using the amber force field implemented in the sybyl software package. it was minimized gradually (hydrogens, side-chains, all) using the constraints in heavy or backbone atoms to alleviate any remaining bad steric contacts. the optimized structure of ndm- was then subjected to evaluation by procheck and profiles- d to examine the stereochemical quality and the structural rationality [ , ] . after verified the rationality, the d structure of ndm- was subjected to the subsequent study. glide calculations were performed with maestro v . (schrodinger, inc.) [ ] . hydrogen atoms and charges were added during a brief relaxation performed using the protein preparation module in maestro with the ''preparation and refinement'' option, and a restrained partial minimization was terminated when the root-mean-square deviation (rmsd) reached a maximum value of . Å in order to relieve steric clashes. the grid-enclosing box was centered on the zn + (i) and defined so as to enclose residues located within Å , and a scaling factor of . was set to van der waals (vdm) radii of those receptor atoms with the partial atomic charge less than . . in the docking process, extra-precision (xp) docking was adopted to generate the minimized pose, and the glide scoring function (g-score) was used to select the final poses for each antibiotic. together with reported study, the reasonable poses were used for the binding mode analysis. all antibiotics used in this study were purchased from j&k scientific ltd., except for kanamycin purchased from sangon biotech(shanghai) co., ltd.. the ndm- gene, which was obtained as a bp pcr product from huashan hospital. a new pcr product with restriction sites (ndei on forward site and xhoi on reverse site) encoding truncation protein from amino acid q to the last amino acid (designated as ndm- - ) of ndm- were constructed into a modified pet vector. as a result, ndm- - were expressed as fusion protein with a n-terminal his -sumo (small ubiquitin-related modifier) tag. the quickchange ii site-directed mutagenesis kit (stratagene, la jolla, ca) was used to introduce all the mutations, including d a,c a,k a,k e, replacing residues of loop ( - , ldmpgfgava) with vim- corresponding residues ( - ,qsfdgavyp), into the gene of ndm- - . the expression vectors were transformed into e.coli strain bl (de ). a -ml overnight culture of these transformed bacteria in luria-bertani (lb) medium containing mg/ml kanamycin was used to inoculate liter of lb medium containing mg/ml kanamycin and mm zncl . bacteria were cultured at uc with shaking, until reach an optical density at nm of . , then transferred to uc, induced by . mm iptg overnight. the bacteria were collected by centrifugation and resuspended in ml lysis buffer containing mm tris, ph . , mm nacl, . % b-mercaptoethanol per liter culture. the bacteria were ruptured by sonication, and the bacteria debris was removed by centrifugation at rpm for min. the cleared supernatant was load onto a ni-column, which pre-equilibrated by lysis buffer, and washed with lysis buffer supplemented with mm imidazole. then ulp- (ubiquitin-like protein-specific protease ) was add into the ni-column, digest the fusion protein at uc overnight. collect the flow through, concentrated and load onto a superdex column, which pre-equilibrated by mm tris, ph . , mm nacl, mm dtt. fractions containing ndm- - and corresponding mutation proteins were pooled and concentrated, then stored at uc freezer. protein purity was more than %, estimated by sodium dodecyl sulfate (sds)polyacrylamide gel electrophoresis. the final proteins concentration were determined by using the molar extinction coefficient at nm of , m cm . the ndm- catalyzed substrate hydrolysation reaction were carried out in uv-starh well microplates (greiner bio-one ltd.) at room temperature within reaction buffer mm hepes, ph . . the antibiotics hydrolysation were monitored by tecan infinite multimode and absorbance microplate readers (tecan group ltd.) in the peak absorbance of various antibiotics. characterization of a new metallo-lactamase gene, blandm- , and a novel erythromycin esterase gene carried on a unique genetic structure in klebsiella pneumoniae sequence type from india emergence of a new antibiotic resistance mechanism in india, pakistan, and the uk: a molecular, biological, and epidemiological study new delhi metallo-beta-lactamase (ndm- ): towards a new pandemia metallo-beta-lactamase: structure and mechanism the mechanism of catalysis and the inhibition of the bacillus cereus zinc-dependent beta-lactamase on the mechanism of the metallo-betalactamase from bacteroides fragilis hybrid qm/mm and dft investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase ccra from bacteroides fragilis biochemical and structural characterization of the subclass b metallo-{beta}-lactamase vim- crystal structure of ndm- reveals a common {beta}-lactam hydrolysis mechanism a structural view of the antibiotic degradation enzyme ndm- from a superbug analysis of the importance of the metallo-beta-lactamase active site loop in substrate binding and catalysis crystallographic investigation of the inhibition mode of a vim- metallo-betalactamase from pseudomonas aeruginosa by a mercaptocarboxylate inhibitor mercaptophosphonate compounds as broad-spectrum inhibitors of the metallobeta-lactamases three-dimensional structure of fez- , a monomeric subclass b metallo-betalactamase from fluoribacter gormanii, in native form and in complex with dcaptopril metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily why are oseltamivir and zanamivir effective against the newly emerged influenza a virus (a/h n )? basic local alignment search tool procheck: a program to check the stereochemical quality of protein structures} a method to identify protein sequences that fold into a known three-dimensional structure glide: a new approach for rapid, accurate docking and scoring. . method and assessment of docking accuracy we gratefully thank dr. xin liu from stanford university for his helpful comments. we deeply appreciate dr. fupin hu from huashan hospital giving us the ndm- pcr fragment. key: cord- -c ytamge authors: da fonseca pestana ribeiro, jose mauro; park, marcelo title: less empiric broad-spectrum antibiotics is more in the icu date: - - journal: intensive care med doi: . /s - - -z sha: doc_id: cord_uid: c ytamge nan antibiotics are administered in approximately % of patients who are admitted to the intensive care unit (icu) and have helped to save millions of lives [ ] . however, up to half of all antibiotic prescriptions may be unnecessary [ ] . antibiotic overuse has contributed to alarmingly high levels of global antibiotic resistance, which is increasing at a rate faster than that at which novel antibiotics are produced. therefore, finding a fine balance between the appropriate use and avoidance of unnecessary administration is crucial to prevent the renaissance of a new world without antibiotics [ ] . antibiotics largely reduce mortality associated with moderate and severe infections, with a historical numberneeded-to-treat estimated in . for severe pneumonia patients [ ] . infection progressing to sepsis is the leading cause of death in icu patients and can be potentially treated using antibiotics, along with organ dysfunction support, and infection source control [ ] . from the cognitive dimension, the fear of patient deterioration due to sepsis favours the empirical use of antibiotics in icu patients. once a severe infection is diagnosed, the early administration of broad-spectrum antibiotics is recommended to decrease the risk of death [ ] . this intuitive recommendation is also based on observational studies that have been carried out in the emergency department [ , ] . in contrast, a randomized study, showed that the pre-hospital administration of antibiotics in septic patients did not reduce the mortality [ ] . furthermore, in a prospective cohort of icu patients with bacteremia, early initiation and appropriateness of antibiotic intervention were not found to impact mortality when adequately adjusted for confounders [ ] . additionally, a pooled analysis of the current literature failed to demonstrate a survival benefit related to antibiotic administration within the first hour or within the first h following a diagnosis of sepsis [ ] . in surgical and trauma patients, a quasi-experimental before and after study demonstrated that more aggressive antibiotic use had similar outcomes and higher antibiotic exposure compared to conservative use [ ] . interestingly, when antibiotics were administered following the diagnosis of shock (mean arterial pressure < mmhg), the mortality of the aggressively-treated group was higher than that of the conservatively-treated group ( % vs. %, p < . ). the authors presented several plausible factors to explain these findings. the adequacy of initial antibiotic treatment was lower in the aggressivelytreated group, which therefore extended the antibiotics exposure. moreover, the waiting time for blood cultures and observation of the clinical course may also disclose alternative diagnosis to infections. at last, up to % of patients initially diagnosed as septic shock did not have an identified infection h after their initial diagnosis [ ] . from the physiological point of view, there is no plausibility that minor time differences in antibiotic administration reduce the intensity of the inflammatory response, and may even be associated with a transient worsening after administration. lastly, it is difficult to differentiate the effect of early antibiotic use per se from the awareness of critical illness and the timely institution of high quality-of-care [ ] . several adverse effects related to antibiotic use are described in the literature; with acquired multidrug resistance (mdr) being the most concerning effect. since *correspondence: marcelo.park@hc.fm.usp.br intensive care unit, emergency department, hospital das clínicas, university of são paulo medical school, são paulo, brazil , antibiotic resistance has been a major fear of sir alexander fleming. currently, mdr bacteria are largely spread across the world [ ] . the real impact of mdrs on the outcomes of icu patients is debatable, but despite this controversy, the incidence of mdrs is related to poor quality-of-care, as an expression of reduced compliance to hand hygiene [ ] , and a high burden of antibiotic exposure [ ] . de-escalation approach, in which the antibiotic spectrum is narrowed or even withdrawn after re-evaluation, has been implemented to reduce exposure to antibiotics. de-escalation has proved to be safe in terms of survival; however, it is associated with an increased icu lengthof-stay, without reducing the incidence of mdrs [ ] . de-escalation decreases the time of antibiotic use, but a short exposure still exists; in this way, a single antibiotic dose may be enough to treat severe infections such as fig. two different mindsets in the decision making process to initiate antibiotics to critically ill patients who are getting worse. a aggressive mindset, in which the antibiotics are initiated as soon as possible to avoid further clinical deterioration; and b conservative mindset, in which antibiotics are only initiated with the infection diagnosis, or in shock patients without non-infectious alternative suspicion. mdr denotes multidrug resistant bacteria. atms denote antimicrobials. kpc denotes klebsiella pneumonia carbapenemase. cre denotes carbapenem resistant enterobacteriaceae. *in the intensive care unit, patients have h of close clinical observation. # the gram-positive cocci absence in the tracheal aspirate has a high negative predictive value to staphylococcus aureus growing in patients with high clinical probability of ventilator associated pneumonia and clinical worsening-new fever, hypothermia, unexplained tachycardia and hyperventilation. laboratorial worsening-leukocytosis, leukopenia, increased c-reactive protein and increased procalcitonin. red boxes⇒no evidence-no randomized study or cohort evaluation on favor the practice, or randomized study against the practice. yellow boxes⇒some evidence-at least one cohort evaluation on favor the practice. green boxes⇒clinical evidence-at least one randomized study on favor the practice meningococcal meningitis [ ] , and to promote profound and sustained microbiome unbalances, therefore facilitating opportunistic infections and damping the potential benefit of the de-escalation approach [ ] . the main step toward the reduction of antibiotic use is the adequacy of hand hygiene in healthcare professionals [ ] . an antibiotic stewardship focusing on feedback, monitoring, persuasion, and audit after each drug prescription is associated with a long term reduction in healthcare associated infections, antibiotic prescriptions, and health care costs, without the deleterious effects on length-of-stay, readmissions, and in-hospital mortality [ ] . furthermore, the decrease in the use of carbapenems, has been associated with an overall reduction in the incidence of mdrs [ ] to ensure patient safety, the early aggressive administration of broad-spectrum antibiotics in the icu setting is common practice [ ] . however, maintaining a conservative mindset with respect to antibiotic use and safety is fundamental to both the patient and environment. mindset modification accomplishes many dimensions; for instance, the reset model which has been applied to dairy cattle farms resulted in a reduction in antibiotic use in this area [ ] . reset dimensions are ( ) (r)ulesan external motivation to reduce antibiotic prescription; ( ) (e)ducation-showing that antibiotic prescriptions are unnecessarily excessive, expensive, and paradoxically unsafe; ( ) (s)ocial pressure-ensuring societal awareness that unnecessary use of antibiotics is dangerously growing; ( ) (e)conomics-the awareness of economic consequences of reduced use of antibiotics to save costs; and ( ) (t)ools-ways to spread knowledge regarding the conscious use of antibiotics. a schematic, aggressive, and conservative mindset to commence antibiotics is presented in fig. . there are several reasons why aggressive early use of broad-spectrum antibiotics should be avoided in icu patients. presence of shock without an alternative diagnosis other than infection, and a diagnosis of infection based on cultures, bacterioscopic examinations, and imaging results for the initiation of antibiotics is currently considered safe practice. furthermore, clinicians can consider investigating feasible alternative diagnosis for shock in unstable icu patients before antibiotics initiation. consideration of antibiotic use in our icus is essential, and if necessary; there is great plausibility in changing our mindset to restrict antibiotic use. the authors declare that they have no conflicts of interest. springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. international study of the prevalence and outcomes of infection in intensive care units ready for a world without antibiotics? the pensières antibiotic resistance call to action treatment of pneumonia with -(p-aminobenzenesulphonamido) pyridine surviving sepsis campaign: international guidelines for management of sepsis and septic shock the timing of early antibiotics and hospital mortality in sepsis empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the first hour: results from a guideline-based performance improvement program prehospital antibiotics in the ambulance for sepsis: a multicentre, open label, randomised trial antibiotic use and impact on outcome from bacteraemic critical illness: the bacteraemia study in intensive care (basic) the impact of timing of antibiotics on outcomes in severe sepsis and septic shock: a systematic review and meta-analysis aggressive versus conservative initiation of antimicrobial treatment in critically ill surgical patients with suspected intensivecare-unit-acquired infection: a quasi-experimental, before and after observational cohort study septic shock with no diagnosis at hours: a pragmatic multicenter prospective cohort study association between state-mandated protocolized sepsis care and in-hospital mortality among adults with sepsis clinical epidemiology of the global expansion of klebsiella pneumoniae carbapenemases interventions to reduce colonisation and transmission of antimicrobial-resistant bacteria in intensive care units: an interrupted time series study and cluster randomised trial effect of short-term carbapenem restriction on the incidence of nonpseudomonal multi-drug resistant gram-negative bacilli in an intensive care unit de-escalation versus continuation of empirical antimicrobial treatment in severe sepsis: a multicenter non-blinded randomized noninferiority trial ceftriaxone as effective as long-acting chloramphenicol in short-course treatment of meningococcal meningitis during epidemics: a randomised non-inferiority study profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to clostridium difficile-induced colitis long-term effects of phased implementation of antimicrobial stewardship in academic icus the reset mindset model applied on decreasing antibiotic usage in dairy cattle in the netherlands key: cord- - vh jg authors: fortané, nicolas title: antimicrobial resistance: preventive approaches to the rescue? professional expertise and business model of french “industrial” veterinarians date: - - journal: nan doi: . /s - - - sha: doc_id: cord_uid: vh jg this article focuses on the development of veterinary medicine in the industrial pig and poultry production sector. in the current context of controversies over the public problem of antimicrobial resistance (amr), the veterinary profession is tending to promote a model of preventive medicine that is supposed to reduce the use of antibiotics in livestock farming. however, veterinarians specializing in pig and poultry production (“industrial vets”) have in fact been adopting such approaches to animal health for several decades. based on interviews with pig and poultry veterinarians practicing or having practiced in western france between the s and the s, the article aims to understand how such a form of professional expertise has developed, and the business model that underpins it. contrary to public discourses which promote preventive approaches as a way to diversify professional expertise and to disconnect veterinary incomes from drug sales, it is indeed this economic model that has allowed the development of such approaches within industrial livestock farming. modern strategies for reducing antibiotic use should therefore seek less to renew the professional expertise of veterinarians than to find new ways to valorize it economically. the french veterinary profession is currently undergoing major changes; or at least it tends to see itself as being at the heart of a period of major challenges that are pushing it to reinvent itself. this is not the first time that it has had to face such a reflexivity test, even in recent history (in the british case, some historians even see a cycle-woods a), but recent literature produced by professional veterinary organizations shows the importance of what is currently perceived as a need for self-analysis and change (ondpv ; vetfuturs france ) . there are several issues that might explain why this period is favourable to such a prospective assessment of veterinary futures. one of the most important concerns the controversies and public policies that have developed over recent years with regard to the issue of antimicrobial resistance (amr), which has directly challenged the economic and professional model of farm animal veterinary practices that were setting drugs (mostly antibiotics) up as a cornerstone of veterinary activity, as a source of both income and professional expertise. cross-fertilization of research on the veterinary profession and drug regulation is not common. although veterinarians have aroused the interest of certain historians and sociologists of professions, this has essentially been in relation to the analysis of this social group's process of professionalization (berdah ; mitsuba ) , its role in animal health or food safety policies (woods b; enticott et al. ; fortané , ) , the dynamics that contribute to its specialization (gardiner ) or feminization (surdez ), or finally to knowledge and professional practices in farm (shortall et al. ; ruston et al. ) and small animal medicine (sanders ; morris ) . as for the regulation of veterinary drugs, there are also several studies by historians on the vaccination of animals against major zoonoses or epizootic diseases (woods ; berdah ) , sometimes on the veterinary pharmaceutical industry (corley and godley ) , and more recently on the amr issue (kirchhelle ). yet unlike the uses of human medicines that medical anthropology has been able to theorize and document for many years (whyte et al. ) , the uses of veterinary medicines, i.e. the conditions under which they are prescribed, dispensed and used, are rarely studied, except in interdisciplinary literature from the field of veterinary sciences (speksnijder et al. ; coyne et al. ) . this article tries to open a way to cross-fertilize these reflections. using recent debates on the amr problem, it proposes to examine the relationship between the development of professional veterinary expertise and of the drug market, based on the case of a specific segment of the profession, namely veterinarians specializing in industrial poultry and pig production in western france. it thus puts the amr issue under a broader lens as it analyses ongoing changes within the veterinary profession not as potential consequence of recent measures aiming to reduce antibiotic use, but rather as a reason for the way the problem is now framed. indeed, it is common to hear professional organizations or public authorities state that in order to reduce their economic dependence on antibiotic sales, vets must rethink their activity by favouring preventive approaches to animal health which would involve a diversified range of services and would contribute to placing vets in an advisory role with a holistic vision of livestock farming or even of the food supply chain (vetfuturs france ) . however, such a form of professional expertise, combined with a particular business model for the practices promoting it, is not fundamentally new. if it is at the heart of contemporary debates, it is because it is based and supported by far earlier dynamics that initially had nothing to do with amr, but which used the opportunity of current controversies surrounding antibiotic use, sale and prescription to reinforce and legitimize a certain vision of veterinary medicine, based on preventive approaches to animal health. poultry and pig medicine in industrial production is an especially interesting area for an analysis of these dynamics. firstly, because approaches to animal health that have developed in this field are very singular and characteristic of the intensive farming methods used in these sectors, particularly in the brittany and pays de loire regions where a large proportion of the production is located. indeed, a certain vision of preventive medicine was developed by pig and poultry vets in the s and s, even if the issue of this form of veterinary expertise has not always been raised in these terms. this article therefore aims to understand the professional knowledge, practices and economic model upon which this kind of expertise is based, and why the current amr context is an opportunity to expand it (or at least attempt to). secondly, pig and poultry vets make up an extremely small and autonomous segment of the profession (which makes it possible to draw up a fairly representative picture) although its homogeneity should not be overestimated. this article thus seeks to provide a thorough analysis of this very particular part of the veterinary profession, the specificities of which have almost never been addressed by the literature. despite their small numbers, "industrial" vets are nevertheless an essential component of the profession, because they manage the health of an economic sector which supplies a considerable share of national animal production. the article opens with a brief presentation of the political context and controversies surrounding the amr problem, and how the french veterinary profession has faced up to this by defending the preventive medicine model. it then describes this form of expertise in the professional segment studied here, showing why pig and poultry vets chose this specialization. the article then looks at the origins of these preventive approaches to animal health, both in terms of knowledge and practices, and the economic model associated with it. finally, it reviews the strategies currently developed by industrial vets to adapt to the constraints of increased control of antibiotic use in livestock. the amr problem and the preventive "solution" the problem of antibiotic use in livestock farming is not new. as soon as these molecules were introduced in agriculture in the late s, there was controversy concerning the development of resistant bacteria in animals and food, and the risks of human contamination (bud ). yet for several decades, this issue has been eclipsed by the belief in a permanent renewal of the therapeutic arsenal, consisting in thinking that the continuous discovery of new antibiotics would compensate for the development of increasingly resistant bacteria (podolsky ) . after the swann report in , a series of measures to control the use of antibiotics as growth promoters was nevertheless adopted in europe, progressively separating the molecules used in agriculture and human medicine (kirchhelle ) . but years later, during the avoparcin crisis , , , these measures were considered ineffective (in the sense that they did not prevent the transmission of resistant bacteria between humans and animals) and the use of antibiotics as growth promoters was finally banned in the european union in (kahn ) . the problem of antibiotic use in livestock farming as we know it today reemerged in the late s, this time focusing on veterinary uses, i.e. on curative or preventive uses with veterinary prescription (fortané ) . veterinarians were directly accused of being responsible for the overuse and misuse of antibiotics (and therefore for the spread of resistant bacteria) on the basis of a fairly simple argument: their supposed professional "conflict of interest". indeed, in france, since the act on veterinary pharmaceuticals, vets have had a dual monopoly on the prescription and supply of medicines (hubscher ) . even if, in theory, delivery is shared between three beneficiaries (veterinarians, pharmacists and approved co-operatives), vets capture the vast majority of the curative drug market (of which antibiotics constitute the main category) (guillemot and vandaële ) . the argument that veterinarians over-prescribe antibiotics in order to increase their incomes then became the main framing of the amr problem. this construction of the problem was in reality carried by a coalition of human health actors (doctors, pharmacists, health administration) whose political agenda was twofold. on the one hand, they defended a measure that crystallized the debates around the years - : the "decoupling" of prescription and delivery, which consists in applying the professional and economic model that prevails on the human drug market, i.e. reserving prescriptions to physicians and sales to pharmacists. decoupling basically means forbidding veterinarians from selling pharmaceuticals, as is the case in countries such as sweden or spain (fortané ) . on the other hand, this coalition supported the concept of "critically important antibiotics", the principle of which is to reserve certain molecules, in particular the latest generations of antibiotics, for human medicine. from a political and institutional point of view, this period was extremely interesting because it put the spotlight on definitional and jurisdictional conflicts between different social groups for the control of the legitimate use of antibiotics. it finally ended in a relative victory for veterinarians who succeeded, at the end of an unprecedented mobilization, in reversing the stigma that human health stakeholders assigned to them. indeed, vets have been able to impose the image of a profession that is not guilty of overusing antibiotics but which is instead accountable for their proper use. the notions of prudent, judicious, rational or responsible use, now widely used in amr debates, are thus a social construct produced by conflicts between social groups for the definition of the legitimate use of antibiotics (fortané ) . this veterinarian victory led to the withdrawal of the two emblematic measures (decoupling of prescription and delivery; ban on critically important antimicrobials) supported by the coalition of human health actors. in return, a stricter framework for the use of antibiotics in animal husbandry was implemented between and : margins on the sale of antibiotics are now limited and the retail price of antibiotics must be the same for every client, and antimicrobial susceptibility tests are mandatory for the prescription of critically important antibiotics. but once again, the most important part of this victory certainly concerns the changes regarding the image of the profession. indeed, veterinarians not only reversed the stigma and positioned themselves as guardians of antibiotics, they were also able to re-appropriate the problem by highlighting the way they could solve it. without denying that the economic model of the profession was too financially dependent on antibiotic sales, and that antibiotic use may have been too prevalent in animal care in the past, vets started to defend the development of preventive approaches which would, according to them, be the only way to ensure the transition towards an economic and professional model guaranteeing responsible use of antibiotics. this view was reinforced and supported by farmers and public authorities who also called for the development of such approaches which are usually promoted by national amr policies ( fig. ) in france and in other countries (badau ; piquerez ) . at the heart of this new prospective narrative for the profession and its role in managing the amr problem, we can observe the construction of a (supposedly) new conception of animal health, which is not based on a strictly clinical approach to diseases but on a holistic vision of animals and livestock farming (biosecurity, hygiene, nutrition, good husbandry practices, etc.). in the posters above, veterinarians are portrayed as the gatekeepers of such an approach, through their transversal role as "health advisors". this professional model, based on the knowledge and practices of preventive approaches to animal health, goes hand law for food, agriculture and forestry n° - of october th, . decree no. - of march th, . when public authorities and the veterinary profession began to conceive this campaign, a third poster was designed, saying: "my vet is much more than a mere drug supplier, he is also a teacher! he prescribes the medicines i need … but above all he talks to my farmer to make sure that i am perfectly fed, sheltered and vaccinated". however this poster was not retained for the campaign because of its relatively sensitive headline. in hand with an economic model where the incomes of veterinary businesses would be more diversified since these new "health advisors" would be able to monetize a wider range of goods and services (hygiene and nutrition products, bacteriological analyses, livestock audits, etc.) than just pharmaceuticals. could we look beyond the symbols and images of professional and political discourses and see whether these preventive approaches that might change the way veterinary medicine is practiced, and how antibiotics are used, rely on actual knowledge and practices and, if so, where and since when? the fact is that this model of preventive veterinary medicine seems in reality to be quite typical of a very particular segment of the veterinary profession, the one this article proposes to describe, namely industrial vets. the remainder of the article thus seeks to address the following two questions: is this form of professional expertise really perceptible in the field, and is its development truly linked to the global context of the amr problem and to recently implemented policy measures, or does it have other origins and raisons d'être that might actually when public authorities and the veterinary profession began to conceive this campaign, a third poster was designed, saying: "my vet is much more than a mere drug supplier, he is also a teacher! he prescribes the medicines i need … but above all he talks to my farmer to make sure that i am perfectly fed, sheltered and vaccinated". however this poster was not retained for the campaign because of its relatively sensitive headline. these two posters were used in the french amr policy ("plan ecoanƟbio"). they are a perfect illustraƟon of how the veterinarian's role was reframed towards prevenƟve approaches to animal health (in parƟcular vaccinaƟon), as a means to reduce the use of anƟbioƟcs. the first poster (on the leŌ) says: "my vet is far more than a mere emergency doctor, he is an expert contribuƟng to good husbandry pracƟces". the second poster (on the right) says: "my vet is far more than a mere hands-on man, he is an advisor, always there to prevent and vaccinate". both conclude with: "ask your vet for advice" . when poultry or pig vets are asked why they chose this specialty, they often point out a huge contrast between what they do and the way they perceive cattle (i.e. "rural") or companion animal vets. they feel that being an "industrial vet" essentially relates to four characteristics. firstly, veterinarians specialized in poultry or pig medicine attach importance to working at the heart of the agri-food system, with livestock farming professionals. many of them have agricultural family origins and believe that they chose this profession in order to maintain a strong link with the rural world. they perceive farmers as animal experts, unlike pet owners, and see their activity as teamwork alongside skilled professionals, with whom it is easier to interact and who can also provide them with knowledge about animals. their clients are therefore also their partners in animal health management: they can trust them, rely on them and delegate tasks to them. secondly, pig and poultry vets consider their work to be a permanent renewal, as opposed to the repetitive and sometimes boring work of cattle vets who constantly reproduce the same gestures and who are rarely motivated or intellectually stimulated by new situations and new challenges. most of them, whether they are young vets or already have or years of experience, tend to compare their professional activity with the image of the "emergency vet" (or "fire brigade" vet), available day and night to care for sick animals. from their point of view, this traditional activity is typical of cattle vets, corresponds to the past and relates to a type of work which is limited to clinical diagnosis, drug prescription and/or surgery (e.g. midnight calving). in their opinion, the only objective of such a way of working is to ensure that clients are satisfied with an occasional intervention and that they will once again call upon veterinary services the next time health problems occur. the point here is not to claim that this is what cattle vets are actually doing, but simply to note that this narrative is widely used to define, by contrast, the professional identity of industrial vets. i am indirectly from a rural family, that is to say that my grand-parents, my uncles, they all worked as farmers, in mixed farming and mixed animal farming, from both sides of my family. it is just my parents who had access during the postwar period to national education programmes and became teachers or researchers. so i am from the third generation but i spent a lot of time at the farm. although some of the characteristics that pig and poultry vets tend to associate with cattle vets have actually been observed in other studies, in particular the fact that cattle vets do not have a high opinion of the technical expertise of the farmers they deal with (shortall et al. ) . these opinions of their clients nevertheless depend to a certain extent on the type of farm and farmers they relate to: cattle vets have better professional relationships with "commercial farmers" (managers of large, modern and business-oriented farms) as the latter tend "to understand the need to use the vet as a disease prevention consultant rather than to treat individual sick animals: i.e. part of vets' desired move from a 'test and treat' to a 'predict and prevent' model of veterinary intervention" (shortall et al. , p. ) . in addition, this shows that a tension between "fire brigade" work and advisory veterinary work is also present within a certain section of the cattle vet profession. i became a vet to take care of farm animals because i like being outside and having an intellectual occupation. so that is the reason why. so at vet school, you didn't think about working with dogs? certainly not (laughs)! that was my nightmare! when you work in the pig sector, what is good is that you work % on farms. because when you work with cattle, most of the time you have to do some small animal work as well. and what i want is to work with professionals who are producing the animals we eat. pig farmers (well, not all of them but most of them) have very good technical skills. pig farming is a very dynamic sector, you never get bored! we often have to upgrade the farms to new standards so it's always evolving. research also moves very fast, the pharmaceutical industry innovates a lot so it's interesting. (…) and to be honest, what interests me the most is this kind of follow-up, not being a "fire brigade" vet. but i can't talk very knowledgeably about the "classic" rural vet as i never was one. but what i do think about this kind of practice is that there is a lot of emergency and "fire brigade" work and i don't think that is very challenging. in pig production, we have been evolving for quite a long time because if we only do "fire brigade" work… well, farmers expect a lot more than that! and for us, that is also what's interesting. pig farming is a batch production, so we have this tendency to always try to do something for the next batch, try to prevent future batches from getting the disease we have now. so having to try this and that is always very dynamic and challenging. so we know that there is always a new batch to come, and that is not the same in cattle farming. thirdly, pig and poultry vets describe their work as being part of an epidemiological rather than clinical approach to animal health, which they associate with the idea of a preventive rather than curative or therapeutic approach to diseases. this conception is closely linked to the two previous points. on the one hand, it refers to the professional proximity that veterinarians maintain not only with their clients but also with technical advisors, often employees of the co-operative to which the farmer belongs or sometimes of a feed mill company. indeed, in pig and poultry farming, technical advisors play an important role as they visit the farms much more frequently than vets. although their role should not involve animal health issues (but rather feeding, housing or husbandry practices), they tend to conceive these aspects as a whole, as do vets when they look at the technical factors (rather than biological and medical ones) of diseases. animal health is thus the work of a professional trio, whose theoretically distinct roles often overlap, encouraging situations of cooperation and also sometimes conflict (adam et al. ). on the other hand, and consequentially, this so-called epidemiological conception of animal health establishes a form of activity which is not limited to a clinical and individual approach to pathology but which, on the contrary, opens up professional expertise to areas often considered as not specifically veterinary, such as hygiene, nutrition, zootechnics or biosecurity. the knowledge and the toolbox of industrial vets are thus extremely varied and cannot be limited to surgery tools or prescription booklets. the veterinarians interviewed often emphasized the "evidence-based" side of their professional expertise (and legitimacy), which is based on the collection and analysis of various data and promotes intellectual stimulations regularly renewed by the diverse situations they must face. they believe all these elements to be part of preventive approaches to animal health and they tend to perceive themselves as health advisers, or "health managers" as thoms ( ) has shown in the case of german poultry vets. i graduated from veterinary school in . then i got a degree in epidemiology. what i realized and particularly interested me during my studies was the difference between individual medicine and herd medicine. so with my education and also my family farming background i realized that individual medicine was more a cost than a profit. so i tried to develop this kind of herd care and preventive approach. i started my professional life in rural medicine in a region that was quite a pioneer in this type of approach, especially regarding reproduction. we have audit grids and we have exploration tools. for example, i have a device to measure co , to dose carbon monoxide. i have a ph-meter, a conductivity meter, a laser. i have a burette to measure the water flow in the feeding system. i have a light meter in case i need it. i have a camera to explore water pipes. i always have smoke bombs in my car to check ventilation in the buildings. so really, we have exploration tools in the form of scissors and gloves to perform autopsies but also equipment for managing the buildings. but aren't you stealing work from the technicians? technicians do autopsies (laughs)! no, it's true that controlling ventilation doesn't mean that i am able to deal with the farm it system. so technicians keep their skills. but i consider that it is my job to explain to the farmer that if he has a colibacillosis it's not because a germ fell from the sky but because his ventilation system doesn't work the way it should. that's part of a vet's job, even though it is the technician who is able to fix the problem. we are doing what i might call an etiological or epidemiological diagnosis. fourthly, the characteristics of pig and poultry medicine must also be related to the type of animals with which these vets work on a daily basis. without necessarily following the epistemological principles of the "animal turn" promoted by certain branches of the social sciences (guillo ) , which consists in analysing the way in which animals themselves shape human interactions or the socio-technical devices within which they take place (notion of "animal agency"), it must be noted that taking care of chickens or pigs has different implications than is the case with cattle, dogs or cats. two elements seem central here and are directly related to the characteristics of pigs and poultry and the farming systems to which they belong. on the one hand, these animals have a relatively short lifespan: only about days for a conventionally raised chicken (between and days in organic or label farming) and about months for pigs (the sows being slaughtered after or years). it is therefore very different from a dairy cow that must remain healthy and productive for an average of years, or pets that live or years, sometimes more. in these conditions, which obviously also depend on the economic structure of the agri-food industry, animal health becomes part of biological and temporal dynamics where the slightest disorder may have pathological consequences that might be seen as "just-in-time diseases", i.e. health issues directly related to, or shaped by, the sociotechnical and economic infrastructures (including the animal bodies themselves) within which they emerged (allen and lavau ) . on the other hand, the health of chickens and pigs is not considered individually, but rather from a population perspective. these are animals that are reared in batches and it is the group of animals that constitutes the epidemiological reference unit for both the vet and the farmer. in certain cases, particularly in poultry farms where the production cycle is very short, many decisions are therefore made not for the current batch but for the following one, in order to avoid repetition of the same problem. overall, all of these aspects are typical of industrial veterinary medicine and, therefore, of this form of expertise and professional legitimacy that can be qualified as preventive veterinary medicine. to sum up, and without prejudging whether or not these elements can be found in other segments of the veterinary profession, we can say that poultry and pig medicine is characterized by (i) a vocation; (ii) a technical and preventive approach; (iii) tripartite work; (iv) animals and farming systems that "call for", or co-construct, this form of expertise. however, when listening to veterinarians talk about their profession, this way of working on industrial farms does not seem to be linked to the rebuilding claimed by the profession since its incrimination in the amr problem, even though certain policy measures recently implemented may encourage the development of this preventive and evidence-based approach, such as the obligation to perform antimicrobial susceptibility tests before prescribing critically important antimicrobials (bourély et al. ) . indeed, the roots of this particular form of veterinary expertise can be traced back to the mid- s/early s, when some pioneers began to specialize in pig and poultry farms-at that time during a massive industrialization and intensification process. the origins of preventive approaches in "industrial" veterinary medicine during the s and s in france, particularly in brittany and pays de loire, poultry and pig farms expanded rapidly (nicourt ) . the mixed crop-livestock model was gradually being replaced by specialist farms which were developing through a twofold process of intensification (increased herd size, confinement and containment of animals, rationalization and (bio)technicization of husbandry methods such as genetics, feeding and pharmaceuticals) and industrialization (concentration and vertical integration of the food chain's stakeholders, and taylorization of farm labour) (diry ) . this movement led to the emergence of new needs in terms of health management. firstly, at that time veterinarians knew little about these animals in terms of medical knowledge or techniques (poultry and pig medicine was rarely touched upon in veterinary schools back then). secondly, the confinement of animals in enclosed buildings led to outbreaks of disease, especially-but not only-infectious diseases which were unknown or at least whose management methods were no longer appropriate. a small number of vets then began to specialize in this type of production, viewing it as a promising and developing market. poultry farming was not taught at all. poultry diseases even less so and the prevention of poultry diseases even less than that. so my gateway to poultry farming was the technical-economic approach to things, and not the purely pathological approach, which i could have done at the time on sheep or cattle. except that there, i was in a completely capitalist system. as you can see, one can adapt to anything (laughs). in the pig sector, it was mainly vets employed by agricultural co-operatives who embarked on the adventure, supported in particular by the creation of the station de pathologie porcine (spp) (national veterinary laboratory specializing in pig health) in ploufragan (north brittany) in (fortané ) . in the poultry sector, which is structured more around industrial groups than around co-operatives, there were more independent vets who were orienting their practices towards this type of clientele. what these veterinarians had in common was the conviction that they could no longer do their job in the traditional way, i.e. as emergency "rural" vets, alone or in partnership in small practices serving a diversified clientele (cattle farmers and pet owners in particular, with a few occasional interventions on poultry or pig farms). moreover, they were convinced that their job was to accompany the development of intensive and industrial livestock farming by providing services adapted to the specific animal health issues of this sector, and that their own organization had to follow and mimic the development of the industry they were working for. the term "industrial vets" therefore refers not only to the kind of clientele they were (and still are) working for, but also to their own state of mind and conception of veterinary medicine, as a profession and as a business. in fact, we were the defenders, the propagators of intensive livestock production. we never denied that, that's what we were employed for. we were just saying "ok, but the conditions for success are this and this and this". at the time, there was a double-digit growth in the sector, so we said: "we must stick to the development of this sector". we were focused on poultry, we had almost given up on pigs. we said: "we have to stick to the leaders". very quickly, in - , we said: "it's x [one of the biggest poultry industrial group], we'll stick to x, we'll stick to the growth of x, like a leech, we'll never let it go". that was our aim in - and it became concrete a little later when we were working for x, even though we weren't their official vets. (…) we had developed well in - , so how could we consolidate our system, how could we really sell it, how could we duplicate it? this is where the notion of "global offer" began. here, you find three activities: the veterinary practice, including advice and training, the medicines and the analysis. when you come here, you have this "global offer": the lab part, the drug part and the advisory part. the way this pioneering generation of pig and poultry vets worked was characterized by their capacity and interest in conceptual innovation and do-it-yourself techniques for responding to the often unknown situations they had to face. on the one hand, it concerned the development of pharmaceutical products adapted to these animals and their husbandry conditions, at a time when the pharmaceutical industry was producing very few medicines for this type of livestock, not considering it to be a worthwhile market. it was therefore not uncommon for veterinarians to order pharmaceutical raw materials (rather than manufactured drugs) in order to themselves prepare a product that could be effective in terms of both pharmacological (e.g. combining an antibiotic and an anti-inflammatory) and galenic properties (e.g. designing a drug in the form of a powder to be spread in bedding rather than to be mixed with food-for dermatological infections in particular). in - , we had outbreaks of staphylococci. obviously, the animals caught it very early because they already started to have small pimples at - days. so the mother was a carrier, so we thought: "what if we use an antiseptic powder?" then we thought: "we need a powder that is very powdery, that adheres well to the skin". we worked on the galenic, excipients and everything. we developed a powder and tried it and the farmers said: "this works well". who were you doing this with? we made the powder ourselves. we had a mixer. in our pharmacy, we had a manufacturing workshop. (...) it was common at the time. we had the right to make extemporaneous preparations that were the result of our prescription and our imagination. on the other hand, this broader conception of the veterinary role could be seen in the holistic vision of health that these professionals were promoting. most of the time, they combined therapeutic intervention with bacteriological analysis and research on animal nutrition (some of these vets were also employed by feed mills). all of the larger practices of this pioneering generation developed a laboratory, sometimes a makeshift one, in order to perform the autopsies necessary for bacteriological tests. x [a pioneering poultry vet] had a very solid clientele of horses and cattle at the time, but he was interested in birds. (...) when the first industrial poultry farms, the large flocks of to chickens, settled in, he moved towards that. very quickly, he realized that the bigger the batches of poultry became, the more the diagnosis had to go through the laboratory in order to be accurate -at least regarding bacteriology and parasitology. since he's a guy who doesn't want to do things by half, he thought: "i can't make a laboratory like that, we suck as vets, i need training". he said to his partner: "i will go to pasteur". further education at that time was unimaginable. (...) then, when he came back, he started his own lab and that was really the beginning of the adventure. in the pig sector, it is interesting to note the extent to which the history of the ploufragan station is still rooted in the north brittany territory, as many generations of veterinarians, still today, have done part of their training there or continue to rely on the expertise of spp's epidemiologists or microbiologists in their daily activity (especially in the case of outbreaks of infectious diseases or to set up clinical trials). oh yes, with regard to emerging diseases, i often contacted the station when we saw pathologies that seemed new to us. this was the case for many diseases. there was streptococcal, there was respiratory coronavirus. at the spp, i called [the vet in charge] and the others, they were not convinced because at that time there was still pseudorabies in the farms. i had to talk to [a pharmaceutical company] about it and then the spp became interested. indeed, veterinary researchers from the spp had developed a preventive approach to animal health called "ecopathology" that had considerable success among pig vets and farmers in the s (fortané ) . it was mostly based on an epidemiological conception of animal health (disease outbreaks are related to multiple variables, particularly "technical", i.e. non-clinical ones), and was adapted to the specific issues and husbandry conditions of intensive livestock farming. in this regard, the type of preventive veterinary medicine which was developed at that time in france would seem to have similar characteristics to that which had flourished in the uk slightly earlier (from the s to s) (woods ) : animal health has to be conceived at the scale of the herd (and not the individual animal), be articulated to non-medical matters such as feeding, housing and genetics, and integrate the economic issues of performance and profitability within the advisory support vets provide to their clients. the most important difference during the process of institutionalizing these preventive approaches in france and uk seems to be the role played by public authorities. while in the uk, the state firmly supported the development of preventive veterinary medicine as a way to accompany the modernization of british livestock farming, in france, except for the spp which was partially founded by local authorities and state veterinary services, most of the preventive approaches that flourished in the s were supported by the private engagement of pioneering vets trying to respond to the challenges of a growing industry and, in the meantime, to capture the market of "industrial" veterinary services. all in all, the point here is not to say that contemporary pig and poultry vets are nowadays using the exact same techniques and knowledge of the preventive approaches developed in the s and s, or even to suggest that all industrial vets of that time were doing exactly the same. it is rather to demonstrate that this type of veterinary medicine has at least a to -year history in these sectors and that some aspects of this can still be seen in the way that modern industrial vets continue to work (and to perceive their job and professional identity), such as the importance of technical expertise, epidemiological knowledge and bacterial laboratory-in other words, that a diversified form of veterinary expertise is required. even though this history has more or less vanished from the profession's official memory, a few unconscious vestiges of it can still be seen in recent amr debates. for example, during the campaign promoting the amr policy in the pig sector in , an implicit link was made between this pioneering medicine and the kind of expertise which is now considered to be the future of the profession and through which veterinarians tend to legitimize their role as the guardians of antibiotics. this is demonstrated by the utilization of the ecopathology icon which expresses the holistic conception of animal health (namely the so-called "ploufragan hexagon") to promote good veterinary practices in antimicrobial use in livestock (fig. ) . all these elements show that what is now called preventive veterinary medicine and which is perceived, within the political context of the amr problem, to be the model of professional expertise towards which veterinarians must turn, is not fundamentally new, at least within the knowledge and practices of pig and poultry vets. but what about the economic model on which this kind of expertise is based and how it is actually related to the use of antimicrobials? although it is in fine difficult to associate the development of preventive approaches with the reaction of veterinarians to their incrimination on the amr issue, contrary to what the sole examination of professional discourses in the press or in various it should also be noted that in the uk the development of preventive approaches concerned farm animal medicine in general (so mostly cattle medicine), while in france this movement was located in "industrial" pig and poultry medicine -although due to local history it would seem that in some regions other forms of preventive medicine were also developed in a small number of cattle veterinary practices as from the late 's (combettes et al. ) . this is indeed the purpose of talking about "preventive approaches" in the plural, i.e. to highlight the fact that these approaches could be rooted in different local histories or individual trajectories yet still share some common principles. while pig vets were mainly referring to ecopathology by virtue of their link with the spp, poultry vets did not use a specific term (preventive, holistic or epidemiological approach, global offer, etc.). nevertheless all industrial vets were (and still are) referring to what they were (are) doing with the same kind of contrasting schemes: epidemiological vs clinical, preventive vs curative, herd vs individual, technical vs medical, etc. which i consider to be the common ground of "preventive approaches to animal health" with, in addition (cf. next section), an economic model based on free-of-charge services funded by drug sales and aimed at "capturing" clients. institutional spaces relating to amr policy-making might suggest, nowadays this model has nevertheless become more visible and contributes to the re-legitimation of the veterinary profession (badau et al. forthcoming) . however, the idea that preventive approaches will make it possible to move away from the economic model placing antibiotic sales at the heart of veterinary income seems more dubious, as the development of said preventive approaches was in fact based on this very system. by the notion of economic model, we mean the way in which veterinary services are monetized. one of the key elements of the criticism against veterinarians with regard to the amr issue has been the fact that their sources of income are largely dependent on drug sales (antibiotics in particular). however, whereas professional discourses seek to explain that the development of a preventive medicine in which antibiotics no longer hold a central place will make it possible to change the "business model" of veterinary practices, it is on the contrary clear that this economic model based on drugs sales has in fact allowed these preventive approaches to flourish. even though it is difficult to concretely assess the accountability of veterinary practices due to a lack of available data (in particular if we wish to distinguish between different segments of the ploufragan hexagon: animal health is dependent on six variables (tillon et al., ) prevenƟon campaign against anƟbioƟc misuse in pig farming, fig. the common principles of past and present preventive approaches in industrial veterinary medicine. -ploufragan hexagon: animal health is dependent on six variables (tillon ) . this famous diagram represents the way animal health (and economic performance of the farm) is conceived within the ecopathological framework: it is correlated to six variables, namely the farmer, the animal, housing, feeding, microbes and husbandry practices. at that time, it was considered quite innovative to claim that veterinary expertise should take into consideration all these aspects and not just focusing on animals and microbes (fortané ). -prevention campaign against antibiotic misuse in pig farming, . this poster used in the amr campaign perfectly reproduces the six "ecopathological" variables (here referred to as the six "pillars" of animal health). it says: "no more antibiotics than needed. with my vet, i manage the health of my animals while limiting the use of antibiotics". this poster therefore illustrates how preventive approaches within veterinary medicine are deemed to be a solution to reduce antimicrobial use profession), we can nevertheless rely on estimates from various literatures. a veterinary thesis on the structure of the drug market considered that drug sales were generating to % of the income of farm animal practices (rivière ) . thirty years later, in the midst of the amr debates, a report by the french food, agriculture and rural areas council estimated this figure to be around % for farm animal vets in general, and up to % (including a high proportion of antibiotics) for industrial vets (dahan et al. , p. ) . so one cannot help but wonder what happened during the three last decades and to what extent this evolution of the economic model of veterinary activity has in fact supported the development of preventive approaches to animal health, contrary to the prospective narrative the profession has constructed to defend its role as the guardian of responsible use of antibiotics. the answer is actually quite simple, and is a classic case in agricultural economics: the sale of inputs funds the advice. in the case of industrial vets, the context in the s and s favoured the emergence of strong competition between practices seeking to capture the growing clientele of pig and poultry farmers. this competition was also heightened by the fact that the supply of veterinary goods and services was still highly heterogeneous, due to the non-existence of standardized pharmaceutical, hygienic or nutritional products adapted to the new health problems caused by the intensification of animal husbandry. consequently, pharmaceuticals, which are the only product on which veterinarians have a monopoly for prescribing (and therefore advice) and dispensing (and therefore sales), became the main means of ensuring client loyalty. since the act, the veterinary drug market has thus been developing into a captive market, where drug sales have gradually become the only monetized exchange between vets and farmers, funding all the services actually offered by veterinarians (visits, diagnosis, analyses, prescription, audit, etc.) (bonnaud and fortané ) . indeed, preventive veterinary medicine developed on the basis of this economic model which corresponded, on the one hand, to that of the few pioneering independent practices which owned bacteriology laboratories, small drug manufacturing factories or wholesale companies and, on the other hand, to that of the agricultural co-operatives which the act established as lawful drug suppliers and which, until , employed veterinary practitioners in this regard. indeed, it was precisely by providing a whole range of "free of charge" services (visits, advice, vaccination, etc.) that these vets were able to disqualify their competitors, i.e. their "emergency" or "fire brigade" colleagues who offered little advice but were able to monetize their occasional interventions. yet were the farmers prepared to pay for their visits, as they would have done with rural vets at the time? because, even the independent vets specializing in group pathologies, so pig and poultry, like those from x [one of the pioneering veterinary practices in industrial medicine], most of the time, they did not charge for their visit, their visit was paid through drug sales. in fact, most farmers were smart enough to understand that if they were satisfied with the services of a vet or a veterinary practice, they should buy drugs to pay them indirectly, even if there were price differences. i think it was like this: "you do me a favour, i need you, you treat, you prevent, we work together, i buy drugs". it was indirect payment. (…) i've always thought that the best way to ensure farmers' loyalty is to be efficient. then they will not even talk about drug prices. there was a time when vets were very active on the farms. if farmers were happy with our services, [they didn't care about] the price of the drugs. at one point, we were a little cheaper but we weren't always cheaper. we were also known for being reasonably priced, so that there wasn't too much competition. sure, we weren't the cheapest on the market, but that's not the issue. but i'm convinced, and i know that's the way it was for a lot of people, the best way to keep them was to meet their expectations. their expectations were simple: "i have problems, i have to solve them, help me solve them, if it takes time ok it takes time". it was up to us to meet farmers' expectations in terms of health. if the farmer was satisfied, the rest would follow, he would take the feed, the genetics, the drugs. we had an indirect commercial role, but we could only do it if we were efficient. (…) but some of them stopped buying our drugs. they told me: "you're too expensive". so i answered: "if we are too expensive, you go elsewhere, but you no longer have the services". what does he want? a cheap price, but with a service that will be what it will be, it may be very good, ok, but the farmer is free to choose. however, he fully understood that he could not ask us to come ten times a year or twenty times and then buy zero medicines. moreover, i tell most people: "we provide you with important services, we know that you also like to work with other people from time to time, at x for example, so don't buy everything from us, but buy a little from us, as we come to see you regularly and we need a return". and then everything was fine, they bought some elsewhere and some from us. the construction of a captive market is therefore a central dimension of what i call here "the economic structures of professional expertise". the development of preventive approaches within industrial veterinary medicine is not only the result of the emergence of new demands or needs from farmers, but it is also and above all the consequence of the intra-and extra-professional competition that veterinarians have had to face after the act. prescribing and dispensing pharmaceuticals, combined with a holistic expertise, is a means of capturing a clientele through a simple and exclusive form of economic contracting (the sale of drugs) while providing a wide range of services (diagnosis, advice, etc.). it is indeed the articulation of these two dimensions that makes it possible to prevent, or at least reduce the risk, that clients are captured by a competitor. in this sense, preventive approaches to animal health must be read simultaneously as a professional and a business model, these two dimensions being constitutive of each other. such economic structures of veterinary expertise have been observed in another context, that of the usa in the s and s. smith-howard ( ) shows how american veterinarians, who did not have a monopoly on the sale of medicines, gradually established themselves as the main distribution channel by coupling their prescriptions with preventive services that provided real added value to farmers, compared with pharmacists or other retailers who were merely supplying the drugs. a linguistic distinction has even emerged between "dispensing" and "merchandising", contributing to (re)establishing the legitimacy of veterinarians on a new basis. in the end, it is therefore in the light of this link between professional expertise (in the sense of type of knowledge and services) and business model (in the sense of how these services are economically valorized) that we must question the current context and controversies surrounding amr. it seems finally a little too simplistic to support the thesis of the professional conflict of interest that human health actors have mobilized to point out veterinarians' responsibility in the amr problem, because of their dual monopoly on the prescription and supply of medicines. in fact, the structure of the veterinary drug market has set up the sale of pharmaceuticals as a quasi-unique way of making professional expertise profitable, even though this expertise was already based on preventive approaches (and thus diversified services) for quite a long time. the current challenge for the veterinary profession is therefore less the development of a preventive medicine than the renewal of the economic model on which it has been based until now. in this regard, it is actually interesting to note that the vets i met in this study clearly mention this issue and have already started to develop strategies to deal with it. that's exactly the issue we now have with my colleague. i'm right thinking this. historically in poultry, no charge is really made for visits. overall, payment is made through [the purchase of] medicines, which is, for me, not a bad thing if it is not excessive. at some point, when we take the example of human medicine, you pay a doctor, you pay a pharmacist, everyone is happy because there is healthcare security. the day there's no healthcare security, i don't know what we're going to do. so that's what i explain to farmers: "the day you have to pay a vet and a pharmacist it's going to cost double". so at the moment, with this system, you only have one cost, so in theory that's good. indeed, there can be misuse, someone who would systematically prescribe medicines even if there is no need. this is clearly an issue and it is difficult to explain, that's our problem. but honestly, every morning when i stand up, i don't say to myself: "i will prescribe kilos there, kilos there and kilos there, and the day is done". that's absolutely not the way i think, but i can understand… and i understand when people are telling me: "yes, but if you sell, you earn". that's all there is to say. it's been on my mind for a year. firstly, particularly in a context where profits on medicines are now more strictly controlled (and therefore more limited), it seems essential for the veterinary profession to be able to charge for services that were previously funded by drug sales. this is the case in particular for visits, technical advice and bacteriological analyses (the latter were generally charged but often below the real cost-which could be high for the veterinary practice that has to employ laboratory technicians). secondly, there are strategies consisting in investing in hygiene and/or nutrition product factories (in particular disinfectants and food additives), in order to be able to sell products other than just pharmaceuticals. it is a strategy of diversification of the professional and economic activity that pioneering independent practices or certain cooperatives employing veterinarians have been using for many years, but which is now tending to become generalized among industrial vets due to the development of franchised practices. company x is a part of group y [a pig co-operative]. [we sell] zero drugs. there is hygiene, so disinfectants and detergents, and also nutrition and probiotics, i.e. products that can be added to food or that farmers can put in drinking water. you have suppliers for these products or you manufacture them yourselves? there are products that we make ourselves, otherwise we choose products from everything we know, and from people we work with. we are doing clinical and zootechnical trials as well. we've written some articles, i did one on swine haemorrhagic dysentery. we did an international article in which we showed that we can prevent it with a certain probiotic. it allowed me to go and see farms in portugal, spain and england as well. i even went to cuba for x. trying to sell products? to preach the good word! we hold meetings on a given theme, for example it might be digestive issues, and we talk about the ecopathological approach. rather than using this or that antibiotic, there are other things that work, and we know this because we have experience with farmers from y. thanks to this experience, and because there were disastrous situations where antibiotics no longer worked, we can tell other veterinary colleagues [that these products work well]. a third strategy consists in developing various forms of contractualization with the clients. for example, the vet interviewed below tries to imagine an annual flat-rate model that would cover all veterinary services, from advice to medicines. this would be based on a form of insurance, where some farmers would ultimately pay a higher price than the actual cost of the services they have received, while others, particularly those facing more health issues, would pay a lower price (although the reverse might be true from one year to the next). in fact, this system is similar to the one set up by the so-called "veterinary groups under contract" in central and south-eastern france, but which was only developed in areas where livestock farming is not widespread i.e. in small and medium-sized cattle or sheep farms connected to local markets; this system is mainly associated with alternative agricultural projects resulting from s protest movements (combettes et al. ) . it would be interesting to know the extent to which such a model might be easily generalizable in the heart of an industrialized agri-food system where farmers are involved in more complex and constraining chains of interdependence with upstream and downstream industries. this trend resonates with certain dynamics currently observable in the uk where farm animal vets are also concerned about the sustainability of their economic model and are trying to develop similar forms of contractual veterinary services, although less than % of the clientele of the practices trying to develop these kinds of contractual schemes have adopted it so far (ruston et al. ). the economic model and the type of goods and services that veterinarians can provide are nevertheless now considered to be key criteria for the sustainability of veterinary businesses (henry et al. ) . so i've been thinking for a year. now i'm going to test a new system, a comprehensive flat-rate package. i'm testing it, it's brand new, with two or three farmers. this is a complete veterinary follow-up, which includes visits and medicines. we don't talk about fees anymore. [...] so i don't know yet. my package system might be good in theory, maybe not good if farmers... because you know, on the farms, there are major variations in antimicrobial consumption. at some point the package is going to be an average. some of the farmers will find my services a little bit too expensive whereas others will like it, but yes perhaps major antibiotic users so it might be a bad influence for them. i'm not claiming victory yet, but i'm trying to find another system. a fourth strategy consists in monetizing certain veterinary services no longer to farmers, but to co-operatives. this relates to at least two types of activity. first of all, it concerns the follow-up of "herd health plans" that co-operatives are obliged to set up if they want to be approved for selling veterinary medicines, in accordance with the act. it is of course an activity that has existed for a long time, but that many cooperatives delegated to their employed vets until . the second activity relating to this strategy is linked with the development of new roles for veterinarians, in particular those of standards controllers or certifiers. indeed, with the development of "antibioticfree" labels, more and more co-operatives are asking vets to help them implement such standards. for example, vets have to perform "pharmaceutical audits" in an attempt to recruit farmers who can comply with such specifications, or to set up protocols to monitor antibiotic use and help farmers reduce it. when the co-op announced its project [antibiotic-free pigs], some farmers called me the day after, or i called them, to be part of this project. so for those who were still using antibiotics in feed there were still some stages to go through but when a farmer calls you, you think that you're going to need him for the project so you have to find alternatives. you have to know if he really needs antibiotics and how to reduce them. so this is where you have to set up a procedure, to find ways to identify the flaws… and in the end this is the perfect way to familiarize farmers with this issue. (…) well the farmer has to be motivated but this is where the bill of specifications helps, because there is an added-value. and there is also glory and self-satisfaction because the added-value isn't much, but there is both. yet these new roles for veterinarians, or more exactly these new ways of monetizing their expertise, are associated with a redefinition of their professional identity that vets are not always comfortable with. while being a health advisor rather than a clinician is perfectly in line with their preventive conception of veterinary medicine, becoming a sort of controller and sometimes even a sales representative in charge of enrolling and accompanying farmers in quality insurance schemes is not necessarily easy. this difficulty has also been noted among uk cattle vets who felt conflicted between their role of practitioner (within the framework of their relationship with their clients) and their role of "enforcers" of biosecurity practices (while implementing policy measures to prevent bovine tuberculosis), although in this case they were acting on behalf of the government and not for market schemes of private stakeholders (enticott ) . the vet interviewed below explains the practical and ethical adjustments he has had to make to accommodate this new way of valuing his professional expertise, and the limits he personally sets to remain in what he considers to be the role of a health advisor. so luckily we have some experience [with following up on bills of specifications], especially with welfare standards. in this standard, the farmers have to use the co-op's animal feed. so our experience allows us to recognize the feed bags. and one day i was on a farm visit, and i saw a feed bag. and i thought "but this is not the feed from the co-op?". because i know that it is normally small granules, and this time it was big granules. so here, clearly, the farmer is not complying with the bill of specifications! so you see, if you look carefully, you can see things. well you can't see everything, especially when farmers don't want you to know… because in this case he even didn't think about it. leaving the bag like that… it is sure that he's going to be in trouble with the co-op. but you won't see the ones who really want to cheat! and in this example, what happened in the end? you just let him know, asked him to be careful, and let it go? or might you impose sanctions at some point? well that's not for me to decide. but the question for me is whether or not i want to report someone. one day the co-op boss asked me [about the co-op's granules] but i replied that i didn't have time to check whether every farmer in the quality insurance scheme actually uses its granules. (…) but no, what i do, mostly, is warn the farmer. i tell him that he has been found out. and i tell him that the coop is fairly meticulous and that if they find out they will take him off the scheme. so for a few months he will lose cents and he won't be happy. so that's the situation. and they are absolutely capable of doing it, without any doubt. so this is what i do, i warn him but i don't think it is my role to report him, or to impose sanctions. conclusion "if i change, i may lose my clients. but if i don't change, i might lose my job" by cross-examining the development of the drug market and the professional expertise of french "industrial" vets, this article has aimed to articulate reflections from the sociology of professions and the anthropology of medicines. the amr problem is a very interesting case-study through which to make such an articulation fruitful. indeed, numerous works of research in the anthropology of medicines invite us to analyse drug use through the lens of the global circulation of pharmaceuticals and not just by focusing on the practices and knowledge of end-users, be they farmers or patients (whyte et al. ; petersen ) . antibiotic use cannot therefore be disconnected from upstream practices (or pharmaceutical "life stages", as anthropologists of medicines would call them) such as production, distribution, prescription and sale. though little is yet known about the structure of the veterinary drug market, we have shown that as key actors at the heart of the veterinary drug chain, involved in many areas of this global circulation of pharmaceuticals, veterinarians play a major role in the regulation of antibiotic use-particularly industrial vets who are not only involved in prescription and delivery but also in some cases in production and distribution. this result is therefore interesting from the point of view of the sociology of professions as it shows that the "jurisdiction" (abbott (abbott , of veterinarians is certainly more complex than them being mere practitioners of animal healthcare. indeed, when we look at the veterinary profession as a whole it becomes quite obvious that veterinary knowledge is involved in many domains of animal health and food safety, from farm to policy and industry fortané , ) . what this article shows, in addition to describing the specificities of a relatively unknown segment of the profession, is that this highly diversified form of professional expertise, and therefore the variety of areas in which it can be exerted, can also be concentrated within a tiny group of professionals, namely pig and poultry vets. moreover, even though it still has to be more broadly demonstrated, it would seem that the trajectory of this particular segment, characterized by the development of specific approaches and economic models, is somehow quite representative and/or influential of more global changes that are now affecting the profession as a whole (at least in farm animal medicine). the expansion of the activity of industrial vets within the drug chain and the "technical" domains of livestock farming indeed corresponds to a (conflicted) evolution of veterinary jurisdictions that echoes the profession's ongoing attempts to renew itself in the context of amr controversies. all in all, articulating reflections from the sociology of professions and the anthropology of medicines has allowed us to highlight the "economic structures of professional expertise" (that is to say that professional practices and knowledge are shaped by the way they are economically valued on a given market), which is of considerable importance for the analysis of the amr problem. indeed, it underlines the fact that amr cannot be addressed by simply focusing on antibiotic use or prescription and, more importantly, it shows that the framing of the amr problem cannot be understood without reconnecting it with the global transformations of the veterinary profession (both in terms of expertise and business model). in this regard, we have shown that the veterinary profession has developed a prospective narrative to defend its role as the guardian of antibiotics (i.e. moving towards preventive approaches in order to prescribe less antibiotics and be less dependent on drug sales) that does not fully correspond to either the history or the actual practices of industrial vets. such approaches have in fact already existed for many years and it is thanks to this diversified veterinary expertise that this segment of the profession has developed. however, the economic model upon which this expertise has been based is in fact the one which is nowadays criticized within amr controversies (i.e. the sustainability of veterinary businesses being highly dependent on antibiotic sales), so that it would appear relatively doubtful, if not ironic, that the profession now brandishes preventive approaches as the undisputable solution to antibiotic overuse or misuse. indeed, drug sales were almost the only way of monetizing veterinary services in the pig and poultry farming sectors and this is how the pioneering generation of industrial vets disqualified their traditional competitors, by "enrolling" clients through the development of a captive drug market. so although promoting preventive approaches is probably the right way to encourage veterinarians to move towards a "health advisor" role where antibiotics are neither the main tool of their activity nor the main source of their income, the profession still has to develop economic models (practice accountability, contractual arrangements with the clients, etc.) that do not rely on drug sales. recent policy measures and incentives are probably pushing in this direction, as are broader trends such as the development of franchised practices and new professional roles and status, but this still has to be empirically confirmed (even though we know that over recent years antibiotic use has already started to decrease). social sciences have a major 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with regard to jurisdictional claims in published maps and institutional affiliations key: cord- -w ig mrl authors: nori, priya; madaline, theresa; munjal, iona; bhar, shubha; guo, yi; seo, susan k.; porrovecchio, andrea; gancher, elizabeth; nosanchuk, joshua; pirofski, liise-anne; ostrowsky, belinda title: developing interactive antimicrobial stewardship and infection prevention curricula for diverse learners: a tailored approach date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: w ig mrl background. to impart principles of antimicrobial stewardship (as) and infection prevention and control (ipc), we developed a curriculum tailored to the diverse aptitudes of learners at our medical center. methods. we integrated case-based modules, group learning activities, smartphone applications (apps), decision support tools, and prescription audit and feedback into curricula of the medical school, medicine residency program, infectious diseases (id) fellowship program, and hospital medicine program operations. interventions were implemented in – using a quasi-experimental before-and-after study design, and this was assessed using pre- and postintervention surveys or audit of antibiotic prescriptions. results. over medical students participated in the as and ipc seminars. after smartphone app introduction, % reported using the app as their preferred source of antibiotic information. approximately % of students felt comfortable prescribing antibiotics for a known infection compared with % at baseline (p = . ), and approximately % were able to identify the appropriate personal protective equipment for specific scenarios. approximately % agreed that they have a role in promoting patient safety and preventing healthcare-associated infections as medical students. at months, appropriateness of trainee antibiotic prescriptions increased by % (p < . ). almost all id fellows indicated that the as and ipc seminar was a vital training supplement. uptake of internist antibiotic recommendations using as decision support tools was approximately %. conclusions. all interventions addressed learning objectives and knowledge gaps and are applicable across a range of environments. evaluating long-term impact of our curriculum is the focus of future study. in , the infectious diseases society of america (idsa) noted that traditional infectious diseases (id) curricula were failing to stimulate active participation, recognize medical students as individual learners, or spark enthusiasm for id [ ] . in , abbo et al [ ] surveyed faculty and residents at teaching hospitals to assess knowledge, attitudes, and perceptions about antimicrobial use and resistance. the majority of respondents desired further education on antibiotics and agreed that better use of antibiotics would reduce resistance, but they did not feel responsible for antibiotic over prescribing. in a follow-up multicenter survey of fourth year medical students, % desired further education on antimicrobial prescribing, but only % were familiar with the role of antimicrobial stewardship (as) in promoting judicious antimicrobial use and preventing multidrug resistance [ , ] . authors also noted that only % of students surveyed completed a clinical id rotation, an underused opportunity to augment id knowledge and explore a potential career path [ ] . likewise, studies in medical student education reveal ( ) poor knowledge and practices of infection prevention and ( ) gaps in understanding of healthcare-associated infections (hais) due to lack of emphasis and suboptimal practices among supervising physicians [ ] [ ] [ ] [ ] . successful strategies in early medical education include active practice and feedback on proper hand hygiene, use of uv hand gel, with reinforcement of best practices in later years of training [ , ] . however, there is no consensus on optimal techniques or implementation of an infection prevention curriculum. stewardship literature has established that education alone cannot sustain improvements in antimicrobial prescribing behaviors [ ] . furthermore, new regulatory requirements will require concerted educational outreach to enable global improvements in antibiotic prescribing. president obama's national action plan for combating antibiotic resistant bacteria proposed a widespread implementation of antimicrobial stewardship programs (asp) to reduce antibiotic use by %- % across all healthcare settings [ ] . the centers for medicare and medicaid services and the joint commission proposed similar asp standards in [ , ] . per ohl and luther [ ] , the goal of stewardship education is not only to reduce total antibiotic use, but also to ensure that antibiotics are prescribed only when indicated, at the correct dose, route, and for the proper duration for each infection. in this study, we describe an integrated, multidisciplinary curriculum developed by the unified antimicrobial stewardship and infection prevention and control programs at the montefiore health system in bronx, new york. it consists of educational strategies designed to bridge perceived learning gaps and lay the foundation for best practices in stewardship and infection prevention in medical students, postgraduate trainees, and mature clinicians. we conducted a series of diverse educational processes across distinct learning environments within our medical center. these were layered over time as an outgrowth of observed patterns of antibiotic prescribing and infection prevention behaviors across the spectrum of our learners. the majority used a quasi-experimental, before-and-after study design with preand postintervention knowledge assessment questions, surveys of learners, or chart review with post-antibiotic prescription audit as methods of evaluation. the χ analysis was used to measure pre-and postintervention differences (microsoft excel). statistical significance was set at a p value of <. where applicable. montefiore medical center institutional review board approval was obtained where appropriate, and remaining studies were registered as quality improvement (qi) initiatives through the montefiore network performance group. the targeted learner, educational strategy, and method of assessment are detailed below. we developed seminars integrated into the microbiology and infectious diseases course for second-year medical students at the albert einstein college of medicine, conducted annually in the medical school's state-of-the-art active learning studio. antimicrobial stewardship and infection prevention seminars were added to the existing curriculum to introduce students to patient-centered topics such as safety, quality, and antimicrobial resistance. attendance at both seminars, conducted over hours each, was a course requirement. in the first seminar on appropriate antibiotic use, stewardship team members presented fundamental concepts of "bug-drug" matches, de-escalation, and use of the hospital antibiogram/ local susceptibility data using case-based multiple-choice questions as reinforcement. in small groups, they assembled a "toolkit" of core stewardship strategies to improve antibiotic use in mock clinical scenarios. in year ( ), a printed antibiogram was provided. in years and ( and ), students downloaded a smart phone application (app) named, "appropriate use, " containing antibiograms and clinical practice guidelines developed by montefiore asp (supplementary figure ). using an audience response system ([ars] turning technologies), students answered questions in primary domains: ( ) general antibiotic use, ( ) principles of microbiology and testing, and ( ) prescribing using the local antibiogram. students additionally participated in an anonymous, voluntary survey about their antibiotic overuse perceptions and preferred antibiotic resources. questions were adapted from a previously published study by abbo et al [ ] . students were introduced to infection prevention bundles, personal protective equipment (ppe), and the transmission-based isolation precautions during a multidisciplinary patient safety seminar. in small groups, students identified appropriate precautions for mock patient scenarios, including clostridium difficile infection and tuberculosis, then practiced hand hygiene and proper donning and doffing of ppe. infection preventionists moderating the small group sessions used uv-reactive wash (glo germ) to identify areas of ongoing contamination and improve technique. they also worked with prevention bundles for hais such as catheter-associated bloodstream and urinary tract infections. a video describing the comprehensive patient safety seminar can be viewed at https://www.youtube.com/ watch?v=p zybuoc vy. at the conclusion of the patient safety seminar, students participated in an anonymous, voluntary survey evaluating the program. students' clinical microbiology/id final examination integrated questions on infection prevention drawn from the session. in , we developed an id core curriculum for the medicine residency program consisting of recurring, -minute, case-based lectures on the recognition and management of typical inpatient infections (eg, community-acquired and healthcare-associated pneumonia, urinary tract infections, skin and soft tissue infections, etc). as an adjunct, we distributed a hospital antibiogram and a syndrome-based pocket antibiotic prescribing guide adapted from national guidelines and tailored to local microbiology (supplementary figure ) . before the first lecture, we distributed an antibiotic pretest with multiple-choice questions on common clinical scenarios designed to assess baseline prescribing knowledge. house staff inpatient antibiotic prescriptions were obtained from queries of the pharmacy's electronic database from november to september . antibiotic regimens recommended by consulting services (ie, id, critical care medicine) were excluded from review, as were antiretroviral and antifungal prescriptions, because these often involved id comanagement. appropriateness of prescriptions was scored using criteria. ( ) were antibiotics indicated for a "true infection" (no alternative noninfectious primary diagnosis)? ( ) did the "selected regimen" cover the infection and pathogens in question? ( ) were antibiotic "dose" and "duration" appropriate? a senior medical resident and id attending physician independently reviewed each chart. antibiotic appropriateness by indication was assessed at month preintervention and month and months postintervention. appropriateness of antibiotic dose and duration was assessed at months postintervention. in , the montefiore medical center and memorial sloan kettering cancer center jointly developed a free, half-day, intensive workshop on as and infection prevention and control (ipc) for id fellows. the first half-session consisted of interactive ipc cases, including emerging infections, hospital outbreaks, hazardous exposures in laboratory personnel, among others. cases varied each year to include practical, everyday scenarios as well as relevant and timely global threats, such as ebola virus, middle east respiratory syndrome coronavirus, and zika virus. the second half-session addressed challenging as scenarios, including drug shortages and conflict resolution with the "obstinate" prescriber. a premeeting survey evaluated fellows' existing participation in as and ipc. fellows answered multiple-choice questions using ars (turning technologies). solutions were discussed openly with a panel of experts from area hospitals (hospital epidemiologists, id pharmacists, and infection preventionists) and the new york city department of health. fianlly, fellows answered a postmeeting survey on perceptions, training needs, and the value of the workshop itself. in , we developed an audit tool containing sepsis criteria, risk stratification for multidrug resistance, and diagnostic criteria for pneumonia, skin and soft tissue infections, and urinary tract infections for a smaller community hospital without fulltime asp (see supplementary figure ). a -month qi initiative was designed to enable internal medicine faculty to serve as asp extensions (stewardship liaisons) to offer antibiotic recommendations to floor teams without providing direct patient care. initially, stewardship liaisons systematically screened all patients initiated on empiric antibiotics upon admission to geriatric units using postprescription audit. liaisons used the audit tool and a validated antibiotic prescribing guide to assist chart review. cases were then discussed with asp, and recommendations on regimens, dose adjustments, or additional management were conveyed to the floor teams by the stewardship liaison in real-time, using one-to-one academic detailing and feedback. electronic medical record was reviewed for patient age, sex, nursing home residence, comorbidities, renal function, allergies, microbiology, imaging results, and length of hospitalization. acceptance rate of recommendations was determined from review of clinical notes and orders. unadjusted hospital length of stay was compared before and the after pilot. one hundred eighty-three students participated per year ( - ), and an average of students answered the voluntary survey per year ( %). eighty percent of survey respondents believed that antibiotics are nationally overused. at least % believed that better use of antibiotics will reduce antibiotic resistance and that strong knowledge of antibiotics is important for success in medicine. forty percent admitted to taking antibiotics for a viral upper respiratory infection, and % reported that their friends have done the same. the appropriate use app was the preferred source of antibiotic information for % of students surveyed. two hundred twenty-two students downloaded the app over years ( downloads in and downloads in ). pre-and post-app, there were no significant differences in the percentage of correct responses to questions on general antibiotic use (p = . ) or principles of microbiology and testing (p = . ). an increase in correct responses from % to % was observed for questions involving antibiogram use (p = . ) ( table ). the app hits peaked at in the immediate time frame after the february session. after app introduction, approximately % of students felt comfortable prescribing antibiotics for a known infection compared with % at baseline (p = . ) [ ] . one hundred eighty-three students participated each year ( and ) and answered the preintervention survey, which revealed that only % of students felt either "very comfortable" or "somewhat comfortable" using ppe. only % of students recognized that central line insertion bundles reduce infection rates. only % were able to identify the appropriate ppe and isolation precautions for measles; however, % identified the appropriate hand hygiene associated with c difficile infection (soap and water instead of alcohol-based rubs). posttest results showed a significant improvement in ppe proficiency and knowledge of hai bundles (table ) . on average, students per year ( %) completed an anonymous survey evaluating the program. the majority of students rated the session as "effective" or "very effective" in achieving the learning objectives ( % and %, respectively, in and ) and answered exam questions about isolation, ppe, and hais correctly (range, %- %). approximately % agreed that they have a role in promoting patient safety and preventing hais as medical students [ ] . one hundred four internal medicine residents completed the antibiotic pretest, and the majority had - of correct responses. one hundred fifty residents received the id core lectures with antibiogram and pocket prescribing card from november to september , with an average of lectures per resident per year. antibiotic orders of unique prescribers were audited for appropriateness, with an average of orders per resident. fifty-four percent of prescribers were interns, % were second-year residents, and % were thirdyear residents. a total of patient charts were analyzed. antibiotics were indicated for a true infection in at least % of all cases reviewed (no alternative noninfectious diagnosis such as congestive heart failure, cardiac ischemia, or pulmonary embolism was encountered). preintervention appropriateness by indication was %, which improved to % at month and % at months postintervention (p = . and p < . , respectively). at months, appropriateness of antibiotic doses and durations was % and %, respectively (table ) . a preand postintervention analysis by syndrome showed a statistically significant prescribing improvement only for urinary tract infections ( % preintervention, % at months postintervention; p = . ) and respiratory infections ( % preintervention, % at months postintervention; p < . ) [ ] . syndrome-specific prescribing improvements for gastrointestinal, skin and soft tissue infections/osteomyelitis, and "other" infections (bloodstream, meningitis, c difficile, etc) were not statistically significant. on average, id fellows attended the course annually, or > % of second-or third-year id fellows, and % of all id fellows in the greater new york area. sixty-four percent of participants reported some formal as and ipc didactics and participation in regular as and ipc activities at their home institutions (ie, committee meetings or approval of restricted antibiotics). although % of participants expressed a professional interest in an ipc or as career after fellowship, more than half felt uncertain about possessing the skills to implement a stewardship program in future employment, and only half felt comfortable managing everyday ipc scenarios. more than % of participants agreed that the program was a valuable supplement to their id training and that case studies are an effective strategy for reinforcing as and ipc concepts. almost all participants desired additional training during fellowship. the primary critique each year was the limited time allotted for the workshop. in , fellows from smaller programs with less as and ipc exposure also attended ( table ). fellows from of local training programs have attended since the inaugural session in [ ] . from august to november , the asp/physician liaison collaborative team reviewed a total of cases from inpatient geriatric units. the mean age of patients was : % were male and % female. the most common syndromes reviewed were skin and soft tissue infections, osteomyelitis, pneumonia, urinary tract infections, and bloodstream infections. thirty-eight percent met sepsis criteria on admission, and % were residents of long-term care facilities. a variety of adjustments were recommended in . % of reviewed cases, including dose reduction for diminished creatinine clearance, penicillin allergy clarification, optimization of gram-negative coverage based on local susceptibility patterns, and facilitation of id consultation. uptake of asp/physician liaison recommendations determined from postprescription audit was . %. as a secondary outcome, we observed a -day reduction in average length of hospitalization compared with a similar time frame in ( . days [august -november ] vs . days [august -november ]) [ ] . the idsa suggests real-time electronic question-answer sessions, peer instruction, and small group discussions as tools to enhance preclinical curricula in id [ ] . these tools can effectively introduce as concepts to medical students, because studies indicate that only % of medicals schools address stewardship in their curricula [ , ] . a recent collaborative study by macdougall et al [ ] at the university of california san francisco suggests that early introduction of core as concepts to both pharmacy and medical students may foster appropriate antibiotic use as a shared responsibility of both professions. since its introduction in , our as student seminar has evolved to better suit students' needs, and it has become a cornerstone of einstein's preclinical clinical microbiology and id curriculum. introduction of the appropriate use app resulted in a % increase in the percentage of students who felt more confident prescribing antibiotics for a given syndrome. likewise, introduction of an id core curriculum and tailored antibiotic guide for medical residents enabled a % increase in appropriate antibiotic prescriptions over time. to further leverage this success, we adapted our antibiotic guide to a smart phone app for all montefiore prescribers, which we launched during the centers for disease control's "get smart about antibiotics" campaign in november . this "version . " of the appropriate use app was downloaded onto over devices and accessed over times within the first months of introduction [ ] . thus, similar tools, adapted across a range of learners, have proven successful and are popular throughout our institution. our experience also suggests that stewardship tools can aid experienced, non-id clinicians select appropriate antibiotic regimens for complex, elderly patients. attending physicians often serve in leadership roles in the medical unit, and they are charged with a myriad of responsibilities, including improving hospital throughput and use as well as teaching and evaluating trainees. challenges of outreach to the mature prescriber include ( ) time constraints, ( ) long-standing prescribing behaviors, ( ) staff turnover, and ( ) emphasis on individual patients over aggregate outcomes. education to improve prescribing at the senior level needs to respect existing attitudes, expectations, and knowledge, and maintain a collegial and collaborative atmosphere. our strategy has focused on recurring feedback sessions to prescriber groups and discrete detailing to individual prescribers. subtle reminders evoking the "public commitment" to responsible prescribing has been referred to as "antibiotic judo" [ ] . our senior prescribers have also benefited from the prescribing tools initially developed for our students and trainees. our ipc session for second-year medical students enforced proper hand hygiene technique and introduced transmission-based isolation precautions and appropriate ppe at an early stage. many students requested additional training before the start of their clinical rotations, and they judged ours to be the most interactive session held in the education center in . after the seminar, students felt much more comfortable identifying the appropriate ppe and isolation precautions for each scenario. our findings suggest that emphasis on ipc best practices in medical school promotes a culture of patient safety and lays the groundwork for sustained infection prevention behaviors as students mature into clinicians. the as and ipc interventions were implemented in different time frames and settings, which served to reduce potential confounding between learner groups. smartphone app was disseminated at the medical center only after it was introduced and studied in medical students. strategies presented herein share common themes and lessons learned (table ) , but collective and individual limitations should be mentioned. we did not conduct an educational needs assessment before study implementation. interventions were designed based on our perceived educational needs extracted from daily interactions with learners. for example, we observed from > stewardship pager interactions per year that %- % of requests are for empiric antimicrobial regimens, often broad spectrum, or intended for patients with remote penicillin allergies, for whom more streamlined β-lactam regimens are more appropriate. quasi-experimental, before and after study design, particularly when applied to small sample sizes, has several limitations, including lack of random assignment and internal validity, generalizability of results, and robustness of conclusions on the effectiveness of educational techniques [ ] . however, this methodology is common to published studies in stewardship and infection prevention. techniques described herein are best suited for adaptation at an academic medical center, because they have not been studied outside this setting. only of the interventions was designed for and implemented in a community hospital. student learners were assessed using pre-and postintervention surveys and knowledge assessment questions, and thus the true impact on prescribing and infection prevention practices is not currently known. in the postgraduate residency curriculum, appropriateness of antibiotic dose and duration was not assessed at month due to time constraints, and an antibiotic posttest was not administered due to a wide distribution of resident rotations across multiple sites throughout the bronx. in addition, a statistically significant improvement in syndrome-based antibiotic prescribing was not demonstrated in all categories due to insufficient sample sizes. in the id fellows' seminar, content of the program, mix of learners, and preand postassessment questions varied slightly each year, which may have affected survey results. although a majority of local id fellows attended our as and ipc workshop, the study was not powered to demonstrate statistically significant differences in pre-and postsurvey responses. past course attendees have not been surveyed to determine the role of as and ipc in their current careers and their perceived preparedness after completion of the workshop. a baseline audit of patient characteristics and antibiotic prescribing on the geriatric units was not conducted before stewardship implementation, and unadjusted length of stay was obtained from hospital discharge data only. reduced length of stay observed during the pilot was likely due to other factors in addition to asp intervention. fianlly, we have not yet studied the long-term impact of the curriculum as a whole or tracked individual learner progress on the path from medical student to mature clinician. the as and ipc curriculum development is a multidisciplinary endeavor of id specialists and clinical pharmacists, infection preventionists, medical school course directors, and residency and fellowship training program directors. we also suggest collaborating with other institutions to benefit from their particular expertise. to our knowledge, this is the first report describing a comprehensive as and ipc curriculum across a range of learners and environments. all strategies achieved intended short-term goals of addressing knowledge and training gaps, increasing confidence, and actively engaging participants. evaluating the long-term impact of individual strategies as part of an integrated curriculum such as ours should be the focus of future study. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. commentary: idsa guidelines for improving the teaching of preclinical medical microbiology and infectious diseases faculty and resident physicians' attitudes, perceptions, and knowledge about antimicrobial use and resistance medical students' perceptions and knowledge about antimicrobial stewardship: how are we educating our future prescribers? implementing an antibiotic stewardship program: guidelines by the infectious diseases society of america and the society for healthcare epidemiology of america hand-hygiene behaviour, attitudes and beliefs in first year clinical medical students now please wash your hands': the handwashing behaviour of final mbbs candidates usage of ultraviolet test method for monitoring the efficacy of surgical hand rub technique among medical students critical gaps in knowledge of the epidemiology and pathophysiology of healthcare-associated infections hand hygiene in medical students: performance, education and knowledge infectious diseases society of america and the society for healthcare epidemiology of america guidelines for developing an institutional program to enhance antimicrobial stewardship new societal approaches to empowering antibiotic stewardship cms issues proposed rule that prohibits discrimination, reduces hospital-acquired conditions, and promotes antibiotic stewardship in hospitals health care provider education as a tool to enhance antibiotic stewardship practices is there an app for that? expanding the stewardship education armamentarium laying the foundation for better infection prevention and control practices through active learning in early medical education improving antimicrobial use starts with our trainees pooling nyc resources to educate fellows about antimicrobial stewardship and infection prevention and control engaging internists to champion antimicrobial stewardship on the wards a comprehensive survey of preclinical microbiology curricula among us medical schools an interprofessional curriculum on antimicrobial stewardship improves knowledge and attitudes toward appropriate antimicrobial use and collaboration is there an app for that . : using an app to help house staff make more informed antimicrobial prescribing choices antibiotic judo working gently with prescriber psychology to overcome inappropriate use the use and interpretation of quasi-experimental studies in medical informatics we acknowledge dr. rosemarie conigliaro (montefiore internal medicine residency program director) for guidance and support for pursuits in medical education.financial support. our preclinical curriculum was supported by funding from the albert einstein college of medicine, grants for excellence in medical education program. dr. susan k. seo is supported in part through the nih/nci cancer center support grant p ca .potential conflict of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -nypnib h authors: olsufyeva, evgenia n.; yankovskaya, valentina s. title: main trends in the design of semi-synthetic antibiotics of a new generation date: - - journal: nan doi: . /rcr sha: doc_id: cord_uid: nypnib h this review summarizes main advances achieved by russian researchers in the synthesis and characterization of semi-synthetic antibiotics of a new generation in the period from to . the following classes of compounds are considered as the basis for modification: polycyclic antibacterial glycopeptides of the vancomycin group, classical macrolides, antifungal polyene macrolides, the antitumour antibiotic olivomycin a, antitumour anthracyclines and broad-spectrum antibiotics, in particular, oligomycin a, heliomycin and some other. main trends in the design of modern anti-infective and antitumour agents over this period are considered in relation to original natural antibiotics, which have been independently discovered by russian researchers. it is shown that a new type of hybrid structures can, in principle, be synthesized based on glycopeptides, macrolides and other antibiotics, including heterodimers containing a new benzoxaborole pharmacophore. the review addresses the influence of the length of the spacer between two antibiotic molecules on the biological activity of hybrid structures. a combination of genetic engineering techniques and methods of organic synthesis is shown to be useful for the design of new potent antifungal antibiotics based on polyenes of the amphotericin b group. many new semi-synthetic analogues exhibit important biological properties, such as a broad spectrum of activity and low toxicity. emphasis is given to certain aspects related to investigation of a broad range of biological activity and mechanisms of action of new derivatives. the bibliography includes references. the review addresses the influence of the length of the spacer between two antibiotic molecules on the biological activity of hybrid structures. a combination of genetic engineering techniques and methods of organic synthesis is shown to be useful for the design of new potent antifungal antibiotics based on polyenes of the amphotericin b group. many new semi-synthetic analogues exhibit important biological properties, such as a broad spectrum of activity and low toxicity. emphasis is given to certain aspects related to investigation of a broad range of biological activity and mechanisms of action of new derivatives. the bibliography includes references. antibiotics are commonly used in the treatment and prevention of various infectious diseases. one of the major problems of modern chemotherapy is the disappointing efficacy when using available drugs against resistant bacterial strains. natural antibiotics, i.e., antibiotics produced by various microorganisms, have been and continue to be an important source of new highly active antimicrobial and antitumour agents. one of the most relevant approaches to the design of new drugs relies on targeted chemical transformations of natural antibiotics. in the world science, considerable efforts are currently underway to combat the problem of resistance of microorganisms to available drugs. however, in comparison with other drugs, the development of new antibiotics is not carried out sufficiently. the design of anti-infective drugs and the creation of marketable products are still a challenge. since the development of medicines for the treatment of chronic diseases is much more profitable and because of high requirements for safety, large cap pharmaceutical companies (big pharma) shut down their antibiotic research projects. currently, small-and medium-sized enterprises are developing a majority of new drugs through investments, venture capital, etc. because of high demands for new anti-infective drugs and extremely high cost of these works, cross-country collaborations are needed for research in this field. only a few new compounds were approved for therapeutic use in human medicine or have completed phase-iii clinical trials. the problems are compounded by the fact that the increasing percentage of the population, particularly in developed countries and russia, suffer from infections that were not earlier dangerous, i.e., from opportunistic infections. this is due to a significant decrease in the immune status of the population caused by natural or man-made factors. the translation of semi-synthetic antitumour antibiotics (e.g., doxorubicin) into clinics resulted in the development of gold standard chemotherapeutic agents. many antibiotics have made a great contribution to understanding of mechanisms of development of resistance in bacterial and tumour cells. due to high innate or acquired drug resistance of cancer cells, chemotherapy of malignant tumours is often ineffective. the international research community has focused its attention on the search for new, more effective and less toxic antitumour agents. one of the most rational approaches to the targeted therapy is based on the search for inhibitors of important tumour cell targets among natural products, primarily antibiotics. even the repurposing of known antitumour antibiotics is considered in order to address the problem of antibiotic resistance of antiinfective agents. researchers of the gause institute of new antibiotics (gina) headed by academician of the ussr academy of medical sciences g.f.gause in the ± s made considerable contribution to the discovery of a series of original antibacterial and antitumour agents (a total of compounds), their characterization and introduction to medical practice. major achievements of the institute during this period are considered in the review. antibiotics comprise an important class of natural products with unique structural diversity. chemical transformations of natural antibiotics imply a change of particular functional groups of the starting molecules with preservation of structural elements responsible for biological activity. the structure determines the possibility of chemical transformation of the antibiotic and reaction conditions. for example, many antibiotics contain nitrogenous and(or) nitrogen-free sugars, which are easily eliminated in acidic or alkaline media. many antibiotics are sensitive to oxidants, are poorly soluble in organic media or, on the contrary, in aqueous solutions, etc. on the other hand, in the case of similar structures of certain moieties [e.g., the presence of nh , co h, oh, c(o), etc. groups)], methods developed for one class of antibiotics can be applied to antibiotics of another class. the goal of synthetic chemists is to transform natural products with preservation of the sites responsible for biological activity. besides, targeted modification can be performed to gain better understanding of the mechanisms of action, in particular in order to investigate the interaction between the antibiotic and the target. in this review, the following classes of compounds are considered as scaffolds for the synthesis of new antibiotics: polycyclic glycopeptides of the vancomycin ± teicoplanin group, classical macrolides, macrolides of the amphotericin b ± oligomycin group, anthracyclines, aureolic acid derivatives, heliomycin, synthetic benzoxaboroles and some other antibiotics. such representatives as eremomycin, carminomycin, olivomycin a, oligomycin a and heliomycin . olivomycin a . . modification of olivomycin a at the aromatic ring of the aglycone . . modification of olivomycin a at the side-chain h -keto group of the aglycone . . modification of the side chain at the c( h ) c ( h the discovery of vancomycin ( ) and teicoplanin ( ) (fig. ) has given impetus to research on polycyclic glycopeptide antibiotics. natural antibiotics and are still used in medical practice and are considered as reserve antibiotics. they are commonly applied for the treatment of infections caused by gram-positive cocci, particularly, methicillinresistant staphylococcus aureus (mrsa) strains. glycopeptide antibiotics bind with high affinity to the terminal d-ala-d-ala group of the growing peptidoglycan chain on the outer bacterial cell wall, thereby inhibiting the enzymes transpeptidase and transglycosylase. the vancomycin resistance in enterococcus strains (vre) (for vana and vanb phenotypes) arises due to replacement of the d-ala-d-ala group by d-ala-d-lactate, which weakly interacts with the antibiotic. semi-synthetic glycopeptide analogues, such as oritavancin, telavancin and dalbavancin, have recently been used worldwide in medicine. these drugs only partially solve the problem of the treatment of infectious diseases caused by vancomycinresistant enterococci. , the search for more effective glycopeptide analogues is an ongoing process. ± eremomycin (see fig. ), the natural antibiotic of this group, was discovered in the gause institute of new antibiotics. this compound differs from vancomycin ( ) by the absence of a chlorine atom and the presence of the additional amino sugar eremosamine in the side group of amino acid (aa ), as well as by the structure of the amino sugar ( h -epivancosamine or eremosamine) at the d-glucopyranose moiety attached to aa . eremomycin ( ) is ± times more active against gram-positive bacteria than antibiotic ; however, drug is also ineffective against vre and vancomycin-intermediate resistant staphylococcus aureus (visa). in recent years, series of new semi-synthetic derivatives of eremomycin, vancomycin and teicoplanin active against resistant vre and visa strains were prepared. ± figure presents main possible directions of modification of the cand n-terminal groups of the peptide core (a and f ), h -amino sugar (b), the amide group of asparagine (asn) (c), sugar elimination (d ) and edman degradation (e) for antibiotics ± . the presence of (benzotriazol- -yl)oxytripyrrolidinophosphonium hexafluorophosphate (pybop) as the peptide coupling reagent afforded a series of new carboxamide derivatives of eremomycin ± (scheme , fig. a ) . ± after the purification, these compounds were isolated in * % ± % yields. eremomycin pyrrolidide ( ) has high in vitro antibacterial activity against sensitive and resistant gram-positive bacterial strains, including mrsa, visa and vre isolates. , besides, compound is much more effective in the treatment of induced sepsis in mice compared to vancomycin ( ) and does not cause a pseudoallergic reaction typical of many antibiotics of this group. compound was successful in preclinical evaluation (in collaboration with the limited liability company`medicine technology') and was recommended for further clinical trials. eremomycin n-adamantan- -ylamide ( ) was synthesized in a similar way as amide (see scheme ). in in vitro assays, compound exhibits activity against mrsa, visa, vre and bacillus anthracis strains. this compound is also effective against ciprofloxacin-resistant strains of bacillus anthracis. model in vivo assays in mice infected with s. aureus or bacillus anthracis showed that compound provides a higher survival rate of animals compared to ciprofloxacin and has pharmacologically relevant properties, exhibiting an excellent distribution in tissues. the synthesis of eremomycin carboxamides containing bulky substituents, such as -aminoadamantane ( -ad) (compound ), in the presence of pybop at ph * . afforded the previously characterized unsubstituted eremomycin amide ( ) as a by-product. compound is produced by the competitive amidation reaction of the antibiotic with ammonia, which is eliminated through transpeptidation of asparagine-containing peptides in an alkaline medium. an original method was developed for the selective introduction of different amino acids containing a hydrophobic substituent into glycopeptide antibiotics or via selective aminoacylation of the h -amino group of the amino sugar moiety of the disaccharide branch. for instance, the reaction of vancomycin with n-fmoc-(n-n-octyl-o- benzyl)-l-alanine n-hydroxysuccinimide (osu) ester gave figure . structures of vancomycin ( ), teicoplanin a - ( ) and eremomycin ( ) and directions of their chemical modifications: amidation (a), acylation (b), alkaline hydrolysis of the c(o)nh group to co h followed by amidation (c), sugar elimination (d ), edman degradation (e) and modification of the n-terminal amino group of the peptide core ( f ). fig. b ) . in this reaction, the n-terminal group of the peptide core of the antibiotic remains intact. the n-fmoc protecting group can easily be removed by the treatment with a % secondary amine solution. compound exhibits high activity against sensitive and resistant clinical strains of gram-positive bacteria, including vre. in order to study in detail the interaction between the antibiotic and the target in the intact bacterial cell by solid-state nmr spectroscopy using the rotational-echo double resonance (redor) technique, nh -or f-labelled substituents were introduced into amino acid residues (aa ) and(or) (aa ) of the peptide chain of the antibiotic eremomycin ( ). the n label was introduced in the vicinity of the binding pocket of the antibiotic. this was accomplished using carboxyeremomycin ( ) , which was synthesized previously by the selective alkaline hydrolysis of compound in a saturated aqueous solution of ba(oh) . under these conditions, vancomycin ( ) decomposes. carboxyeremomycin [ n]-bisamide was synthesized by the reaction of compound with appropriate amines in the presence of pybop (scheme , fig. a ,c ) . eremomycin -fluorophenyl-n-piperazide ( ) was synthesized by the conventional amidation method in the presence of pybop. the redor experiments were performed using intact staphylococcus aureus cells, which were grown in a culture medium containing bioprecursors with isotope-labelled atoms (e.g., c-amino acid). the n-or f-containing antibiotic that was added to the medium inhibits bacterial growth by forming a stable complex with c-labelled peptidoglycan moieties (see fig. , hydrogen bonds are indicated by dashed lines). , the study of the complex with compound provides an estimate of the distance from the distance between the c-terminal [ n]-amide of eremomycin ( ) and l-[ c( )]ala of the peptidoglycan stem is . # a (see fig. , a solid arrow). consequently, higher activity of eremomycin amide (compared to antibiotics or ) against resistant visa staphylococci can be attributed to the fact that this compound interacts with the peptidoglycan not only via a classical model (i.e., with the d-ala-d-ala target) but also with the l-[ c( )]ala group of its stem. besides, there is an additional binding site of derivative to the target, which can also account for its high antibacterial activity against vre and visa. previously, it was shown that the elimination of sugars (see fig. d ) and the introduction of a hydrophobic residue into the aglycone can give rise to aglycone derivatives of antibiotics exhibiting activity against different types of enveloped viruses. the modification of the eremomycin aglycone ( a), its de-d-meleu analogues (hexapeptide, a), which was produced by the cleavage of amino acid (aa ) using the edman method (see fig. e), and the teicoplanin aglycone ( ) gave a series of new hydrophobic derivatives. ( -adamantylmethyl)amide of the eremomycin aglycone ( b) and its hexapeptide analogue ( b) are derived by the reaction of -adamantylmethylamine with a or a in the presence of diphenylphosphoryl azide (dppa) (scheme ). diphenylphosphoryl azide rather than pybop is the reagent of choice for the amidation of aglycones, because the reactions in the presence of pybop often afford by-products containing the pybop moiety in the phenol group of the aglycone at aa . the acylation of compound with di-tert-butyl dicarbonate (boc o) followed by amidation under standard conditions in the presence of pybop gives the disubstituted derivative Ð ( -adamantyl)amide of the n-boc-teicoplanin aglycone ( ) . the acylation of with -adamantylmethyloxy carbonate (adoc o) affords the n-adoc-teicoplanin aglycone ( ) (see fig. f, scheme ). compounds b, b and ± exhibit high in vitro activity against different corona-and flaviviruses, in partic-ular feline infectious peritonitis virus (fipv) and the coronavirus (sars-cov). the most interesting data were obtained when studying antiviral activity of ( -adamantylmethyl)amide of the eremomycin aglycone ( b) and its de-(d-meleu) analogue ( b) against human immunodeficiency viruses (hiv): ic = . and . mmol l for hiv- , . and . mmol l for hiv- , respectively. compounds of type b are promising selective anti-hiv agents because they cannot bind to bacterial targets. apparently, they cannot induce resistance of bacteria during long-term application and can be used in the future for the prevention of hiv infections. the doubly modified teicoplanin derivative Ð n-bocprotected -adamantylamide of the teicoplanin aglycone Ð exhibits high in vitro activity against a series of flaviviruses: hepatitis c virus (hcv), yellow fever virus (yfv), japanese encephalitis virus (jev), tick-borne encephalitis virus tbev) and dengue virus (denv). , compound is unique in that it can inhibit replication of the closely related denv and hcv viruses by different mechanisms: in the former case, the inhibition occurs in the stage of virus entry in the host cell; in the latter case, after virus entry. protein kinases play an essential role in the virus entry in the cell and virus replication. hence, analogues of the eremomycin and teicoplanin aglycones (including compounds a,b, a,b and ± ) were tested on a panel of recombinant human protein kinases (pks) and two rat liver pks (ck and ck ). these compounds were shown to inhibit pk activity by % at a concentration of < mmol l and by % at a concentration of mmol l . teicoplanin aglycone derivatives and exhibit higher activity against many pks compared to eremomycin derivatives b and b, which also correlates with their higher activity against many types of enveloped viruses. the kinetic analysis of the inhibition of protein kinase ck a demonstrated that teicoplanin n-adoc-aglycone does not compete with atp and peptide substrates. on the available data, it was suggested that one of the mechanisms of antiviral activity of glycopeptide derivatives can be based on the inhibition of serine/threonine protein kinases. the synthesis of hybrid analogues containing covalently bonded compounds of different classes (dual-acting antibiotics) with different spectra of antibacterial activity is a promising approach to the search for new antibacterial agents to combat antibiotic resistance of bacteria. , boronic acids and benzoxaboroles are compounds capable of interacting with various biologically important components of the living cell, such as alcohols, amino alcohols, carbohydrates, rna and some peptides. a new class of synthetic antibiotics possessing antifungal, antimicrobial and antiparasitic activity was designed and synthesized based on benzoxaboroles and is currently developed by anacor pharmaceuticals (usa). certain starting benzoxaboroles used in the synthesis also exhibit biological activity (see below). series of hybrid analogues ± linked to the borole or benzoxaborole moiety either directly or through a spacer were synthesized for the first time from glycopeptides and . to introduce a substituent containing a boronic acid moiety into molecule or , it is necessary to employ picolinic acid as a protecting group, which is easily removed in a weakly acidic medium (scheme ). the amidation of the carboxyl group of antibiotics and with -or -aminomethylphenylboronic acid picolinate esters in the presence of pybop gave new carboxamides of these antibiotics ( a ± a). the hydrolysis of the picolinic group under mild conditions in a weakly acidic aqueous medium affords derivatives b ± b containing the unprotected boronic acid moiety. borole-containing derivatives ± were found to be as effective as the starting antibiotics and . eremomycin derivative b exhibits the highest activity against gram-positive bacteria and is more effective against resistant staphylococcus strains (visa) compared to compounds and . a series of vancomycin conjugates containing different types of benzoxaborole substituents were synthesized: amido derivatives a,b, n-acyl derivatives ( ) n-alkyl derivatives ( ) (scheme ). similar schemes were applied to synthesize benzoxaborole derivatives of eremomycin ( ) (see scheme ) and the teicoplanin aglycone (scheme ). carboxamides of eremomycin ( ) (see scheme ), vancomycin ( a) (see scheme ) and the teicoplanin aglycone ( a) (see scheme ) were synthesized by a standard procedure based on the treatment of compounds , and , respectively, with -(aminomethyl)benzo[c] [ , ] oxaborol- ( h)-ol in the presence of pybop. the reaction of compound or with o-amino-n-alkylamines affords the corresponding amides b and b,c (n = , and ) containing a longer spacer. the reactions with osu-activated esters of the same in situ generated compounds were used to synthesize n-[ -( -hydroxy- , -dihydrobenzo[c] [ , ] oxaborol- -yl)propanoyl] derivatives of vancomycin ( ) and the teicoplanin aglycone ( a). the alkylation of vancomycin ( ) with appropriate aldehyde in the presence of nabh cn affords n,n hdi( -hydroxy- , -dihydrobenzo[c] [ , ] oxaborole- -methyl)vancomycin ( ) in quantitative yield (see scheme ) . the amidation of n-acyl-substituted teicoplanin aglycone a with appropriate amine (in a similar way as the synthesis of amides and a) gave disubstituted teicoplanin aglycone derivative b. the five-membered oxaborole ring cleavage is not observed in various reactions of benzoxaboroles (see scheme ) . the presence of peaks at m/z . [m oh], . and lower ( . and . ) in the tandem mass spectrometry (esi-ms/ms-mrm) spectrum of compound indicates that the antibiotic molecule contains a substituent in the n-terminal amino group of the peptide core rather than in the amino sugar n( h ) group of vancosamine (fig. ) . vancomycin derivatives a, and proved to be less effective against gram-positive bacteria than the starting compound , except for amide a, which exhibits activity comparable with that of vancomycin . hybrid derivatives, in which benzoxaborole and the teicoplanin aglycone are linked by a spacer with a particular length, exhibited the highest antibacterial activity against clinical isolates of gram-positive bacteria. -amino-n-( hydroxy- , -dihydro[c] [ , ] oxaborol- -yl)propylamide of the teicoplanin aglycone ( c, n = ) possesses particularly high activity, in particular against vancomycin-resistant strains. besides, this compound exhibits moderate activity against vancomycin-resistant enterococci (vre); the minimum inhibitory concentration (mic) is ± mg ml . an increase or a decrease in the spacer length and the introduction of two benzoxaborole substituents into the n-and c-terminal groups of the peptide were found to decrease antibacterial activity. the broad-spectrum antibacterial drug kanamycin a ( a) is an important antibiotic of the aminoglycoside (aminocyclitol) class, which is still used in medicine for the treatment of many infectious diseases and also in agriculture. aminoglycosides are active against gram-positive and gram-negative bacteria. the mechanism of their action is related to the interaction with the decoding site (a site) of the s subunit of ribosomal ribonucleic acid (rrna), which leads to disturbance of translation, i.e., protein biosynthesis. according to the literature data, a number of semi-synthetic derivatives of a new generation were synthesized based on aminoglycosides. various heterodimeric aminoglycoside conjugates with other antibiotics were reported, and some of them are used in medicine. , the synthesis of hybrid kanamycin a conjugates with glycopeptides and was described for the first time in our publication. kanamycin a ( a) was conjugated with compounds or via an amino group of the antibiotic at the position of -deoxy-d-streptamine. the acylation of this amino group is known to reduce the risk of the development of resistance, because it prevents deactivation of the antibiotic by enzymes. the amino group at the position of -deoxy-dstreptamine and the h -amino group of h -deoxy- h -amino-d-glucopyranose of aminoglycoside a were protected by the benzyloxycarbonyl group (cbz). , h -bis-(cbz)-kanamycin a ( b) was synthesized by the reaction of the zinc complex of compound a with cbzcl in the presence of a base (et n) using a modified method (scheme ). (mic * ± mg ml for compounds , a,b) and vre stains (mic = mg ml for compound a). based on the results of these studies, methods were developed for the selective introduction of functional groups at the amino sugar amino group of vancomycin ( ) or eremomycin ( ), with the terminal methylamino group of the peptide core of the antibiotic remaining intact. the amidation of the terminal carboxyl group of these antibiotics with various amines, including amines with bulky substituents, was studied in detail. , , an unusual byproduct of amidation (previously unknown for these classes of antibiotics) was isolated, and the optimal conditions were found for the amidation providing the target products in high yields. , the introduction of various groups into glycopeptides at certain positions of the molecule can give new derivatives active against bacteria that are resistant to the initial antibiotics Ð glycopeptide-resistant enterococci. , this resulted in the discovery of compounds exhibiting high activity against glycopeptide-resistant enterococci (mic = ± mg ml ) and staphylococcus aureus with intermediate resistance to glycopeptide antibiotics (mic = ± mg ml ). generally, eremomycin derivatives possess higher in vitro antibacterial activity than analogous vancomycin derivatives and show significant advantages over vancomycin in the treatment of animals in a mouse model of staphylococcal sepsis. , conditions were found for the selective introduction of isotopic labels at both the terminal carboxyl group and the asparagine residue (aa ) of the peptide core of eremomycin, with carbohydrate moieties and other labile functional groups remaining intact. the investigation of interactions of these compounds with native cells of gram-positive bacteria by the redor technique confirmed the mechanisms of action of this group of antibiotics proposed in our previous studies. , modifications of glycopeptide aglycones at the carboxyl and(or) amino group were performed in a series of studies. ± this resulted in the discovery and characterization of a new class of polycyclic peptides exhibiting antiviral activity at micromolar concentrations against hiv- and hiv- , as well as against the enveloped viruses hcv, denv and many other. ± the correlation between antiviral and pk inhibitory activities was established for a class of hydrophobic derivatives of glycopeptide aglycones. the first heterodimeric conjugates of glycopeptide antibiotics with boroles, , and with kanamycin a were synthesized. the conjugates exhibit activity against resistant vre and(or) visa strains. the synthesis of chimeric (heterodimeric) macrolide-based antibiotics is a promising area of research to search for new antimicrobial agents. these antibiotics are among the most effective broad-spectrum antibacterial agents. the semi-synthetic antibiotics clarithromycin ( ) and azithromycin ( ) are commonly used in medicine for the treatment of various infectious diseases caused by many gram-positive and gram-negative bacteria (fig. ) . azithromycin ( ) has the best pharmacological profile among macrolide antibiotics. the mechanism of action of macrolides is based on the inhibition of protein synthesis. the target of macrolides is the peptidyl transferase centre on the large s subunit of bacterial ribosome. however, clarithromycinand azithromycin-resistant clinical isolates of bacteria were isolated. researchers at the gause institute of new antibiotics have developed methods for the conjugation of macrolide antibiotics with benzoxaboroles or polycyclic glycopeptide antibiotics and synthesized series of new chimeric antibiotics. conjugates based on clarithromycin ( ), azithromycin ( ) and various substituted benzoxaboroles were synthesized by the targeted modification of macrolides at the c( ), c( h ) and c( hh ) atoms and the c( ) ± c( ) bond (see fig. a ± d ). according to the literature data, the introduction of arylalkyl groups at the hh position of the cladinose moiety may help antibiotics overcome resistance caused by methylation of the macrolide-binding site of s rrna of the large ribosomal subunit. a method was developed for the introduction of aminobenzoxaboroles at the c( hh ) atom of the cladinose moiety of the antibiotic through the carbamoyl group. hybrid structures containing hydroxamic acid-derived benzoxaborole at the c( ) keto group of the aglycone were prepared, because modification of this group does not lead to the loss of antibiotic activity. scheme shows the synthesis of conjugates based on clarithromycin via the introduction of benzoxaborole groups (a and b) into the antibiotic molecule at the c( ) atom of the aglycone or at c( hh ) o-cladinose with acetyl protection of the c( h ) oh group of desosamine. the former approach is based on the treatment of clarithromycin ( ) with aminoacetic acid giving intermediate clarithromycin -syn(anti)-(o-carboxymethyl)oxime ( a). the reaction of a with aminobenzoxaboroles ha figure . structures of the macrolide antibiotics clarithromycin ( ) and azithromycin ( ) . arrows indicate the directions of modification: at the position of the aglycone (a), at the c( h ) oh group of desosamine (b), at the c( hh ) atom of cladinose (c), the formation of c( ),c( )-cyclic carbonate and modification of the c( ) atom (d ). or hb gives the corresponding amides of clarithromycin (e/z)- -carboxymethoxime b,c (see scheme ). another approach was accomplished by a modified procedure involving the following four steps: the protection of the c( h ) oh group of desosamine by the acetyl group giving h -oac-clarithromycin ( ), the transformation of the latter into activated h -oac-clarithromycin hh -o- h-imidazole- -carboxylate ( ) by the treatment with carbonyldiimidazole (cdi), the amidation of with amines ha or hb in the presence of the peptide coupling reagent , -diazobicyclo [ . . ]undec- -ene (dbu) giving h -oac-substituted carbamoyl derivatives of clarithromycin a,b, and the deacetylation of a,b by heating in methanol to form target unprotected carbamoyl derivatives of clarithromycin a,b. compounds b,c and a,b exhibit the inhibitory effect against staphylococci and streptococci comparable with the activity of starting compound . in these assays, derivatives at the c( hh )-cladinose position were found to be more effective than the derivatives at the c( ) position of the aglycone of antibiotics b and c. compound b is the most effective against the strains staphylococcus epidermidis atcc and streptococcus pneumoniae atcc . clarithromycin analogues c and b possess an opposite activity against gram-negative bacteria, such as sensitive strains of e. coli and resistant strains of e. coli (tolc and tolc puc erm ). thus, compound c is more active than b. in the former case, e. coli tolc and tolc puc erm are bacterial strains containing the outer membrane protein tolc, which is responsible for antibiotic efflux from the cell. in the latter cases, the strain contains, apart from tolc, the puc plasmid cloning vector and methylase erm . attempts were made to extend the method developed for the synthesis of c( hh )-substituted clarithromycin ± benzoxaborole conjugates to the synthesis of related azithromycin conjugates (scheme ). it appeared that the success of introducing the aminobenzoxaborole moiety into a macrolide antibiotic depends on the structure of antibiotics and , as well as on the structure of aminobenzoxaborole. the acetylation of azithromycin ( ) giving the h -oac derivative ( ) followed by the treatment of the latter with n,n h -carbonyldiimidazole in the presence of et n produces the desired activated imidazole derivative Ð azithromycin h -oac- hh -o- h-imidazole- -carboxylate ( ) (see scheme ) . however, unlike the synthesis of clarithromycin analogue a, the amidation of compound with -(hydroxy- , -dihydrobenzo[c] [ , ] oxaborole)methylamine in the presence of dbu does not give the desired outcome. the introduction of the latter amine was accomplished using the trisubstituted derivative, the , -cyclic carbonate azithromycin h -oac- hh -o- h-imidazole- -carboxylate as the substrate. compound the same conditions as those used for was not successful (see scheme ) . meanwhile, this reaction with another amine containing an aminoethyl spacer gives the corresponding azithromycin carbamoyl derivative (see scheme ) . however, the elimination of the h -oac group finally results in the decomposition of the deacetyl derivative during its purification on silica gel. an alternative procedure for the introduction of benzoxaboroles into molecule using carboxy derivatives and diaminoalkane spacers (scheme ) proved to be more successful. the treatment of imidazole derivative with stronger bases, such as diaminoethane or , -diaminopropane, in the presence of dbu resulted in the formation of aminoalkylcarbamoyl derivatives (n = ) and (n = ). the subsequent acylation of the latter with various benzoxaborole acids under standard conditions (dcc, hobt) gives a series of acylaminoalkylbenzoxaborole-containing carbamoyl derivatives of , -cyclic carbonate, h -oacazithromycin a ± a (see scheme ) . the deacetylation of these compounds affords the corresponding cyclic carbo-nates b ± b containing the free c( h ) oh group of the desosamine moiety (r = h) in quantitative yields. compound b and its h -oac analogue a were synthesized from azithromycin h -oac- hh -o- h-imidazole- -carboxylate through intermediate h -oac analogues (n = , ) (scheme ). therefore, the synthesis of compound a and its h -oac analogue b showed that the introduction of the acylaminoalkylbenzoxaborole moiety can be accomplished using a scheme described above without protection of the c( ) oh and c( ) oh groups by cyclic carbonate. the evaluation of antibacterial activity of hh -o-substituted derivatives , a ± a (n = ), b ± b (n = , ) and b (n = , ) compared with that of compound showed that the activity of compounds , ± and against gram-negative bacteria ( isolates) is lower than that against gram-positive bacteria ( isolates). for example, the activity of compounds , a (n = ), a (n = ) and b (n = ) against the gram-positive strains streptococcus pyogenes atcc and propionibacterium acnes atcc is comparable with that of the starting com- pound , while conjugates b (n = ), a (n = ), b (n = ) and b (n = ) are more effective than compound against the strains streptococcus pneumoniae atcc or enterococcus faecium. the presence of the h -oac group or , -cyclic carbonate in analogous hybrid antibiotics was found to have almost no effect on antibacterial activity. for compounds a (n = , ), a (n = , ), a (n = ), b ± b (n = ) and b (n = , ), the mechanism of antibacterial activity was studied using the prfpcer-trpl a reporter construct, which responds to inhibitors of translocation of the ribosome along the matrix nucleic acid (mrna). all compounds were found to inhibit the peptide chain growth at the exit from the ribosome tunnel like typical macrolide antibiotics. it is worth noting that one of the starting benzoxaborole acids, -( -hydroxy- , -dihydrobenzo[c] [ , ] oxaborol- -yl)propanoic acid (see schemes and , marked with an asterisk), also exhibited activity in this assay. . . azithromycin ± benzoxaborole conjugates at the -oh group of the aglycone , -cyclic carbonate can be used not only as the protecting group for two hydroxyl groups but also as the activated group to introduce benzoxaborole substituents at the position of antibiotics. the reaction of , -cyclic carbonate azithromycin h -oac derivative , which was generated from azithromycin ( ) in two steps (treatment with ethylene carbonate followed by acylation of the h -o group of the desosamine moiety), with diaminoalkane gave h -oacetylazithromycin -aminoalkylcarbamates (n = , ) (scheme ). the acylation of compound with benzoxaborole acids under standard conditions (dcc, hobt) produced a series of azithromycin h -oac derivatives a ± a. the deacetylation of these compounds afforded target benzoxaborole derivatives b ± b. new hybrid antibiotics b ± b exhibit broader-spectrum antibacterial activity against gram-positive and gram-negative bacteria compared to azithromycin ( ) and tobramycin. compound b proved to be the most effective compound in this series, but its activity is lower than that of compound . the modified antibiotics do not overcome the antibiotic resistance in mrsa strains (strain atcc ). higher activity of these three compounds against the sensitive strain s. pneumonia atcc compared to tobramycin (mic is . ± . versus mg ml ) is a particularly valuable property. , or , or , dcc, hobt; dcc is n,n h -dicyclohexyl carbodiimide, hobt is -hydroxybenzotriazole; in the former case, the reaction of azithromycin -aminoalkylcarbamates (n = , ) with antibiotics , or in the presence of pybop affords the corresponding derivatives of vancomycin ( , ) , eremomycin ( ) or the teicoplanin aglycone ( , ) (scheme ). in the latter case, , -cyclic carbonate azithromycin hh -o-alkylaminocarbamoyl derivatives and are amidated with antibiotics , or in the presence of pybop (scheme ). after the removal of the h -o-acetyl protecting group from compounds a ± a and the column chromatographic separation on silanized silica gel followed by sephadex lh- chromatography, five new conjugates b ± b were isolated in % ± % yields based on the corresponding starting antibiotic. antibacterial activity of derivatives ± modified at the c( ) oh group of the aglycone was evaluated compared to the starting antibiotics vancomycin ( ) and azithromycin ( ) on a panel of gram-positive and gramnegative bacterial strains ( and strains, respectively). none of the conjugates exhibited activity against gramnegative bacteria, which attests to the absence of the effect of the azithromycin moiety active against gram-negative bacteria. generally, compounds ± display similar or somewhat lower activity against gram-positive bacterial strains compared to compounds and(or) , the activity against staphylococci being higher than that against the streptococci s. pneumoniae atcc and s. agalactis - . azithromycin ± teicoplanin aglycone conjugate containing a long spacer (n = ) exhibits higher activity against all tested gram-positive bacterial strains (staphylococci and derivatives at the hh -cladinose position show a similar tendency. thus, they are inactive against gram-negative bacteria. the fact that the hybrid structures are ineffective against e. coli atcc and other gram-negative bacterial strains indicates that they cannot penetrate the outer phospholipid layer of the bacterial cell. in all the tested gram-positive bacterial strains, compounds ± exhibited activity comparable to or higher than that of azithromycin ( ) and vancomycin ( ) . their activity is provided by the presence of the glycopeptide moiety. unlike hybrid vancomycin analogue b, hybrid eremomycin analogue b displays significant activity against the vancomycin-resistant enterococci (vre) strains enterococcus faecium and enterococcus faecalis (mic = . and . mmol l ), which can be attributed to the effect of the azithromycin moiety attached to the c-terminal group of the peptide core of antibiotic . , the mechanism of action against gram-positive bacteria was confirmed by quantum chemical calculations of the energy of interaction dg in relation to hybrid antibiotics b and b with the model d-ala-d-ala ligand typical of glycopeptides. these studies resulted in the development of methods for the synthesis of macrolide-based hybrid antibiotics containing benzoxaborole as a new pharmacophore. , , the behaviour of the macrolide antibiotic aglycone in chemical reactions was found to be affected by its structure, in particular it depends on the presence of an additional methylamino group in azithromycin ( ) . , the position of the benzoxaborole substituent was shown to influence the antibacterial activity of antibiotics and . it was established that the c( )-substituted analogues are less effective inhibitors of gram-positive and gram-negative bacteria compared to hh -substituted analogues. , the presence of , -cyclic carbonate or the h -o-acetyl group in the azithromycin molecule was shown to have no significant effect on the antibacterial activity of the conjugates, while an increase in the spacer length generally leads to an increase in activity of the final compounds. a method was developed for the synthesis of a series of chimeric antibiotics based on glycopeptides and azithromycin ( ) . the activity of almost all the synthesized compounds against the tested gram-positive bacterial strains, including vancomycin-resistant strains, is similar to or higher than that of the starting antibiotic. the range of antibacterial activity of the resulting hybrid derivatives and quantum chemical calculations suggest that the antibacterial activity is determined by the presence of the glycopep- carbohydrate-containing polyene macrolides are commonly used in medicine for the treatment of both superficial and systemic mycoses due to their high activity and a broad spectrum of action. , the mechanism of action of polyene macrolides is related to their ability to interact with sterol-containing cytoplasmic membranes and form pores (channels) in these membaranes, by which ions leave the cell causing its death. the efficacy of polyenes against fungal pathogens is due to their stronger binding to fungal membrane ergosterols compared to cholesterol present in human and animal cell membranes. nystatin ( a), partricin and pimaricin are administered locally, whereas amphotericin b (amb, a) is the only polyene that is applied for the treatment of systemic mycoses. unfortunately, polyenes are rather toxic agents because of their low selectivity for fungal versus mammalian cell. poor solubility of polyenes in water, their high hematotoxicity and nephrotoxicity and a number of other adverse effects have stimulated an extensive search for new, less toxic and more effective agents. previously, it was shown that toxicity of compound a and other polyenes can be reduced by chemical modification, which leads to a decrease in side effects. , the toxic effect of compound a on blood cells (haemolysis) is particularly dangerous. in order to improve antifungal properties, cytotoxic and therapeutic characteristics and to study the mechanisms of action, series of new semi-synthetic derivatives based on amb ( a) and bioengineered analogues s hp ( a), bsg ( a), bsg ( a), bsg ( ), bsg ( a) and bsg ( ) were synthesized (in collaboration with the company biosergen, norway) (scheme ). ± the structural diversity of the above-mentioned polyenes a ± a, , a and was provided by using methods of genetic engineering to alter genes encoding the nystatin-producing strain streptomyces noursei. new analogues compare favourably with nystatin ( a), primarily due to the presence of a double bond (instead of a single one) at c( ) ± c( ) characteristic of a and other polyenes ± . the heptaene group of the aglycone imparts rigidity to the antibiotic structure and improves antifungal activity. new monosubstituted polyene macrolides at the terminal -co h group of the aglycone were synthesized based on compounds a and a; monosubstituted polyene macrolides at the mycosamine h -amino group were prepared based on a, a and a. , the synthesis of doubly modified analogues of antibiotics a and a was reported. the related amido derivatives ( b ± h) substituted in a similar way at the c( )-carboxamide group of s hp were prepared. ± the yields of c( )-amido derivatives were * % ± % depending on the structure of the starting amine and the antibiotic. the antibiotic structure was found to have almost no effect on antifungal activity against the fungal strains candida albicans (atcc ), cryptococcus humicolus (atcc ), aspergillus niger (atcc ) and fusarium oxysporum (vkm f- ). the activity in each pair of the derivatives containing the same substituents is almost the same in magnitude. carboxamides b,d,g and b,e,i were found to be the most effective against the above-mentioned strains (mic & . ± mg ml ). the major directions of chemical modification of s hp ( a) and bsg ( a) at the mycosamine h -amino group in alkylation and aminoacylation reactions, the aminocontaining reagents are protected by the -fluorenylmethoxycarbonyl (fmoc) group. conventional h -n-alkyl derivatives of polyenes, such as the h -n-( -dimethylaminobenzyl)-substituted compounds s hp ( l) and bsg ( c) and the n,n-di(aminopropyl)-substituted compounds s hp ( m) and bsg ( d), were synthesized by reductive alkylation of compounds a and a with appropriate aldehydes in the presence of nacnbh (see scheme , conditions b and c). the yields of compounds m and d with respect to the starting antibiotics are * % ± %. h -n-acyl derivatives n and e were synthesized by the reaction of antibiotics a and a with n a ,n e -(fmoc) -l-lysine in the presence of pybop in * % ± % yields (see scheme , conditions d ). the removal of the fmoc group from intermediate derivatives o,p and f,g with a % piperidine solution in dmso affords the corresponding h -n-aminoacyl derivatives m,n and d,e in * % ± % yields. the evaluation of the influence of substituents in the terminal group at the c( ) atom of the aglycone and the mycosamine amino group on the antifungal activity of polyenes showed that the replacement of the co h group by me has no significant effect on antifungal activity against the tested strains. the activity of s hp ( a) and its analogue k is similar to that of bsg ( c) and its analogue b. thus, the effect of the same modifications on the activity of the initial antibiotics s hp and bsg with very close values of antifungal activity can be multidirectional. the mic values are changed in the following series: a = a, k = b, l > c, m > d, n < e. ( ) . the removal of the fmoc protecting group from compound a gave h -n-(l-lysyl)-s hp n-( -dimethylaminopropyl)amide ( b). an alternative scheme involves the initial synthesis of fmoc-protected h -n-aminoacyl derivatives of s hp followed by their transformation into the corresponding c( )-carboxamides (scheme ). the reaction of compound a with n-fmoc- -aminomethylbenzoic acid in the presence of pybop affords h -n-(n-fmoc- -aminomethylbenzoyl)-s hp ( ) . the amidation of the latter with appropriate amines in the presence of pybop gives h -n-(n-fmoc- -aminomethylbenzoyl)-s hp dmae-amide ( a) and -hydroxypropylamide ( a). known compound p, which was prepared by the reaction of a with n a ,n e -(fmoc) -l-lys in the presence of dcc and hobt, was used to synthesize n-( -dimethylaminoethyl)amide ( a) and -hydroxypropylamide ( a) of n a ,n e -(fmoc) -l-lysyl-s hp. the removal of the fmoc group from compounds a ± a under mild conditions gave target products b ± b containing free amino groups (see scheme ) . the evaluation of antifungal activity of doubly modified s hp derivatives ± against the above-mentioned four fungal strains compared to the corresponding monomodified s hp c( )-carboxamides b,c demonstrated that the additional modification of the mycosamine h -amino group of carboxamide b has no significant effect on antifungal activity against these fungal and yeast strains (mic * . ± mg ml ). meanwhile, the corresponding modifications of s hp -hydroxypropylamide lead to a considerable decrease in antifungal activity. in the series of doubly modified derivatives, s hp -n,n-dimethylethylamides ( and , respectively), prepared via the amadori rearrangement with d-glucose or d-galactose, exhibit the highest activity, similar to that of the starting antibiotics a and a. experiments in animals play a significant role in the selection of lead antifungal agents. since only rather toxic amb ( a) is used for the treatment of systemic fungal infections, compounds exhibiting the highest in vitro activity are currently tested for the haemolysis and(or) acute toxicity. new genetically engineered polyene macrolides a, a, a and a, the semi-synthetic derivatives dmae-s hp ( b), h -n-lys-bsg ( e) and doubly modified h -n-( deoxy-d-fructos- -yl)-s hp dmae ( ) were evaluated for antifungal activity in the treatment of candida albicansinduced sepsis in mice and tested for toxicity. , the largest margin between the therapeutic and toxic doses was observed for compounds b and . compounds, the effective dose was % and % of the maximum tolerated dose (mtd), respectively, whereas amb ( a) is effective only at a dose of % of mtd. the antifungal activity of c( )-methyl-c( )-decarboxypolyenes against four fungal strains changes in the following order: bsg [c( ), c( )] ( a) > bsg [c( )] ( ) > bsg [c( ), c( )] ( ) . this confirms the pattern of changes in the activity against c. albicans observed previously in the series of c( )-carboxy-containing antibiotics with a similar arrangement of hydroxyl groups at c( ) c( ): s hp ( a) > bsg ( ) [c( )] > bsg ( a) [c( ), c( )]. the following amides were synthesized from polyenes a, a and a and -(n,n-dimethylamino)ethylamine according to the conventional amidation method in the presence of pybop: dmae-s hp ( b), dmae-bsg ( b) and dmae-bsg ( b) (see scheme ) . , the activity of these compounds, like that of the starting antibiotics, changes in a similar series: dmae-s hp ( b) > dmae-bsg ( b) > dmpe-bsg ( b). it is worth noting that low antifungal activity of compounds b and b was confirmed also by animal experiments related to the treatment of murine candida sepsis. these studies clearly demonstrated that the c( ) c( ) group of the polyol moiety plays a critical role in antifungal activity, although this group has not previously been considered of importance in the model of antibiotic binding to the target. compounds containing a single hydroxyl group at the position of c( ) c( ) ( a and ) exhibit low activity against the tested fungal strains. polyenes containing two hydroxyl groups at the and positions ( a and ) are inactive. antibiotics and semi-synthetic derivatives containing hydroxyl groups at the and positions (amb, a,b) and at the c( ) and c( ) atoms [s hp ( a,b) and bsg ( a,b)] displayed the best results. the design of hybrid analogues of antibiotics containing pharmacophore moieties, which affect targets different from those used by the starting antibiotics, is a promising line of research. , some benzoxaborole-containing compounds exhibit pronounced antifungal activity. methods were developed for the synthesis of dual-action antibiotics based on amb ( a) and different types of benzoxaboroles. the following five types of conjugates were synthesized depending on the nature of the functional group in benzoxaborole, which can be used to attach the latter to the amb molecule: c ( ) h -n-sulfo derivative and h -n-mono-and h -n,n-dialkyl derivatives a and (scheme ). amide was produced by the standard procedure that was applied to prepare the above-described amides; however, the yield of was low ( %). apparently, the amidation interferes with the formation of the aminoborole complex with amb. as mentioned above, the yields of amb carboxamides in this reaction using other amines are higher than %. h -n-derivatives a ± a were prepared from amb ( a) using in situ generated osu-activated esters. h -n-sulfo derivative was synthesized by the reaction of a with the appropriate sulfochloride in the presence of pyridine (py); h -n-alkyl analogues a and were prepared by the reaction of a with the appropriate aldehyde in the presence of nabh cn. the amidation of derivatives a and a with n,n-dimethylethylenediamine in the presence of pybop gave b and b, respectively (scheme ). an attempt to synthesize disubstituted h -n-alkyl-dmae analogue b according to a similar scheme from h -n-alkylamino derivative a failed (see scheme ) . nevertheless, compound b was prepared using an alternative approach by the alkylation of c( )-amide derivative b with -hydroxy- , -dihydrobenzo[c] [ , ] oxaborole- -carbaldehyde in the presence of nabh cn (see scheme ). tandem mass spectrometry (esi-ms/ms-mrm) studies showed that different fragmentation patterns are possible depending on the modification of the starting polyene (scheme ). in many cases, the introduction of the benzoxaborole substituent leads to a decrease in cytotoxicity and haemolytic activity with retention of high antifungal activity. these facts were confirmed by membrane activity assays. the results are given in table . semi-synthetic amb derivatives b,d,e, a,b, a, b and a,b were shown to have a significant pore-forming ability in artificially formed sterol-containing membranes. compounds with high antifungal activity and low haemolysis have higher selectivity for ergosterol-containing fungal membranes (c chol /c erg ) versus cholesterol-containing human cell membranes compared to compound a. for example, the high selectivity ( . ae . ) of compound b correlates with low haemolysis of human erythrocytes ( %). on the contrary, high haemolysis ( %) is determined by low or even reverse selectivity (c chol /c erg = . ae . ). for amb ( a) and its derivative b, the corresponding parameters have intermediate values (c chol /c erg = . ± . , haemolysis % ± %). amphotericin b ( a) was selectively modified at the mycosamine h -amino group or the c( ) carboxyl group. the developed approaches were extended to the related polyenes s hp ( a), bsg ( ) and other genetically engineered polyenes, which differ from the starting amb by the substituent at the c( ) atom and the positions of hydroxyl groups at c( ) ± c( ) of the aglycone moiety. the structure ± activity relationship analysis of new semisynthetic derivatives of polyene macrocycles revealed several general features of antifungal activity. in particular, antibiotics and, consequently, their semi-synthetic analogues containing two hydroxyl groups in this region at the and positions (amb, a) or the and positions (s hp and bsg ) exhibit high activity. a series of new semi-synthetic derivatives were shown to have pore-forming ability in artificially formed sterol-containing membranes. it is worth noting that they have selective activity against ergosterol-containing fungal membranes and lower haemolysis compared to amphotericin b. the aim of chemical modifications of the antibiotic oligomycin a ( a) (fig. ) acting as the f f -atp synthase inhibitor is to prepare new analogues possessing selective antitumour or anti-infective activity and to elucidate the mechanisms of sensitivity of microorganisms to this agent. oligomycin a ( a) (hereinafter oligomycin) belongs to macrolides Ð -membered a,b-unsubstituted macrolactones. it is a highly specific inhibitor of oxidative phosphorylation in the mitochondria of eukaryotes. oligomycin inhibits adenosine triphosphate (atp) synthesis and causes cell death. note. cerg is the minimum concentration of the compound that causes the pore formation in the dphpc/erg bilayer; cchol/cerg is the ratio of the minimum concentrations of the polyene in the dphpc/chol and dphpc/erg bilayers (dphpc is , -diphytanoyl-sn-glycero- -phosphocholine, chol is cholesterol, erg is ergosterol). the oligomycin molecule ( a) was found to contain a functional group, the chemical modification of which can produce the largest number of semi-synthetic analogues with various biological activities. the docking study of the interaction between the antibiotic and the target of the enzyme f f -atp synthase showed that the c( ) c ( ) side chain is not directly involved in the formation of this complex. a series of -substituted oligomycin derivatives were synthesized using -deoxy-o-mesyl oligomycin ( ) as the key compound, which was prepared by the selective treatment of a with methanesulfonyl chloride in a dmap ± py mixture (scheme ). the nucleophilic substitution of the group r via the s n or s n mechanism using various reagents gave the following -substituted derivatives: -(s)-oligomycin a ( b), -deoxy- -(s)-thiocyanooligomycin ( ), -deoxy- -(r,s)-bromooligomycin ( ) and -deoxy- -(s)-azidooligomycin ( ) (see scheme ) . the racemization is observed only for bromo derivative . the -epimer of this antibiotic, -(s)-oligomycin a ( b), was synthesized by the solvolysis of -(r)-deoxy-omesyl oligomycin ( ) with an aqueous mixture of tiourea and methyl cellosolve on heating. the reaction involves the walden inversion of configuration at the c( ) atom through a plausible mechanism presented in scheme . the biological activity assay of compound b revealed that the inversion of the hydroxyl group decreases activity against the actinobacteria streptomyces fradiae, while the antifungal activity remains at the same level. -(s)-oligomycin a ( b) exhibits somewhat higher activity against tumour cells compared to the starting analogue a. both antibiotics are able to overcome different drug resistance phenotypes and have low toxicity to non-malignant cells. the treatment of oligomycin with % formic acid afforded c( )-o-formyloligomycin ( ) (see scheme ) . formylated derivative retains the ability to inhibit tumour cell growth, whereas the activity against most other test cultures, including non-malignant cells, decreases. due to selectivity against tumour cells, c( )-o-formyloligomycin ( ) holds promise for further investigation. -deoxy-o-mesyl oligomycin ( ) can be quantitatively converted into -dehydrooligomycin ( ) by the kornblum oxidation in a dmso ± et n mixture at c (see scheme ) . attempts to oxidize the oh group at the c( ) atom of oligomycin ( a) to the keto group using different oxidizing agents failed. the cited study is interesting because this structure was previously presented as a new natural compound. however, the structure of this compound was not described in detail and its biological activity was not evaluated. derivative exhibits twice lower activity against s. fradiae atcc- compared to com- pound a; its activity against candida spp. and other filamentous fungi is very similar to that of compound a. docking studies of the binding of derivative to f f -atp synthase also showed that the affinity for the enzyme decreases compared to the starting antibiotic a. a method for the synthesis of , -disubstituted , , triazoles of oligomycin was developed based on -azido- -deoxyoligomycin . the method involves the regioselective [ + ]-dipolar cycloaddition of the -azido group to monosubstituted alkynes (scheme ). the reaction of azide with alkynes (phenylacetylene, propiolic acid and methyl propiolate) in a tert-butanol ± water mixture ( : ) can be performed both in the presence of a catalyst (cu i ) or without catalysts. this approach was applied to synthesize -deoxy- -( -phenyltriazol- -yl)oligomycin ( ), -deoxy- -( -methoxycarbonyltriazol- -yl)oligomycin ( ) and -deoxy- -( -carboxytriazol- -yl)oligomycin ( ) in %, % and % yields, respectively. compound served as the starting compound for the synthesis of water-soluble -deoxy- -[( -dmae-carbonyl)triazol- yl]oligomycin amide ( ) exhibiting selective antitumour activity. oligomycin a undergoes a retro-aldol rearrangement accompanied by dehydration in the presence of bases (scheme ). the structure of alkaline degradation product a was established by the detailed h and c nmr study, including heteronuclear correlation, combined with tandem mass spectrometry (esi-ms/ms-mrm). the structure of the carbon skeleton of the starting antibiotic a undergoes a significant transformation at c( ) c( ) (the cleavage pathways a, b and c) giving open-ring compound a. the mechanism of alkaline degradation of oligomycin a presented in scheme accounts for the formation of derivative a (through intermediates c,d) but not for the formation of b (through intermediates e,f). as opposed to compound a, compound a does not exhibit activity against proteasomal f f -atp synthase at a concentration of mmol l because of the loss of conformational rigidity. the hydrogenation of oligomycin ( a) on a palladium catalyst occurs both at the , -unsaturated bond of lactone and the diene system at c ( ) the hydrogenation of compound a under other conditions leads to the sequential selective reduction of keto groups Ð first at the c( ) atom and then at the c( ) atom. thus, the use of nabh(oac) latter with nabh in ethanol afforded ( s, r)-tetrahydrooligomycin ( ) (see scheme ) . the hydrogenation of double bonds of the macrolactone ring causes a decrease in the activity of compound a both against actinobacteria and fungal and mammalian cells. this may be attributed to the loss of conformational rigidity and the fact that the geometry of the macrocycle favourable for the interaction with the target (f f -atp synthase) is changed because of destruction of the diene system of the starting antibiotic a. the retention of activity of the starting compound against some strains of candida spp. supports the previous suggestion that there are additional targets in yeast cells of this genus, the binding to which is apparently independent of the geometry of the macrocycle. the reaction of compound a with m-chloroperoxybenzoic acid (m-cpba) in dichloromethane on decreasing the reaction temperature to c allows the selective epoxidation of oligomycin at one of c = c bonds to form unstable intermediate epoxide (scheme ). in the presence of formic acid, the latter compound gives a stable disubstituted oligomycin derivative Ð , -dihydro- s, s-dihydroxy- , -diformyloligomycin ( ). previously, -bromo derivative of this antibiotic was synthesized using n-bromosuccinimide as the brominating agent (see scheme ). the addition of hydroxylamine and related compounds to a was studied. the comprehensive study of the resulting compound by h and c nmr spectroscopy, including heteronuclear correlation, made it possible to establish the structure of nitrone a and exclude the possible existence of isomer b. it was found that an additional ring involving the c( ) ± c( ) atoms is formed, the activity of the antibiotic against f f -atp synthase being reduced. the reaction of antibiotic a with aminopyridinium and -dimethylaminopyridinium iodides in pyridine affords cyclic derivatives of pyrazolo [ , -a] pyridine and -methylpyrazolo[ , -a]pyridine a,b, respectively, annulated to the macrocycle (see scheme ) . their structures were established by h and c nmr spectroscopy, including heteronuclear correlation, and structure c was excluded. biological assays of new derivatives of oligomycin ( a) demonstrated that, in most cases, modifications reduce biological activity of the starting antibiotic against s. fradiae. , ± the growth inhibition assay of the strain s. fradiae atcc sensitive to very low concentrations of oligomycin (< . nmol ml or . nmol per disc surface) and hypersensitive to most of the known antibiotics was used to study the mechanism of resistance of microorganisms. mutant strains of this microorganism sensitive to analogues of compounds (ref. ) and a, as opposed to the starting antibiotic a and other derivatives, were produced under experimental conditions. the results of assays demonstrated that antibiotic a has several biotargets. these data confirm the conclusion that both the diene system of the macrocycle and its hydroxypropyl side chain play an important role in biological activity. therefore, the chemical modification of the antibiotic oligomycin ( a), a highly active f f -atp synthase inhibitor, was performed for the first time. more than new semi-synthetic oligomycin derivatives were prepared and the mechanism of their action was studied. analogues with selective antitumour or anti-infective activity were synthesized. the chemical modification of antibiotic a, which enables the efficient modulation of its biological activity due to a decrease in the binding to f f -atp synthase, was found. this provides the possibility to optimize pharmacological properties. olivomycin a ( ) (hereinafter olivomycin) is a highly effective antibiotic with a unique mechanism of antitumour activity discovered in the gause institute of new antibiotics , , (fig. ) . its structure consists of the aglycone olivin and two carbohydrate chains attached to the aglycone at the and positions. the antibiotic is a dna duplex minor groove ligand, which binds to the guanine-cytosine (gc)-rich region. compared to other antibiotics of the aureolic acid group (mithramycin and chromomycin a), olivomycin has better therapeutic efficacy. in recent years, antibiotics of this group have attracted increasing interest. , antibiotics of this group were shown to be able to prevent the development of resistance of tumour cells to other antitumour agents, in particular via a mechanism involving the inhibition of transcription of the mdr gene, overexpression of which is responsible for multidrug resistance of tumour cells. mithramycin is used to treat paget's disease and testicular carcinoma. chromomycin is a drug of limited use in japan for the treatment of gastrointestinal cancer. olivomycin ( ) was applied in the ussr for the treatment of ovarian cancer, reticulosarcoma and some other tumours. however, serious adverse effects limit the therapeutic potential of these drugs. various aspects of antitumour activity of antibiotics of the aureolic acid group were addressed in detail; however, chemical modifications of this class of antibiotics are poorly known. selective modifications of olivomycin ( ) at the c( ) atom (a), the c( ) oh (b) and c( h ) = o groups (c), the c( h ) c( h ) bond (d ) and the residues a and e (e) (see fig. ) were developed in the gause institute of new antibiotics. the selective acylation of compound at the phenolic hydroxyl group at the c( ) atom with a ac o py mixture affords -o-acetylolivomycin ( ) (scheme ). an investigation of the reaction of olivomycin ( ) with aryldiazonium salts showed that the azo coupling gives aryldiazenes monosubstituted at the position of the aglycone accompanied by the elimination of the disaccharide branch at the c( ) atom: -(phenyldiazenyl)olivomycin ( ), -( -sulfamidophenyldiazenyl)olivomycin ( ), -( methoxyphenyldiazenyl)olivomycin ( ), -( , -dichlorophenyldiazenyl)olivomycin ( ) and -( -methylphenyldiazenyl)olivomycin ( ) (see scheme ) . to explain the outcome of this reaction, the frontier electron density in the highest occupied molecular orbital (homo) was calculated by the semiempirical quantum chemical am method (fukui indices f). alternative directions of the nucleophilic attack by the phenyldiazonium cation were chosen by considering possible anionic forms of olivomycin ( a ± c) (scheme a). it was found that the position in anion a is the most favourable for electrophilic attack giving compound (the fukui index f homo is . ). meanwhile, the nucleophilicities of the c( ) and c( ) atoms are lower ( . and . , respectively). the formation of anion a in an alkaline medium is confirmed by the above-mentioned selective acylation of compound giving acetate at the same hydroxyl group at the c( ) atom in high yield (see scheme ) . the calculated energy parameters of alkaline hydrolysis of the disaccharide branch are in agreement with the experimental data. thus, the hydrolysis proceeds very rapidly in the presence of the diazenyl substituent at the position, while the storage of in an alkaline medium (used for the azo coupling) on cooling to ± c for h in the absence of diazonium salt does not lead to hydrolysis. the azo coupling of aryldiazonium salts with the aglycone of olivomycin Ð olivin ( ), which was synthesized by quantitative acid hydrolysis of compound , was investigated. aryldiazenyl derivatives of olivin a ± c containing the same substituents as compounds , and (scheme ) were synthesized. the geometric configurations of the most probable tautomeric structures a ± d of derivative a were determined (scheme ) and the total energies of each tautomeric form were calculated by the density functional theory at the b lyp/ - g(d) level of theory. the h nmr spectroscopic data also indicate that compounds a ± c exist as equilibrium mixtures of isomeric forms a ± d. the reaction of olivomycin ( ) with (o-carboxymethyl)hydroxylamine affords h -(carboxymethoxime)olivomycin (cm) (scheme ). the introduction of the carboxyl group into molecule makes it possible to subject this compound to further modification. the reaction of compound with appro- the introduction of the carboxyl group into molecule , as in the case of long acid , provides a route to its further modification. the reaction of short osa with appropriate amines in the presence of pybop or diphenylphosphoryl azide (dppa) affords osa n-methylamide it is worth noting that the method developed for the synthesis of intermediate osa ( ) can be applied to prepare the related derivative of mithramycin bearing a similar side chain at the c( ) atom of the aglycone. hence, short' mithramycin acid becomes more available compared to the combinatorial biosynthesis and can be used for further chemical modification of mithramycin. olivomycin a ( ) has two carbohydrate chains bearing the acetyl group at the a position of the oliose moiety and the isobutyryl group at the e position of the olivomycose moiety. a series of analogues of compound , which differ in the set of functional groups, were synthesized in order to elucidate the influence of acyl substituents in carbohydrate chains on biological activity. two analogues, de-e -isobutyrylolivomycin a ( ) and de-e -isobutyryl-de-a -acetylolivomycin a (or de-e isobutyrylolivomycin c) ( ), were synthesized by selective alkaline hydrolysis of the e -isobutyryl group of olivomycin a ( ) or c ( ), respectively (scheme ). it is worth noting that the hydrolysis of the e -isobutyryl group in olivomycin ( ) antibiotics (de-e -isobutyrylolivomycin a) and (de-e -isobutyryl-e -acetyl-olivomycin a or olivomycin b) were isolated from the natural olivomycin complex produced by fermentation of the streptoverticillum cinnamoneum strain. after the purification by silica gel column chromatography and semipreparative hplc, compounds and were isolated in % and % yields, respectively. , these compounds are identical to the previously characterized natural olivomycins c and b, respectively. the modification of antibiotic at the c( ) phenol group of the aromatic ring (compound ) was found to have no effect on antiproliferative activity against cancer cell lines and does not alter its ability to inhibit topoisomerase i. the transformation of giving diazenyl derivatives accompanied by elimination of the disaccharide branch from the aglycone (compounds ± ) leads to a sharp decrease in antiproliferative activity. compared to the starting olivomycin , compounds , and acquire considerable selective activity against human immunodeficiency viruses hiv- and hiv- in assays in the human t-lymphocyte cell line (cem). the evaluation of antiproliferative activity of olivomycin ( ) and its analogues modified at the side-chain h -keto group of the aglycone (cm amides ± and ) against the leukaemia cell lines k and l showed that these compounds are more effective than the starting acid but are less active than compound . for derivatives of antibiotic with a shorter aglycone side chain (osa, ) and its amides ± , the evaluation of antiproliferative activity in the human chronic myeloid leukaemia cell line k and the human colon the evaluation of antiproliferative activity of olivomycin analogues ± against hct cells showed that acyl groups in carbohydrate chains of antibiotic play a significant role. the activity decreases with elimination of acyl groups from molecule ; ic is . (for ), . (for ), . (for ) and > mmol l (for compounds , and ). these results correlate with the data on the ability of these compounds to inhibit dna-dependent topoisomerase i. in the absence of antibiotics, the relaxation of supercoiled (sc) dna leads to the disappearance of inhibitory activity and the formation of a set of topoisomers. the inhibition of topoisomerase i is detected from the presence of residual amounts of sc-dna and a decrease in the amount of rapidly migrating topoisomers. a decrease in the inhibitory activity of the enzyme is consistent with a decrease in the antiproliferative activity in the series of compounds > > . the removal of the e -isobutyryl group from the trisaccharide branch has a lower effect than the removal of the a -acetyl group from the disaccharide branch. a similar pattern of activity is observed in another group of olivomycin derivatives. compound displays low antiproliferative activity and is inactive against topoisomerase i. h -(carboxymethoxime)olivomycin n-( -adamantyl)amide ( ) is active in both assays. h -(carboxymethoxime)olivomycin n-(tert-butyl)amide ( ) and h -(carboxymethoxime)olivomycin n-( , -dihydroxy- -methylpropan- -yl)amide ( ) are even more effective inhibitors of the enzyme, capable of inhibiting sc-dna relaxation even at concentrations of . mmol l . the data on antiproliferative activity of some analogues of antibiotic do not correlate with the activity against topoisomerase i. for example, the analogue of olivomycin osa ( ), which exhibits weak antiproliferative activity, displays inhibitory activity against topoisomerase i similar to that of olivomycin a ( ), whereas dmae-osa ( ) possessing high antiproliferative activity is a weaker inhibitor of this enzyme. , recently, it was shown that highly effective analogue can act as a dna duplex minor groove ligand in another assay. it can disrupt the key epigenetic dna methylation process with the dnmt a enzyme on an equal basis with antibiotic . both compounds inhibit the formation of the dna ± enzyme intermediate covalent bond, required for the methylation, at nearly equal micromolar concentrations. olivomycin complexes with model oligonucleotide ± dna duplexes were studied by circular dichroism (cd) and fluorescence titration (ft). according to hartree ± fock - g calculations of the d structure of the dimer [ ] mg + , the presence of the dmae group in compound leads to an increase in the binding constant (k a ) of the mg + complex with the dna duplex by an order of magnitude compared to the acid osa ( ) (k a = . versus . mol l , as evaluated by ft). however, the presence of the bulky adamantyl substituent in compound results in a decrease in the binding constant of the dimer [ ] mg + with the dna duplex by an order of magnitude (k a = . mol l ). the elimination of one acyl substituent also leads to a decrease in the antiproliferative activity compared to that of antibiotic due probably to a decrease in its affinity for dna. the molecular docking of complex of with dna shows that the antibiotic can bind only to gc-rich regions in the minor groove of the dna duplex. carbohydrate chains of olivomycin interact with the sugar ± phosphate backbone of dna, and the aglycone interacts with nucleic acid bases. the sites of responsible for the interaction with dna (an additional hydrogen bond with the nh group of the g base) and the complexation of the antibiotic with dna were identified. the structural fragment, which is not directly involved in the interaction with dna but models the affinity of the antibiotic to the target Ð the minor groove of the dna duplex, was determined. based on these data, a schematic model of the interaction between olivomycin a and dna was proposed (scheme ). two semi-synthetic olivomycin derivatives ( and ) with the modified aglycone side chain were chosen based on the evaluation of antiproliferative activity in animal assays. compound is more effective in the treatment of p murine leukaemia than the starting antibiotic due to a decrease in toxicity and the absence of the cumulative effect. , compound (olivamide) is also more effective in this assay compared to the starting antibiotic . detailed preclinical assays in transplanted syngeneic tumours confirmed the efficacy of the agent based on compound for further clinical trials. ± these studies enabled the development of methods for selective chemical modification of the antibiotic olivomycin a, resulting in the synthesis of a series of semi-synthetic derivatives of this antibiotic; besides, structure ± activity relationship analysis was performed. , many of these compounds exhibited high antiproliferative activity in different tumour cell lines. some aspects of the mechanism of action of olivomycin a and its natural and semi-synthetic analogues were considered. , , , ± it was concluded that high antitumour activity of these compounds is related to their high affinity to the dna duplex. based on the results of in vitro assays, compounds were chosen for the evaluation of antitumour activity in in vivo assays. after the preclinical evaluation of antitumour activity and toxicity in laboratory animals, semi-synthetic olivomycin analogue Ð olivamide Ð was recommended for further clinical trials. ± anthracycline antibiotics are important chemotherapeutic agents commonly used in the treatment of malignant tumours. daunorubicin ( a), which was independently discovered under the name of rubomycin in the gause institute of new antibiotics (gina), is applied mainly for the treatment of leukaemia in children and adults. doxorubicin ( -hydroxydaunorubicin, dox) ( a) is used in combination chemotherapy of breast cancer, smallcell lung cancer, sarcoma, tumours in children and haemoblastosis. an original method for the one-pot preparation of semi-synthetic doxorubicin from rubomycin was developed in the gina. carminomycin ( a), which was also discovered in the gina, has lower cardiotoxicity than other anthracyclines and can inhibit the growth of doxorubicin-resistant tumours ( a). the structures of anthracycline antibiotics a, a and a are shown in fig. . the mechanism of cytotoxic activity of anthracycline antibiotics is related mainly to the inhibition of nucleic acid synthesis via intercalation between nitrogeneous base pairs, dna damage and inhibition of dna topoisomerases. an adverse effect of anthracyclines is the potentially irreversible and cumulative dose-related cardiotoxicity, apparently associated with the free-radical damage of myocardial cell membranes. the chemical modification of anthracycline antibiotics was extensively studied in the gina for a long period of time. in recent years, efforts were focused on the synthesis of new semi-synthetic analogues of drugs with improved anticancer properties. daunorubicim ( a) and carminomycin ( a) were modified at the c( ) atom (b), the c( ) = o bond (c) and the daunosamine h -amino group (d, e) (see fig. ). h -n-alkyl or h -n-aminoacyl derivatives exhibit high antitumour activity, because they retain the amine function at the daunosamine moiety. this function is required for the primary interaction of the antibiotic with the sugar ± phosphate backbone of dna. however, the drawback of reductive alkylation of anthracyclines a and a with aldehydes in the presence of nabh cn is that it is accompanied by the reduction of the c( ) = o group as the side reaction giving n-alkyl- -dihydro derivatives of daunorubicin ( b) and carminomycin ( b), respectively (scheme ). these analogues are less active than the related compounds containing the c( ) = o group. ± -dimethyl ketals of -bromo derivatives of daunorubicin ( c) and carminomycin ( c) were used to avoid this side reaction (see scheme ) . the reductive alkylation of compounds c and c in the presence of nabh cn can be accomplished using d,lglyceraldehyde and aldoses (the monosaccharide arabinose and the disaccharide melibiose) to form the following bromo-substituted -dimethyl ketals in quantitative yields: the antiproliferative activity of compounds e and against leukaemia cells k is virtually as high as that of derivative e, but is lower than that of carminomycin ( a). the activity of -hydroxycarminomycin derivative evaluated in the same assay is an order of magnitude lower than that of the starting anthracycline a, and the activity of doxorubicin e is two orders of magnitude lower than that of compound a. it should be emphasized that -hydroxycarminomycin derivatives and are equally active against the wildtype human breast adenocarcinoma cell lines mcf- and k and resistant pgp-expressing cell lines (mcf- dox, k i/s ). the antitumour activity of compound e evaluated in the murine leukaemia cell line p compares favourably with that of analogue a. thus, an increase in life span (ils) of mice bearing p leukaemia after a single admin-istration of mg kg of compound e is the same as that observed after administration of analogue a at a dose of mg kg (ils %). it was shown that anthracycline antibiotics a, a and a, which are known to inhibit dna topoisomerase ii at micromolar concentrations, can inhibit dna topoisomerase i at the same concentrations. new derivatives e, e, and have higher inhibitory activity against topoisomerase i compared to compounds a and a. the introduction of polyhydroxylated substituents at the h -amino group of the daunosamine moiety of anthracycline antibiotics increases the inhibitory activity of anthracyclines against topoisomerase a method was developed for the preparation of new watersoluble depot forms of doxorubicin ( a) Ð conjugates with high-molecular-mass polysaccharides. , galactomannan davanat ( ) was used as the polysaccharide. the latter was prepared by controlled partial hydrolysis of water-insoluble high-molecular-mass , -b-d-galactomannan isolated from seeds of cyamopsis tetragonoloba or guar gum. the molecular mass of compound , determined by gel chromatography on a sephadex g- column calibrated with pullulans, is * kda. to conjugate compound with a, the former is activated by the oxidation with periodate using a deficient amount of the oxidizing agent ( . ± . equiv. with respect to the total amount of sugar residues). this gives rise to schiff bases between the aldehyde groups of the oxidized polysaccharide ( a ± c) and the h -amino group of the antibiotic (scheme ). different structures of the final products are possible ( a ± c). the content of the starting antibiotic a in conjugate is mass % (determined from the content of the chromophore per unit mass of the dried powder by uv spectroscopy at nm). in order to increase the doxorubicin content in the conjugate with davanat , the antibiotic molecule was attached to the polysaccharide through a spacer giving h -n-l-lysyldoxorubicin ( ) (scheme ). compound contains two amino groups (while doxorubicin contains one amino group), which may facilitate the formation of the schiff base. besides, it is known that a series of n-acyl conjugates of daunorubicin or doxorubicin with amino acids possess high antitumour activity. h -n-l-lysyldoxorubicin ( ) was synthesized by the acylation of the amino group of doxorubicin ( a) with n a ,n e -(fmoc) -l-lysine osu-ester followed by the deprotection of the fmoc-protected intermediate with a morpholine solution. the schiff base in the resulting conjugate can have either a linear ( a) or cyclic structure ( b). scheme presents the possible structures for one of the oxidized subunits of activated davanat . it should be noted that h -n-l-lysyldoxorubicin can be attached to conjugate through either the a-amino-or e-amino group of h -n-l-lysyldoxorubicin (is not shown in scheme ). the introduction of the lysine spacer between compounds a and allows an increase in the antibiotic content in the conjugate to mass % with retention of water solubility. the conjugates were purified by gel chromatography on a sephadex g- column and dialysis against deionized water using a membrane with molecular weight cut-off (mwco) m w > kda. the molecular masses of conjugates and evaluated by gel chromatography on a sephadex g- column calibrated with pullulan standards are * and * kda, respectively. the antiproliferative activity of the doxorubicin conjugates was tested in three tumour cell lines: the murine melanoma cell line b -f , the breast cancer cell line mcf- and the colon cancer cell line ht- (htb- ). the ic values for conjugate (taking into account the percentage of antibiotic a in the conjugate) are . ± . , . ± . and . ± mg ml , respectively; for antibiotic a, . ± . , . ± . and . ± . mg ml . despite the fact that the cytotoxicity of conjugate is * ± orders of magnitude lower (data were not reported) than that of doxorubicin ( a), these results indicate that conjugate is an active depot form of doxorubicin ( a). the antiproliferative activity of the h -n-l-lysyldoxorubicin ± davanat conjugate ( ) (ic > mg ml ) against these tumour cell lines is much lower compared to cytotoxicity of conjugate . this can be due to the fact that the imine bonds in the h -n-l-lysyldoxorubicin ± da-vanat conjugate ( ) are more stable than those in conjugate . it should be noted that h -n-l-lysyldoxorubicin is not released in in vitro assays. therefore, a biological model, which would provide release of , is apparently required to evaluate the therapeutic potential of conjugate . based on these studies, a method was developed for the introduction of polyhydroxylated substituents of different types and different length into anthracycline antibiotics, which was used to synthesize a series of new hydrophilic h -n-alkyl derivatives of doxorubicin and -hydroxycarminomycin, including those containing mono-and disaccharide residues. , this modification was found to enhance the inhibitory activity of anthracyclines against topoisomerase i with retention of antitumour activity of the antibiotics. the new -hydroxycarminomycin derivatives, unlike doxorubicin derivatives, were shown to suppress the tumour cell growth insensitive to doxorubicin. a new water-soluble depot form of doxorubicin Ð a conjugate with the highmolecular-mass polysaccharide galactomannan dava-nat Ð was prepared. , this depot form exhibits antiproliferative activity against the above-mentioned three tumour cell lines. the antibiotic heliomycin (resistomycin, , , , -tetrahydroxy- , , -trimethyl- h-benzo[cd ]pyrene- , -dione) ( ) with a broad spectrum of biological activity (scheme ) was discovered in the gause institute of new antibiotics. first of all, this antibiotic is highly effective against grampositive and some gram-negative microorganisms, including drug-resistant strains. more recently, heliomycin was found to exhibit antifungal and antiviral (anti-hiv) activity. besides, compound can block proliferation of some tumour cells in in vitro assays. in the soviet union, heliomycin ( ) was produced on a commercial scale and was used as a gel for topical treatment of skin infections and healing of burn wounds. the chemical modification of heliomycin is poorly known. hence, structure ± activity relationship studies require the development of method for the synthesis of new semi-synthetic derivatives and evaluation of their biological properties. the main goal is to prepare series of derivatives with improved water solubility in order to expand their practical application. a method was developed for the synthesis of aminomethyl derivatives at the position of compounds (where x is an amine moiety or a nitrogen-containing heterocycle). typical synthetic procedures are presented in relation to compounds a ± c (see scheme ) . , the mannich aminomethylation of compound can be performed using amines and formaldehyde in dmf (see scheme b ). an alternative procedure for the synthesis of derivatives is based on the use of pre-prepared stable iminium salts (see scheme , conditions a). in the case of aminomethylation of compounds with polyfunctional amines, the amino group is protected with boc (see scheme c) and then deprotected with acid (see scheme d ). the reaction of compound with n,n-dimethylamino(methylene)ammonium chloride afforded -[(n,n-dimethylamino)methyl]- , , , -tetrahydroxy- , , -trimethyl- -h-benzo[cd ]pyrene- , -dione hydrochloride ( a). -[(tert-butylamino)methyl]- , , , -tetrahydroxy- , , -trimethyl- h-benzo[cd ]pyrene- , -dione hydrochloride ( b) is produced by the treatment of compound with tertbutylmethylamine in the presence of formaldehyde. the treatment of compound with tert-butylpiperidin- -ylcarbamate in the presence of a formaldehyde solution gives -( -boc-aminopiperidinomethyl)- , , , -tetrahydroxy- , , -trimethyl- h-benzo[cd ]pyrene- , -dione, which is quantitatively converted to the corresponding amine dihydrochloride ( c) upon the treatment with hcl meoh. the antiproliferative activity (ic ) was evaluated by the colorimetric determination of cell metabolic activity (mtt assay) using a standard procedure in eight tumour cell lines, including both drug-sensitive and drug-resistant cell lines. the resulting compounds inhibit tumour cell proliferation in a low submicromolar to micromolar concentration range, similar to that of doxorubicin ( a). however, most of these compounds significantly outperform doxorubicin in terms of the drug-resistance index. these compounds block the growth of the wild-type cell lines k and hct and the following multidrugresistant cell lines: the k / subline isogenic to p-glycoprotein (pgp)-positive multidrug resistance and the hct p ko subline with p gene deletion. the development of multidrug resistance in these tumour cell lines is the crucial factor responsible for a decrease in activity of antitumour drugs. as opposed to compound , derivatives a ± c show a high level of induced apoptosis in the t bladder cancer cell line model. the introduction of the -aminomethyl moiety enhances the dna-binding affinity and the inhibitory activity against dna topoisomerase i. hence, compound c is the most promising candidate for preclinical trials. based on these studies, methods were developed for chemical modification of heliomycin ( ). series of new analogues, water-soluble salts of amino-containing derivatives, were synthesized and they were shown to exhibit high antiproliferative activity against many tumour cell lines and inhibitory activity against various targets. the value of these studies is that the majority of aminomethyl derivatives of heliomycin are active against both wild-type and drugresistant cancer cells at micromolar or submicromolar concentrations. the development of new-generation drugs is a challenging problem because of the increasing risk of the development of drug resistance in microorganisms. different approaches to the search for new compounds were developed in recent years. particular attention is given to semi-synthetic derivatives based on available natural antibiotics, since there are numerous examples of the successful application of this approach. some semi-synthetic derivatives based on macrocyclic glycopeptides have advantages over the gold standard chemotherapeutic agent Ð vancomycin. , , the distinguishing features of new representatives of this class are selectivity against multidrug-resistant pathogenic bacteria and higher bioavailability. the new semi-synthetic vancomycin analogue telavancin (vibativ) (manufactured by theravance and astellas pharma, us) was approved for use in the united states and europe. two semi-synthetic derivatives of glycopeptide antibiotics have completed phase clinical trials and were approved by the united state food and drug administration (fda): chloroeremomycin (discovered by eli lilly, acquired by the medicine co in ) and dalbavancin (discovered by lepetit; acquired by pfizer in ). , the drawbacks of vancomycin are the poor accumulation within tissues, because of which it is not used in the treatment of, for example, pneumonia, and a pronounced pseudoallergic reaction typical of glycopeptides. research in international cooperation showed the promise of chemical transformations of the antibiotic eremomycin belonging to this group of glycopeptide antibiotics. eremomycin is a highly active domestic antibiotic that suppresses the growth of gram-positive organisms; it is ± times more effective than vancomycin but is inactive against drug-resistant strains of staphylococci and enterococci. original approaches and methods were developed under the supervision of professor m.n.preobrazhenskaya in the gause institute of new antibiotics. these methods can be applied to prepare derivatives of antibiotics of this group with desired properties. in , the method for the synthesis of glycopeptide analogues was protected by an international patent. promising analogues, various n h -derivatives and carboxamides of eremomycin, were synthesized. these derivatives compare favourably in efficacy against drug-sensitive and drug-resistant strains of staphylococci and enterococci with the related vancomycin derivatives and they are even more effective in a number of assays. ± some carboxamides show no allergenicity. other derivatives (e.g., the adamantane derivative of eremomycin) are promising as a protection against biological risks because they were found to be active against the bacterium bacillus anthracis, including fluoroquinolone-resistant strains. high activity of the resulting hydrophobic glycopeptide derivatives can be attributed to the dual mechanism of action on gram-positive bacteria. , modifications of aglycones of glycopeptide antibiotics with hydrophobic substituents resulted in the discovery of a new class of polycyclic peptides active against a large group of enveloped viruses, such as hiv or hepatitis c virus. studies on the mechanisms of antiviral activity are currently ongoing. it was suggested that protein kinase is one of possible targets for this agluco analogue, because antiviral activity was shown to correlate with the inhibition of serine/ threonine protein kinases. comprehensive research on the synthesis and characterization of heterodimeric conjugates based on different classes of antibiotics was initiated in the gause institute of new antibiotics under the supervision of professor m.n.preobrazhenskaya. the following hybrid antibiotics were synthesized: glycopeptide ± macrolide, glycopeptide ± aminoglycoside and hybrid compounds containing the benzoxaborole chromophore. the literature data provide evidence that this line of research holds promise. , macrolides modified through the carbamoyl group at the hh position can acquire activity against drug-resistant bacterial cell lines. generally, conjugates containing a long spacer exhibit higher activity than the related compounds with a shorter spacer. , investigations of interactions between different benzoxaboroles and antibiotics made a significant contribution to the chemistry of not only antibiotics with complex structures but also the relatively poorly studied borole compounds. benzoxaboroles were found to be quite stable under different reaction conditions. in particular, the acylation, amidation and reductive alkylation with reactive agents and on heating are virtually not accompanied by oxaborole ring opening. the introduction of the benzoxaborole substituent into the polyene macrolide amphotericin b (amb) also enhances biological activity. the resulting compounds possess valuable properties, such as lower cytotoxic and haemolytic activity compared to amb combined with high antifungal activity. the efficiency of the approach to the design of antibiotics of a new generation was demonstrated in relation to antifungal polyene macrolides. it is based on a combination of genetic engineering techniques and methods of organic synthesis ± and is protected by an international patent. the chemical modification of polyene antibiotics, which were obtained via the genetic engineering of nystatin a biosynthesis at the norwegian university, gave a series of agents exhibiting lower toxicity and higher activity compared to amphotericin b in animal assays. the dependence of antifungal activity on the structure of the polyol region [c( ) ± c( )] of these antibiotics was revealed for the first time by preobrazhenskaya et al. pioneering studies on the development of methods for selective chemical modification of the unique macrolactone oligomycin a, a specific f f -atp synthase inhibitor, and the original antitumour antibiotic olivomycin a of the aureolic acid group were performed. in both cases, examples of chemical modifications of related compounds for these antibiotics are absent in the literature. these results are of great scientific value. investigations of f f -atp synthase inhibitors are of considerable interest because this enzyme is involved in the development of resistance in microorganisms. chemical transformations of oligomycin a using different reagents were studied in detail. alkaline hydrolysis reactions were performed and conditions for the selective reduction of double bonds and keto groups, cyclization, etc. were found. the replacement of the c( )-hydroxyl group by the activated mesyl group has proved to be particularly successful. this modification has no significant effect on biological activity of the antibiotic but provides a possibility to optimize its pharmacological properties. , only transformations via the biosynthesis were described for the aureolic acid group antibiotics mithramycin and chromomycin. , these natural antibiotics, which have a limited use in the treatment of some malignant tumours, have attracted increasing attention of researchers in different fields. , the synthesized compounds were tested for antiproliferative activity. based on the results of in vitro studies of a series of new olivomycin a analogues of different types, compounds were selected for the in vivo evaluation. after preclinical trials in laboratory animals (evaluatrion of antitumour activity and toxicity), one olivomycin a analogue was recommended for further clinical trials. ± a systemic approach applied to series of new semisynthetic analogues of olivomycin a allows a detailed study of the molecular mechanism of antitumour action of this antibiotic. ± in particular, it was shown that olivomycin and its analogues, acting as dna duplex minor groove ligands, can inhibit topoisomerase i and the dnmt a enzyme responsible for the disruption of the key epigenetic dna methylation process. , the structural fragments of olivomycin a critical for antitumour activity were identified. a model of the interaction of the antibiotic and some its analogues with the dna duplex was proposed. new analogues of anthracycline antibiotics with substituents of different types and different length, including those containing mono-and disaccharide residues, were prepared. the evaluation of the effect of polyhydroxylated moieties of doxorubicin and -hydroxycarminomycin on antitumour activity showed that this modification does not lead to the loss of activity of anthracyclines ± and enhances inhibitory activity against topoisomerase i. -hydroxycarminomycin derivatives proved to be particularly valuable because these compounds, as opposed to related doxorubicin derivatives, inhibit the proliferation of both doxorubicin-sensitive and doxorubicin-resistant tumour cell lines. a new water-soluble depot form of doxorubicin with the high-molecular-mass polysaccharide galactomannan davanat was constructed and it was shown that it exhibits antiproliferative activity against three tumour cell lines. , series of new heliomycin analogues Ð water-soluble salts of amino derivatives Ð were synthesized and these compounds were shown to have high antiproliferative activity against many tumour cell lines and inhibitory activity against different targets. the value of these studies is that the majority of aminomethyl derivatives of heliomycin are active against both wild-type and drugresistant cancer cells at micromolar or submicromolar concentrations. the method is protected by a patent. targeted chemical modifications of antibiotics are not only performed in order to prepare new potential drugs of a new generation but are used as an efficient tool for investigation of the mechanisms of action on bacterial or tumour cells. it should be emphasized that many potent antibiotics are indispensable tools for molecular biology research of the living world. such comprehensive studies can lead to the design and synthesis of new-generation drugs, which would be more effective than the starting antibiotics and which are of theoretical interest as new compounds with high biological activity. figures , , and were composed by the authors based on the cited publications (the references are given in the figure captions). new approaches to natural anticancer drugs. springer briefs in pharmaceutical science and drug development antibiotics: challenges, mechanisms, opportunities markovnikov congress on organic chemistry (book of abstracts) handbook of experimental pharmacology doctoral thesis in chemical sciences, m.v.lomonosov institute of fine chemical technology glycobiology and drug design. (acs symp. ser. ) carbohydrates and drug design. (asc symp. ser. ) key: cord- -tmhce p authors: kalil, andre c.; timsit, jean-francois title: less is more: critically ill status is not a carte blanche for unlimited antibiotic use date: - - journal: intensive care med doi: . /s - - - sha: doc_id: cord_uid: tmhce p nan administration of antibiotics, is the accelerating drive of bacterial resistance-then, a begging question must be answered: who is responsible for most intravenous antibiotic use? given that more than half of icu patients receive antimicrobial therapy [ ] , it should not take a rocket scientist to estimate the answer. which patients end up receiving the majority of empiric intravenous antibiotics? the answer is obvious-critically ill patients. and where critically ill patients are most commonly located? in the emergency department before hospital admission and in the intensive care unit (icu) after the hospital admission. what health-care providers who take care of critically ill patients (emergency department physicians, intensivists, anesthesiologists, pulmonologists, infectologists, clinicians and surgeons) can do to curb the fate of antibiotic loss? compliance with individual hand hygiene, hospital infection control measures and antibiotic stewardship programs are critical to win the fight against bacterial resistance, and this has been discussed elsewhere [ , ] . in addition, we propose that health-care providers can bring concrete and direct benefits to each of our critically ill patients at the bedside by preventing the excessive use of unnecessary antibiotics. how can this be done? the clinical deterioration of mechanically ventilated patients may be associated with a new infection process; however, the majority of ventilator-associated events leading to antibiotic administration is related to noninfectious processes [ ] ; thus, the appropriate antimicrobial de-escalation is essential and can be safely done if culture results are negative [ , ] . of note, if the clinical deterioration progresses to septic shock, then microbiological samples should be taken and antibiotics be immediately started. for many decades, critically ill patients have been treated with antibiotics during two to three weeks for severe infections including pneumonias, abdominal and urinary infections, all of which still comprise the majority of infections leading to sepsis and admission to the intensive care unit. this practice was based on zero scientific evidence! however, physicians are also creatures of habits, good and bad habits, and the habits of giving prolonged courses of antibiotics have been the standard of care around the world. more recently, several randomized controlled trials have brought relevant findings to our clinical practice, specifically regarding the efficacy of short-course antibiotics in the setting of several bacterial infections. table shows the proven treatments with short course of antibiotics. another important way to reduce both the development of resistance and the unnecessary prolongation of antibiotics is by administrating antibiotics according to the most optimal pharmacokinetics and pharmacodynamics (pk/pd) parameters. the appropriate antibiotic dosing will clear the infection faster than suboptimal dosing and consequently will speed up the clinical cure rate, which will give the clinician the indication that is safe to de-escalate antibiotics [ ] . in fact, the hospital-acquired pneumonia (hap) and ventilator-associated pneumonia (vap) guideline from the infectious disease society of america and the american thoracic society [ ] recommends the use of pk/pd for antibiotic dosing in patients with hap or vap. considering that respiratory infections are the most common cause of sepsis worldwide, it is no surprise that pneumonia is among the main drives of antibiotic use in the icu. the vast majority of hospital-acquired and ventilator-associated pneumonias can be safely treated with an average of days of antibiotics independent of the microbial etiology [ ] . the benefits from the pk/ pd approach have also been demonstrated in patients with sepsis and septic shock [ , ] . there are three other respiratory syndromes that are responsible for a substantial overuse of antibiotics in the icu: copd exacerbation, ventilator-associated tracheobronchitis (vat) and health-care associated pneumonia (hcap). copd exacerbation is not and should not be treated as pneumonia, and evidence clearly supports a very short course of just a few days of antibiotics, if any, because one-third or more of these exacerbations are caused by viruses [ ] . vat is an ill-defined syndrome with lowquality scientific evidence, poorly predictive of progression to vap and not associated with higher mortality than icu patients without vat; this led the idsa/ats guideline to recommend against the use of antibiotics in patients with suspected vat [ ] . hcap has now been eliminated from both the hap/vap and the cap guidelines [ , ] because the most current evidence does not support the historical assumption that the hcap definition could distinguish patients with versus without mdr pneumonia. hence, the avoidance of empiric antibiotics in patients with suspected hcap or vat without vap can further prevent a substantial amount of unnecessary antibiotic overuse in the icu. in addition, antibiotics should be avoided in patients with positive urine culture with normal urine analysis, except in certain immunocompromised patients, such as renal transplant recipients. another area of interest is regarding the use of combination versus monotherapy for critically ill patients. while we agree that the use of combination antibiotic table practical bedside recommendations to minimize unnecessary antibiotic exposure in the critically ill patient for the empiric treatment of severe infections in critically ill patients may be a reasonable strategy while microbiology tests are being processed, we do not recommend combination therapy when the infectious pathogen and susceptibilities are known, i.e., targeted/directed therapy. evidence suggests that combination antibiotic therapy does not prevent development of resistance, is associated with more side effects and does not improve survival compared to monotherapy [ ] [ ] [ ] [ ] . for the high mortality risk cases of bloodstream infection due to carbapenemase-producing enterobacteriaceae, the potential value of combination over monotherapy remains to be determined. lastly, we cannot emphasize enough the critical importance of an aggressive source control of the infection process in the critically ill patient. more antibiotics and prolonged courses will not suffice if there is an uncontrolled source of infection (e.g., abdominal abscess, infected central venous catheter, empyema). in fact, the antibiotic escalation may do more harm than good in this situation. on the other hand, antibiotic de-escalation can produce further benefits when patients are presenting clinical improvement. importantly, the lack of deescalation (i.e., unnecessary prolonged courses) can harm patients and lead to more antibiotic resistance [ , [ ] [ ] [ ] . it is time to take action and protect our critically ill patients from the harmful effects of unnecessary antibiotic overexposure. this will not only benefit our current patients at the bedside by preventing serious antimicrobial side effects and c difficile colitis, but will also save future patients from dying due to multi-drug-resistant infections. our bedside actions to prevent antibiotic overuse can curtail the development of antibiotic resistance and beat the blade runner's gloomy prediction for . antibiotic resistance threats in the united states quantifying drivers of antibiotic resistance in humans: a systematic review antimicrobial consumption and resistance in adult hospital inpatients in countries: results of an internet-based global point prevalence survey rationalizing antimicrobial therapy in the icu: a narrative review antimicrobial resistance and antibiotic stewardship programs in the icu: insistence and persistence in the fight against resistance. a position statement from esicm/escmid/waaar round table on multi-drug resistance ventilator-associated events: prevalence, outcome, and relationship with ventilator-associated pneumonia management of adults with hospital-acquired and ventilator-associated pneumonia: clinical practice guidelines by the infectious diseases society of america and the antimicrobial deescalation in critically ill patients: a position statement from a task force of the european society of intensive care medicine (esicm) and european society of clinical microbiology and infectious diseases (escmid) critically ill patients study group (esgcip) continuous versus intermittent beta-lactam infusion in severe sepsis. a meta-analysis of individual patient data from randomized trials prolonged versus short-term intravenous infusion of antipseudomonal betalactams for patients with sepsis: a systematic review and meta-analysis of randomised trials short-course antibiotic treatment in acute exacerbations of chronic bronchitis and copd: a meta-analysis of double-blind studies diagnosis and treatment of adults with community-acquired pneumonia. an official clinical practice guideline of the antibiotic combination therapy for patients with gramnegative septic shock short-course adjunctive gentamicin as empirical therapy in patients with severe sepsis and septic shock: a prospective observational cohort study effect of empirical treatment with moxifloxacin and meropenem vs meropenem on sepsis-related organ dysfunction in patients with severe sepsis: a randomized trial effect of aminoglycoside and beta-lactam combination therapy versus beta-lactam monotherapy on the emergence of antimicrobial resistance: a meta-analysis of randomized, controlled trials excess antibiotic treatment duration and adverse events in patients hospitalized with pneumonia: a multihospital cohort study short-course empiric antibiotic therapy for patients with pulmonary infiltrates in the intensive care unit. a proposed solution for indiscriminate antibiotic prescription comparison of vs days of antibiotic therapy for ventilator-associated pneumonia in adults: a randomized trial key: cord- -kx kmdej authors: herbers, alexandra; de pauw, ben e. title: acute myelogenous leukemia and febrile neutropenia date: - - journal: managing infections in patients with hematological malignancies doi: . / - - - - _ sha: doc_id: cord_uid: kx kmdej aggressive chemotherapy has a deleterious effect on all components of the defense system of the human body. the resulting neutropenia as well as injury to the pulmonary and gastrointestinal mucosa allow pathogenic micro-organisms easy access to the body. the symptoms of an incipient infection are usually subtle and limited to unexplained fever due to the absence of granulocytes. this is the reason why prompt administration of antimicrobial agents while waiting for the results of the blood cultures, the so-called empirical approach, became an undisputed standard of care. gram-negative pathogens remain the principal concern because their virulence accounts for serious morbidity and a high early mortality rate. three basic intravenous antibiotic regimens have evolved: initial therapy with a single antipseudomonal β-lactam, the so-called monotherapy; a combination of two drugs: a β-lactam with an aminoglycoside, a second β-lactam or a quinolone; and, thirdly, a glycopeptide in addition to β-lactam monotherapy or combination. as there is no single consistently superior empirical regimen, one should consider the local antibiotic susceptibility of bacterial isolates in the selection of the initial antibiotic regimen. not all febrile neutropenic patients carry the same risk as those with fever only generally respond rapidly, whereas those with a clinically or microbiologically documented infection show a much slower reaction and less favorable response rate. once an empirical antibiotic therapy has been started, the patient must be monitored continuously for nonresponse, emergence of secondary infections, adverse effects, and the development of drug-resistant organisms. the averageduration of fever in serious infections in eventually successfully treated neutropenic patients is – days. adaptations of an antibiotic regimen in a patient who is clearly not responding is relatively straightforward when a micro-organism has been isolated; the results of the cultures, supplemented by susceptibility testing, will assist in selecting the proper antibiotics. the management of febrile patients with pulmonary infiltrates is complex. bronchoscopy and a high resolution computer-assisted tomographic scan represent the cornerstones of all diagnostic procedures, supplemented by serological tests for relevant viral pathogens and for aspergillosis. fungi have been found to be responsible for two thirds of all superinfections that may surface during broad-spectrum antibiotic treatment of neutropenic patients. antibiotic treatment is usually continued for a minimum of days or until culture results indicate that the causative organism has been eradicated and the patient is free of major signs and symptoms. if a persistently neutropenic patient has no complaints and displays no evidence of infection, early watchful cessation of antibiotic therapy or a change to the oral regimen should be considered. only years ago, dealing with a patient with a disseminated malignant disease was relatively simple. there were no curative options and information on the inevitable dismal prognosis was not shared with the patient or his family. the mid sixties of the twentieth century witnessed the first successes of chemotherapeutic agents. this encouraged investigators to explore this route further, thereby escalating the dosage of the cytostatic drugs in the expectation of better results. it became rapidly clear that the destructive effects of cytotoxic compounds were not limited to malignant cells. infection has emerged as a prominent complication of chemotherapy, which was particularly worrisome in the sixties, a decade without powerful broad-spectrum antimicrobial agents. since a possible cure of the cancer was seen as the primary goal, complications of rigid cytotoxic regimens were taken for granted and when they occurred, treatment was more or less improvised. this situation remained unchanged until bodey [ ] pointed out that patients in remission of their underlying disease could die suddenly of an overwhelming infection during cytotoxic therapy-induced neutropenia. neutropenia was and remains defined as an absolute neutrophil count of less than . × /l ( /mm ) or a count less than . × /l ( , /mm ) expected to fall below . × /l ( /mm ) [ ] . he even showed a positive correlation between the severity and duration of neutropenia and the risk of acquiring a life-threatening bacterial infection. this risk appeared even more pronounced in individuals who were treated for an acute leukemia or lymphoma as these disorders interfered directly with vital components of the immune system. next to gram-negative bacilli, staphylococcus aureus earned a notably bad reputation [ ] . a few years later, schimpff and co-workers demonstrated convincingly that early administration of antimicrobial agents covering the above suspected pathogens while waiting for the results of the blood cultures saved lives. his so-called empirical approach became an undisputed standard of care [ ] . however, better options to manage infections encouraged hematologists to intensify their antileukemic regimens further in an attempt to improve the remission rates in previously refractory cases. these intensifications, in turn, inspired more thorough clinical research into potentially more effective antimicrobial regimens, which was facilitated by the booming development of new antimicrobial agents such as broad-spectrum synthetic penicillins, third and fourth generation cephalosporins, fluoroquinolones, and carbepenems in conjunction with a keen eagerness of the respective pharmaceutical companies to put their compounds to test in large clinical trials that were usually conducted by cooperative trial groups [ , ] . a cycle of several subsequent rounds of broader-spectrum antibiotics and further intensification of chemotherapeutic regimens has eventually lessened the mortal risk of neutropenia to only one of many problems in today's clinical practice. modern anti-leukemic therapy is inherently associated with ulceration of the pulmonary and gastrointestinal mucosa thereby allowing micro-organisms originating from the damaged mucosal tracts easy access to the body [ , ] . these pathogens may be part of the original indigenous flora but are commonly acquired during hospitalization [ ] . in the s, it was considered logical to prevent invasion of the body by indigenous flora by prophylactic administration of anti-infective agents. since such prophylactic agents were mainly targeted against the gram-negative enterobacteriaceae, a shift from gram-negative to gram-positive micro-organisms, including coagulase-negative staphylococci, viridans streptococci, and enterococci, as the primary cause of fever in neutropenic patients was seen [ ] [ ] [ ] [ ] [ ] [ ] [ ] . in the meantime, therapeutic regimens in the treatment of hematological malignancies have become so complex that use of surgically implanted venous access devices became universal in spite of the risk of catheter-associated infections and thrombosis [ , ] . an epidemiological survey among hospitalized patients treated for hematological malignancies between and in the united states showed that approximately % ( % in and % in ) of all microbiologically confirmed febrile episodes were due to gram-positive bacteria and % ( % in and % in ) due to gram-negative bacilli [ ] . this change in pathogens was facilitated by increased use of central venous catheters and other medical devices. introduction of immunomodulatory monoclonal antibodies into the therapeutic arena has extended the treatment-related immunodeficiency to t-cell functions and innate immunity. this, in turn, has brought viral and fungal infections, including pneumocystis jeroveci, into play, particularly when impaired cellular immunity coincided with prolonged, severe neutropenia [ , ] . the modern chemotherapeutic regimens designed to treat acute lymphoblastic leukemia incorporate high doses of corticosteroids. as a result, patients treated with such regimens are at increased risk of infections typically related to an impaired cellular immunity. in addition, allogeneic bone marrow transplantations have become a fully accepted treatment modality for many hematological malignancies. nowadays, infections still account for substantial morbidity and mortality among patients who undergo myeloablative therapy for a hematological malignancy. in spite of all changes in the spectrum of infectious agents, gram-negative pathogens remain the principal concern because their virulence accounts for serious morbidity and high early mortality rate [ , ] . administration of potentially curative chemotherapy is the starting point in treating acute leukemias. giving cytotoxic drugs is relatively straightforward since internationally accepted antitumor protocols have defined the optimal dosages. once the chemotherapy has been administered, the hematologist must wait patiently for the desired outcome a few weeks later. however, while the scientist in the hematologist has completed this first task, the general clinician in him or her has to step forward to monitor the patient, as the natural host defense system gradually disintegrates. close surveillance of the patients with attention to the emergence of infectious complications is mandatory. management of infections during this time of danger must be individualized because fixed protocols and algorithms are of limited usefulness given the complexity of infectious diseases management [ , ] . it is here that the science and art of medicine meet; listening to the patient's complaints and meticulous physical examinations constitute the crucial factors for timely therapeutic interventions and eventual success. this applies to both patients who are treated with intensive chemotherapeutic regimens and to recipients of a stem cell transplant. during this period of neutropenia, appropriate coordination of information coming from different sources is important, since, next to the patient, family members, nurses, microbiologists, pulmonologists, radiologists, and pathologists can assist in the timely discovery of an emerging complication. different cancer centers approach these tasks in different ways but it occurs to us that the hematologist who is responsible for treating the underlying hematological disease must also act as the captain of the ship. this coordinating role obliges him or her to have at least some basic knowledge of likely infection problems and, perhaps even more importantly, to have fine communication skills to keep all parties on board as well as incorrect on the same course. since the symptoms of an incipient infection are usually rather subtle due to the absence of granulocytes, teamwork is crucial to ensure that antibiotics are administered at the first signs or symptoms of infection [ ] . in most cases, fever defined as a single oral temperature of more than , °c ( °f) or a temperature of more than , °c ( , °f) for more than h, will serve as a trigger for action. at the onset of fever, attempts to identify the cause of fever deserve absolute priority (see table - ), immediately followed by institution of appropriate broad-spectrum antibiotic therapy preferably within one hour of fever [ ] . fever in a neutropenic patient is a warning sign that should be taken very seriously because self-limiting infection is virtually • consider determination of crp, galactomannan antigen, and viral serology nonexistent in neutropenic patients irrespective of whether they have been treated for acute leukemia or lymphoma or received a stem cell transplantation. in anticipation of the results of the diagnostic evaluation, fever denotes infection until proven otherwise. absence of phagocytic cells in combination with a damaged skin and mucosal surfaces allows micro-organisms residing at a superficial site of infection easy access to the bloodstream. under these circumstances, a relatively small inoculum, that easily can escape detection when limited volumes of blood are sampled for culturing, can cause a serious septic syndrome [ ] . therefore, withholding antibiotics while waiting for a blood culture to become positive is a bad idea, even though fever can be of noninfectious origin [ ] . a sudden onset of fever accompanied by chills, tachycardia with or without a drop in blood pressure, and tachypnea is associated with a higher rate of positive blood cultures. shock at the onset of fever is an ominous clinical sign but neither clinical manifestations nor the pattern of fever during neutropenia can serve as an indicator of a particular causative agent, not even when the most notorious pathogens such as pseudomonas aeruginosa or staphylococcus aureus are involved [ , ] . a substantial minority of patients with true infections will have an insidious onset of fever. although more frequently related to noninfectious causes than acute fever, a slow rise of temperature does not exclude an infectious origin, although gram-negative rods, viridans streptococci, and staphylococcus aureus are less prevalent amongst these patients. acute fever following transfusion is often related to the presence of irregular blood group antigens or to cytotoxic antibodies acquired during previous transfusions or a pregnancy [ ] . of note, relative bradycardia in patients who did not receive antiarrhythmic medication suggests either a viral or noninfectious origin of the fever. a possible relation between fever and frequently used drugs such as allopurinol, antibiotics, bleomycin, and cytarabine or with the underlying disease process itself should always be kept in mind [ , ] . a dysfunctional immune system is presumed to be responsible for the high rate of drug allergy in patients with active acute leukemia; the allergy may abate when complete remission is achieved [ ] . this phenomenon is well known in patients with infectious mononucleosis or acquired immunodeficiency syndrome. until recently, coagulase-negative staphylococcal bacteremia was thought to be entirely related to the use of central venous catheters but recent work points at mucosal sites as important portals of entry [ ] [ ] [ ] . the clinical spectrum of catheter-related infections ranges from asymptomatic bacteremia as a manifestation of intraluminal colonization or a process confined to the site of insertion to marked inflammation of the tunnel tract and septicemia with metastatic emboli in the skin and other organs. suspicion of a tunnel or exit line infection should arise when the catheter tract becomes painful, red, or swollen or when signs of inflammation are visible at the exit site. malfunction of the catheter, illustrated by problems drawing blood through the line, is a common first warning of a possible lumen infection [ , ] . in the selection of the initial antibiotic regimen, one should consider the type, frequency of occurrence, and antibiotic susceptibility of bacterial isolates recovered from other patients at the same hospital. in addition, the use of certain antibiotics may be limited by special circumstances, such as drug allergy, liver function disturbances, or renal insufficiency. despite numerous clinical studies, since the s, no single empirical antibiotic regimen has been shown to be superior for initial treatment of patients who become febrile during a neutropenic episode after therapy with chemotherapy drugs for hematological malignancies (see table - ) [ , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . however, there is world-wide consensus that any initial antibiotic regimen should include drugs with reliable activity against escherichia coli, pseudomonas aeruginosa, klebsiella species, other enterobacteriaceae, and staphylococcus aureus [ ] . three basic intravenous antibiotic regimens have evolved: initial therapy with a single b-lactam, the so-called monotherapy; a combination of two drugs, a b-lactam with an aminoglycoside, a second b-lactam or a quinolone but without a glycopeptide; and, thirdly, a glycopeptide in addition to b-lactam monotherapy or combination. numerous extensive studies have shown that traditional combinations, consisting of an antipseudomonal b-lactam and an aminoglycoside, are not more effective than monotherapy in the empiric treatment of uncomplicated episodes of fever in neutropenic patients. a third or fourth generation cephalosporin, a carbapenem, as well as piperacillin-tazobactam, have been found to be effective single agents in the majority of cases [ , ] . it appears appropriate to reserve two-drug regimens for complicated cases or if antimicrobial resistance is a potential problem. the major disadvantages of an aminoglycoside are nephrotoxicity and ototoxicity, and the necessity to monitor serum levels [ ] [ ] [ ] . combination of drugs such as amphotericin b, cyclosporine, and cisplatinum with an aminoglycoside is best avoided because of their additive renal toxicity, whereas high sodium content may limit the simultaneous use of two b-lactam antibiotics in elderly patients. an extensive study by european organization for research and treatment of cancer -national cancer institute of canada [ ] showed unambiguously that vancomycin can be withheld and not administered empirically for persistent fever despite appropriate initial monotherapy or combination antibiotic treatment until the results of the cultures indicate the need for vancomycin. vancomycin must be included in an initial empiric regimen for patients known to be colonized with penicillin-and cephalosporin-resistant pneumococci, viridans streptococci, or methicillin-resistant staphylococcus aureus or in situations where b-lactam resistance is likely such as a catheter-associated cellulitis where coagulase-negative staphylococci predominate . the choice to implement a particular antibiotic regimen is, at least partly, based on the results of clinical trials as reported in the literature. yet, the results of such trials should be interpreted with great caution. definitions for response as well as inclusion and exclusion criteria for clinical study protocols are usually very rigid and quite different from common clinical practice [ , ] . conduct of clinical trials in febrile neutropenic patients was a booming business in the mid-seventies and eighties when many new broad-spectrum antibiotics became available. the data derived from these trials expanded our knowledge of the possible infectious complications tremendously. for instance, analyses of these studies revealed that only half of the patients who develop fever during neutropenia will have a clinically or microbiologically documented infection, the majority being pulmonary infiltrates and bacteremias (see table - ) [ , ] . furthermore, it was obvious that neutropenic patients without a documented infection generally defervesced within a few days, whereas those with a clinically or microbiologically documented infection showed a much slower and less frequent fever defervescence rate [ , , ] . this very consistent observation suggests that it might be prudent to select different antibiotic regimens for patients with different symptoms. although there is no statistically valid evidence to support a more individually tailored approach, it appears reasonable to assume that patients might benefit from timely administration of the antibiotics with the highest intrinsic potency against a given micro-organism. a known or suspected focus of infection, if present at the time of initial fever, could help in the selection of additional case-specific anti-infective agents because the location of an infection is, at least to a certain extent, predictive of specific infective pathogens (see table - ) [ ] . likewise, results of surveillance cultures and knowledge of clinically documented infection fever accompanied by a clinical infection, but pathogens cannot be identified, e.g., cellulitis, pneumonia microbiologically documented infection fever accompanied by a localized infection and microbiologically plausible evidence, or fever without a localized infection, but infectious agents can be demonstrated in a (blood) culture the common complications associated with particular antileukemic regimens may offer valuable input to individualizing appropriate initial treatment of a neutropenic patient with fever. a damaged integument probably plays a major etiologic role in virtually all infections that occur following aggressive cytoreductive therapy for a hematological malignancy but its involvement is most obvious in infections of the skin and gastrointestinal tract. the use of high-dose cytarabine in conjunction with the occurrence of diarrhea were found to be independent risk factors for streptococcal infections among patients evaluated during first episodes of neutropenic fever [ ] . it has been recognized that bacteremias due to oral streptococcus mitis and streptococcus oralis may result in serious complications such as sepsis or adult respiratory distress syndrome, which carry high mortality [ ] [ ] [ ] . similarly, bacteremias due to staphylococcus aureus, pseudomonas aeruginosa, and clostridium species as well as candidemias are more frequently encountered in patients with acute leukemia who suffer from neutropenic enterocolitis or typhlitis, the most serious disturbance of the delicate balance between mucosal damage and microbial flora in the setting of prolonged exposure to antibiotics after intermediate or high-dose cytarabine chemotherapy. the signs and symptoms of chemotherapy-induced enterocolitis or typhlitis vary considerably from patient to patient and include nausea, vomiting, abdominal cramps, and severe abdominal pain with virtually no formed bowel movements but accompanied by profuse, watery diarrhea. many patients are in such pain that they only gain relief from narcotic analgesics which, in turn, induce constipation by reduction of bowel movements. this may create a very alarming situation as the clinical picture in severe cases resembles that of gut perforation, acute pancreatitis, or even toxic megacolon. because there is a high mortality rate for surgical interventions in neutropenic and thrombocytopenic patients with acute leukemia, it is essential for physicians to be aware of the existence of neutropenic enterocolitis/typhlitis with the accompanying symptoms. ultrasonography or ct, showing pathological thickening of the bowel walls, may be useful to establish the diagnosis of typhlitis. patients treated for acute myeloid leukemia with a bowel wall thickness of more than mm had a significantly higher mortality rate than did those with a bowel thickness of less than mm [ ] . disproportional bacterial overgrowth in the gastrointestinal tracts of neutropenic patients with damaged mucosa can serve as a source of bacteremia for the endogenous gastrointestinal flora as well as for otherwise exclusively enteric pathogens such as clostridium septicum [ , ] and bacteroides fragilis. in contrast, salmonella species are rarely found in the stool or blood of granulocytopenic patients; these organisms are obviously not major players in this field. this is also true for pathogens like campylobacter and shigella species. therefore, an adequate antibiotic regimen for patients with abdominal symptoms should cover gramnegative rods but due consideration should be given to the use of compounds with activity against anaerobes. next to glycopeptides and carbapenems, metronidazole is an attractive adjunct to a standard monotherapy/combination regimen under these circumstances. pseudomembranous colitis caused by clostridium difficile [ ] [ ] [ ] [ ] [ ] constitutes a related but distinct entity that can be severe and even fatal. the stool should be tested immediately for clostridium difficile toxin if the diagnosis is suspected. enteric clostridia infections necessitate oral antibiotic therapy with either vancomycin or metronidazole. relapses are frequent and may follow cancer chemotherapy or courses with antibiotics such as clindamycin. relapse is harder to document because toxin may persist in the stool of successfully treated patients. diagnostic problems account for underestimating enteric viruses as causative agents in gastrointestinal infections. although a compromised cell-mediated immunity is known to predispose for parasitic and protozoan infections, their incidence is surprisingly low in patients who are treated for a hematological malignancy [ , ] . folliculitis and cellulitis are the most common manifestations of infectious processes in the skin. sometimes it is difficult to differentiate infectious lesions from drug-induced toxic skin eruptions. infection-associated erythema and swelling are usually mild but, if left untreated, infiltration and abscess formation will involve extensive areas of the skin with necrosis and gangrene. since the lesions associated with the various organisms are rather alike, a simple needle aspiration or biopsy should be performed to establish an accurate diagnosis as early as possible in the course of the disease. causative micro-organisms include streptococci, staphylococci, and, less commonly, gram-negative bacilli and fungi [ ] [ ] [ ] [ ] . localized infections of the skin, particularly in the face, are usually caused by gram-positive bacteria that arise more frequently in carriers of organisms like staphylococcus aureus. none of the standard empiric regimens is the optimal choice for treating skin infections caused by the prevalent but usually indolent nons. aureus gram-positive cocci that are often methicillin-resistant, but the morbidity from these infections should not be underestimated either. pseudomonas aeruginosa acquired in a hot jacuzzi may cause a folliculitis that occasionally progresses to a destructive ecthyma gangrenosum [ ] . this characteristic entity should be distinguished from similar lesions caused by other rare pathogens, such as actinomyces, stenotrophomonas maltophilia [ ] and fungi [ , ] as well as from pyoderma gangrenosum, a noninfectious cutaneous process in patients with a myeloid malignancy [ , ] . sweet's syndrome, a dense, tender infiltration by neutrophils of the dermis on the head, neck, and upper extremities is associated with a leukocytosis [ ] . varicella zoster is the leading dermatologic complication in patients with impaired cell-mediated immunity [ ] [ ] [ ] . if skin or mucous membrane lesions due to herpes simplex or varicella-zoster viruses are present, even if they are not the cause of fever, treatment with valacyclovir or another suitable antiviral is indicated with the intention to speed healing of lesions that could become potential portals of entry for bacteria and fungi. the results of several prospective studies do not indicate a general need for a glycopeptide as part of the front-line therapeutic regimen unless one has a particular reason to suspect the presence of methicillin-resistant staphylococcus aureus or penicillin-resistant viridans streptococci on the basis of local patterns of resistance or surveillance cultures. nevertheless, most physicians intuitively prefer an up-front glycopeptide-containing regimen to cover catheter-related infections as these are frequently due to coagulase-negative staphylococci, although early glycopeptide treatment does not contribute to improved survival from these usually indolent infections. hence, when coagulase-negative staphylococci are involved, a few days of watchful waiting for a possible clinical response and the results of the cultures will have no detrimental impact. most catheter-associated infections will respond to antibiotic therapy without the removal of the catheter. rotation of antibiotics through each lumen of multilumen catheters to avoid microbial sequestration in one of the lines and the use of antibiotic-containing heparin lock solutions to supplement systemic therapy have been proposed by some investigators but such practices remain controversial. pulling the catheter is most likely to be required for the cure if a concurrent venous thrombosis is found, the tunnel tract appears involved, or if the infection, regardless of the etiology, is recurrent, or if after several days of therapy an eventual response to antibiotics appears doubtful [ ] . gingivostomatitis and periodontal lesions occur frequently in patients with acute leukemia [ ] . oral mucositis is characterized by pain, edema, erythema, superficial lesions, pseudomembranous formation in conjunction with excessive mucous production, reduced saliva secretion, and bleeding. a wide array of pathogens can be found and include herpes simplex, gram-negative bacilli, streptococci, anaerobes, and candida species [ ] . with the introduction of aggressive chemotherapeutic regimens, hitherto unusual pathogens such as stomatococcus and aerococcus are increasingly seen in patients with mucositis. mixed and polymicrobial infections are more or less standard [ , ] . given the range of prevalent pathogens, there is little need to deviate from one of the standard regimens, although, on theoretical grounds one might prefer to select a carbapenem, fourth generation cephalosporin, or extendedspectrum penicillin given their superior intrinsic activity against viridans streptococci and pneumococci. the course of herpes simplex stomatitis is usually prolonged in patients treated for leukemia or lymphoma, and relapses are common [ ] . herpes simplex lesions are most commonly white painful plaques with or without serpiginous borders on the gums, tongue, buccal mucosa, or oropharynx and may be difficult to discriminate from oropharyngeal candidiasis and, indeed, co-infections do occur. swallowing can be so painful that saliva is expectorated and intake of food and fluids drastically reduced. it is not uncommon for oropharyngeal herpes simplex and candida infections to extend to the esophagus. although neither herpes nor candidiasis belong to the category of diseases that requires an empiric approach, it is generally accepted that early treatment with valacyclovir and fluconazole, respectively, is important to prevent extension into the esophagus and further dissemination, particularly among bone marrow transplant recipients. when the paranasal sinuses are involved in the infectious process, moulds have to be considered as possible causes. direct inspection of the nasal turbinates and a computer-assisted tomographic scan of the sinuses can be helpful to establish or reject the diagnosis. management of pulmonary infiltrates that are responsible for % of all fatal infections in febrile neutropenic patients is complex [ ] [ ] [ ] . the importance of classic clinical complaints of cough, pain, and dyspnea should not be neglected but bronchoscopy and radiological examination of the chest by a computerassisted tomographic scan represent the cornerstones of all diagnostic procedures. typically, chest radiographs performed early in the evolution of infection in patients with profound granulocytopenia fail to show infiltrates. it may take more than days for the infection to generate enough necrosis with hemorrhage and edema to produce a visible infiltrate. the critical decision faced by the clinician at the bedside of patients with pulmonary infiltrates is whether to undertake invasive procedures such as bronchoscopy with or without bronchoalveolar lavage, transbronchial biopsy, transthoracic aspiration, thoracoscopy-guided biopsy, or open lung biopsy. the exact role of these diagnostic procedures in the optimal management of patients is still controversial because the yield depends on the collaboration and skills of various specialists. moreover, concurrent thrombocytopenia precludes simple invasive diagnostic procedures such as transbronchial biopsies in many patients. the radiologic pattern of a possible infiltrate is often suggestive of its cause. a diffuse opacity, usually of both lungs, is seldom of bacterial or fungal origin. although viruses and pneumocystis jeroveci typically cause diffuse, bilateral pulmonary infiltrations, it should be kept in mind that a similar picture of pneumonitis can be seen secondary to radiation, fluid overload, cytotoxic drugs such as methotrexate, cytarabine and bleomycin, and in pulmonary hemorrhage. pneumocystis jeroveci pneumonia is manifested in patients with deficient cellular immunity as fever, progressive hypoxemia with dry cough, and dyspnea, typically beginning after discontinuation of corticosteroid therapy given for other reasons [ ] . high-dose trimethoprim-sulfamethoxazole with adjuvant corticosteroids for hypoxemic patients (po < mmhg) has become the preferred therapy for these infections [ ] . alternatives include intravenous pentamidine, oral dapsone in combination with trimethoprim, or oral atovaquone suspension alone. antiviral drugs are indicated only if there is clinical or laboratory evidence of viral disease. with the exception of a cytomegalovirus-related pneumonitis in allogeneic bone marrow transplant recipients with graft-versus-host disease, there appears to be no need for empiric coverage of respiratory viruses, such as respiratory syncytial virus, influenza [ , ] , and adenoviruses. ganciclovir, valganciclovir, and foscarnet have established activity in the treatment of cytomegalovirus infection and their timely use might be lifesaving. mycoplasma pneumoniae with or without cold agglutinins is remarkably infrequent in patients treated for leukemia. in more acutely ill patients, the possibility of acute lung injury following transfusion of a cellular blood product or respiratory distress syndrome related to streptococcal sepsis should be considered. patients with an infection by streptococcus mitis, which has been linked with severe mucositis and high-dose cytarabine are at particular risk [ , ] . the incidence of acute respiratory distress syndrome in such cases is more than % and mortality is substantial. the pathophysiology of adult respiratory distress syndrome following streptococcal bacteremia in a neutropenic patient is poorly understood. probably several factors are involved, such as deleterious effects of sepsis superimposed on preexisting tissue damage. even patients who had received appropriate antimicrobials at the onset of fever were reported to experience shock and death [ ] [ ] [ ] . therefore, in addition to antibiotics, corticosteroids should be considered in the management of patients affected by ards and streptococcal bacteremia. bacterial infections of the lung, accompanied by bacteremia in about % of cases, usually create infiltrates on a computer-assisted tomographic scan that are confined to one or more lobes. pneumonias caused by pseudomonas aeruginosa and staphylococcus aureus do have a bad reputation but enterobacteriaceae [ , ] , haemophilus influenzae and streptococcus species are hardly less dangerous. given the uniformly poor outcomes of pulmonary infections in clinical trials, the empiric use of a combination of antibiotics is recommended with the addition of vancomycin in centers that face resistance of s. pneumoniae to penicillin and macrolides. outbreaks of legionella pneumophila, an infection characterized by patchy interstitial or nodular pulmonary infiltrates and sometimes accompanied by headache or gastrointestinal symptoms, have been observed among compromised patients in units with contaminated water systems [ ] . therefore, if a case of legionellosis is encountered, other patients with similar symptoms on the same ward should be treated with a macrolide or a fluoroquinolone from the start of antimicrobial therapy. a nodular pattern of pulmonary infiltrates should lead the physician to consider the possibility of atypical pneumonia or, more commonly, a pulmonary fungal infection. in the latter case, diagnostic procedures rather than immediate institution of antifungal drugs should be given priority. especially in patients with concomitant impairment of the cell-mediated immunity, pulmonary aspergillosis has to be distinguished from tuberculosis. infections with mycobacterium tuberculosis in patients with impaired cell-mediated immunity are manifested as either localized pulmonary disease or devastating miliary tuberculosis. nontuberculous mycobacteria are still rather rare in patients with acute leukemia, but the introduction of purine analogues such as cladribine and fludarabine, which cause severe and prolonged depression of cellular immunity, may change this picture in the near future [ ] . urinary tract infections are astonishingly uncommon in patients who are treated for leukemia or lymphoma and, since gram-negative bacteria are the predominant urinary tract pathogens, the choice for a single broad-spectrum b-lactam is fully justified. malignant otitis externa is a very serious infectious complication that can emerge after administration of aggressive chemotherapy for a hematological malignancy. at the outset, the patient will complain of a painful, discharging ear, and physical examination will reveal a reddened edematous ear canal. local maceration and humid conditions favor the growth of pseudomonas aeruginosa which, indeed, can be isolated frequently from swabs taken from superficial lesions of the external canal. untreated, the infection will penetrate into underlying soft tissues, threatening the retromandibular and parotid area. likewise, spread to the middle ear, the mastoid air cells, and adjacent temporal bone is possible. once osteomyelitis becomes established, extension to the base of the skull with invasion of the cranial nerves and local thrombosis poses a direct danger to the patient's life. a computer-assisted tomographic scan may be helpful to identify tissue damage in the early phase. prolonged antibiotic therapy with ceftazidime, ciprofloxacin, or other antipseudomonal antibiotics in combination with surgical debridement constitutes the treatment of choice [ ] . occasionally, a similar clinical picture can be the result of an infection by staphylococcus aureus or aspergillus fumigatus. in such cases, surgery should be combined with an antistaphylococcal penicillin or vancomycin, or with voriconazole, respectively. an insidious onset of fever accompanied by headache and confusion might be indicative of meningitis when causation by leukemia or lymphoma has been excluded by cytologic examination of the cerebrospinal fluid. in cases of infection, the cerebrospinal fluid is usually clear with moderate protein elevation. the prevalent pathogens are listeria monocytogenes, cryptococcus neoformans, and toxoplasma gondii [ ] . recovery of one of listeria monocytogenes [ ] and cryptococcus neoformans from blood cultures should, provided that no intracranial hypertension is detected, always prompt a lumbar puncture even in the absence of neurological symptoms. considering their low incidence and the relatively reliable diagnostic possibilities, there is no need to cover for these infections with a specific empiric regimen. outpatient management of infections in patients with hematological malignancies is discussed in more depth in chap. . when potent oral broad-spectrum antibiotics became available in the late eighties, many clinicians felt tempted to use these drugs in the treatment of febrile neutropenic patients. several groups around the world assessed the options and limitations of this seemingly revolutionary approach [ ] [ ] [ ] systematically. these analyses showed that it is possible to define risk factors that can be used to classify patients into low or high-risk categories. in fact, these studies offered nothing more than identification of objective parameters that corroborate the gut's feeling of the experienced clinician. since the time of bodey [ ] , it was already obvious that patients with absolute neutrophil count between , and . × /l ( - /ml) carry a minor risk compared to those with a granulocyte count of less than . × /l ( /ml). but now other risk factors have been identified. patients with concurrent mucosal damage or impaired cellular immunity, as well as those with clinically documented infections or unstable vital signs, are at high risk and deserve increased vigilance. patients with these additional risks cannot be considered candidates for antibiotic treatment on an out-patient basis. the vast majority of patients with acute leukemia are considered high-risk patients and should continue to receive intravenous broad-spectrum antibiotics in the hospital or similar setting. the remaining low-risk patients, namely those with unexplained fever who are clinically stable, may be safely treated with oral antibiotics provided that they have been seen at a qualified medical center promptly after the onset of fever [ , ] . the possible use of antibiotic prophylaxis does not pre-empt the need for a thorough check-up but limits the choice of drugs that can be used for treatment. patients with increasing granulocyte counts are considered to be better candidates for outpatient therapy than are patients without an indication of bone marrow recovery. among the oral regimens that have been evaluated are ofloxacin, ciprofloxacin, and ciprofloxacin plus amoxicillin-clavulanate. it is crucial to make sure that the patient is informed about the risk of unremitting fever during a neutropenic episode and that he or she fully understands the importance of seeking immediate medical advice in case any unexpected incident occurs. vigilant observation at home by a relative or professional health care worker and prompt access to appropriate medical care must be available h per day, days a week [ ] [ ] [ ] [ ] . as an alternative to initial outpatient therapy, early discharge with continued outpatient therapy for selected patients may be considered after a brief admission during which intravenous therapy is initiated, fulminant infection is excluded, and appropriate culture specimens are taken [ , ] . two studies have demonstrated that children who lack signs of sepsis and severe mucositis, who are afebrile for > h, who have neutrophil counts of > cells/mm (> . × /l), and who are at low risk for complications may have their intravenous antibiotic treatment safely stopped to be substituted by oral cefixime [ , ] . after starting empiric antibacterial treatment, fevers will persist or return in about one third of patients. the average duration of fever in serious infections, in eventually successfully treated neutropenic patients is - days (table - , fig. - ) [ , , , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . although fever can be inconvenient for the patient, it is important to realize that it is part of the body's defense system [ ] . indeed, some retrospective studies have suggested that fever is associated with improved survival and shortened disease. uncontrolled studies have reported an association of increased mortality with the absence of fever in polymicrobial or gram-negative sepsis and in elderly patients with community acquired pneumonia [ , ] . so, when the body temperature remains above normal during or days on apparently effective broad-spectrum antibiotics, this should not be considered a complete waste of time, particularly not if the time is used for an appropriate diagnostic work-up. it should be kept in mind that empiric administration of antibiotics is only meant as an immediate cover for rapidly fatal bacteria such as gram-negative rods and staphylococcus aureus, thereby, so to say, buying time for consideration of the next therapeutic interventions and for waiting for the results of the diagnostic procedures. when the results of the cultures become available and the infection has had time to blossom clinically, there is a more solid basis for decisions on necessary adjustments of an antibiotic regimen. unfortunately, all large, randomized clinical trials on empiric antibiotic therapy in the febrile neutropenic patients during the past years have been pharmaceutical company-driven for purposes of attaining governmental agency approval [ , ] . as a consequence, the design of these studies focused primarily on the efficacy of a particular drug in comparison with another drug or combination of drugs. according to the protocols for these trials, only patients who survived the febrile episode without a change in the allocated regimen could be labeled as successes, whereas any change in therapy, independent of the trigger, was denoted a failure, even if the patient survived unscathed and the infection was eradicated. therefore, modification of the test regimens was discouraged, which constitutes a rather artificial situation, as clinicians are inclined to adjust an antibiotic regimen for no other reason than a subjective feeling of unease with the original choice of antibiotics. changes often reflect impatience, nervousness, and lack of confidence on the part of the clinician concerned over the still febrile neutropenic patient rather than any deficiency in the original antibiotic regimen used. when restrictions surrounding a clinical trial do not apply, juggling antibiotics against an undulating line on a temperature chart is a well-known frequent occurrence on a ward full of patients suffering with hematological malignancies. indeed, in daily practice, many modifications are not based on objective criteria and are made outside office hours, i.e., by less experienced physicians on call [ , ] . however, it is generally recognized that exposure to many different antibiotics as a result of haphazard changes of regimens enhances the risk of drug-related adverse events and seldom improves the outcome of the patient under treatment. moreover, such a policy of endless therapeutic trials of antibiotic changes might wrongly decrease the perceived need for further diagnostic procedures in poorly responding patients. since there is evidence from clinical trials on what to do after the empiric phase, some experts have been promoting the so-called algorithms of planned progressive antibiotic therapy to treat neutropenic patients with fever. a planned progressive strategy involves adjustment of therapy every - days, until the patient becomes febrile or until all the potential causes of infection are covered by the best available microbial agents, irrespective of the development of additional symptoms. it is clear that algorithms featuring planned progressive therapy are destined to lead to overtreatment with unnecessary expenses and drug exposures [ ] . it appears more intellectually attractive not to rely on fixed algorithms but to weigh several different, patient-specific parameters, including fever and clinical response, as a guide for modification of an empiric regimen. it goes without saying that spending time at the bedside is crucial for those who feel attracted to the role of attending physician because careful observation often provides early clinical clues for a rational adaptation of the original empirical antibiotic regimen. the need for individualization is not only dictated by variations in the signs and symptoms of the patient that accompany persisting fever but also by differences in skills and expertise amongst attending specialists in various centers. for example, centers with excellent and interested departments of medical microbiology and pathology will rely more heavily on their findings than do centers with poorly functioning departments, whereas units with an active radiology service may benefit from the locally available know-how in this particular field. once an empiric antibiotic therapy has been started, the patient must be monitored continuously for nonresponse, emergence of secondary infections, adverse effects, and the development of drug-resistant organisms. this implies that the start of antibacterial agents cannot be seen as an impetus to stop diagnostic procedures. daily blood cultures are certainly justified as long as patients remain febrile and when a new temperature peak occurs because breakthrough bacteremia or fungemia may develop. close monitoring of sites that are prone to infection should start before the onset of fever and has to be continued after empirical antibacterial therapy has commenced. subtle changes must bring diagnostic tools into play to confirm or exclude the presence of an infectious focus. regular ct-scans of the chest, preferably in combination with serological monitoring for aspergillosis antigen, have an established value in patients who are at increased risk of fungal infections [ ] . as a rule, approximately % of patients without a focus of infection, which includes % overall with positive blood cultures, will show some clinical improvement after days of broad-spectrum empiric coverage in spite of persisting fever. in most cases, defervescence will follow rapidly. elements that should be incorporated in clinical decision making include the course of fever and clinical condition with special attention to the vital signs, evolving symptoms of infection in relation to the granulocyte count, c-reactive protein levels, antigen monitoring, and risk for relapses of latent viral infections determined by pretreatment antiviral titers. the results of all cultures taken at the onset of fever have to be assessed and it is recommended to analyze surveillance cultures, if any, to identify possibly colonizing resistant organisms. without clinical deterioration or proof of an infection caused by a micro-organism resistant to the initial antibiotic regimen, persisting fever after - h of empiric therapy in and of itself is an unsatisfactory basis for changing the original empirical antibacterial regimen. it is better to alter the regimen only when there are objective reasons to do so: deterioration of vital signs, isolation of a resistant pathogen without clinical improvement, persistence of a pathogen, antibiotic-related adverse events, occurrence of a new focus of infection or progression of an existing focus in the absence of granulocyte recovery, unexplained fever persisting for more than days, new fever, a new pathogen or recognition of a local outbreak with a resistant organism (tables - and - ). in most patients, antimicrobial therapy can be adjusted objectively on the basis of clinical or microbiologic findings but such an individually tailored approach requires careful daily assessment of all possible parameters collaborating with consulting specialists, including microbiologists, pulmonologists, and radiologists. in contrast to the moment of the onset of fever, there is ample time for deliberation and contemplation in a situation where the patient's fever persists for or more days while on antibiotics because the origin of fever is obviously not a rapidly fatal microorganism that needs immediate treatment. fever that persists for more than days suggests that the patient has a nonbacterial infection, a resistant bacterial infection, a second infection, or a drug fever [ , ] . despite extensive cultures, only around % of all febrile patients will be shown to have microbiologically defined infections. in % of patients, organ involvement is already apparent with the initial fever and an additional % will show clinically defined infection within the next h (see fig. table - ) . patients belonging to each of these three categories may have either a microbiologically documented infection, a clinically documented infection, or an explained fever. all these factors that are partly subjective and partly objective can be exploited to steer the modification of an empiric regimen when there is a perceived need to do so. ultimately, only - % of patients with a persisting unexplained fever should require a continued empirical rather than a clinical or microbiologically directed approach after h of broad-spectrum antibacterial therapy. whichever modification is planned, it cannot be overemphasized that maintenance of appropriate antigram-negative cover is mandatory as long as a patient is febrile and neutropenic. when the patient is improving or stable, there appears to be no imminent need to adjust an antibiotic regimen. depending on the micro-organism isolated, a change to an oral regimen could be considered with caution. when a gramnegative isolate is identified, broad-spectrum antibiotic coverage should be maintained in full dose. whereas the clinical relevance of a blood culture positive for gram-negative bacilli is never a matter of controversy, the implication of recovery of particular gram-positive cocci is less clear. single blood cultures positive for s. aureus, s. pneumoniae, or enterococcus faecalis in neutropenic patients should be regarded as significant and indicative of the need for further treatment. viridans group streptococci, with an average mortality of - %, are perhaps the most feared among the bacteremias today [ ] [ ] [ ] . although viridans streptococci are common blood contaminants in the general population, positive blood cultures in patients with oral mucositis should not be disregarded, certainly not when s. mitis or related streptococci are isolated [ , ] . isolation of rare micro-organisms should prompt evaluation of the appropriateness of the starting antibiotic regimen, especially when the patient is not responding optimally. on the other hand, isolation of in vitro resistant organisms such as coagulase-negative staphylococci and, more rarely, stenotrophomonas maltophilia, from the blood of a clinically, evidently improving patient, pose an interesting challenge. many would be inclined to modify the initial regimen but in many cases other bacteria that were not recovered on the culture plate may have been the culprits in the current fever. a blood culture that yields candida species or another fungus should be taken very seriously and dictates immediate institution of antifungal therapy [ ] [ ] [ ] . the availability of the candins has extended the therapeutic options [ ] [ ] [ ] . adaptations of an antibiotic regimen in a patient who is clearly not responding is relatively straightforward when a micro-organism has been isolated; the results of the cultures, supplemented by susceptibility testing, will assist in selecting the proper antibiotics. all clinical trials so far have demonstrated consistently that patients diagnosed with a clinically documented infection respond much slower and remain febrile for a longer time than those without a focus of infection [ , , ] . moreover, due to problematic penetration into avascular sites, infections associated with abscesses or prosthetic devices usually respond poorly to antimicrobial therapy. attending physicians should, therefore, be more hesitant to change antibiotics in patients who are not deteriorating. on the other hand, there are indications that early addition of specific agents might be useful for more rapid control of clinically documented infections. for instance, considering the probable involvement of anaerobes, switching to a carbapenem, if not given initially, or addition of metronidazole to a standard anti-gram-negative regimen, appears a logical choice when fever is accompanied by abdominal symptoms. in cases with a clinically documented site who do not improve or stabilize, coverage of micro-organisms known to prevail at the involved site of infection (see table - ) appears appropriate. clinically documented infections that emerge later during the course of febrile neutropenia carry a dismal prognosis and are presumed to be related to the occurrence of resistant microorganisms, including invasive fungi, in combination with persisting immunodeficiency often as a result of a refractory underlying disease. if the patient with an unexplained fever clinically improves or remains stable after h of empirical treatment and re-evaluation by physical examination and diagnostic tests yields no new information, and no isolate was found, the initial antibiotic regimen can be continued or can be switched to an oral compound. the latter option is more reasonable clinically if neutropenia is expected to resolve within the ensuing days. if vancomycin is a component of the initial antimicrobial regimen, withdrawal of the drug should be considered if the results of the cultures do not support its use. deteriorating cases without any microbiological or clinical sign of infection pose a dilemma. unexplained fever accompanied by deterioration can imply that the patient has a nonbacterial infection or a noninfectious cause of fever, but foremost, a resistant bacterial infection or the emergence of a second infection should be taken into account [ , ] . an initial response rate of about % may be expected in patients with shock, compared with % in patients without shock, which suggests the possible presence of an undetected toxin-producing pathogen in the former. addition to the original empirical antibacterial regimen is mandatory in critically ill patients, independent of the level of fever. escalation might include filling theoretical gaps in antibiotic spectrum and enhanced monitoring for any changes in the patient's condition. under these circumstances, the selection of agents should be guided by knowledge of locally prevalent virulent pathogens and actual susceptibility patterns, which implies the necessity of close cooperation with the local microbiology laboratory. addition of vancomycin appears reasonable in view of the fact that the spectrum of antibacterial drugs in traditional empiric regimens usually does not cover coagulase-negative staphylococci, methicillin-resistant staphylococcus aureus, enterococci, and some strains of penicillin-resistant s. pneumoniae and viridans streptococci. on the other hand, liberal use of vancomycin has confronted the medical community with vancomycin-resistant enterococci and staphylococci, which has led to increasing use of new agents like quinupristindalfopristin and linezolid in the treatment of febrile neutropenic patients. when the starting regimen consists of a single, broad-spectrum b-lactam, addition of an aminoglycoside is an attractive option to provide a better coverage when infections by resistant gram-negative rods are suspected. however, it has to be emphasized that development of resistance during therapy is extremely rare and that aggressive gram-negative organisms typically cause the infection to deteriorate rapidly to a stage beyond cure within a few days after first fever in most cases. hence, if the local resistance pattern or a particular concern in an individual patient prompts the use an aminoglycoside for resistant gram-negative bacteria, then aminoglycosides should be prescribed from the start in optimal doses with monitoring of the peak and trough serum levels. clinical deterioration in a persistently neutropenic patient with unexplained fever is an important but rather rare event in daily practice and applies to only a quarter of the overall % of cases that deteriorate while on broadspectrum antibacterial treatment. moreover, it is noteworthy that the success rate of empiric modifications is less than %, whereas more than % of cases will respond to specifically customized modifications [ ] . invasive fungal infections are encountered in up to % of autopsies in patients with hematological malignancies. fungi have been found to be responsible for two thirds of all superinfections, which surface during broad-spectrum antibiotic treatment of neutropenic patients. more than years ago, when diagnostic capabilities were virtually nonexistent and the choice of effective antifungal agents limited, two prospective, randomized trials laid the scientific foundation for the addition of systemically active antifungals even though neither study was adequately powered to reach a statistically valid conclusion [ , ] . this strategy appeared to reduce the incidence of invasive fungal infections in patients without any further sign of a clinically documented infection. solid statistical evidence to support the validity of this empiric approach was never obtained subsequently in further placebo-controlled trials because empirical antifungal treatment had become widely accepted as the standard of care. this so-called empiric antifungal therapy has remained popular as it seemed to make life easy for clinicians. the lack of reliable diagnostic tools combined with very poor outcomes of invasive fungal infections that were not timely treated contributed greatly to this popularity [ ] [ ] [ ] . however, in most cases in , antifungals prescribed empirically for fever alone are unnecessary because invasive fungal infection is present in a minority of cases. a better understanding of the pathophysiology of invasive fungal disease in combination with use of better diagnostics allows for a more individualized approach [ , ] . an optimal diagnostic work-up in conjunction with careful clinical observation will likely render routine empiric antifungal therapy superfluous in most cases because appropriate application of presently available diagnostic tools enables timely pre-emptive institution of appropriate antifungal therapy by experienced clinicians [ ] [ ] [ ] . the most common initial presentation of invasive aspergillosis is unremitting fever despite broadspectrum antibacterial treatment, accompanied eventually in most patients by pulmonary infiltrates or sinusitis. clinicians should suspect the diagnosis in a patient with pleuritic pain, hemoptysis, or a localized pleural rub. the halo sign (a dense central nodule with surrounding less dense infiltrate) on a computer-assisted tomographic scan of the chest, though not pathognomonic, is highly suggestive of an early phase of pulmonary aspergillosis or other mould pneumonia in immunosuppressed patients [ ] [ ] [ ] . even when gramnegative pathogens, including pseudomonas aeruginosa and enterobacter cloacae, are isolated from the sputum or blood of such patients, aspergillosis should be the leading consideration when nodular chest ct findings are present. if no infiltrate is found in a high-risk patient with persisting fever, the investigation should be repeated within a few days, preferably supported by bronchoalveolar lavage if indicated and additional assays such as screening for the presence of galactomannan in the blood [ ] . even in patients with aspergillosis who are responding adequately to antifungals, the computerassisted tomographic chest scan will usually show some enhancement of the lesion when the neutrophils return with eventual development of cavitation within the infiltrate, the so-called air-crescent sign [ ] [ ] [ ] . this finding is suggestive of aspergillosis, although mucormycosis and other moulds may cause an identical picture. whether the increased incidence of non aspergillus mould is due to more extensive use of the new azoles like voriconazole or to the use of more intensive immunosuppressive treatment schemes remains to be seen [ , ] . isolation of an aspergillus species from sputum or bronchoalveolar lavage specimens connotes either invasive infection or bronchial colonization, the latter conferring high risk for invasive aspergillosis. when voriconazole or posaconazole have been used as prophylaxis, it is sensible to select an antifungal compound with a different mode of action when therapy becomes mandatory [ , ] . surgery is indicated for patients in whom lesions near the pulmonary hilus pose a direct threat of invasion of a major vessel with the risk of fatal hemorrhage or for debridement of dead tissue after a period of antifungal therapy [ ] . low risk patients who test negative for aspergillus in all diagnostic procedures do not need to be started on intravenous antifungals. treatment should be stopped for those patients started on antifungals pending diagnostic test results. a more conservative wait-and-see approach can be implemented successfully once clinicians learn to accept that negative diagnostic results constitute sufficient evidence that there is no fungal infection in many persistently febrile neutropenic patients [ , ] . fluconazole given as prophylaxis has virtually eliminated infections with candida albicans. however, candida species or other fungi are still occasionally identified as causes of disseminated infections in humans, albeit with a shift from candida albicans to nonalbicans species [ , ] . a candidemic patient typically presents with an irregular fever sometimes accompanied by polymyalgia and polyathralgia. in about % of cases, characteristic pinkishpurple, nontender subcutaneous nodules may arise anywhere on the body. biopsy specimens should be cultured and histologically screened at multiple levels in an attempt to establish a final diagnosis. candida ophthalmitis is seldom seen in leukemic patients since the distinctive retinal exudates are the result of an inflammatory response that involves granulocytes. upon the return of the neutrophils or tapering of corticosteroids, complaints of abdominal discomfort and elevation of alkaline phosphatase levels with or without hepatosplenomegaly may emerge. at this stage, an abdominal ultrasound or computer-assisted tomographic scan will display rather distinctive multiple abscesses in the liver and/or spleen, known as "bull's-eyes" [ , ] . mortality from an invasive yeast infection may be as high as %, particularly when the start of antifungal therapy has been delayed. trichosporonosis and fusariosis can produce a clinical syndrome identical to candidemia [ ] [ ] [ ] . up to now, empirical antimicrobial therapy has been the backbone of improving survival of febrile neutropenia in leukemic patients. hematopoietic growth factors have been studied as adjunctive therapy for febrile neutropenic patients in several randomized, controlled trials. g-csf (filgrastim) and granulocytemacrophage colony-stimulating factor (sargramostim) when used as part of the treatment of febrile neutropenic patients were shown to consistently shorten the duration of neutropenia defined as a neutrophil count below . × /l ( /ml). however, the duration of absolute neutropenia, i.e., count of less than . × /l ( /ml), was not influenced, which might help to explain why neither a decrease in infection-related mortality rates nor a significant effect on morbidity, including duration of fever and use of anti-infectives, were observed [ , ] . therefore, the use of growth factors should be restricted to complicated cases for which there appears to be no rational alternative therapeutic option [ ] [ ] [ ] . this concept also applies to the use of granulocyte transfusions. transfusion of high numbers of granulocytes harvested after administration of g-csf, with or without dexamethasone, to a donor is done by some clinicians without there being any unequivocal evidence of its efficacy. patients with prolonged profound neutropenia and an uncontrolled clinically documented infection, such as severe cellulitis or sinusitis, appear to be the primary candidates for treatment with granulocyte transfusions, whereas administration of a colony-stimulating factor (g-csf) should be preferred when a return of the neutrophils is imminent. significant toxicities in granulocyte-transfusion recipients include transmission of cytomegalovirus, alloimmunization associated with fever, graft-versus-host reactions if granulocytes are not irradiated, progressive platelet refractoriness, and, possibly, respiratory insufficiency associated with concomitant administration of amphotericin b. new approaches with agents designed to protect the mucosa, like recombinant human interleukin and keratinocyte growth factor palifermin, show promising results in terms of reducing severity of mucositis and occurrence of fever and bacteremia in neutropenic patients [ ] [ ] [ ] . it is widely believed that antibiotic treatment should be continued for a minimum of days or until culture results indicate that the causative organism has been eradicated, infection at all sites has resolved, and the patient is free of major signs and symptoms. ideally, the neutrophil count should be > mm ( . × /l) before treatment is stopped [ ] . when no infection has been identified after days of treatment and the patient has become afebrile for h in association with a neutrophil count that has exceeded cells/mm ( . × /l), antibiotic therapy may be stopped. in addition, if a persistently neutropenic patient has no complaints and displays no clinical, radiological, or laboratory evidence of infection, cessation of antibiotic therapy or a change to oral antimicrobials should be considered after days without symptoms. if antibiotics are discontinued while the patient is still neutropenic, the patients must be monitored closely and intravenous antibiotics restarted immediately with recurrence of fever or any other evidence of bacterial infection, since the initial infection may have only been suppressed, not eradicated. one should consider continuous administration of antibiotics throughout the neutropenic period in patients who have profound neutropenia, mucous membrane lesions of the gastrointestinal tract, or any other identified risk factor. some experts suggest, in patients in whom hematological recovery cannot be anticipated, a change from the therapeutic regimen to a prophylactic scheme after weeks of therapy with intravenous antimicrobials. when the suspicion of a noninfectious cause of the fever is high, interruption of antibiotic therapy after ~ days seems warranted in clinically well patients without any evidence of infection apart from persisting fever. under these conditions, meticulous monitoring has to be maintained to guarantee the patients timely protection against subsequent infections that are likely to occur. the decision to start antifungals may appear complex but is not as difficult as the decision to discontinue. if a systemic fungal infection has been identified, the course of antifungal therapy will be determined by the causative agent and the extent of the disease. in patients with pulmonary infiltrates or other suspicious lesions, it is essential to see a clinical and, preferably, a radiological response before one ponders cessation of antifungal therapy. however, if no fungal infection is found, it is not clear how long antifungal drugs should be administered [ ] . for clinically well patients with prolonged neutropenia, it is suggested that antifungal agents can be stopped after weeks of treatment, provided that no conspicuous lesions can be found by clinical evaluation or by computer-assisted tomographic scanning of the chest and the abdominal organs. in the patient who appears ill or is at high risk, continuation of antifungal therapy throughout the neutropenic episode is recommended. conversely, when neutropenic fever subsides, the patient is clinically well and computer-assisted tomographic scan of the abdomen and chest reveals no suspicious lesions; antifungals may be discontinued, particularly when the criterion for commencing antifungal therapy had been simply fever unresponsive to antibiotics. this approach also applies when the presumptive diagnosis becomes questionable during the course of granulocytopenia. when a patient diagnosed with and treated for a proven or probable invasive fungal disease requires further chemotherapy or bone marrow transplantation, protection against the offending pathogen has to be provided, even if the patient responded completely to initial antifungal therapy. the risk of relapse of invasive fungal disease is so high that secondary prophylaxis is warranted, requiring that a full dose of the most effective antifungal is administered [ , ] . after introduction of routine ct scanning it became apparent that solitary lesions caused by invasive fungal disease are rare and this observation reduced the enthusiasm for surgical interventions. however, if the number of lesions is limited or a difficult-to-treat pathogen, such as a zygomycosis, has been found, surgical excision has to be considered, especially when the lesions are located close to a large vessel [ ] . modern chemotherapy offers hope of a cure to many cancer patients, but it confronts the medical community with new challenges continuously. infection remains an inevitable side-effect of the myeloablative therapy for acute leukemia and is the principal cause of morbidity and mortality amongst these patients. optimal care can be delivered only by those who pay scrupulous attention to the patient's clinical condition and are aware of the evolving therapeutic and diagnostic modalities. it cannot be denied that time remains an important factor in the management of infectious complications but we must try to distinguish more accurately between patients truly in need of immediate therapy and those who are not. fixed treatment algorithms are only acceptable if they allow individual interpretation and reasonable deviations. maintaining guidelines that dictate second line treatment of a population in which more than half of the patients do not have true infection is not justifiable in view of potential adverse events and the economical burden. the demand for an alternative strategy, built on clinical skills, modern and more accurate laboratory tests and imaging techniques, has become apparent and a broad application of this principle may change the approach to antimicrobial treatment in neutropenic patients completely. overuse of antimicrobial agents, both antibacterial and antifungal, has become all too common in the belief that broader coverage will benefit the patient. unfortunately, prescription of antimicrobials according to a preset scheme may give a false sense of security with reduced or delayed diligence in pursuing a diagnosis. diagnostic considerations should prevail whenever patients do not respond satisfactorily to an antibacterial regimen. in addition, neutropenia can no longer be seen as the major compass to steer antimicrobial therapy in a febrile patient because neutropenia is not the one and only factor predisposing for infection. a damaged integument and impairment of t cell-mediated immunity have altered the incidences of causative 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patients with previous invasive aspergillosis impact of previous aspergillosis on the outcome of bone marrow transplantation surgical resection of persistent pulmonary fungus nodules and secondary prophylaxis are effective in preventing fungal relapse in patients receiving chemotherapy or bone marrow transplantation for leukemia key: cord- -bnl i oy authors: wright, gerard d title: q&a: antibiotic resistance: where does it come from and what can we do about it? date: - - journal: bmc biol doi: . / - - - sha: doc_id: cord_uid: bnl i oy nan antibiotics target essential bacterial physiology and biochemistry, causing microbial cell death or the cessation of growth. there are five major antibiotic targets: the bacterial cell wall, the cell membrane, protein synthesis, dna and rna synthesis, and folic acid (vitamin b ) metabolism ( figure ). these bacterial targets are different or nonexistent in eukaryotic cells (including those of humans), which means that antibiotics are relatively nontoxic drugs. for example, the β-lactam antibiotics such as penicillins, cephalosporins and carbapenems block the synthesis of the bacterial cell wall. this structure is absent in higher organisms but is essential for bacterial survival. the bacterial ribosome is the target of the tetracycline, aminoglycoside, macrolide and other antibiotics, and is sufficiently different from the eukaryotic ribosome that cross-inhibition does not occur. resistance to antibiotics occurs through four general mechanisms: target modification; efflux; immunity and bypass; and enzyme-catalyzed destruction ( figure ). target modification can occur through mutation of the targets themselves -for example, the topoisomerases that are the target of the fluoroquinolone antibiotics -or by the production of enzymes that modify antibiotic targets, as, for example, in ribosomal methylation. vancomycin resistance is a version of target modification where new biosynthetic machinery is engaged to alter cell-wall structure. efflux occurs through a large family of protein pumps that eject antibiotics from inside the cell. in immunity, antibiotics or their targets are bound by proteins that prevent the antibiotic binding to its target. arguably, the most specific and evolved mechanism of antibiotic resistance are enzymes that recognize antibiotics and modify them in such a way as to eliminate the functional characteristics that enable them to interact with their targets. for example, β-lactamases hydrolytically cleave the core β-lactam ring that is characteristic of the class and essential to antibiotic action. resistance to antibiotics was recorded even before the first clinical use of penicillin in the early s. in the intervening years, resistance to all classes of antibiotics has emerged, and there are no antibiotics for which resistance does not exist. there are two general strategies for resistance. one comprises mechanisms that transfer resistance vertically from a bacterium to its progeny. examples are mutations in chromosomal genes that give rise to drug-insensitive products, such as the point mutations in the genes encoding dna gyrase or topoisomerase iv that result in resistance to fluoroquinolone antibiotics such as ciprofloxacin. the second strategy includes the actions of genes that can be transmitted both vertically to progeny and horizontally to other bacteria, even those of different genera. these genes are located on mobile genetic elements such as plasmids, which can carry one or more resistance genes. many of the β-lactamase genes that confer resistance to the penicillin, cephalosporin, penem and monobactam antibiotics are located on such elements, as is the glycopeptide-resistance gene cluster vanhax, which provides resistance to vancomycin. the prevalence and mobility of resistance genes in previously sensitive pathogenic bacteria has now reached crisis levels in many cases because new antibiotics are no longer being developed at a rate that can keep pace with microbial evolution. in the past two decades we have witnessed: • the rise of so-called extended spectrum β-lactamases (esbls), which are mutants of enzymes that previously could only inactivate penicillins but now have gained activity against many cephalosporins; • carbapenemases such as kpc and ndm- that inactivate all β-lactam antibiotics; • plasmid-mediated (and thus horizontally disseminated) resistance to fluoroquinolone antibiotics; • the spread of virulent mrsa (methicillin-resistant staphylococcus aureus) in the community; • the rise of multi-drug resistant neisseria gonorrhoea; • the emergence and global dissemination of multi-drug resistant acinetobacter baumannii, pseudomonas aerugi nosa, klebsiella pneumoniae and enterobacteriaceae; • the spread of extensively drug resistant mycobacterium tuberculosis; • the development of resistance to the two newest antibiotics to be approved for clinical use -daptomycin and linezolid. resistance is relentless and unavoidable as long as we use antibiotics. antibiotic resistance is the evolutionary response to the strong selective pressure that results from exposure to these compounds. the horizontal dissemination of resistance genes into bacterial species and genera that are not themselves intrinsically resistant, as well as the maintenance of resistance mutations vertically through populations is likely to be the result of contemporary use of these drugs in the clinic and on the farm. support for this hypothesis is the infrequency of antibiotic resistance in collections of pathogenic bacteria that pre-date the antibiotic era. nevertheless, antibiotic resistance is a natural phenomenon. it has been recognized for decades that the resistance mechanisms that have emerged in the clinic parallel those that are intrinsic to the bacteria that produce antibiotics. recent studies of non-pathogenic soil bacteria have revealed that the majority of environmental bacteria tested are multi-drug resistant. this reflects the fact that these microbes live and have evolved in an environment where small bioactive molecules, some toxic, some benign, are plentiful and diverse. bacteria have simply evolved to interact with them and control their biological effects. pathogens, on the other hand, are often more virulent forms of our commensal bacteria and simply have not been exposed to the diversity and types of small molecules found in the environment; as a result, they have not required the gamut of resistance genes found in some environmental bacteria. furthermore, the genes and proteins responsible for resistance in environmental bacteria are homologous to those found circulating in pathogens, strongly suggesting contemporary horizontal gene transfer. opportunistic pathogens with environmental reservoirs -for example, p. aeruginosa and a. baumannii -are highly drug resistant and have a remarkable capacity to acquire new resistance genes. the environment is therefore a large reservoir of potential resistance genes: the environmental 'resistome' . given the vast numbers of bacteria on the planet and the massive selection pressure provided by antibiotics, the movement of antibiotic-resistance elements from benign, but resistant, microbes into previously susceptible pathogens is simply a matter of time and opportunity. antibiotics themselves are the source of the evolutionary pressure that eventually renders them obsolete. limiting exposure of microbes to antibiotics therefore makes good sense to reduce the opportunity for the selection and dissemination of resistance. the inappropriate use of antibiotics by clinicians and the agricultural community needs to be curtailed. over the past several years, the medical community in particular has made concrete efforts to curb the improper use of antibiotics. the european union has taken the lead in limiting the nontherapeutic use of antibiotics in food animals. robust surveillance networks that span the clinic and the farm need to be supported in order to monitor the impact of resistance and the emergence of new threats in real time. in north america, efforts such as the strategies to address antimicrobial resistance act seek to diminish antibiotic use in agriculture and improve surveillance. furthermore, there have been several successful campaigns to educate the public on the importance of antibiotics and the proper use of these drugs. while none of these efforts is perfect, there is much to be celebrated and encouraged. these measures all serve to reduce antibiotic use and, as a result, delay the emergence of resistance. furthermore, by decreasing selection pressure, the opportunity for the rise of particularly clinically challenging or virulent organisms should be lessened. all strategies that reduce the incorrect use of antibiotics are welcome, but in the end new drugs will always be needed because of the inevitability of resistance. unfortunately, in the developing world, access to antibiotics is frequently not regulated and their use in agriculture is often rampant. these facts make antibiotic stewardship especially challenging. in an era of rapid intercontinental travel, pathogens are no longer geographically contained and can move from country to country with ease. the recent examples of transcontinental spread of the severe acute respiratory syndrome (sars) virus from guangdong province in china to hong kong and then canada in , and the ndm- carbapenemase, which inactivates all β-lactam antibiotics and appears to have originated in the indian subcontinent but is now found in north america, the uk and europe, make the point. the growing problem of resistance fuels a continuous need for new antibiotic drugs. the enterobacteria that produce carbapenemase are just one example of antibiotic-resistant enterobacteria. other gram-negative pathogens resistant to virtually all antibiotics include multi-drug resistant a. baumannii and p. aeruginosa. the expanding problem of mrsa, and the global challenge of extensively drug-resistant m. tuberculosis (also called extreme drug-resistant m. tuberculosis), require new therapies. there are some promising new candidates on the horizon, especially for the treatment of infections caused by gram-positive pathogens such as mrsa and enterococci. as already mentioned, two new drugs active against this microbial spectrum -daptomycin and linezolid -have been introduced in the past decade. tigecycline, a third-generation semi-synthetic tetracycline antibiotic approved in , also has activity against mrsa. the semi-synthetic glycopeptide antibiotic telavancin recently received approval in the united states and the fifth-generation cephalosporin ceftobiprole is available in some european countries and canada. however, there are few candidates in late-stage clinical trials suitable for the problem of gram-negative pathogens. here, often the choice of last resort is colistin, an antibiotic discovered more than years ago and seldom used in the past because of adverse affects, including kidney toxicity; however, it is now increasingly used. there are a number of reasons, some economic, for the paucity of new antibiotics. they include challenging and shifting processes of government regulatory approval that add to the risk for the pharmaceutical industry. furthermore, considerations of return on investment favor drugs for chronic diseases, which are taken by patients over long periods of time, often decades. in contrast, antibiotics cure disease and are taken for short periods of time. other reasons for the decline in antibiotic discovery and development are scientific. the first wave of antibiotics discovered five decades ago have been termed the 'low hanging fruit' . despite the discovery of numerous compounds with antibiotic properties in the years since, few have had the requisite properties to become drugs. most antibiotics are natural products or their derivatives that have been isolated from soil bacteria. some researchers have suggested that this source might now be exhausted. furthermore, the promise of the genomic era and the reality of hundreds of available bacterial genomes have so far failed to deliver the hoped-for new molecular targets for antibiotics. other new technologies, such as highthroughput screening of libraries of synthetic molecules, have not resulted in new drugs, although this may reflect a poor choice of chemical classes in the screens, emphasizing molecules more active in human biology than as antibiotics. test compounds were often skewed in favor of small lipophilic molecules with physical properties meeting the criteria of lipinski's rule of . however, though helpful in assessing the prospect of a compound to be an orally active drug for human disease, this strategy has been shown to fail when searching for antibiotics. well, natural chemicals have significant advantages. although the first antibiotics introduced into the clinic were the synthetic sulfonamides, the majority of antibiotics in current clinical use are bacterially produced natural products or their derivatives; only a few are completely synthetic in origin. the reasons for this in part reflect the history of antibiotic discovery postpenicillin, and the relative ease of discovery of suitable molecules through screening the products of soil microbes compared with libraries of synthetic compounds. many of these 'natural' antibiotics have desirable drug-like qualities, such as good bioavailability, the ability to cross the cell membrane (and outer membrane in the case of compounds with gram-negative activity) and the ability to evade efflux systems, and chemical structures that favor binding to vital cellular targets, supporting the idea that natural products encompass privileged structures in antibiotic drug discovery. however, the increasing difficulty of identi fying new chemical compounds with equally suitable drug-like characteristics from natural sources has caused natural-product-based screening programs to fall out of favor in many pharmaceutical firms over the past few decades. instead, the ability of parallel synthesis methods to generate hundreds of thousands of synthetic molecules suitable for modern high-throughput screening has shifted the focus in favor of synthetic molecules in commercial antibacterial drug discovery. the advantages of synthetic compounds are not insignificant: pure lead molecules can easily be produced in quantity and quality suitable for clinical trials, and are relatively easily modified to improve target affinity. however, after two to three decades of emphasis on such molecules and millions of dollars spent on high-throughput in vitro and cell-based screens, no new synthetic antibiotics have emerged. linezolid, the one synthetic antibiotic to be brought to market in the past decade, was discovered using traditional medicinal chemistry in a research program with a plant-disease focus in the early s. they do have great advantages, although a direct comparison of the success and failure of synthetic as against natural product libraries is unfair. microbial natural products have evolved over millennia to interact with biological molecules, whereas the synthetic chemical libraries used in antibiotic drug-discovery screens were generally developed with a focus on eukaryotic drug-discovery campaigns, as noted earlier. efforts to develop physical-property rules for antibiotics and to incorporate natural-product-like chemical complexity in libraries of synthetic chemicals will no doubt improve success in identifying new synthetic antibiotic leads. ironically, at the same time that the pharmaceutical industry was abandoning natural-product libraries, university researchers were making remarkable advances in understanding the molecular details of natural-product biosynthesis by bacteria. many bacteria, especially the actinomycete group of common environmental bacteria, are prodigious producers of natural products. these are termed secondary metabolites to contrast with molecules of primary metabolism, such as carbohydrates, amino acids and so on. secondary metabolites range in molecular weight from around daltons (da) to up to , da and they have diverse biological activities, including induction of cell death (antibiotics such as tetracycline, vancomycin and daptomycin, and anticancer agents such as adriamycin), iron sequestration (for example, enterobactin), facilitation of cell-cell communication (γ-butyrolactones), protection from oxidizing agents (phenazines), and a host of others. the bacterial natural products that are most important as antibiotics include polyketides, such as the macrolides and tetracyclines, and non-ribosomal peptides -that is, peptides that are not synthesized on ribosomes -which include β-lactams and glycopeptides such as vancomycin. these are produced in the cell in assembly-line fashion on large dedicated enzyme platforms called, respectively, polyketide synthases and non-ribosomal peptide synthetases. following assembly the compounds are then 'decorated' by a series of modifying enzymes, such as glycosyltransferases. the end result is a molecule of often complex structure, with multiple chiral centers and functional groups such as sugars, halogens, sulfates, acyl groups and others. in general, bacterial genes that encode the production of natural products are clustered together in the genome, greatly facilitating analysis and prediction of biosynthetic pathways and structures. indeed, several software packages (for example, np.searcher) have been developed based on rules-based understanding of natural-product biosynthesis. the availability of cheap, rapid genome sequen cing means that time-consuming construction and screening of gene libraries for natural-product clusters can now be bypassed. genome sequencing has also revealed a hitherto unrealized richness in the quantity and variability of natural-product biosynthetic clusters. sequenced genomes of bacteria of the actinomycetes class reveal to biosynthetic clusters in each organism. furthermore, natural-product producing bacteria from non-soil environments are being investigated and these have already resulted in new chemical matter, suggesting that there is a fantastic wealth of untapped chemical diversity waiting to be discovered. perhaps some of this diversity will include new antibiotic chemical scaffolds. we are in a remarkably productive time for naturalproduct research that is serving to reinvigorate interest in this sector. at the same time, the application of synthetic biology approaches to this field could serve to improve issues of yield and expand chemical diversity. yes. first, existing discarded antibiotics can be reexamined. the development of daptomycin is instructive. daptomycin was discovered by the antibiotic group at eli lilly in the s, but was not fully developed because of toxicity concerns. the antibiotic was obtained by researchers at cubist in and by altering the dosing, this group was able to bring the antibiotic to market in , since when it has proved highly successful in treating infections caused by gram-positive pathogens. certainly, there are other 'old' antibiotics discovered by the pharmaceutical industry but not developed at the time that could be resurrected as leads for new drugs. a second option is the combination of antibiotics with each other and with other drugs to improve efficacy. infectious-disease physicians often combine antibiotics in an effort to achieve synergy, and this well-established practice has resulted in formulated drug combinations, such as co-trimoxazole (trimethoprim and sulfa methoxazole). combination of antibiotics with non-antibiotics deserves investigation as well. several natural products have been discovered by satoshi omura's group that potentiate the activities of antibiotics such as imipenem in s. aureus by unknown mechanisms. other antibiotic adjuvants are inhibitors of resistance mechanisms. the tremendous commercial and clinical success of augmentin (ampicillin together with the βlactamase inhibitor clavulanic acid) and other similar combinations speaks to the power of such combinations. our growing understanding of the mechanisms of resistance should fuel such approaches. inhibitors of efflux pumps, for example, have been discovered, and though challenging to implement in organisms with multiple redundant systems, are worthy of continued investigation. finally, other strategies orthogonal to antibiotics must be on the table. we should never forget vaccines as proven and outstanding protective agents against infectious diseases. bacterial viruses (bacteriophages) were used extensively to treat bacterial infections in the former soviet union and could find new application in the face of outbreaks of multi-drug resistant bacteria, especially in settings such as hospital infections. the use of enhancers of innate immunity, such as cationic antimicrobial peptides, is also an approach worth investigating. we need antibiotics to maintain our current standard of health care. as already stated, resistance is a natural evolutionary phenomenon that cannot be stopped. through judicious use of current drugs and the development of new ones, the pace of resistance development can be controlled without impairing our ability to control disease. the need for new drugs is, however, acute. antimicrobial stewardship alone cannot fulfill our requirement for new antibiotics. we are in a remarkably exciting time for fundamental research in antibiotics. the rapidity of genome sequencing, the maturing of our knowledge of natural product biosynthesis, a growing understanding of the physical properties of ideal antibiotics, the development of new strategies to develop synthetic compounds with improved antibiotic properties, and the possibilities of synthetic biology combine to suggest that we are entering a highly productive period of antibiotic discovery. the challenges of moving these advances into the clinic fast enough to keep pace with resistance are significant, but with concerted effort between scientists, funders, industry, regulators and clinicians, i believe they can be overcome. where can i go for more information? antibiotic-resistant bugs in the st century -a clinical super-challenge ecology and evolution of antibiotic resistance bad bugs, no drugs: no eskape! an update from the infectious diseases society of america developing a new resource for drug discovery: marine actinomycete bacteria antibiotics for emerging pathogens emergence of a new antibiotic resistance mechanism in india, pakistan, and the uk: a molecular, biological, and epidemiological study has the era of untreatable infections arived? beta-lactams and beta-lactamase-inhibitors in current-or potential-clinical practice: a comprehensive update the antibiotic resistome: the nexus of chemical and genetic diversity xanthoradones, new potentiators of imipenem activity against methicillin-resistant staphylococcus aureus, produced by penicillium radicum fki- - : i. taxonomy, fermentation, isolation and biological properties research in the author's lab on antibiotic resistance is supported by a canada research chair, the canadian institutes of health research and the natural sciences and engineering research council. key: cord- -dd gw t authors: armbruster, walter j.; roberts, tanya title: the political economy of us antibiotic use in animal feed date: - - journal: food safety economics doi: . / - - - - _ sha: doc_id: cord_uid: dd gw t this chapter examines the evidence for antibiotic resistance in the united states and globally, the public health implications, and the impact of—and related industry and political responses to—antibiotic use in animal feed. in , the swann report in the united kingdom noted a dramatic increase in antibiotic-resistant bacteria in food animals receiving low levels of antibiotics in their feed. while the food and drug administration of the united states sought to control antibiotics in animal feed as far back as , only in were such regulations fully implemented. the farm-level costs of such controls are estimated by the us department of agriculture’s economic research service to be minimal, while the centers for disease control and prevention’s estimates of the public health costs of antibiotic resistance without implementing controls are $ billion annually. the complex interactions which exist between economic interests, regulatory policy, and human and animal health are explored in this chapter. antibiotic resistance has been widely recognized as a serious public health problem. hence, there is a major public good to be realized in safeguarding the effectiveness of existing antibiotics and creating new ones. antibiotics are used to treat human infections and used in animal agriculture. while many drugs are dual-use, others are animal-or human-use specific. the production benefits of sub-therapeutic levels of antibiotics in animal agriculture have been recognized since the late s (cast ) . in animal agricultural production, antibiotics are used at therapeutic levels to treat infections and at sub-therapeutic levels to prevent infections and promote animal growth (sneeringer et al. ; van boeckel et al. ; who ) . as the organizational complexity of the animal agricultural supply chain increased, the number of economic stakeholders in on-farm antibiotic use has also increased. the major stakeholders include pharmaceutical companies, production integrators, feed suppliers, farm groups, producers, restaurants, food retailers, the public, the medical community, the scientific community, government regulators and policy makers. each of these stakeholders faces a different set of incentives and disincentives related to on-farm use of antibiotics in animal agriculture. knowledge of these incentives and disincentives has evolved with the accumulation of scientific and economic research. to understand the regulatory outcomes governing antibiotic use in agriculture, it is important to recognize the political economy context in which they are developed. the various stakeholders are driven by the relative benefits they receive under policies as they affect their industry segment (zilberman et al. ). alexander fleming, who discovered penicillin, warned that "…misuse of the drug could result in selection for resistant bacteria" (rosenblatt-farrell ) . antibiotic resistance (ar), a term sometimes used interchangeably with antimicrobial resistance, occurs when bacteria change in ways that make antibiotics less effective in treating infections, thereby allowing the bacteria to survive, multiply, and cause additional harm. ar has been recognized as a serious public health problem among the medical and scientific communities. antibiotics are used to treat human infections and used in animal agriculture. particularly concerning is resistance for those antibiotics that are of value in treating human health issues, the so-called medically important antibiotics. the use of antibiotics along with other advances in agricultural technology has facilitated the concentration of animal production on farms in the united states (us) and elsewhere. for example, in , % of all us sales of hogs and pigs were by the % of farms with , or more head, and % of all layers were produced on the less than % of farms that sold , or more to egg producers (nass ) . the majority of the production of hogs, broilers, and eggs occurred under contractual arrangements between growers and integrators, with the integrators prescribing certain production practices, including the use of antibiotics for treating infections, for disease prevention and for promoting growth. many of the antimicrobial drugs administered to food-producing animals are also important in treating humans, worldwide. domestic sales of medically important antimicrobial drugs for use in food-producing animals in the united states accounted for % of the domestic sales of all antimicrobials approved for use in food-producing animals. and, % of domestic sales of all medically important antimicrobials approved for use in food-producing animals are labeled for therapeutic use only . importantly, animal drug sales data represent products sold or distributed by manufacturers through various outlets for intended sale to the user. since veterinarians and others in the supply chain may have substantial inventory on hand for possible use, these numbers do not accurately reflect the amount of product ultimately administered to animals. given the number of humans versus a much larger number of animals in each of the species, as well as other confounding factors, no definitive conclusions from any direct comparisons between the quantities of antimicrobial drugs sold for use in humans versus animals can be drawn (fda a) . there are obvious situations where antibiotics are required to treat sick animals in agriculture, but the proper therapeutic use versus prophylactic use remains in question among stakeholders. farm groups and others in the food animal supply chain recognize that antibiotics in animal feed keep animals healthy and meat costs down. but over medical doctors and other healthcare providers signed petitions to congress asking for new legislation to reduce non-therapeutic antibiotic use in food animals (miller ) . the animal health industry is very concerned that needed preventative use will be threatened by the recent fda ban on use of medically important antibiotics for growth. fda classifies as therapeutic those antimicrobials targeted for treatment, control, and prevention of bacteria or disease identified on the product label. fda explicitly states that the use of antibiotics in animal feed for growth promotion is not allowed. those who characterize preventative use as routine overlook the difference between treating animals versus humans. if preventative measures are not taken and a disease outbreak occurs and spreads rapidly within a flock or herd, it risks large numbers of animals developing a deadly, high mortality disease. waiting until a disease is clearly evident makes successfully treating the active infections very difficult due to the large number of animals involved. by contrast, a human patient can generally be quickly diagnosed and treated. while some are concerned that producers will continue to use antibiotics for growth under the guise of prevention, the fda-approved label is specific about dose and duration for a specified bacterium or disease. off-label use of antibiotics in animal production is illegal, and fda only allows a veterinarian to decide whether to use or not to use a preventative treatment based on their judgment of a disease threat (carnevale ) . in an economic framework, antimicrobial resistance can be considered as an unwanted side effect, or externality, associated with the use of antibiotics. the efficacy of antibiotics can be considered as a public good that must be managed with government involvement. this is because the costs of overuse by any single individual are borne by society and, in the case of antibiotics, globally. hence, not only is there a role for government involvement with the animal agriculture industry in managing the stock and use of antibiotics as an important public good, but it must be done cooperatively across countries. in , the united kingdom's (uk) parliament received the swann report, which concluded that using antimicrobials at sub-therapeutic levels in food-producing animals created risks to human and animal health (joint committee on the use of antibiotics in animal husbandry and veterinary medicine ). it noted a dramatic increase in numbers of animal-origin bacteria strains which showed resistance to one or more antibiotics and that these strains could transmit resistance to other bacteria. it recommended that only antimicrobials that are not medically important for humans should be used without prescription in animal feed and that antimicrobials should only be used for therapeutic purposes under veterinary supervision. the primary reason that producers were using these sub-therapeutic doses of antibiotics was to promote faster weight gain in the animals. in , a us food and drug administration (fda) task force was charged to do a comprehensive review of antibiotic use in animal feed (fda ). its report found that sub-therapeutic use of antimicrobials in food-producing animals was associated with development of resistant bacteria and that treated animals might provide a reservoir of antimicrobial-resistant pathogens capable of causing human disease. the task force recommended that medically important antimicrobial drugs meet certain guidelines they identified or be prohibited from growth promotion or other sub-therapeutic use by certain dates. further, antimicrobials not meeting the guidelines should be limited to short-term therapeutic use only under veterinarian control. in the s, the animal health institute (ahi), a us trade association for the animal drug industry, funded an on-farm study to determine the impact of adding low-dose antibiotics to chicken feed. within week of adding tetracycline, the intestinal flora in the chickens "…contained almost entirely tetracycline-resistant organisms" (levy et al. ). the antibiotic resistance was not located in the dna of the bacteria which is hard to transfer among bacteria but in plasmids located on the outside surface of the bacteria. plasmids are easily exchanged among bacteria living in the intestine. importantly, the tetracycline-resistant bacteria in the chicken's intestines were resistant to multiple antibiotics. furthermore, some members of the farm families began to harbor these same antibiotic-resistant bacteria in their intestines within months. in , the fda proposed withdrawing the new animal drug approvals for the sub-therapeutic uses of human medically important penicillin and tetracycline in animal feed based on lack of evidence to show they were safe. however, the us congress intervened and asked for more research first. the ahi was one of the groups advocating in congress to delay regulation pending additional research, then and now. in congressional testimony, richard carnevale, vice-president at ahi, testified that while it is possible for human antibiotic resistance to be caused by antibiotic use in farm animals, "…it does not happen enough that we can find it and measure it" (carnevale ) . this statement contradicted the data produced by the ahi-funded study by levy (levy et al. ) that was published in the prestigious new england journal of medicine in . richard carnevale also mentioned in his testimony that prior to joining ahi he was deputy director of new animal drug evaluation in fda and had worked at usda in the food safety and inspection service (fsis). his testimony illustrates two points in the political economy of food production: ( ) how industry has an opportunity to influence regulators' decision-making via the revolving door of employment and ( ) how industry carefully selects its facts to present a point of view that bolsters their profits, namely, for drug companies in this case (oreskes and conway ) . another example of the political economy in action involved usda prohibiting an agency research microbiologist from talking about the significant levels of antibiotic-resistant bacteria detected in the air near midwest hog confinement operations (union of concerned scientists ). a third element of the political economy is shown by industry efforts to influence policy makers through campaign contributions and strong lobbying of proposed legislation which may affect their bottom line. pharmaceutical companies spent at least $ million and agribusiness companies another $ million during , in large part to fight possible limits on antibiotic use in animal feed (mason and mendoza ) . in response to congressional pressure in the late s, fda withdrew its proposal and instead funded three studies to determine the impact of using low levels of antibiotics in animal feed (industry won this round, obtained a delay in regulations, and funded more reports): . in , the national academy of sciences reported that there was limited epidemiological research on the topic. available evidence at that time did not prove nor disprove dangers of seven therapeutic antimicrobials in animal feed, but that did not preclude the existence of hazards (national academy of sciences ). . in , the fda funded the seattle-king county department of public health to analyze salmonella and campylobacter, which were chosen as models to estimate the flow of potentially pathogenic bacteria from animals to humans through the food chain. their report was based on sampling retail meat and poultry and investigating salmonella and campylobacter enteritis cases in humans. isolates from human illness cases and retail foods were analyzed for antibiotic resistance of these pathogens, using plasmid analysis and serotyping. the report found that campylobacter was a more common cause of enteritis than salmonella and appeared to flow from chickens to humans through consumption of poultry products, with tetracycline resistance being plasmid-mediated (seattle-king county department of public health ). . in , the institute of medicine (iom) undertook a fda-requested independent quantitative risk assessment of human health impacts from sub-therapeutic use of penicillin and tetracycline in animal feed. based on a risk-analysis model of salmonella infections that resulted in human death, the iom did not find substantial direct evidence that sub-therapeutic use in animal feed posed a human health hazard. however, they found a considerable body of indirect evidence implicating both sub-therapeutic and therapeutic use of antimicrobials as a potential health hazard and strongly recommended additional study of the issue (institute of medicine ). numerous research results quantifying the extent of the antimicrobial resistance problem have been published in the scientific literature and indicate a growing and serious threat to human health. the many channels for ar to affect humans are shown in fig. . . the two main channels for food animals are ( ) ar bacteria in the food animal's gut can contaminate the meat or poultry eaten and ( ) environmental contamination, such as manure used to fertilize fields that contain ar bacteria, may contaminate the environment and some of the food crops grown on these fields. consumer reports (cr) tested products sold in us supermarkets and found resistance to multiple antibiotics in the following percent of samples: beef %, shrimp %, turkey %, and chicken % (consumer reports ). cr also found that ground beef from conventionally raised cows was twice as likely to contain antibiotic-resistant pathogens as ground beef from cows raised without antibiotics. like other threats to human health, ar is best managed across national boundaries. increasing international trade may spread antibiotic resistance through imported food products as more trade agreements are approved. this scenario could be exacerbated to the extent fsis approves additional international facilities, local regulations, and inspections as "equivalent to the united states." future trade agreements will need to include provisions which address reduced use of medically important antibiotics in producing food animals. numerous trusted institutions from the united states (us) and the united kingdom (uk) as well as international organizations such as the world health organization (who), the united nations' food and agriculture organization (fao), and the world organization for animal health (oie) have acknowledged the threat of antibiotic resistance related to use in producing food animals. the fol- lowing excerpts from a few recent reports highlight the role that low-dose antibiotic use in animal feed plays in spreading ar. the centers for disease control and prevention ( b) reported that: each year in the united states, at least million people acquire serious infections with bacteria that are resistant to one or more of the antibiotics designed to treat those infections. at least , people die each year as a direct result of these antibiotic-resistant infections. many more die from other conditions that are complicated by an antibiotic-resistant infection. antibiotic-resistant infections add considerable and avoidable costs to the already overburdened u.s. healthcare system. in most cases, antibiotic resistant infections require prolonged and/or costlier treatments, extend hospital stays, necessitate additional doctor visits and healthcare use, and result in greater disability and death compared with infections that are easily treatable with antibiotics. the total economic costs of antibiotic resistance to the u.s. economy has been difficult to calculate. estimates vary but have ranged as high as $ billion in excess direct healthcare costs. adding on the costs for lost productivity brings the total societal costs (sic) for ar to $ billion a year ( dollars). (cdc a, p. ) this cdc report also indicates that foodborne cases are responsible for % of human ar infections ( fig. . ). thus, societal costs of these ar foodborne illnesses could total $ billion annually of the $ billion/year total costs to the us economy. these societal costs could be prevented if the foods were free of contamination with ar pathogens. there may be additional costs associated with environmental pathways of human contamination from use of antibiotics in meat production, such as exposure to contaminated water. in , who stated: "antimicrobial resistance (ar) is an increasingly serious threat to global public health. ar develops when a microorganism (bacteria, fungus, virus or parasite) no longer responds to a drug to which it was originally sensitive. this means that standard treatments no longer work; infections are harder or impossible to control; the risk of the spread of infection to others is increased; illness and hospital stays are prolonged, with added economic and social costs; and the risk of death is greater-in some cases, twice that of patients who have infections caused by non-resistant bacteria. the problem is so serious that it threatens the achievements of modern medicine. a post-antibiotic era-in which common infections and minor injuries can kill-is a very real possibility for the st century" (who , p. ) . in , oie noted: "today, in many countries, including developed countries, antimicrobial agents are widely available, directly or indirectly, practically without restriction. of countries recently evaluated by the oie, more than do not yet have relevant legislation on the appropriate conditions for the import, manufacture, distribution and use of veterinary products, including antimicrobial agents. consequently, these products circulate uncontrolled like ordinary goods and are often falsified." to date, there is no harmonized system of surveillance on the worldwide use and circulation of antimicrobial agents. that information is necessary, however, to monitor and control the origin of medicines, obtain reliable data on imports, trace their circulation, and evaluate the quality of the products in circulation. it is in this context that the oie was mandated by its member countries to gather that missing information and create a global database for monitoring the use of antimicrobial agents, linked to the oie's world animal health information system (wahis). that mandate is also supported by fao and the who within the framework of the who's global action plan on antimicrobial resistance. the database will form a solid basis for the three organizations' work to combat antimicrobial resistance (oie , p. ) . in , a uk evaluation of academic, peer-reviewed research articles addressing antibiotic use in agriculture determined that only % found no link and % found a positive link between antibiotic use in animals and antibiotic resistance (ar) in humans (o'neill ) . taken to evaluate proposals to ban the use of growth-promoting or sub-therapeutic levels of antibiotics in food animals, usda's economic research service (ers) economists added questions on antibiotic use to the agricultural and resource management survey (arms). arms is a nationally representative survey of farms administered jointly by ers and usda's national agricultural statistics service (nass). hog producers were surveyed in and , and broiler producers were surveyed in and . ers also drew upon their research using data in the national animal health monitoring system (nahms) to develop a model to estimate the impacts of withdrawing antibiotics for other than therapeutic use in food animals. using monte carlo simulations, ers estimated the impacts of eliminating antibiotic use for growth promotion of poultry and pork, not just the fda-specified "medically important" antibiotics (table . ). simulation results showed less than . % reduction in output and an approximate . % increase in wholesale prices, netting pork producers greater total revenue of . % and poultry producers . %. ers concluded that these small effects were not statistically significant (sneeringer et al. ) . these ers results are consistent with research studies post- indicating that productivity gains from using antibiotics for growth promotion were lower than earlier research had found (teillant and laxminarayan ) . another report suggested that phase out of growth promotion use in food animals over a -year period would avoid most of the % projected global growth in such use and cost agricultural sectors a small portion of the costs of ar in each country. further, reduced infection risk and costs of medications would cover most farm-level costs of improving animal husbandry practices to offset loss of antimicrobials for production purposes (laxminarayan and chaudhury ) . presuming that any new antibiotic classes probably will not be made available for veterinary medicine, it is important to preserve the effectiveness of existing antibiotics which are necessary for treatment of infectious diseases to maintain animal health (teillant and laxminarayan ) . an alternative to encourage development of new antibiotics would be to delay or not approve drugs which mimic others, but for which the applicant company has not performed antibiotic research (amábile-cuevas ). even better, several production practices may be used to enhance animal health in the absence of using antimicrobials for growth or for prophylactic disease prevention (sneeringer et al. ; who ; macdonald and wang ) . these include: • improved management practices, such as more space per animal and better control of the housing environment • tightened biosecurity to prevent diseases and improve productivity by avoiding introduction of infectious agents by wild animals, domestic pets, and nonessential workers or other humans; through increased cleanliness of production facilities; and from timely removal of dead animals • optimized nutrition to increase growth and mitigate stress-related factors and provide vitamin and mineral supplements to reduce disease susceptibility • improved gut microflora to improve feed efficiency by providing enzymes, organic acids, prebiotics, probiotics, and immune modulators • vaccinations to prevent some diseases • hazard analysis critical control point plans to improve productivity in the absence of using sub-therapeutic antibiotics in animal production generally, these practices may raise production costs modestly at the farm level because of the need for more resources required to successfully manage them. since ers found no statistically significant evidence that antibiotics reduce the costs of producing pork or broilers, we conclude that there are small or no costs to producers from withdrawing growth-promoting or prophylactic uses of antibiotics in production of food animals. in contrast, the public health benefits of withdrawing these antibiotics from agriculture are significant. as reported above, cdc estimates that the medical costs and productivity losses of ar illnesses attributed to agriculture are $ billion us dollars annually. the benefit/cost analysis becomes $ billion in public health protection benefits vs. the very small costs to animal production from withdrawing antibiotics from non-therapeutic use. in other words, the protection of the public health will come at little or no cost to agriculture. furthermore, this benefit/cost analysis provides a conservative estimate of public health protection benefits. the cdc public health protection benefits do not include estimates for protection from an increasing number of "superbugs" that would be created if low-level antibiotics would continue to be used. and cdc does not include the costs of long-term health outcomes caused by foodborne pathogens (see chap. ). aside from costs to agricultural producers, there are also other societal costs related to ar and connected to antimicrobial use in animal production, both in their production and use/misuse, affecting human and environmental health. in economic terminology, these costs are considered negative externalities to society from the individual use of antibiotics. moreover, since the science of ar is unfolding, there may be additional unknown human health and environmental risks associated with the use of antibiotics in food animal production. pharmaceutical production. a major issue involved with manufacturing of active ingredients for antibiotics and the effluent from factories producing them is the potential to contaminate nearby water systems. pharmaceutical factories often contaminate the environment, since guidelines for pharmaceutical waste discharge focus on chemicals used in manufacturing, rather than active pharmaceutical ingredients. this is a primary concern in countries outside the united states, but international trade makes it a worldwide problem. use and misuse. worldwide, antibiotics are used heavily in animal agriculture. this practice has created resistance problems transmissible from animals to humans. for example, china has mrc- colicin resistance in pork and salmonella resistance to cephalosporins at higher levels than in the united states (zhang et al. ) . their practice of applying human waste on fields and the closeness of population centers to agriculture contribute to cross-mixing of pathogens in china. parasites are common in chinese soil and can contaminate pork. and low levels of chlorine in chinese water supplies allow accumulation of biofilms containing antibiotic-resistant pathogens in water pipes. in india, manufacturing of pharmaceuticals and waste disposal practices lead to contamination of water and soil. further, over-the-counter antibiotics are available and heavily used there. farm antibiotic use is of concern in india and china in poultry and pigs (apua newsletter ). the threat of superbugs via food is worldwide, due to the distribution of animal food products from china (zhang et al. ; zhu et al. ) . rosenblatt-farrell ( ) drew upon existing literature to identify additional environmental paths to exposure to antibiotic resistance. veterinary antibiotics are frequently excreted intact from food animals (table . ). for the widely used tetracycline, - % of the antibiotic is excreted in the feces or urine and not metabolized by the food animal. the transfer of this animal waste to croplands may transfer antibiotics and possibly ar pathogens. in one study, ar genes in soil increased fourfold after manure from hog and dairy farms was applied to the soil (moyer ) . runoff from farms, feedlots, or cropland can lead to antimicrobial resistance problems in soil, surface water runoff, and groundwater. animal waste held in lagoons allows birds and insects to become contaminated with antibioticresistant bacteria, and flies around food animal facilities can carry antibioticresistant enteric bacteria which increases potential human exposure. migratory birds and seagulls which become infected with antibiotic-resistant bacteria or viruses can widely transmit resistance to other birds as well as marine life. others note that antibiotics should never be used to compensate for poor hygiene and husbandry practices or conditions in livestock production (van boeckel et al. ) . veterinary medicine should only use antibiotics to treat diagnostically determined bacterial infections not otherwise treatable and only those antibiotics authorized for the diagnosed pathogenic indication and the specific bacteria involved. further, given the potential for acute diseases that require immediate treatment, it is important that routine testing (surveillance) be carried out for farm-specific pathogens for all relevant antibiotic classes (silley and stephan ) . who also emphasizes the need for surveillance and monitoring antimicrobial use in food-producing animals to evaluate the extent to which their guidelines are implemented. fda has increased regulation of antibiotic use in food animals. as noted in sect. . above, fda attempted to withdraw new animal drug approvals for subtherapeutic uses of human medically important penicillins and tetracyclines in animal feed based on lack of evidence to show they were safe. after industry opposition and congressional intervention to require further study, this early policy response was withdrawn. subsequently, the us congress gave something to each group when it enacted the animal drug availability act (adaa) in . this act both table . , fda in recent years issued three core documents to implement a policy framework for judicious use of medically important antimicrobial drugs in food animals: on january , , fda announced that it had completed implementation of the guidance for industry # . this means that medically important antimicrobials provided to food-producing animals may no longer be used for growth promotion purposes and may be used to treat, prevent, or control animal illnesses only under direction of a veterinarian. fda worked with industry participants to implement this voluntary compliance to slow development of antimicrobial resistance and preserve effectiveness of medically important antibiotics. more than percent of new drug applications subject to gfi # were converted from over-the-counter to prescription status, applications were withdrawn, and all applications indicating production use withdrew that specified use. fda also indicated plans to work with industry stakeholders to support antimicrobial stewardship in food animal production and to evaluate the effectiveness of strategies to reduce antimicrobial resistance development under the allowed uses (fda ). some industry stakeholders in the supply chain are actively engaged in responding to consumer and general public health concerns about ar in the food supply chain amidst mounting scientific evidence, but responses vary considerably by country, place in the supply chain, and individual company. aside from farm groups, stakeholders include feed companies, pharmaceutical companies, integrators or meat processors, restaurant chains and other retail outlets, and consumer and other interest groups. pharmaceutical companies. in the case of pharmaceutical companies, little evidence exists that they are responding to the ar problem yet. as described earlier, most antibiotics are produced in india and china, and their production has resulted in significant risk, especially environmental risk. regulators need to set minimum standards for the treatment of manufacturing waste before it is released into the environment. other industries which purchase these pharmaceuticals need to establish higher standards through their supply chains to help correct this environmental pollution (o'neill ). furthermore, the drug companies are not required to compensate victims who become ill or die from either the environmental or food exposure. the drug companies and their trade associations have resisted more regulation to prevent misuse of antibiotics. the companies therefore have been getting a "free ride" at the expense of the ill consumers and the general public. integrators and meat processors. some chains and food retailers have recently responded to customer concerns by restricting the use of antibiotics in their food supply chains. large meat processors committing to judicious use of antibiotics have already led many producers to eliminate the use of antibiotics for production enhancement purposes. in a case study of voluntary labeling in the broiler industry, "raised without antibiotics" (rwa) label claims by tyson foods and by perdue farms in , respectively, numbers one and three in total broiler production, resulted in mixed outcomes. at that time, usda fsis had not published a standard for such claims, nor was a clear definition established. perdue and tyson developed their own standards and submitted the label claims to fsis for approval along with supporting documentation. after initially approving both firms' label claims, fsis determined in september that tyson's claim was false and misleading and gave them the opportunity to submit a revised label claim. however, tyson continued their advertising of the rwa claims. the diverse label claims in which tyson and their competitors were using different standards for their claim resulted in consumer confusion, and eventually court challenges were filed jointly by sanderson farms, the fourth largest producer, and perdue against tyson. the suit was upheld in court in april . tyson was found not to have delivered the rwa attribute promised to the marketplace and to thereby have harmed competitors, while tyson profited from introducing a false and misleading claim. in june , fsis rescinded tyson's qualified rwa label claim and required its removal within weeks, after the claims and advertising had continued for more than a year. the authors found no evidence that the events had any impact on tyson's brand, suggesting that companies may have incentives to introduce misleading label claims since the size of penalties is uncertain (bowman et al. ) . perdue farms inc. was the only major chicken producer to eliminate all medically important and animal-specific antibiotics from use in its chicken production as of . by replacing antibiotics with vaccines and improving its production facilities and practices, it has been able to produce chicken at virtually the same cost as when using antibiotics. perdue estimates that its conventional chicken sales are increasing by not more than % annually, while sales for product raised without antibiotics are growing - % annually (bunge ) . gnp company, a leading provider of premium natural chicken products, is adopting antibiotics-free production of chicken products. its gold'n plump brand will feature a "no antibiotics-ever" claim. this will go well beyond what many companies are currently focusing on-eliminating the use of medically important antibiotics, rather than all antibiotics. usda regulations allow this label claim only for chicken never having received antibiotics, even inside the egg. the company will continue to treat flocks for illness as necessary, but not market them under their premier gold'n plump brand. the company plans extensive media and in-store support to educate consumers about the transition to its chicken products raised totally without antibiotics (gnp company ). tyson foods, a leading producer of chicken, pork, and beef and products thereof, adopted a position to eliminate the use of human-use antibiotics in broiler production by september . they stopped the human antibiotic use in their hatcheries and reduced usage in producing broilers by % since . they also have worked with farmers and others in the beef, pork, and turkey supply chains to explore ways to reduce human antibiotic use at the farm level. tyson is employing alternative husbandry strategies such as use of probiotics and essential oils, improved housing, and selective breeding to offset the potential impact of eliminating the use of the antibiotics. they are also interacting with the food industry and other involved supply chain participants, as well as academics, to increase research on disease prevention and alternatives to replace antibiotics (tyson foods ). feed companies. the feed companies are also getting into the discussion to address public health concerns about antibiotic resistance and the relationship to livestock production uses of antibiotics. phibro animal health corporation recently launched a website animalantibiotics.org to "…provide accurate and credible information while still creating open dialogue about animal agriculture in the use of antibiotics." it will address all issues involving animal antibiotics and changes underway within the industry to promote responsible use of antibiotics in livestock (johansen ) . this is very consistent with the historical pattern of the animal agriculture industry making its case in the political economy in reaction to the strong push to limit use of antibiotics to help quell rising antibiotic resistance of medically important drugs. restaurant chains. an interesting example of restaurant chains and poultry producers working together is provided by panera bread co. and perdue farms inc. panera is one of the restaurant companies for which perdue supplies chickens raised without antibiotics. when panera pioneered antibiotic-free chicken in its restaurant products over years ago, they paid a % premium versus chicken produced using antibiotics. with improved production practices, the cost differential has virtually disappeared (bunge ) and is thus consistent with the ers estimates cited earlier. consumer and other interest groups. in the process of developing these new fda regulations, activist groups petitioned the federal courts. for example, in may , the natural resources defense council (nrdc), center for science in the public interest (cspi), food animal concerns trust (fact), public citizen, and union of concerned scientists (ucs) filed a case against the fda. they charged that fda failed to ban penicillins and tetracyclines used at low doses in animal feed for growth promotion, despite evidence fda put forth in that penicillin and most tetracyclines were not shown to be safe and may pose a risk to human health (apua ). in , the federal court ruled in favor of these petitioners. in a later ruling in , the federal court directed fda to reexamine its decision on five other classes of "medically important drugs" used as growth promoters addressed in two citizen petitions (filed in and ) to ensure the safety and effectiveness of all drugs sold in interstate commerce (ibid). given that most governments have neglected to acknowledge and address the problem of increasing antibiotic resistance, international organizations with a role in health issues have been stymied from doing so. it will take more concerted action by societies around the globe to successfully address this cross-border issue (amábile-cuevas ). us consumers, in general, have much less information about the product than does the seller (chaps. and ). this asymmetric information can offer opportunity for the selling firm behavior that is detrimental to the interests of the consumer, as when a product is labeled as containing or not containing certain desirable or undesirable attributes. in the case of many products known as credence goods, it is impossible to determine whether the attributes are as stated, even when the product is used or consumed. this market failure can be addressed either through government regulations or through voluntary steps by the sellers to assure that the stated attributes are factual. the latter could be accomplished through advertising to build and maintain the firm's brand and reputation, and competition with other sellers could result in consumers having increased variety of product choices. however, some consumers may not trust private companies' word about product attributes and prefer certification programs which monitor products against some standard established either by the private sector or by government agencies. lusk (lusk ) argues that voluntary labels are dynamically efficient in responding to changes in market conditions and encouraging innovation more than mandatory labels implemented through regulations, since the latter are more subject to manipulation by those with vested interests. further, usda's agricultural marketing service (ams) process-verified and certification programs are very effective in helping to assure the credibility of voluntary labeling, while accommodating innovation from the private sector. gnp's adoption of antibiotics-free production discussed in . is an example of dynamic market efficiency through use of voluntary labeling to innovate in response to changing consumer demand usda's food safety inspection service (fsis) currently employs an animal production claims protocol for evaluating and allowing or denying labeling claims. labeling applications must provide supporting documentation such as operational protocols detailing production practices and affidavits or testimonials about production practices. fsis then evaluates whether protocols support the accuracy of the proposed label. also, feed formulations must be provided and reviewed to ensure they do not include substances not permitted by the claim. commonly approved claims relevant to the use of antibiotics include "raised without added hormones" (only allowed for use in beef cattle and lamb production) and "raised without antibiotics." claims not allowed include that animal products are antibiotic-, hormone-, or residue-"free" (fsis ) . given the current trend among meat producers, restaurants, and retail livestock product marketers, it can be anticipated that there will be increasing attention to labeling the lack of antibiotic use for other than therapeutic purposes. this will likely result in animals that have been raised with antibiotics to promote growth and uniformity of size consistent with processor contract agreements being diverted to marketing outlets where such promises do not exist. the impact of labeling in this manner will vary according to how much consumers know about the use of antibiotics in livestock production and their ability to currently purchase antibiotic-free livestock products (lusk et al. ) . o'neill and his british colleagues emphasize improving transparency as a major step in addressing antimicrobial resistance related to the livestock production. recent attention by companies such as food retailers, wholesale producers, and fastfood chains, as well as investors, for reducing antibiotic use in their supply chains, has been in response to consumer pressure. providing greater transparency through voluntary approaches is helpful in the short term, but it may be necessary to mandate transparency requirements about how antibiotics are used in the supply chains to have longer-term impacts. labeling that refers to antibiotic use could improve consumer knowledge to allow them to make better informed decisions. they also argued that third-party validation of support from independent institutions to monitor progress may be beneficial (o'neill ). improved transparency by food producers about antibiotics used in producing meat could help consumers make better informed purchasing decisions. but there are large gaps in data needed to allow monitoring of types and quantities of antibiotics used in animal agriculture and their impacts (cfi ), as well as on emergence and spread of resistance in animals. the who also identified major gaps in surveillance and data sharing on emergence of antibiotic resistance in bacteria and its impact on animal and human health. who called for integrated surveillance systems harmonized across countries to enable better comparison of data from foodproducing animals, food products, and humans (who ). in the united states, fda requires drug companies to voluntarily submit data on drugs sold for use in food animals. the publicly available data are not detailed, and % of the sales of medically important antimicrobials are over-the-counter (otc). tetracyclines are primarily added to feed and accounted for % of domestic sales of animal drugs that are "medically important" to human medicine in (fda b) . from to , domestic sales and distribution of tetracycline products approved for use in food-producing animals increased by %. while levy et al. ( ) discovered how rapidly tetracycline created antibiotic resistance in the gut of chickens, years later, the public does not have access to information on what antibiotics are used in which food animals at what stage of life. this will change somewhat in fda implementation of gfi # (fda ) that will identify whether the sales are intended for use in cattle, sheep, hog, or poultry. fda ( b) issued a final rule amending an existing requirement that sponsors of drug products containing antimicrobial active ingredients report annually the amount of each such ingredient in the drug products sold or distributed for use in food-producing animals. effective july , , drug sponsors were required to submit species-specific estimates of product sales as a percent of their total sales. additional reporting requirements are expected to facilitate better understanding of antimicrobial drug sales for specific food-producing animal species and the relationship between such sales and antimicrobial resistance. as reported above, drug sponsors have all adopted voluntary revision of fda-approved labels for use of new medically important antimicrobial animal drugs administered through feed or water. under this rule, sponsors all voluntarily removed the growth promotion and feed efficiency uses and brought the remaining therapeutic uses under veterinarian oversight by the end of december . the rule makes it illegal to use medically important antibiotics for production purposes. despite the scientific and economic evidence, many comments to the proposed final regulation reflected ongoing resistance to the elimination of food animal production use of medically important antibiotics. data available on antibiotics used in the us livestock industry is derived primarily from two nationally representative surveys of farms conducted by the usda's economic research service (ers) and national agricultural statistics service (nass). the agricultural and resource management survey (arms) is designed to collect information on farm finances, production practices, and resource use focuses on three commodities annually, livestock included. different types of livestock are resurveyed every - years and represent commercial producers in states producing % of production for that livestock type. some questions have been included in these surveys on antibiotic use for hogs and broilers. the hog surveys ask about use of antibiotics in feed or water for growth promotion, disease preven-tion, and/or disease treatment in breeding, nursery, and finishing hogs. given the widespread use of hog production contracts under which farm operators may receive feed from integrators, the surveyed operators may not know if antibiotics are included in it. for broilers, there is only a single question about whether they were raised without antibiotics in feed or water other than for therapeutic treatment of illness. production contracts dominate the broiler industry, so surveyed farm operators are in a similar situation as hog producers in not necessarily knowing whether antibiotics are included in the feed provided. a further complication is that arms does not separate traditional antibiotics and ionophores, which are not used in human medicine (sneeringer et al. ) . the national animal health monitoring system (nahms) consists of national studies to provide essential information on livestock and poultry health and management. major food livestock species are surveyed about every years to provide current and trend information important to industry participants, researchers, and policy makers. each study includes states that represent at least % of the targeted animal population and at least % of the farm operations involved and provides statistically sound information for decision-making. a nahms study is a collaborative, voluntary, confidential, scientifically sound product. descriptive reports are prepared along with information sheets which briefly address very specific topics, such as biosecurity practices (aphis ). the nahms focuses on animal health and management, providing information on disease occurrence and disease prevention practices, as well as more detailed information on antibiotics used in production, including by specific purpose. however, the information collected on antibiotics varies greatly across commodities, as well as over time with the same commodities. further, arms focuses on hog production operations with or more head versus nahms focus on or more head. this complicates comparison of statistics across surveys, assuming smaller operations may have different characteristics than larger ones (sneeringer et al. ) . to track antimicrobial resistance changes over time, the national antimicrobial resistance monitoring system-enteric bacteria (narms) was established by cdc in . the program is a collaboration between state and local public health departments and three federal agencies to monitor changes in antimicrobial susceptibility for certain enteric bacteria from ill people (cdc), retail meats (fda), and food animals (usda) in the united states. it provides information about emergent bacterial resistance, the ways resistance is spread, and how resistant infections differ from susceptible ones (narms ). the world organization for animal health (oie) plans to address antimicrobial resistance as a major risk to the international community, in the face of concern about agriculture's role in increased antimicrobial resistance. the goal is to preserve effectiveness of antimicrobials used in animal medicine, protect animal welfare, and help maintain important antimicrobials for use in human medicine. oie has already developed international standards, most recently revised in . the new strategy introduced at the th oie general session in may outlines plans to help nations improve legal frameworks to preserve antibiotics, communicate about the ar problem, train animal health workers, and monitor antibiotic use in animals. they are currently working to create a database of information on the use of antimicrobial agents in animals and develop performance indicators to assist countries by increasing information flow and transparency in their use of antimicrobials. further, the oie expert network is working to reinforce scientific knowledge about new technologies and replacement solutions for current antimicrobials (mitchell ) . the eu has banned the use of antimicrobials in food animal production, other than by veterinarian prescription for specific therapeutic use. some other countries have adopted similar bans, and, as discussed above, the united states fully implemented voluntary guidelines in requiring current drug sponsors to withdraw antibiotics for growth promotion. however, the animal health institute's carnevale has said that the new fda guidance on antibiotics may not decrease the total quantities of antibiotics used in animal food production (moyer ) . generally, variations among countries in implementing regulations have resulted in the spread of resistance. there is ample evidence to support the need for global coordination to prevent continued spread of antimicrobial resistance, and elements of a framework to make such global coordination effective have been posited (so et al. ) . the uk review on antimicrobial resistance final report proposes three broad steps to deal with reducing unnecessary use of antibiotics in animals. first, establish -year targets for reduction in use, with milestones to support progress consistent with countries' economic development. this could encourage farmers to reduce non-therapeutic use to be able to allocate the resulting reduced amounts of antibiotics to treating sick animals. second, implement restrictions or bans on certain types of highly critical last-line antibiotics for humans from being used in agriculture. this would require a harmonized approach to identify the most important human health antimicrobials across countries and good systems of veterinarian oversight to assure compliance. third, improve transparency from food producers on antibiotic use in meat production to allow consumers to make better informed buying decisions. voluntary industry efforts may be one of the most practical approaches to reduce antibiotic use in the near term, but third-party validation to monitor progress would be beneficial (o'neill ) . generally, voluntary industry approaches require monitoring by an outside party to assure both industry participants and consumers that standards are being met as required. the uk medical research council (mrc) recently made three large grants focused on antimicrobial resistance through an initiative established in to address the growing ar issue. the projects will use new technology to exploit natural compounds, develop a better and faster diagnostics tool, and study how the body's immune system can be harnessed to better fight infections. the goal is not only to develop antibiotics but also explore alternatives to antibiotic use, working with other uk research councils to bring to bear a wide range of disciplines to tackle ar (mrc ). the need to focus increased attention to developing new antibiotics is supported by cdc data which shows that many of the most widely used drugs have developed resistance. the number of years to develop resistance varies greatly but never extends more than a couple of decades, and more recent antibiotic introductions have been resistant for only a year or two. for example, the widely used tetracycline was introduced in and developed resistance to shigella by . this is near the midrange of years to resistance reported (cdc a). given this scientific fact, the slow pace of adopting policies to proscribe use of human-use antibiotics in animals and to encourage greater investment in developing newer antibiotics or alternatives is unacceptable. increasing detection of bacteria resistant to last-resort drugs has driven stakeholders to countenance accelerating government efforts to increase surveillance of drug use and to develop new antibiotics (fda week ). promising approaches which provide more rapid assessment utilizing newer technologies such as genomics are now being utilized by scientists. microbiologists are embracing high-throughput genomics to quickly examine individual organisms or entire microbial communities. a project underway at the university of california, davis, the k foodborne pathogen genome sequencing project, will sequence , foodborne isolates for the most important worldwide foodborne illness outbreak organisms. it involves a consortium of academic, government, and industry to create a massive database of genome signatures for the most significant foodborne disease-causing microbes. the goal is to allow public health agencies and the food industry supply chain to trace any foodborne illness outbreaks to their source. by comparing the pathogen genome to the database which includes millions of pieces of information on previously detected strains, including their exact location, the contamination source will be positively identified. bioinformatics and the analytics involved can be used to turn the vast amount of genomic information into actionable knowledge. these event sequencing approaches will enable new diagnostic and public health approaches to manage foodborne disease to facilitate improved public health. the database will increase ability to detect and mitigate pathogenic organisms in food, the environment, and livestock. that capacity is now constrained by continual genetic evolution of pathogens which hinders the ability to defend the food supply. this project will facilitate speedy testing of raw ingredients and finished products from outbreak investigations with precision and accuracy unparalleled using existing methods of analysis. genomics enabled diagnostics with molecular tools will allow surveillance, risk assessment, and diagnosis of foodborne pathogens directly throughout the global food chain. the result will be a genetic catalog for some of the most important outbreak organisms impacting human health. the database will provide insights into molecular methods of infection and drug resistance for use in creating new vaccines and therapies. and importantly, it will assist in systematic definition of biomarker gene sets associated with antibiotic resistance (weimer ). a recent innovative metagenomics study also provides new insights on possible impacts of antibiotic use in food animal production and ar in humans. the research investigated antimicrobial resistance potential-the resistome-by tracking specific pens of intensively managed cattle from feedlot through slaughter to market-ready beef products. study results found no antibiotic-resistant determinants (ards) in the beef products beyond the slaughter facility. this suggests that intervention during slaughter minimizes potential for antibiotic-resistant determinants passing through the food chain. the results also highlight potential risks through indirect environmental exposures to the feedlot resistome through wastewater runoff, manure application on cropland, and wind-borne particulate matter. the insights provided can be used to better inform future agricultural and public health policy. however, this first of its kind study suggests the scientific community must develop a better understanding of the risk of different resistomes and resistance genes. it also identifies a pressing need to standardize ard nomenclature so that databases and analyses are comparable across studies (noyes et al. ) . the world health organization has recently developed guidelines to mitigate human health consequences from use of medically important antimicrobials in food-producing animals (who ). the guidelines are evidence-based recommendations and include best practices for use of medically important antimicrobials in food-producing animals, especially antimicrobials deemed critically important to human medicine. they also can help preserve effectiveness of antimicrobials for veterinary medicine. the recommendations include: • an overall reduction in use of all classes of medically important antimicrobials in food-producing animals. • complete restriction for use in growth promotion. • complete restriction of use to prevent infectious diseases that have not yet been clinically diagnosed. • antimicrobials designated as critically important for human medicine should not be used to control spread of clinically diagnosed infectious disease identified within a group of food-producing animals, nor for treatment of food-producing animals with a clinically diagnosed infectious disease. • for best practices, any new class of antimicrobials for use in humans will be considered critically important for human medicine unless otherwise categorized by who. further, medically important antimicrobials not currently used in food production should not be so used in the future. these guidelines apply universally, and improved animal health management can be used to reduce the need for antimicrobials including improvements in disease prevention strategies, housing, and husbandry practices as noted in sect . above. economic incentives in regulations were addressed in a recent article. in some european countries, capping total antimicrobial use per animal through regulations has been successful in reducing use by more than half while maintaining competitive livestock sectors. the second option was to impose user fees on veterinary antimicrobials, applied at the point of manufacture or wholesale purchases for imported products, which could also reduce use significantly. as a policy option, some combination of these two strategies would significantly reduce antimicrobial use in food animal production (van boeckel et al. ) . finally, as discussed in chap. , sweden does not allow use of antibiotics in broiler production. if there is the political will, strong regulations can provide strong economic incentives to control antibiotic use. to promote the understanding and implementation of the fda's new veterinary feed directive, the farm foundation and the pew charitable trusts sponsored a series of meetings with livestock and farming communities throughout the united states. twelve educational workshops provided livestock producers, feed suppliers, veterinarians, and support service organizations information and insights on the new policies. the workshops also provided opportunity for participants to interact with fda and usda's animal and plant health inspection service (aphis) personnel about implementation challenges. among livestock producers attending the workshops, small-and medium-sized operators, as well as many veterinarians, were unaware of the pending requirements. lack of understanding about responsibilities under the revised vfd rule means that producers and veterinarians need education. some land grant university extension services are now offering balanced education programs to inform these audiences about their obligations going forward, rather than having interested parties in the food animal industry be the primary source of information to producers and veterinarians about the requirements. while seeing positives of improved public perception and livestock management as result of the new rules, workshop participants were concerned about increased costs in animal health due to restrictions on access to antibiotics and lack of veterinary services. perhaps the biggest challenge is that many small producers do not have established relationships with veterinarians needed to establish a veterinarianclient-patient relationship (vcpr). this may be particularly challenging in remote rural and urban fringe areas where fewer veterinarians are available to treat foodproducing animals. in sum, workshop participants saw a need for education and outreach; continuing dialogue between industry representatives, consumers, and state or federal regulators; and the need to provide better access to veterinary services for food animals. there is widespread agreement that the scientific evidence indicates a global human health and environmental crisis due to antibiotic resistance, in part resulting from production practices in animal agriculture. government action in regulating the animal agriculture industry, to date, has done little to slow the advance of ar. most countries still need to pass legislation to establish appropriate conditions for the import, manufacture, distribution, and use of veterinary products, including antimicrobial agents. continued easy access to antimicrobial drugs for use on the farm is not acceptable. important stakeholders in the animal production industry include pharmaceutical companies, feed companies, livestock production integrators, and some farm groups, each with their own set of incentives and supporters. they must be engaged in the effort to reduce agriculture's role in contributing to development of ar, which cdc estimates at % (fig. . ) . even so, other major industry groups must be engaged to significantly reduce their % contribution to resistance development. in the united states, some progress was made with the passage of the animal drug availability act in and its very gradual implementation through various regulations over the past two decades. however, there are serious gaps in these regulations. given the gridlock that has prevailed in the us congress and the power of the pharmaceutical lobby at the national level, state actions are leading the way to responsive regulation in the public interest. for example, california is the first us state to prohibit all human antibiotic use in food animal production. in contrast to the halting actions of governments and industry, consumer and interest group actions are being at least partially successful in getting fast-food and retail establishments to not market animals fed human-use antibiotics for growthpromoting purposes. this suggests that a productive approach may be finding ways to provide information to and educate consumers about the risks of antibiotic resistance to enable them to make better informed decisions. there is an important role for educators to extend scientific information in a nontechnical way to the lay public. the drive to use antibiotics more responsibly and in the public interest may be facilitated by recent economic results that show that reducing antibiotic use in animal production need not come at a significant economic cost to producers or consumers. since the benefits of using antibiotics for livestock growth promotion appear to have resulted in increasingly smaller productivity gains, independent producers where input mix is a farmer-driven choice based on farm-level economics may be better off to substitute good management practices rather than using antibiotics for prophylactic disease prevention. however, much of meat animal production on us farms is produced under contract, where the integrator provides inputs, often including antibiotics, that the grower is required by contract to use. recent actions by integrators and meat processors to reduce antibiotic use and substitute alternative strategies to protect animals from diseases and maintain productivity are an important development, especially since production-purpose use of antibiotics is now prohibited. presuming that any new human-use antibiotic classes will probably not be made available for veterinary medicine, it is important to preserve the effectiveness of existing antibiotics. some policy makers and industry now recognize the urgency to identify new antibiotics. this will require increased antibiotic research funding and judicious use of existing antibiotics. the ban of human-use antibiotics in animals for production purposes is expected to help slow the growth of antimicrobial resistance, giving more time to discover new antibiotics for animal uses and for human health uses. to the extent they can be developed and used separately, the potential for animal antibiotic use leading to antimicrobial resistance for important human antibiotics will be mitigated. the ban on antibiotics used for humans also being used for animal production purposes will necessitate adopting improved cultural practices to reduce the poten-tial for disease and to increase feed efficiency. this calls for research on best management practices to accommodate today's supply chain requirements for food safety, production efficiency, and attribute verification. moreover, there is a need to educate producers-for example, through the usda-state cooperative extension service-about safe production practices for managing ar. this will allow producers to maintain efficiency in their operations and assure that they comply with current regulations to address the growing concern about antimicrobial resistance in the food supply chain. improved data collection and analysis to allow tracking of potential antimicrobial resistance development are essential to facilitate the food animal industry implementation of cultural practices to reduce the potential for contributing to antimicrobial resistance. it would also allow policy makers to better understand the need for any necessary interventions. these investments in the public good can be very cost-effective, though not without additional public investment or internal agency budget reallocation. increasing international trade may spread antibiotic resistance through imported food products as more trade agreements are approved. this scenario could be exacerbated to the extent fsis approves additional international facilities, local regulations, and inspections as "equivalent to the united states." in many developed and developing countries, antimicrobial agents are readily available. policies need to be implemented establishing appropriate conditions for use of veterinary products, including antimicrobial agents. future trade agreements will need to include provisions which address reduced use of medically important antibiotics in producing food animals. to date, there is no harmonized system of surveillance on the worldwide use and circulation of antimicrobial agents. that information is necessary to monitor and control the origin of medicines, obtain reliable data on imports, trace their circulation, and evaluate the quality of the products in circulation. the oie initiative to create a global database for monitoring the use of antimicrobial agents is an important step that can provide valuable information for private sector and public policy leaders worldwide. the serious implications of growing antibiotic resistance require a concerted effort across all stakeholders and society generally. increased attention to this issue is emerging in the medical community where overuse of existing drugs and inadequate sanitary precautions account for % of the resistance. lack of development of new antibiotics exacerbates the problem, and industry focus and perhaps government policy are needed to improve this situation. animal agriculture stakeholders need to improve production practices to reverse the other % of resistance attributable to foodborne sources. government policy and agencies have been slow to acknowledge the seriousness of antibiotic resistance and appropriately address it. public and private sector collaboration internationally is necessary to successfully deal with this critical societal issue. changes in the measurement of antibiotics and in evaluating their impacts in agroecosystems: a critical review society must seize control of the antibiotics crisis animal and plant health inspection service, united states department of agriculture apua. major developments in u.s. policy on antibiotic use in food animals. alliance for the prudent use of antibiotics farm antibiotic use remains worrisome in india. alliance for the prudent use of antibiotics raised without antibiotics: lessons from voluntary labeling of antibiotic use practices in the broiler industry perdue chickens now free of antibiotics antibiotic resistance and the use of antibiotics in animal agriculture: hearing before the subcommittee on health of the house committee on energy & commerce across the divide: the importance of antibiotics for animal health antibiotic resistance threats in the united states estimates of foodborne illness in the united states. centers for disease control and prevention tracking animal antibiotic use in food animals. the center for foodborne illness research and prevention america's antibiotic crisis council for agricultural science and technology (cast). . antibiotics in animal feeds the judicious use of medically important antimicrobial drugs in food-producing animals. guidance for industry # summary report on antimicrobials sold or distributed for use in foodproducing animals anti-microbial animal drug sales and distribution reporting. fda, department of health and human services fda announces implementation of gfi # , outlines continuing efforts to address antimicrobial resistance stakeholders: colistin-resistance shows need for congressional action animal production claims: outline of current process. fsis, u.s. department of agriculture gnp company. gold'n plump to add 'no antibiotics-ever' and humane certified attributes. . perishable news.com report of a study: human health risks with the subtherapeutic use of penicillin or tetracyclines in animal feed. committee on human health accurate, credible info on animal antibiotics. phibro animal health report presented to parliament by the secretary of state for social services, the secretary of state for scotland, the minister of agriculture, fisheries and food and the secretary of state for wales by command of her majesty antibiotic resistance in india: drivers and opportunities for action changes in intestinal flora of farm personnel after introduction of a tetracycline-supplemented feed on a farm consumer information and labeling consumer demand for a ban on antibiotic drug use in pork production foregoing sub-therapeutic antibiotics: the impact on broiler grow-out operations pressure rises to stop antibiotics agriculture antibiotic discussions intensify in wdc. pork network world animal health organization sets out action on antibiotic resistance. poultry news the looming threat of factory-farm superbugs mrc announces cross-council awards worth nearly £ m to tackle antibiotic resistance department of health and human services, cdc united states summary and state data the effects on human health of subtherapeutic use of antimicrobial drugs in animal feeds. committee to study the human health effects of subtherapeutic antibiotic use in animal feeds resistome diversity in cattle and the environment decreases during beef production tackling drug-resistant infections globally: final report and recommendations. the review on antimicrobial resistance world organization for animal health merchants of doubt: how a handful of scientists obscured the truth on issues from tobacco smoke to global warming the landscape of antibiotic resistance prepared for united states department of health and human services, public health service, food and drug administration, bureau of veterinary medicine prudent use and regulatory guidelines for veterinary antibiotics-politics or science? economics of antibiotic use in u.s. livestock production an integrated systems approach is needed to ensure the sustainability of antibiotic effectiveness for both humans and animals restricting the use of antibiotics in food-producing animals and its associations with antibiotic resistance in food-producing animals and human beings: a systematic review and meta-analysis economics of antibiotic use in u.s. swine and poultry production position statements: antibiotic use scientific integrity in policymaking: an investigation into the bush administration's misuse of science insights: reducing antimicrobial use in food animals veterinary feed directive a rule by the food and drug administration on / / . illustrative examples of probable transfer of resistance determinants from food animals to humans: streptothricins, glycopeptides, and colistin weimer bc k genome project . veterinary medicine, uc davis antimicrobial resistance: global report on surveillance. summary. world health organization who guidelines on use of medically important antimicrobials in food-producing animals. geneva: world health organization ctx-m- producing salmonella enterica serotypes typhimurium and indiana are prevalent among food-producing animals in china diverse and abundant antibiotic resistance genes in chinese swine farms political economy of biofuel acknowledgments we deeply appreciated the conversations with and review comments from mary ahearn in developing and writing this chapter. any remaining errors, mistakes, or omissions are of course ours. w. j. armbruster and t. roberts key: cord- -gwikyux authors: wong, joshua guoxian; aung, aung-hein; lian, weixiang; lye, david chien; ooi, chee-kheong; chow, angela title: risk prediction models to guide antibiotic prescribing: a study on adult patients with uncomplicated upper respiratory tract infections in an emergency department date: - - journal: antimicrob resist infect control doi: . /s - - - sha: doc_id: cord_uid: gwikyux background: appropriate antibiotic prescribing is key to combating antimicrobial resistance. upper respiratory tract infections (urtis) are common reasons for emergency department (ed) visits and antibiotic use. differentiating between bacterial and viral infections is not straightforward. we aim to provide an evidence-based clinical decision support tool for antibiotic prescribing using prediction models developed from local data. methods: seven hundred-fifteen patients with uncomplicated urti were recruited and analysed from singapore’s busiest ed, tan tock seng hospital, from june to november . confirmatory tests were performed using the multiplex polymerase chain reaction (pcr) test for respiratory viruses and point-of-care test for c-reactive protein. demographic, clinical and laboratory data were extracted from the hospital electronic medical records. seventy percent of the data was used for training and the remaining % was used for validation. decision trees, lasso and logistic regression models were built to predict when antibiotics were not needed. results: the median age of the cohort was years old, with . % being male. temperature and pulse rate were significant factors in all models. the area under the receiver operating curve (auc) on the validation set for the models were similar. (lasso: . [ % ci: . – . ], logistic regression: . [ % ci: . – . ], decision tree: . [ % ci: . – . ]). combining the results from all models, . % of study participants would not need antibiotics. conclusion: the models can be easily deployed as a decision support tool to guide antibiotic prescribing in busy eds. supplementary information: the online version contains supplementary material available at . /s - - - . upper respiratory tract infection (urti) is one of the most cited reasons for use of antibiotics [ ] . in the majority of urtis, the routine use of antibiotics is not recommended [ ] [ ] [ ] [ ] [ ] . in the united states (u.s.), it was estimated that antibiotics have been prescribed for over % of uncomplicated urtis in adults and increasingly so for broad-spectrum antibiotics [ ] [ ] [ ] [ ] . between and , million ( . %) emergency department (ed) visits in the u.s. were for acute respiratory tract infections, with almost half ( . %) of patients with infections being administered antibiotics inappropriately [ ] . from to , adults had the highest rate of inappropriate antibiotic use for acute respiratory tract infections (urtis, influenza, and viral pneumonia), with antibiotic prescriptions per ed visits for adults aged - years and per visits for those aged > = years [ ] . in singapore, while primary care clinics are highly accessible in the community, there are individuals who preferred to seek care at the ed for urti, accounting for a substantial proportion of ed attendances [ ] . urti accounted for - % of ed visits by non-frequent attenders ( - ed visits in one year) and up to % of ed visits by frequent attenders (≥ ed visits in one year) [ ] . a previous study at an adult general hospital has reported that % of adult patients attending at ed for urti were inappropriately prescribed antibiotics, with the penicillin class of antibiotics being the most commonly prescribed [ ] . studies have shown a strong link between antibiotic prescribing and antimicrobial resistance [ , , ] . in addition, a population-wide study on us pharmacy records showed that antibiotic use and resistance appears to be closely linked to broadly distributed low-intensity prescribing [ ] . as a consequence, antimicrobial resistance has risen to dangerously high levels globally. a global study estimated that escherichia.coli and klebsiella pneumoniae resistant to third-generation cephalosporin caused . million bloodstream infections and . million serious infections in . carbapenem-resistant strains were estimated to cause . million bloodstream infections and . million serious infections [ ] . antimicrobial resistance is associated with higher medical cost, prolonged hospital stays, increased mortality and economic burden [ , ] . hence, there is an urgent need to ensure the prudent use of antibiotics for common illnesses predominantly of viral etiology such as urtis. in singapore, considerable efforts have been made to address antibiotic resistance [ ] . although computerized decision support systems have been developed to guide antibiotic prescribing, they are largely based on guidelines drawn by expert consensus and not on actual data derived from local patients [ ] . furthermore, most studies on antibiotic prescribing focus on understanding behaviors and perceptions or finding associative factors for antibiotic prescribing decisions [ ] [ ] [ ] [ ] . to date, prediction models to guide antibiotic prescribing has been confined largely to pediatric populations [ ] [ ] [ ] . differentiating bacterial and viral infections is not straightforward in adult urtis. in uncertainty avoidance, physicians tend to over-prescribe antibiotics. in this study, we aim to develop prediction models based on local clinical and laboratory data to guide antibiotic prescribing for adult patients with uncomplicated urti with the ultimate goal of deploying them as an evidencebased clinical decision support tool for routine practice. seven hundred-fifteen patients were recruited from the ed at tan tock seng hospital (ttsh), the second largest adult hospital in singapore between june and november . eligible patients were years and above attending at ttsh ed for the first time with a primary diagnosis of uncomplicated urti (icd -am j -j ) within days who provided informed consent. ttsh ed is the busiest ed in the country, attending to an average of patients daily. at discharge from the emergency department, the patients were invited to participate in the study and consent was obtained. patients who were subsequently admitted were excluded from the study. a nasopharyngeal swab was taken to determine the presence of respiratory viruses using multiplex pcr (seeplex® rv ace detection). the panel detects major respiratory viruses including adenovirus, bocavirus / / / , coronavirus e/nl and oc , enterovirus, influenza a and b, metapneumovirus, parainfluenza , , and , respiratory syncytial virus a and b, and rhinovirus. we chose not to include the bacterial respiratory pcr panel in the study, as commensal bacteria are common in the upper respiratory tract and detection on pcr does not necessarily indicate a bacterial infection. a lower respiratory tract sample (such as sputum) was also not practicable for every participant. instead, we performed a point-of-care c-reactive protein (crp) test on a drop of capillary blood obtained from a finger prick (quikread go® crp). crp is widely used in clinical settings as a supportive test to diagnose bacterial infection [ ] . our main outcome of interest was to identify patients for whom antibiotics were clearly not recommended ( = nabx) from those for whom the physician should review the need for antibiotics ( = rabx). we defined nabx as patients with a respiratory virus detected via pcr and crp < mg/l or patients who did not have a respiratory virus detected via pcr and crp ≤ mg/l [ ] . patients who did not fall into these categories were assigned to the rabx group. demographic, clinical and laboratory data documented as part of the patients' routine care were extracted from the hospital electronic medical records. these include age, gender, ethnicity, visit date, pre-existing comorbidities, respiratory symptoms, full blood count, kidney/liver panels, and biochemistry tests. according to comorbid status of the participants, charlson's comorbidity index was calculated [ ] . additionally, epidemiologic data on smoking, influenza vaccination, travel history, and prior medical consultation and antibiotic consumption were obtained from an interviewer-administered questionnaire. descriptive statistics were performed and differences between the nabx and rabx groups compared using mann-whitney u-test for continuous variables and chisquared test for categorical variables. where appropriate, fisher's exact tests were used to account for small cell sizes. variables with more than % of data missing were excluded from the analysis. categorical variables with data missing were recoded as under the assumption that presence of any clinical covariates would have been recorded. continuous variables were imputed according to their group medians. with ease of use in mind, we decided to perform predictive modeling using methods that could subsequently be easily deployed for implementation: logistic regression, lasso regression and classification and regression trees (cart). the models were derived using % of the participants as training set. the optimal cutoffs for each model were decided by taking the predicted probability that achieved the highest sensitivity with specificity of at least . . the final model performance was validated by calculating the area under the receiver operating characteristic curve (auc), sensitivity, specificity, positive predictive value and negative predicative values on the remaining % data. univariate analysis was performed on all candidate variables. demographic factors, clinically relevant variables and significant variables from univariate models were fitted into the final multivariable model via stepwise elimination using a cutoff of p < . . in stepwise regression, it is often difficult to tell the effect after removal of each variable. model selection may also be difficult in datasets with a huge number of variables. lasso regression addresses this by shrinking the coefficients of features that are less relevant or exhibit collinearity to zero. this reduces the problem of overfitting of prediction model and the variance without substantial increase in bias. we performed this by selecting a minimum optimal shrinking parameter of λ = . through a -fold cross validation of the training dataset, giving a set of coefficients governed by eq. . cart is a popular tool in supervised learning for classification as they are distribution-free and robust to outliers. unlike generalized linear models, classification trees make an excellent tool for overcoming problems due to multicollinearity and skewed covariates. it uses the gini index to iteratively split branches based on purity. this feature is an added benefit as important interactions can be easily detected. it also has the ability to identify patient subgroups that are more predictive than others. in our analysis, we created a maximum tree depth of and a minimum of subjects in a node before a split is attempted to prevent overfitting. the choice of the final tree size was decided by finding the number of splits that produce the smallest crossvalidation error. analyses were performed using r . . and stata . at a % significance level. lasso and cart models were developed using the glmnet, rpart and rattle packages in r [ ] [ ] [ ] . the study participants were young, with a median age of years (iqr: - years) and a slight preponderance of males ( . %). (table ) two-thirds ( . %) had no pre-existing comorbidities and one-third ( . %) had received influenza vaccination in the prior months. almost two-thirds ( %) of the patients presented with fever. while . % of the patients had nasal problems like running and blocked nose, . % of them had a sore throat. almost half ( . %) of the patients had a respiratory virus detected. influenza ( . %) and rhinovirus ( . %) were common respiratory viruses detected. influenza circulated year-round, with bimodal peaks observed in november and may-june, with rhinovirus dominating in the inter-influenza periods. (data not shown) the median crp level was mg/l (iqr - mg/l) and its (fig. ) . in total, ( . %) patients were classified as nabx (fig. ) . baseline covariates were largely similar between patients in the rabx and nabx groups. patients were less likely to have prior consultation days before the ed visit in the nabx group compared with the rabx group ( . % vs . %, p = . ). influenza vaccination uptake rates were similar in both groups ( . % vs . %, p = . ). there was no evidence of comorbidity being associated with antibiotic need, except those with steroid use and cancer. median time from earliest symptom onset to ed visit was similar between both groups at days (iqr: - days). rabx patients were more likely to present with symptoms of fever, body ache, sore throat and vomiting. nabx patients were likely to display symptoms of shortness of breath and giddiness. patients in the rabx group had a higher median maximum body temperature and lower median systolic and diastolic blood pressures than those in the nabx group (table ) . highest temperature and highest pulse rate were commonly identified to be important predictors in all logistic, lasso and cart models ( table ; fig. ). in addition, age, the presenting symptoms of fever, giddiness and shortness of breath were identified to be significant predictors in the final logistic regression model. similarly, indian ethnicity, fever, giddiness and cancer status were included in the lasso model. (table (table ). in addition, we looked at the corresponding metrics at a probability cut-off of . . the models have marked improvement in sensitivity, but specificity fell below . (logistic: sen = . , spe = . ; lasso: sen = . , spe = . ; cart: sen = . , spe = . ). detailed documentation on different probability cutoffs can be found in additional file . a qualitative study previously conducted in our hospital revealed that ed physicians were confident with their clinical decisions. however, doctors had a lower threshold for prescribing antibiotics for older patients who were immunocompromised and suffering from chronic conditions. junior physicians were observed to be uncomfortable not prescribing antibiotics for urti patients [ ] . patients with bacterial and viral infections present with similar symptoms and differentiation of patients requiring antibiotics from those who do not is problematic. our algorithms developed using three rigorous statistical methods together with laboratorybased confirmatory tests served as a good guide for physicians in their decisions on antibiotic prescribing for urti patients. a recent cochrane systematic review provided evidence that patient satisfaction and clinical outcomes were similar between those for whom antibiotic prescribing was delayed and those not prescribed antibiotics at all. delayed prescribing of antibiotics has been found to be associated with marked reduction in antibiotic use [ ] . our results showed that the performance of all prediction models were similarly modest. while we tried to be pragmatic with our algorithms, we also carried out similar analysis on more complex classification trees and random forests, both of which showed minimal or no improvement in performance (auc . ). a recent systematic review showed that there was minimal improvement using machine learning techniques over traditional regression models [ ] . relevant literature on prediction models for antibiotic prescribing in adults are limited and tended to focus on life-threatening infections. several clinical prediction models were built for pneumonia and serious bacterial infections in children mostly using either logistic regression or decision trees [ , , ] . the findings from this study add to the limited knowledge on clinical decision support tools for antibiotic prescribing in an adult ed setting. we found that fever and pulse rate were significant factors in all models. most studies on viral respiratory infections have focused on influenza with a high temperature identified as a significant risk factor in both younger and older adults [ ] [ ] [ ] [ ] . heart rate was found to be significant in a group of patients presenting with influenza-like illness at a hospital emergency department [ ] . a significant proportion of patients with influenza infection present with tachycardia. this could be due to the physiologic response to fever although cardiac manifestations are not uncommon with complications of influenza [ ] . shortness of breath and giddiness were also found to be significant predictors in two of our models. while these symptoms could be non-specific, we believe that it would have to be significant enough for adult patients to volunteer these symptoms to their physicians when they had them. as physicians often have to make antibiotic prescribing decisions based on subjective symptoms reported by their patients, we believe that our clinical decision support tool, developed from three different models, will provide physicians with a reliable tool when making antibiotic prescribing decisions for patients with urti at the point-of-care. there are a few limitations in our study. firstly, the ability to predict well is dependent on the richness of the data. our study is limited to the information obtained at the time that the patient medically attended at ed. knowledge on baseline vital signs and trajectories prior to ed visit may be important information that could improve our models. a study by stanford university on wearable devices detected that anomalies in skin temperature and heart rate corresponded to periods of high crp levels [ ] . secondly, we did not consider laboratory parameters like full blood count, renal and liver function panels in our model as % of patients did not receive a full blood count, and even fewer had our data reflected this as % of patients had prior consultation although the time between the earliest symptom onset to ed visit was only days on average. the local literature on vaccination uptake in the community is limited. to our knowledge, there is only one population health survey on influenza vaccination uptake in older adults done in [ ] . the authors found that the influenza vaccination uptake in this population was only . %. our patient cohort had a higher vaccination rate ( %) than in the community. however, this does not invalidate our findings and we believe that the impact on the generalizability of our models is minimal. nonetheless, our study had its strengths. we were able to take seasonality into account as the study spanned two years covering two influenza seasons each of northern and southern hemispheres. the use of pcr together with appropriate crp cutoffs were based on findings from several international studies and selected to be the most conservative estimates. the cutoff point for crp was set lower to increase sensitivity of the rabx group [ , , ] . we also note that the proportion of positive viral pcr among the crp < and crp > groups were quite similar (fig. ) . patients with high crp and positive viral pcr represent patients with secondary bacterial infection. in a sub-group analysis of patients with complete blood count performed, those with high crp levels of > and positive viral pcr were almost twice as likely to have leukocyte counts of > . × /l as those with crp < and positive viral pcr ( . % vs. . %, p = . ). this supports our exclusion of patients with high crp and positive viral pcr from the nabx group. comprehensive assessment of medical records was performed by two clinically trained individuals with standardization in data extraction methods and definitions to ensure data accuracy and consistency. analysing the data with different methods not only allowed us to compare models but also allowed us to triangulate the findings from all our models. notably, maximum pulse rate and highest temperature were considered as important variables in all models. finally, our models were either coefficient or rule based. they can easily be entered into an excel sheet or the hospital electronic system without the need to integrate complicated programming codes. combining the results from the three models, . % of study participants would not need antibiotics. moving forward, physicians could use this tool as a useful complement to their clinical judgement in their practice to guide their decisions on antibiotic prescribing. antibiotics should be prescribed with caution even during low influenza periods as there are still other viruses circulating throughout the year. at the time of writing, we have developed a mobile application (app) named the "abx stew-ards" to provide clinical decision support for busy physicians practicing in the ed on antibiotic prescribing for urti (fig. ) . ed physicians are required to fill in parameters all on one screen. all fields are mandatory, and the app will provide a recommendation either to review the need for antibiotics or that antibiotics was not needed, based on the predicted outcomes of all validated models. a validation study is underway. it is hoped that evidence-based clinical decision support tools accessible at the point-of-care can lead to better antibiotic prescribing decisions and the reduction of antibiotic resistance. antibiotics for the common cold and acute purulent rhinitis. cochrane database of systematic reviews excessive antibiotic use for acute respiratory infections in the united states principles of appropriate antibiotic use for treatment of acute respiratory tract infections in adults: background, specific aims, and methods antibiotics for acute bronchitis. cochrane 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and crp for detecting serious bacterial infections in patients with fever of unknown origin: a systematic review and meta-analysis publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations ms. ong lay see and grace tin for collecting the data, staff of ttsh ed who helped with study recruitment, and patients who participated in the study.authors' contributions ac, dcl, and cko conceived the study and designed the study. ac obtained research funding. ac supervised the conduct of the trial and data collection. cko implemented the study including providing oversight of patient recruitment. jgw provided statistical oversight to the study. jgw, aah, and wxl analysed the data. jgw, aah, wxl, and ac drafted the manuscript, and all authors contributed substantially to its revision. ac takes responsibility for the paper as a whole. all author(s) read and approved the final manuscript. the online version contains supplementary material available at https://doi. org/ . /s - - - .additional file : appendix a. training diagnostic performance at different probability cutoffs. appendix b. x tables for the actual vs predicted values on the training and validation set using the best probability cutoff all authors have no conflict of interest related to the submitted work. key: cord- -iuu yes authors: mainous, arch g.; hueston, william j. title: upper respiratory infections and acute bronchitis date: - - journal: management of antimicrobials in infectious diseases doi: . / - - - - _ sha: doc_id: cord_uid: iuu yes upper respiratory infections include the following: uncomplicated upper respiratory infections also known as the “common cold,” acute otitis media, pharyngitis/tonsillitis, and acute sinusitis. these conditions, along with acute bronchitis, are very common illnesses that are commonly seen in outpatient settings and are widely treated with antibiotics. in fact, these conditions are the primary indications for outpatient antibiotic prescriptions. these conditions tend to have overlapping clinical characteristics yet evidence regarding the utility of antimicrobial treatments varies across conditions. upper respiratory infections include the following: uncomplicated upper respiratory infections also known as the "common cold," acute otitis media, pharyngitis/tonsillitis, and acute sinusitis. these conditions, along with acute bronchitis, are very common illnesses that are commonly seen in outpatient settings and are widely treated with antibiotics. in fact, these conditions are the primary indications for outpatient antibiotic prescriptions. these conditions tend to have overlapping clinical characteristics yet evidence regarding the utility of antimicrobial treatments varies across conditions. uncomplicated upper respiratory infections (uris) are characterized by rhinorrhea, nasal congestion, sneezing, sore or "scratchy" throat, and cough [ ] . the incubation period varies between and h. while a low-grade fever in some cases is present, in adults, temperature elevation is rare. early symptoms may be minimal and limited to malaise and nasal symptoms. the nasal discharge is initially clear and watery. there is a subsequent transition period where the nasal discharge becomes viscous, opaque, and discolored (white, yellow, green) [ ] . the color of the secretions is not predictive of a bacterial infection. the clinical presentation is similar in both adults and children. the episode tends to be self-limited. the median duration of a cold is week, with most patients improving by the th day; however, lingering symptoms may last up to weeks. uris, or the "common cold," are exactly as the name implies -common. uris are consistently one of the five most common diagnoses in ambulatory physician office visits [ , ] . adults have two to four uris annually, and children in day care have as many as six or seven [ , ] . the significant costs of uris can be conceptualized as both direct and indirect costs. the direct costs of uris include the costs associated with the substantial number of office visits. uris account for more than million physician office visits a year [ ] . in addition, microbiologic and laboratory diagnostic tests are sometimes performed but are of dubious clinical value and, therefore, contribute unnecessarily to the cost of uris [ ] . the total economic impact of non-influenza-related uris has been estimated to approach $ billion annually (direct costs, $ billion per year; and indirect costs, $ . billion per year) in the united states [ ] . indirect costs for uris include productivity losses related to lost workdays for adults who are sick as well as adults who have to deal with sick children. other indirect costs that are many times overlooked are the impact of uris on missed opportunities to immunize young children. although the interpretation of guidelines by the american academy of pediatrics and the advisory committee on immunization practices, particularly for fever and moderate illness, rests with the clinician [ , ] , a large proportion of children are not immunized on schedule due to visits for uris [ ] . this finding also suggests additional visits for immunizations thereby requiring additional direct costs and indirect costs inherent in taking children to the physician's office. the mechanisms of transmission suggest that uris can be spread through contact with inanimate surfaces [ ] and hand-to-hand contact [ ] . uris have a seasonal variation with an increased prevalence in the united states between september and march. it is unclear why this variation exists, although it may be related to increased crowding of indoor populations in the colder months. temperature is not the key to seasonal variation without the presence of a pathogen. evidence from antarctica showed that spacious well-ventilated rooms reduced transmission of uris as compared to crowded poorly ventilated rooms regardless of temperature [ ] . viruses have been shown to be the major pathogens in uris [ ] . one study established viral etiology in % of uris [ ] . rhinoviruses were found in % of the patients by viral culture or pcr assay. coronaviruses were the second most common group of causative agents, followed by influenza a or b virus. identified bacterial pathogens were chlamydia pneumoniae, haemophilus influenzae, streptococcus pneumoniae, and mycoplasma pneumoniae. none of the patients had beta-hemolytic group a streptococcus. in terms of bacterial pathogens, infections without evidence of a viral infection occurred in only . % of the cases. a variety of studies in the s showed a high rate of prescribing antibiotics for uris [ , ] . more recent data have indicated a drop in the prescribing of antibiotics; however, the use of antibiotics is still far from optimal [ ] . controlled trials of antimicrobial treatment of uris have consistently demonstrated no benefit [ , ] . in eight trials of antimicrobial treatment of uris, six found no difference between the groups either in terms of improvement or in terms of complications. complications tend to be minimal and occur at a rate of - %. one trial found some slight benefit in decreasing the presence of purulent rhinitis [ ] . another found a decrease in rhinorrhea at day but no difference between the groups at day [ ] . similarly, an additional trial attempted to isolate "bacterial colds" for which antibiotics might be effective treatments [ ] . although there was some indication of patient improvement at day , the differences were gone by day . it is important to remember that the normal presentation of a uri is a week to days. few successful treatments have been identified. vitamin c, zinc gluconate, and echinacea have all shown mixed results [ , ] . antihistamines, with a few exceptions, have not been shown to be effective treatments [ ] . the most effective symptomatic treatments are over-the-counter decongestants [ ] . acute sinusitis has considerable overlap with uris in its constellation of signs and symptoms. one half to two thirds of patients with sinus symptoms seen in primary care are unlikely to have sinusitis [ ] . in patients who presented with a uri, % had radiographic evidence of maxillary sinusitis but had no symptoms of sinus infection [ ] . uris are often precursors of sinusitis, and, at some point, symptoms from each condition may overlap. sinus inflammation from a uri, without bacterial infection, is also common. in a series of children undergoing computerized tomography (ct) for non-sinus-related diagnoses, % had evidence sinus inflammation with no clinical signs of sinusitis and with complete resolution following their viral illness [ ] . acute sinusitis tends to start with a uri that leads to sinus ostial obstruction. the signs and symptoms that increase the likelihood that the patient has acute sinusitis are a "double sickening" phenomenon whereby the patient seems to improve following the uri and then deteriorates, exhibiting symptoms such as maxillary toothache, purulent nasal discharge, poor response to decongestants, and a history of discolored nasal discharge [ , ] . other authors have stressed that the symptoms need to persist longer than week to distinguish sinusitis from a uri [ ] . it should be pointed out that the commonly used sign of facial pain or swelling has low sensitivity for acute sinusitis [ ] . since sinusitis is most often a complication of upper respiratory viral infections, it follows the same seasonal pattern as colds. this pattern produces a winter peak with more cases seen than those exposed to upper respiratory tract infections. in children seen in a large health system, sinusitis is frequently found as a comorbidity with otitis media. nearly half of all children with sinusitis also had otitis media [ ] . children are also more likely to have posterior ethmoidal and sphenoid inflammation, while adults have mainly maxillary and anterior ethmoidal sinusitis [ ] . some medical conditions may increase the risk for sinusitis; these include cystic fibrosis, asthma, immunosuppression, and allergic rhinitis [ ] . cigarette smoking may also increase the risk of bacterial sinusitis during a cold because of reduced mucociliary clearance. sinus inflammation can be caused by viral, fungal, and bacterial infections as well as allergies. the majority of acute sinusitis is caused by viral infection. as indicated above, many cases of the common cold have concomitant sinus inflammation. the inflammation associated with viral infections clears without additional therapy. bacterial superinfection of uris is rare and occurs in only . - % of colds. studies examining the treatment of sinusitis confirm that response rates to antibiotics are either small [ ] . when sinusitis is confirmed by a ct scan, response rates to antibiotics are improved [ ] . cultures of material obtained from patients with sinusitis show that the most prevalent organisms are strep. pneumoniae and, especially in smokers, h. influenzae. these two organisms are present in % of cases of bacterial acute sinusitis [ ] . when antibiotics are used for the treatment of bacterial sinusitis, the selection of antibiotics should include sufficient coverage of these two organisms. fungal sinusitis are very rare and usually occur in immunosuppressed individuals or those with diabetes mellitus [ ] . antibiotics are commonly prescribed for adult patients who present with complaints that are consistent with acute sinusitis. the effectiveness of antibiotics is unclear. three recent placebo-controlled, double-blind, randomized trials in general practice settings have yielded mixed results [ , , ] . two of these trials showed no beneficial effect of antibiotics [ , ] ; the third trial, however, demonstrated a significant effect of penicillin and amoxicillin [ ] . the trial showing an effect used more stringent enrollment criteria than the other two; the criteria in the trial are more consistent with those used in daily practice by primary care physicians. these data suggest that patients with more severe signs and symptoms may benefit from an antibiotic. if an antibiotic is to be used, some evidence with trimethoprim/sulfamethoxazole suggests that short-duration treatment (e.g., days) is as effective as longer treatment [ ] . further, narrow-spectrum agents seem as effective as broad-spectrum agents [ ] . in patients with severe signs and symptoms, antibiotics have some utility in treating acute sinusitis. if antibiotics are to be used, then short-course therapy with narrow-spectrum agents is recommended. the key to the judicious use of antibiotics is to first make an accurate diagnosis of sinusitis rather than overtreating uris. the evaluation and management of otitis media has been subject to a wide variance in approaches. the variation in management of otitis media is typified in an examination of the management of otitis media in nine countries in the mid- s [ ] . in this study, antibiotics were used over a wide range ( - %) of episodes of otitis media with similar variation in the types of antibiotics used and duration of therapy. to help bring some consensus to the process, the american academy of pediatrics issued a guideline for the evaluation and treatment of otitis media in [ ] . while the guideline suffers from a lack of definitive evidence in several areas of care, the recommendations are an effective tool for bringing some clarity to an issue that has suffered from a wide variation in management strategies. the aap guideline recommends that the diagnosis of otitis media requires three essential components: an acute onset of illness, presence of a middle ear effusion, and signs and symptoms of middle ear inflammation. middle ear effusion is evident in children with bulging of the tympanic membrane, reduced or absent mobility of the membrane with pneumatic otoscopy, an air-fluid level behind the membrane, and pain in the effected side. inflammatory signs noted in the report include erythema of the tympanic membrane along with pain on that side. in considering all these factors, the combination of reduced mobility, erythema, and a bulging tympanic membrane is the best predictor of otitis media. the most essential step in managing otitis media is assuring that the diagnosis is correct. otitis media may be overdiagnosed, especially in younger children, which complicates the evaluation of treatment effectiveness. studies show that a physician's certainty about the diagnosis of otitis media is dependent on the patient's age. in a multinational study, it was found that physicians were certain of the diagnosis in only % of children under the age of [ ] . this increased to % in those between year and months of age and up to % in those over months of age. historically, acute otitis media has been one of the most common pediatric conditions seen in primary care. however, since the introduction of vaccines against common respiratory pathogens, there is evidence that the frequency of this problem has decreased considerably. in the netherlands, visits to general practitioners for otitis media with effusion in children under the age of fell by % between and [ ] . a similar decrease in visits for acute otitis in children has been reported in a large health system in the united states [ ] , with a smaller reduction in visits noted in the emergency department setting [ ] . the introduction of h. influenzae b vaccine in the s, followed by universal childhood immunization with conjugated strep. pneumoniae, may be responsible for the reduction in otitis media cases encountered. since otitis media is a complication of an upper respiratory infection, it has a peak incidence in the winter when colds are most likely to occur. unlike sinusitis, which is more likely to affect adults, otitis media is predominantly a disease of younger children with a peak incidence between and months of age [ ] . otitis media occurs with varying frequency in children. in a large population study, it was found that during the first years of life about a third of children never had otitis media and another third had one or two episodes, while the remaining third had three or more episodes. otitis media occurs more often in males, children in lower socioeconomic groups, and in certain ethnic groups such as native americans. because of differences in the mechanics of the posterior pharynx and eustachian tube, children born with craniofacial congenital abnormalities such as cleft lip/palate and those with trisomy also are more likely to have otitis media as a complication of a cold. otitis media arises from eustachian tube dysfunction that accompanies uris or allergic rhinitis. inflammation of the eustachian tube and middle ear results in tube occlusion and fluid accumulation in the middle ear space. eustachian tube obstruction is more common in younger children because of less cartilage support of the tube making collapse more likely. the eustachian tube obstruction not only causes entrapment of existing fluid but also produces a negative pressure in the middle ear that results in additional fluid accumulation that characterizes serous otitis media. contamination of this fluid with bacteria results in acute suppurative otitis media. suppurative otitis media is most often caused by the same organisms that result in sinusitis. studies of middle ear aspirates suggest that strep. pneumonia is the most common bacterial cause of otitis media and is found in about % of effusions. h. influenzae accounts for approximately another %. b. catarrhalis and staphylococcus aureus each make up fewer than % of cases. in neonates, gram-negative species also should be considered as potential etiologic agents. otitis media also may result from noninfectious obstruction of the eustachian tube. allergic rhinitis, as noted above, is one such mechanism. other causes include enlargement of the adenoids and posterior pharyngeal tumors. treatment recommendations from the aap/aafp guidelines for the management of acute otitis media suggest that observation rather the initial use of antibiotics is appropriate depending on the child's overall health, age, severity of illness, and likelihood that they can follow-up if necessary. for healthy children over the age of , antibiotics are recommended only if the child is severely ill; if the child is mildly ill or if the diagnosis is uncertain, then observation is acceptable. for children younger than this, antibiotics are recommended for a certain diagnosis of otitis media and for those under age months where the diagnosis is uncertain. antibiotics are not recommended for use in healthy children between months and years who have an uncertain diagnosis (aap subcommittee). if patients who are observed fail to improve in - h, then antibiotic therapy is recommended. based on the aap/aafp guidelines, routine observation or "wait and see protocol (wasp)" as an alternative to universal antibiotic use has been evaluated in emergency room setting. a randomized trial of the wasp approach compared with routine antibiotics showed that antibiotic use was reduced from to % with no differences in prolonged fever, ear pain, or unscheduled subsequent visit for the ear infection [ ] . despite evidence that the wasp or observation period is effective, primary care physicians have been slow to adopt this in practice [ ] . when antibiotics are selected for the management of acute suppurative otitis media, selection of an agent should provide coverage for the two most common organisms, the aap/aafp recommends initial treatment with amoxicillin at a dose of - mg/kg per day. second, the duration of antibiotic treatment is unclear. in a meta-analysis of trials that compared short-duration antibiotic therapy with the traditional day course, no benefit was found of using longer courses of treatment; however, methodologic problems may complicate the interpretation of these results [ ] . in their guidelines, the aap/aafp recommends that a - day course of antibiotics should be sufficient for treatment. in addition to short-course therapy, a single intramuscular dose therapy of ceftriaxone has been shown to be equally beneficial to longer courses of amoxicillin [ ] , cefaclor [ ] , or trimethoprim-sulfamethoxazole [ ] for the treatment of acute suppurative otitis media. where antibiotic resistance to s. pneumonia is high or where patient compliance is an issue, ceftriaxone may be a viable alternative. in addition, some studies have evaluated the use of a single dose of azithromycin ( mg/kg) for treatment of uncomplicated otitis media. in a review of these studies, the overall success rate was % [ ] . macrolide resistance to s. pneumoniae was the largest impediment to success. based on this, it was suggested that single-dose azithromycin may be an alternative in areas with resistance to s. pneumoniae is uncommon. the primary concern in the treatment of otitis media is a primary treatment failure (i.e., persistent illness or an early recurrence of disease following initial therapy of a new otitis episode) [ ] . a meta-analysis of randomized trials supports initial antibiotic use demonstrated no significant differences in failure rates when comparing "standard" or first-line (penicillin, amox/ampicillin, erythromycin, and sulfamethoxazole) and "extended-spectrum" or second-line antibiotics or with duration of therapy. the only factor that appears to be consistently linked to a higher likelihood of a primary treatment failure is a child's age [ , ] , with children younger than years of age having treatment failures in - . % of cases. for older children, treatment failures occur in - % of episodes [ , ] . also of concern is how to manage a new case of otitis media when a previous treatment failure has occurred. in a study that examined failure rates in new infections for children who had a previous treatment failure, there was no benefit of starting therapy with an extended-spectrum agent compared to "first-line" drugs. thus it appears that in a case of previous treatment failure, new cases should be managed with narrow-spectrum agents such as amoxicillin or tmp-smx [ ] . the use of second-line antibiotics when a first-line agent will suffice creates two problems. first, in most cases the use of broad-spectrum drugs adds significant expense to therapy. others have reported that use of second-line agents compared to amoxicillin or smx-tmp adds % to the overall cost of the episode [ ] . since the results of this study show comparable failure rates for first-and second-line antibiotics, there appears to be no justification for this additional cost. second, the injudicious use of broad-spectrum antibiotics may increase the potential for future development of antibiotic resistance. the overuse of antibiotics has been proposed as one reason for the observed growth in antibiotic resistance reported in common childhood organisms such as s. pneumoniae. otitis media is a condition in which antibiotics are frequently prescribed for children and where broad-spectrum antibiotics may be used unnecessarily. limiting the use of broadspectrum drugs to situations in which they are beneficial (i.e., managing the resistant case of otitis) may help reduce further development of drug resistance in children. sore throat is a common reason that patients consult with a physician. most of these are viral infections related to upper respiratory infections, but about - % are secondary to infection with group a beta-hemolytic streptococcus. the primary role of the physician is to differentiate streptococcal pharyngitis from viral illnesses. since most patients with sore throats probably do not visit their doctor, it is difficult to state with any certainty how often sore throats occur in healthy populations. however, pharyngitis is one of the most common diagnoses for physician office visits. estimates from suggest that more than million visits in the united states each year are for pharyngitis [ ] . frequently antibiotics are prescribed for these conditions without evidence of a bacterial etiology. both viral and group a streptococcal pharyngitis have peak occurrences in the winter and early spring. streptococcal infection, in particular, can be recognized in epidemic patterns frequently affecting groups that spend considerable time together in close quarters such as day cares, schools, and places of employment. strep throat also is related to patient age. while infection in the very young (< year old) is uncommon, the peak occurrence for strep throat is between and years of age with diminished risk over the age of . the most common causes of pharyngitis are respiratory viruses. adenovirus and the rhinoviruses account for about % of cases of sore throat in children that are seen by physician [ , ] . coxackievirus, herpesvirus, and epstein-barr virus can cause tonsillitis but are less common that adenovirus [ ] . adenovirus, coxackievirus, and epstein-barr virus can cause exudative pharyngitis that can mimic the appearance of streptococcal infection. while exudative tonsillitis is thought to be a hallmark of group a streptococcal infection, this sign is actually present more often from adenovirus than streptococcus. it is important to identify group a streptococcal infections because trials of antibiotics in undifferentiated sore throat populations show little benefit [ ] . group a beta-hemolytic streptococcus can cause an acute tonsillopharyngitis and may colonize the oropharynx without symptoms. the asymptomatic carrier rate of group a strep ranges from about to % of healthy children, a rate that nearly matches the true infection rate [ , ] . this means that in testing for group a streptococcus, positive tests are just as likely to occur from carriers of group a strep who have a concomitant virus as those actually infected with the organism. in contract to group a streptococcal tonsillopharyngitis, treatment of the carrier state is not necessary and does not reduce symptoms or reduce complications [ ] . the reasons for antibiotic treatment of beta-hemolytic group a streptococcal pharyngitis are to alleviate symptoms, reduce the spread of disease, and reduce the risk of suppurative and nonsuppurative complications. although some authors have suggested that antibiotics are not justified to reduce the risk of rheumatic fever, a complication of beta-hemolytic group a streptococcal pharyngitis, the american heart association in still recommends antibiotic treatment [ , ] . differentiating group a streptococcal pharyngitis from viral disease is the most vexing problem in the management of acute sore throat. the clinical impression of the treating physician has been shown to be fairly inaccurate at making this differentiation [ ] [ ] [ ] . a clinical prediction rule for presence of strep throat that has some utility uses the presence of tonsillar exudate, pharyngeal exudate, or exposure to strep throat infection and the absence of tender anterior cervical nodes, tonsillar enlargement, or exudate. no individual element of history-taking or physical examination is accurate enough by itself to rule in or rule out strep throat [ ] . another dilemma in identifying group a strep in patients with pharyngitis is the sensitivity of rapid group a antibody kits compared to a throat culture. many studies have shown that a rapid test is less sensitive than the culture for identifying the presence of group a strep. the rapid tests have a high degree of specificity, but their sensitivity in clinical practice can be unacceptably low. sensitivities for the rapid test compared to a standard blood agar culture vary considerably but are generally in the range of - %. studies also have demonstrated that in circumstances when the colony counts are low, rapid tests are more likely to miss the presence of group a streptococcus. however, when the seroconversion of aso titers is used as the gold standard for infection, rapid tests perform very well [ ] . it is likely that rapid tests miss patients who have a small number of organisms and who are likely to be colonized instead of infected. thus, rapid testing may be more specific in identifying patients with actual strep-related disease than cultures, which also identify those who are likely to be carriers. this comparison suggests that follow-up throat cultures are not necessary and may actually confuse treatment decisions. rapid strep testing without culture also has been shown to be the most cost-effective approach to managing acute pharyngitis [ ] . as indicated above, reports regarding the role of chlamydia and mycoplasma indicate that these two organisms also may be associated with acute pharyngitis. however, there have been few treatment trials that demonstrate any benefit of treating non-group a streptococcus with antibiotics that would treat either of these organisms. in a study using erythromycin to treat non-group a strep pharyngitis [ ] , patients who received placebo had the same speed of symptom resolution as those treated with active antibiotics. once group a streptococcus has been implicated in the infection, the choice of antibiotic is controversial. with only scant evidence that treatment reduces the symptomatic period and a low risk of complications from untreated group a streptococcal pharyngitis, some investigators suggest that antibiotic treatment carries more risks than not treating and encourages future health seeking and antibiotic expectations for future sore throats [ ] . however, formal decision analyses suggest that in cases of moderate probability of strep throat ( - %) with symptom duration of days or less, rapid strep testing and treatment is beneficial [ ] . selection of an appropriate antibiotic and duration of therapy are important considerations in treating strep pharyngitis. penicillin v resistance in group a strep as well as erythromycin resistance has led to investigations of other drugs for management of strep throat. since streptococcal pharyngitis is a self-limited problem even without antibiotic therapy, much of this resistance has been based on positive throat cultures following the termination of treatment. this may be misleading since colonized patients may continue to harbor streptococcus even after therapy. when drug failure rates are examined with penicillin, cultures remain positive in - % of treated patients [ , ] . however, single-dose therapy with amoxicillin at mg/kg/day for days appears to be very successful resulting in excellent clinical responses and low rates ( - %) of posttreatment carrier rates [ , ] . treatment with other agents such as azithromycin and clarithromycin produces no better results than amoxicillin or penicillin v [ ] [ ] [ ] ; however, these treatments amount to a much greater expense. attempts at "short-course" therapy have been studied with azithromycin [ ] . both short-course treatment with azithromycin and days of cefaclor have exactly the same clinical cure rates ( %) by day of therapy. however, patients treated with cefaclor were less likely to become recolonized with group a strep over the next days than those treated with the short course of azithromycin ( % vs. %). since the significance of rapid recolonization is still unclear, shortcourse therapy with azithromycin or other antibiotics still requires additional investigation. while the carrier rate does not require treatment [ ] , some clinicians attempt to eradicate those colonized by group a strep to prevent spread to other family members and close contacts. a regimen of intramuscular penicillin v plus oral rifampin has been shown to reverse the carrier status in % of patients treated [ ] . there have been no studies performed more recently that have explored whether this regimen remains effective with increased group a strep resistance to penicillin. despite evidence that chlamydia and mycoplasma may be associated with acute pharyngitis, there have been no studies that have shown a benefit from treatment of patients with non-group a streptococcal pharyngitis with antibiotics: studies with penicillin [ ] , which would not be expected to cover these agents, and macrolides [ ] , which would have not shown any significant improvement over placebo. until specific tests that can rapidly identify these organisms are developed which would allow for targeted treatment and studies can demonstrate that treatment reduces symptoms and complications, indiscriminate antibiotic therapy for non-group a strep pharyngitis should be avoided. acute bronchitis is an inflammatory condition of the tracheobronchial tree usually associated with a generalized respiratory infection. cough begins early in the course of the illness and is the most prominent feature of the condition. an initially dry cough may later result in sputum production which characteristically changes from clear to discolored in the later stages of the illness. the cough may last for a significant time. although the duration of the condition is variable, one study showed that % of patients had a cough for more than weeks and % had a cough for more than weeks [ ] . patients with acute bronchitis usually have a viral respiratory infection with transient inflammatory changes that produce sputum and symptoms of airway obstruction. acute bronchitis is essentially a diagnosis of exclusion. the history should include information on cigarette use, exposure to environmental toxins, as well as medication history (e.g., use of angiotensin-converting enzyme inhibitors). the chronicity of the cough should be established to distinguish acute bronchitis from chronic bronchitis since they have different treatments. both acute bronchitis and pneumonia can present with fever, constitutional symptoms, and a productive cough. while patients with pneumonia often have rales, this finding is neither sensitive nor specific for the illness. when pneumonia is suspected on the basis of a presence of a high fever, constitutional symptoms, severe dyspnea, and certain physical findings or risk factors, a chest radiograph should be obtained to confirm the diagnosis. asthma and allergic bronchospastic disorders can mimic the productive cough of acute bronchitis. when obstructive symptoms are not obvious, mild asthma may be diagnosed as acute bronchitis. further, since respiratory infections can trigger bronchospasm in asthma, patients with asthma that occurs only in the presence of respiratory infections resemble patients with acute bronchitis. asthma should be considered in patients with repetitive episodes of acute bronchitis. patients who repeatedly present with cough and wheezing can be given full spirometric testing with bronchodilation or provocative testing with a methacholine challenge test to help differentiate asthma from recurrent bronchitis. finally, nonpulmonary causes of cough should enter the differential diagnosis. in older patients, congestive heart failure may cause cough, shortness of breath, and wheezing. reflux esophagitis with chronic aspiration can cause bronchial inflammation with cough and wheezing. bronchogenic tumors may produce a cough and obstructive symptoms. acute bronchitis in the otherwise healthy adult is one of the most common medical problems encountered in primary care [ , ] . the prevalence of acute bronchitis peaks in the winter and is much less common in the summer. viral infection is considered the primary cause of most episodes of acute bronchitis. a wide variety of viruses have been shown as causes of acute bronchitis including influenza, rhinovirus, adenovirus, coronavirus, parainfluenza, and respiratory syncytial virus [ ] . nonviral pathogens including mycoplasma pneumoniae and c. pneumoniae (twar) have also been identified as causes [ , ] . the etiologic role of bacteria like h. influenzae and s. pneumoniae in acute bronchitis is unclear since these bacteria are common upper respiratory tract flora. sputum cultures for acute bronchitis are therefore difficult to evaluate since it is unclear whether the sputum has been contaminated by pathogens in the nasopharynx. usually, laboratory and imaging tests are not needed in the diagnosis of acute bronchitis. however, a new test under consideration might be helpful in differentiating viral acute bronchitis from more serious bacterial infections such as pneumonia. by measuring procalcitonin, a precursor to the hormone calcitonin, christ-crain and colleagues have been able to distinguish patients at high risk for bacterial infections (those with higher procalcitonin levels) from those with low risk for bacterial infection. evaluation of this method in the emergency department has led to reductions in antibiotic prescribing without any differences in clinical outcomes for patients presenting with acute cough syndromes [ ] . while a point-of-care version of the test for procalcitonin has been developed that can be done quickly in a physician's office, the test is still expensive and has not been evaluated outside the emergency department. antibiotic treatment for acute bronchitis is quite common with evidence indicating that - % of adults visiting a doctor for acute bronchitis receiving an antibiotic [ , ] . clinical trials of the effectiveness of antibiotics in treating acute bronchitis have had mixed results. one reason for the lack of consensus is that in each of the nine trials, different antibiotics were used as well as different outcomes. in an effort to quantitatively review the data, two different meta-analyses were recently conducted [ , ] . in the fahey et al., meta-analysis resolution of cough was not affected by antibiotic treatment and neither was clinical improvement at reexamination. importantly, the side-effects of antibiotics were more common in the antibiotic groups compared to placebo. the smucny et al., meta-analysis concluded that antibiotics may be modestly effective for a minority of patients with acute bronchitis, although it is unclear which subgroups might benefit. the conclusion of both meta-analyses was that the benefits or antibiotics are marginal and are not useful for the general group of patients with acute bronchitis. recent data from clinical trials suggest that bronchodilators may provide effective symptomatic relief to patients with acute bronchitis [ , ] . treatment with bronchodilators demonstrated significant relief of symptoms including faster resolution of cough, as well as return to work. one study evaluated the effect of albuterol in a population of patients with undifferentiated cough and found no beneficial effect [ ] . since a variety of conditions present with cough, there may have been some misclassification in generalizing this to acute bronchitis. • upper respiratory infections and acute bronchitis are common illnesses that are account for a large proportion of total outpatient healthcare utilization as well as nearly % of prescribed outpatient antibiotics. • evidence does not support the use of antibiotics for the common cold, acute bronchitis, initial cases of otitis media with effusion, and non-group a streptococcal pharyngitis. these conditions are self-limited and currently are optimally treated with symptomatic medicines. • although the data are mixed regarding the utility of antibiotic treatment for acute sinusitis, otitis media, and group a streptococcal pharyngitis, antibiotics may have some benefit. short-course therapy with narrow-spectrum antibiotics appropriate for the likely pathogen is recommended. rhinovirus infections in an industrial population. ii. characteristics of illness and antibody response the common cold national ambulatory medical care survey: summary. vital health stat ( ) advance data from vital and health statistics clinical trial examining effectiveness of three cough syrups ineffectiveness of recombinant interferon-beta serine nasal drops for prophylaxis of natural colds national ambulatory medical care survey: summary microbiology and laboratory diagnosis of upper respiratory tract infections the economic burden of noninfluenza-related viral respiratory tract infection in the united states report of the committee of infectious diseases general recommendations on immunization: recommendations of the advisory committee on immunization practices the contribution of missed opportunities to childhood underimmunization in baltimore chemical disinfection to interrupt transfer of rhinovirus type from environmental surfaces to hands potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus and rhinovirus rhinovirus infections in an isolated antarctic station. transmission of the viruses and susceptibility of the population viruses causing common respiratory infections in man viruses and bacteria in the etiology of the common cold antibiotics and upper respiratory infection: do some folks think there is a cure for the common cold? antibiotic prescribing for adults with colds, upper respiratory tract infections, and bronchitis by ambulatory care physicians declining antibiotic prescriptions for upper respiratory infections antibiotics and chemotherapeutic agents in the treatment of uncomplicated respiratory infections in children evaluation of orally administered antibiotics for treatment of upper respiratory infections in thai children amoxycillin and co-trimoxazole in presumed viral respiratory infections of childhood: placebo-controlled trial randomised controlled trial of antibiotics in patients with cough and purulent sputum effects of antibiotic treatment in the subset of common-cold patients who have bacteria in nasopharyngeal secretions vitamin c for preventing and treating the common cold non-antibiotic treatments for upper-respiratory tract infections (common cold) randomized controlled tiral of clemastine fumarate for treatment of experimental rhinovirus colds usual care and outcomes in patients with sinus complaints and normal results of sinus roentgenography correlation of clinical sinusitis signs and symptoms to imaging findings in pediatric patients use of symptoms, signs and blood tests to diagnose acute sinus infections in primary care: comparison with computed tomography does this patient have sinusitis? diagnosing acute sinusitis by history and physical examination introduction and definition of sinusitis prevalence of clinical sinusitis in young children followed up by primary care pediatricians prevalence of sinusitis signs on mri in a non-ent paediatric population a -year report on childhood sinusitis: clinical presentations, predisposing factors and possible means of prevention primary-case-based randomised placebo-controlled trial of antibiotic treatment in acute maxillary sinusitis randomised, double blind, placebo controlled trial of penicillin v and amoxycillin in treatment of acute sinus infection in adults diagnosis and management of sinusitis the end of antibiotic treatment in adults with acute sinusitis-like complaints in general practice? a placebo-controlled double-blind randomized doxycycline trial randomized controlled trial of vs days of trimethoprim/sulfamethoxazole for acute maxillary sinusitis antimicrobial treatment in acute maxillary sinusitis: a meta-analysis diagnosis and antibiotic treatment of acute otitis media: report from international primary care network diagnosis and management of acute otitis media trends in doctor consultations, antibiotic prescription and specialist referrals for otitis media in children trends in otitis media treatment and relapse national trends in emergency department antibiotic prescribing in children with acute otitis media otitis media in children: to treat or not to treat? wait-and-see prescription for the treatment of acute otitis media: a randomized controlled trial management of acute otitis media by primary care physicians: trends since the release of the treatment of acute otitis media with a shortened course of antibiotics single-dose intramuscular ceftriaxone for acute otitis media in children single-dose ceftiraxone versus days of cefaclor for otitis media comparison of ceftriaxone and trimethoprimsulfamethoxasole for acute otitis media single-dose azithromycin for the treatment of children with acute otitis media overall cost in the treatment of otitis media acute otitis media: who needs post treatment follow-up? follow-up visit after acute otitis media treatment of recurrent otitis media after a previous treatment failure: which antibiotics work best? streptococcal pharynfitis in the general population controlled studies of streptococcal pharyngitis in a pediatric population sore throat, tonsillitis, and adenoiditis open randomised trial of prescribing strategies in managing sore throat prevalence of chlamydia trachomatis and mycoplasma pneumonia in children with and without pharyngitis diagnosis of streptococcal pharyngitis: differentiation of active infection from the carrier state in the symptomatic child effect of antibiotic therapy on the clinical course of streptococcal pharyngitis protective effect of antibiotics against serious complications of common respiratory tract infections: retrospective cohort study with the uk general practice research database prevention of rheumatic fever and diagnosis and treatment of acute streptococcal pharyngitis towards a better diagnosis of throat infections (with group a beta-hemolytic stretococcus) in general practice a clinical score to reduce unnecessary antibiotic use in patient with sore throat a scoring system for predicting group a streptococcal throat infection the rational clinical examination. does this patient have strep throat does culture confirmation of high-sensitivity rapid streptococcal tests make sense? a medical decision analysis the effect of erythromycin on resolution of symptoms among adults with pharyngitis not caused by group a streptococcus reattendance and cmplications in a randomised trial of prescribing strategies for sore throat: the medicalising effect of prescribing antibiotics management of children with acute pharyngitis: a decision analysis once daily therapy for streptococcal pharyngitis with amoxicillin randomized, single-blinded comparative study of the efficacy of amoxicillin ( mg/kg/day) versus standard-dose penicillin v in the treatment of group a streptococcal pharyngitis in children comparison of clarithromycin suspension and amoxycillin syrup for the treatment of children with pharyngitis and/or tonsillitis azithromycin versus penicillin v in the treatment of paediatric patients with acute streptococcal pharyngitis/tonsillitis. paediatric azithromycin study group evaluation of the efficacy, safety and toleration of azithromycin vs. penicillin v in the treatment of acute streptococcal pharyngitis in children: results of a multicenter, open comparative study. the swiss tonsillopharyngitis study group azithromucin versus cefaclor in the treatment of pediatrci patient with acute group a beta-hemolytic streptococcal tonsillopharyngitis penicillin plus rifampin eradicates pharyngeal carriage of group a streptococci a randomized controlled trial of doxycycline in the treatment of acute bronchitis common colds and related diseases mycoplasma pneumoniae and adenovirus respiratory illnesses in military and university personnel chlamydia pneumoniae (twar): a common agent in acute bronchitis effect of procalcitonin-guided treatment on antibiotic use and outcome in lower respiratory tract infections: clusterrandomized, single-blinded intervention trial current management of acute bronchitis in ambulatory care: the use of antibiotics and bronchodilators are antibiotics effective treatment for q acute bronchitis? a meta-analysis quantitative systematic review of randomised controlled trials comparing antibiotic with placebo for acute cough in adults symptomatic effect of inhaled fenoterol in acute bronchitis: a placebo-controlled double-blind study albuterol delivered by metered-dose inhaler to treat acute bronchitis a randomized controlled trial of oral albuterol in acute cough key: cord- -c z n ij authors: mungrue, kameel; brown, tessa; hayes, ivory; ramroop, savatri; thurston, portio; pereira, lexley pinto title: drugs in upper respiratory tract infections in paediatric patients in north trinidad date: - - journal: pharm pract (granada) doi: nan sha: doc_id: cord_uid: c z n ij objective: we explored the prescribing patterns of physicians in north trinidad in treating upper respiratory tract infections (urti) in paediatric patients and the appropriateness of drugs prescribed. methods: a retrospective observational study was conducted, with a sample size of paediatric patients, diagnosed with an urti during the period of june to june . the study was conducted at five primary health care facilities in north trinidad. results: the three most frequent urtis diagnosed were non-specific urti, common cold, and acute tonsillitis in rank order. four patterns of prescribing were identified, ( ) no drug therapy [ . %]; ( ) antibiotic therapy alone [ . %]; ( ) antibiotic and symptomatic therapy [ . %]; and ( ) symptomatic therapy alone [ . %]. the, most frequently prescribed antibiotics were penicillins (amoxicillin [ . %] and amoxicillin/clavulanate [ . %]) and a macrolide (erythromycin [ . %]). the three symptomatic agents most frequently prescribed were paracetamol [ . %]; diphenhydramine [ . %]; and normal saline nasal drops [ . %]. in cases with swab analyses done, of these, . % revealed a growth of commensals only, while . % grew pathogenic micro-organisms. of the cases showing commensal growth only, . % were treated with an antibiotic, . % were treated with symptomatic agents alone and . % received no drug therapy at all. conclusions: a large proportion of paediatric patients diagnosed with an urti in north trinidad was prescribed antibiotics although not indicated the inappropriate use of antibiotics can potentiate the worldwide trend of antimicrobial resistance. objetivo: exploramos los patrones de prescripción de los médicos en trinidad norte para el tratamiento de infecciones del tracto superior respiratorio (urti) en pacientes pediátricos y la adecuación de los medicamentos prescritos. métodos: se realizó un estudio observacional retrospectivo, con un tamaño de muestra de pacientes pediátricos diagnosticados con una urti entre junio y junio de . este estudio fue realizado en centros de atención primaria en trinidad norte. resultados: las urti más frecuentemente diagnosticadas fueron, por orden, urti no específicas, resfriado común, y amigdalitis aguda. se identificaron patrones de prescripción, ( ) sin tratamiento farmacológico [ [ , %] ; y gotas de suero salino normal [ , %] . en casos con análisis de torundas, de los que el , % reveló crecimiento de comensales, mientras que en el , % crecieron microorganismos patógenos. de los casos que mostraron crecimiento de comensales sólo, se trataron con antibiótico el , %, con agentes sintomáticos solos el , % y el , % no recibió tratamiento alguno. conclusiones: a una gran proporción de pacientes pediátricos diagnosticados con una urti en trinidad norte se le prescribió antibióticos aunque no estaban indicados. el uso inadecuado de antibióticos puede potenciar la tendencia mundial hacia las resistencias antimicrobianas. an upper respiratory tract infection (urti) is a nonspecific term used to describe acute infections involving the para-nasal sinuses, middle ear, pharynx, epiglottis and larynx. , upper respiratory tract infections are among the leading cause of acute morbidity and the most frequent cause of health service access worldwide. , according to estimates from the united states national ambulatory medical care survey, acute urtis were the fifth most common reason for seeking care and accounted for million physician visits in . in addition - % medical consultations and - % were in children. consequently respiratory tract infections are the second most common indication for antibiotic prescriptions in primary care accounting for % of all prescriptions annually in ambulatory practice. data from the national centre for health statistics in the united states indicate that in recent years, approximately % of all outpatient prescriptions for antimicrobial medications have been issued primarily for five conditions: otitis media, sinusitis, bronchitis, pharyngitis or non-specific urtis. the majority of urtis are of viral origin, due to rhinovirus, parainfluenza virus, coronavirus, adenovirus, coxsackie virus, and influenza virus. however, pharyngitis and the common cold have the greatest probability of being of viral origin. , only % of urtis has been attributable to bacterial aetiology , with the three most common organisms being streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis. the development of antimicrobial resistance has occurred predominantly among streptococcus pneumoniae, haemophilus influuenzae, and moraxella catarrhalis in paediatric patients. trinidad and tobago has a two tier system of health care namely public health care and private health care. the former is free of cost to the client at all levels and for all services. while all pharmaceutical agents are free they are limited in range and the majority are generic brands. this service is managed by the ministry of health and funded by the state. private health care is based upon fee for service, is costly and affordable mainly by high income earners. prescribing an antibiotic for urtis is a common practice in the medical profession. , , watson et al reported that visits for any upper respiratory tract complaint resulted in an antibiotic being prescribed in % of the consultations , particularly for pharyngitis where antimicrobial therapy should not be prescribed in the absence of diagnosed group a streptococcal or other bacterial infection. mohan et al in reported that the five most frequent urtis presenting in children in trinidad are the common cold, pharyngitis, tonsillitis, sinusitis and acute otitis media in rank order. further only % of physicians would request laboratory tests before prescribing antimicrobials; . % of physicians considered them unnecessary; % felt that a clinical diagnosis was sufficient; and . % said the long waiting periods for results rendered laboratory impractical. the frequent and unnecessary use of broadspectrum antimicrobial together with the use of second-generation macrolides has been demonstrated unequivocally to lead to antimicrobial resistance. [ ] [ ] [ ] the majority of antibiotic prescriptions are for respiratory infections and occur in primary care. , children are the principal recipients of a disproportionate quantum of these prescriptions. this study examined the prescribing patterns for urtis in paediatric patients attending primary care clinics in north trinidad, and the appropriateness of prescribed agents. we also determined the proportion of paediatric patients who actually had a bacterial urti based on culture and sensitivity tests. this was a retrospective observational study of paediatric patients with a physician diagnosis of an urti during the period june to june . five public health facilities were randomly selected for this study, four of which had independent routine swab analysis performed by the national surveillance unit. a paediatric patient was a subject years or below and an antibiotic was defined as a substance with bactericidal or bacteriostatic effects. the term is often extended however to include synthetic antibacterial agents, not produced by microbes , such as sulfonamides and quinolones, which was adopted in this study. the diagnoses of urtis for the purposes of this study are: the common cold, acute pharyngitis, acute tonsillitis, sinusitis, acute otitis media, viral urti, influenza and non-specific urti. exclusion criteria were ( ) age equal or lower , ( ) subjects immunocompromised, malnourished or infected by laboratory confirmed resistant strains of pathogens and chronic respiratory tract diseases and ( ) a subject without a definite diagnosis of urti. data were analysed using minitab version . data from throat swabs performed under the national surveillance programme conducted at four ( ) of the health facilities studied were collected and used for analysis. swabs were taken from children presenting with complaints of an upper respiratory tract infection and were obtained on the same day as the physician's visit and were independent of physician consultation. these swabs were transported in commercially available transport media to the microbiology department of the port of spain general hospital where they were initially plated on blood agar containing antibiotic strips to detect sensitivity. the common cold and non-specific urti were also the only two diagnoses made in children over years of age. disease occurrence and gender were not associated except for otitis media in which ( %) of the cases occurred in boys. four patterns of prescribing were observed, ( ) there was a significant association between antibiotic prescribing and therapy for relief of symptoms [p= . ] so that antibiotic prescription was likely to be given with a prescription for symptom relief. in of the cases studied throat swabs were analysed for culture and sensitivity. in [ . %] participants growth of commensals only was reported, and only two subjects had pathogenic organisms; one with streptococcus pyogenes and the other with staphilococcus aureus. in children harbouring commensals, . % were diagnosed with a nonspecific urti, and . % had the common cold. in the one patient in whom staphlococcus aureus was isolated, a diagnosis of the common cold was made, the patient received amoxicillin/clavulanate and the sensitivity report indicated resistance to ampicillin. in the patient with streptococcus pyogenes, the child had non-specific urti, received amoxicillin, and the sensitivity report indicated resistance to amoxicillin. in the participants in whom commensal growth was reported, . % were treated with antibiotics and symptomatic agents and . % were treated with an antibiotic alone. the three most frequent urti's diagnosed in children were non-specific urti, common cold and acute tonsillitis. the diagnosis of non-specific urti's may reflect difficulty by physicians in our setting to precisely identify the diagnosis and aetiology. the recognition by physicians that bacterial urti's are infrequent is in part due to the lack of local evidence that emphasises this feature of urti's which in turn facilitates the misconceptions regarding antibiotics and urti's. there were no gender differences in the occurrence of urti except for acute otitis media in which there were more boys [ . %] than girls [ . %] . we find this difficult to explain as did pukandor et al who reported similar findings. four patterns of prescribing prevail in community health care in trinidad: ( ) a large percentage [ . %] of patients was prescribed antibiotics for urtis contrary to evidence based practice. , the factors contributing to this prevailing pattern of prescribing in our setting is a complex process involving both patient and physician factors. public misconceptions on the effectiveness of, and indications for, antibiotics exist. patients presenting with an acute febrile illness often believe that infection is the problem and antibiotics is the answer. thus patient expectations significantly influence prescribing even if the physician judges that antibiotics are not indicated. lack of continuing medical education among primary care physicians not presently a legal requirement for continuing to practice may also contribute, as more primary care physicians are more likely to initial see these patients than paediatricians. amoxicillin was the most frequently prescribed antibiotic a finding similarly reported by britt et al. however, in our setting, the choice of this antibiotic may be influenced by the ease of availability at public health pharmacies where antimicrobials are often available without prescription. in addition, % of patients with the common cold received an antibiotic contrary to evidence based guidelines. even with a mucopurulent rhinitis (thick, opaque, or discoloured nasal discharge) which frequently accompanies the common cold antimicrobial treatment is not indicated unless it persists without improvement for to days. more than % of patients with a non-specific urti received an antibiotic which is not recommended as it does not enhance illness resolution or alter the rates of complications. a large percentage ( . %) of patients with other urtis (acute tonsillitis, acute otitis media, viral urti, influenza, and acute pharyngitis) also received an antibiotic. almost all patients ( / ) with a diagnosis of acute tonsillitis were prescribed antibiotics. thus is not unusual as physicians are more concerned with the prevention of rheumatic fever especially as laboratory support is inadequate and treatment of group a streptococcal infection with antimicrobial therapy should be initiated within days of onset to be effective in the prevention acute rheumatic fever. , all patients diagnosed with acute otitis media were treated with antibiotics. while antimicrobials are indicated for treatment of acute otitis media, diagnosis requires documented middle ear effusion and symptoms and signs of acute local or systemic illness. the pressures of large volume clinics and the difficulty to follow up patients may strongly influence physicians to use antimicrobials. eight of the patients diagnosed with acute otitis media received amoxicillin. any decision to treat children with acute otitis media with an antibacterial agent, requires that amoxicillin be prescribed because of its safety, low cost, acceptable taste, and narrow microbiologic spectrum. , treating influenza without established secondary bacterial infection with antibiotics has not proven beneficial , yet eight of the nine patients diagnosed with influenza received antibiotics. only [ . %] of the children who had swab analyses showed growth of bacterial pathogens supporting the evidence that most urtis are of viral origin. the main limitation of the study was the use of nurses at the health facility to take the throat swabs although the technique was explained to them we had no way of validating the procedures. future studies to evaluate the resistance patterns of organisms commonly implicated in urtis in trinidad and tobago are recommended. in conclusion we provide evidence justifying the need to modify the current approach to the management of urti in the paediatric setting in trinidad. mainly as a result of the large proportion of paediatric patients diagnosed with an urti who were treated with an antibiotic. although this study was conducted in a small developing country, there are global implications as inappropriate use of antibiotics can potentiate the worldwide trend of antimicrobial resistance. upper respiratory tract infections. cleveland clinic. department of infectious disease clinical pharmacy and therapeutics physician behaviour for antimicrobial prescribing for pediatric upper respiratory tract infections: a survey in general practice in trinidad, west indies antibiotics for upper respiratory tract infections. follow up utilization and antibiotic use national ambulatory medical care survey, summary. hyattsville, md: national centre for health statistics. vital health statistics current estimates from the national health interview survey, .. vital health stat american college of physicians, american society of internal medicine, american academy of family physicians, infectious diseases society of america. principles of appropriate antibiotic use: part ii. nonspecific upper respiratory tract infections trends in antimicrobial drug prescribing among office-based physicians in the united states systematic review of the treatment of upper respiratory tract infection the merck manual of diagnosis and therapy. section -ear, nose, and throat disorders and chapter -pharyngitis pocket essentials of clinical medicine principles of judicious use of antimicrobial agents for pediatric upper respiratory tract infections antimicrobial resistance among pediatric respiratory tract infections: clinical challenges antimicrobial use for pediatric upper respiratory infections: reported practice, actual practice, and parent beliefs pharyngitis-principles of judicious use of antimicrobial agents prevention of infections due to antibiotic-resistant bacteria confronting the problem of increasing antibiotic resistance increased use of second generation macrlide antibiotics for children in nine health plans in the united states reduced antibiotic use in a paediatric practice: practical office strategies based on current evidence antibiotic prescribing by primary care physicians for children with upper respiratory tract infections outpatient antibiotic use in europe and association with resistance: a cross-national database study the pharmacological basis of therapeutics dorland's illustrated medical dictionary mosby's medical nursing and allied health dictionary minitab release . state college occurrence and recurrence of acute otitis media among children antimicrobial prescribing for acute purulent rhinitis in children: a survey of paediatricians and family practitioners the general public's perception and use of antimicrobials in trinidad and tobago beach bettering the evaluation and care of health. a study of the common cold -principles of judicious use of antimicrobial agents rheumatic heart disease -a challenge febrile exudative tonsillitis: viral or streptococcal? otitis media -principles of judicious use of antimicrobial agents american academy of family physicians (aafp) and american academy of pediatrics (aap). diagnosis and management of acute otitis media available at url bacteriologic and clinical efficacy of high dose amoxicillin for therapy of acute otitis media in children prevention of complications of respiratory illness in paediatric practice: a double-blinded study none declared. key: cord- -ua w xki authors: cooper, emily; jones, leah; joseph, annie; allison, rosie; gold, natalie; larcombe, james; moore, philippa; mcnulty, cliodna a. m. title: diagnosis and management of uti in primary care settings—a qualitative study to inform a diagnostic quick reference tool for women under years date: - - journal: antibiotics (basel) doi: . /antibiotics sha: doc_id: cord_uid: ua w xki background: to inform interventions to improve antimicrobial use in urinary tract infections (utis) and contribute to a reduction in escherichia coli bloodstream infection, we explored factors influencing the diagnosis and management of utis in primary care. design: semi-structured focus groups informed by the theoretical domains framework. setting: general practice (gp) surgeries in two english clinical commissioning groups (ccgs), june to march . participants: a total of gp staff within focus groups. results: staff were very aware of common uti symptoms and nitrofurantoin as first-line treatment, but some were less aware about when to send a urine culture, second-line and non-antibiotic management, and did not probe for signs and symptoms to specifically exclude vaginal causes or pyelonephritis before prescribing. many consultations were undertaken over the phone, many by nurse practitioners, and followed established protocols that often included urine dipsticks and receptionists. patient expectations increased use of urine dipsticks, and immediate and days courses of antibiotics. management decisions were also influenced by patient co-morbidities. no participants had undertaken recent uti audits. patient discussions around antibiotic resistance and back-up antibiotics were uncommon compared to consultations for respiratory infections. conclusions: knowledge and skill gaps could be addressed with education and clear, accessible, uti diagnostic and management guidance and protocols that are also appropriate for phone consultations. public antibiotic campaigns and patient-facing information should cover utis, non-pharmaceutical recommendations for “self-care”, prevention and rationale for days antibiotic courses. practices should be encouraged to audit uti management. ( ) by purposively selecting ccgs with different sociodemographic characteristics and then inviting surgeries to participate in a random order, we were able to reduce bias and get input from surgeries with a range of antibiotic prescribing rates. ( ) we were able to speak with staff members from practices with various roles in the management pathway. this allowed us to explore the behaviour of non-prescribers. ( ) general practices that were more overburdened or going through changes were more likely to decline to participate, and their views may not have been captured. ( ) using the theoretical domains framework to develop our focus group schedule allowed us to explore all areas of behaviour and fed into intervention development. ( ) nesting this piece of research within a project that included the development of uti resources for all ages, including a uti flowchart and leaflet for older adults, could have biased discussion to focus more on management in older adults (which is seen as more complex by clinicians) even when general feedback was prompted for during the discussion. escherichia coli is the main cause of bloodstream infection in the uk and is responsible for more than one-third of bloodstream infection cases in england each year [ , ] . yearly rates of e. coli bloodstream infections (ecbsis) increased by % between and ( . / , population in to . / , population in ) [ ] . modelling, using english mandatory surveillance data in , showed that if rising trends are not influenced, there will be a . % year-on-year increase in incidence of ecbsis by / [ ] . this will be even higher for community onset cases ( . %) [ ] . because most cases of ecbsi ( % of cases) are attributed to an underlying urological condition, infections of the urogenital tract contribute the highest number of deaths when comparing days all-cause mortality in people with ecbsi [ , ] . independent risk factors for ecbsi related to the urogenital tract include experiencing or having treatment for a uti in the previous month, having a short-or long-term urinary catheter, and being a woman [ , [ ] [ ] [ ] . we may be able to prevent and reduce ecbsis if we effectively diagnose and manage community acquired utis in adults [ ] . antimicrobial stewardship policies and interventions over the last decade have focused on improving management of common infections presenting in primary care [ , ] . however, key challenges of inappropriate prescribing and diagnosis remain for uti and overuse has continued to drive antimicrobial resistance in gram-negative organisms causing utis and bsis. one-fifth of antibiotic prescriptions between and in england were for uti-related conditions [ ] . in , english uti antibiotic guidelines changed to suggest nitrofurantoin as first-line treatment for lower uti, and in / , a reduction in the trimethoprim:nitrofurantoin prescribing ratio was included in the quality premium [ ] . this has probably contributed to the significant decreases in trimethoprim use (by % since ) and a decrease in e. coli-resistant trimethoprim within uti samples in england ( . % to . % between and ) [ ] . however, we know that these improvements have varied significantly between health authorities across england and more needs to be done to support the universal use of national prescribing guidance [ ] . greater trimethoprim prescribing (compared to nitrofurantoin) is associated with a higher incidence of bsi, uti-related trimethoprim-resistant e. coli bsi, and increased incidence of trimethoprim-resistant bloodstream infection [ ] . to help inform interventions to improve the management and diagnosis of utis within primary care, the authors explored gp staff's diagnosis and management of uti in adults under years. this coincided with a planned review of the public health england (phe) diagnosis of urinary tract infections: quick reference tool for primary care [ ] . specific aims of this review included: i. determine the practices of primary health care staff when diagnosing and treating utis in patients under years in the primary health care setting, ii. identify where there are current barriers and facilitators to appropriate diagnosis and treatment, and iii. identify how these gaps may be addressed through resource development or other measures. although the aims of the review included the whole population of england, large parts of the focus group discussions were focused on women under years, and this is the focal group for the qualitative findings highlighted in this paper. we aimed to attain views from primary health care staff with a range of experience around the diagnosis and management of uti in england. therefore, we purposively sampled in two areas with different demographics/populations: gloucestershire and nottingham city (ccgs). these two clinical commissioning groups (ccgs) were chosen as they provided different types of urban/rural, socioeconomic and ethnic population breakdowns based on information from the uk national census ( ccgs commission medical care for gp practices, deciding what services are needed for diverse local populations, and ensuring that they are provided. most people who reside in the uk have access to primary care through a gp practice. practices vary in their rates of urine submission to local laboratories, and this may be associated with differing staff views on the management of uti. to account for this, practices in each ccg were stratified by higher, middle or lower rates of local laboratory urine specimen submission. to try and reduce sampling bias and to avoid only enrolling practices with an interest in utis, gp practices in each stratum were randomised and then approached by letter and telephone in random order until one practice per strata in each region was recruited. invitation letters from phe contained study information sheets and a consent form. each participant was offered a £ high-street voucher incentive to participate. response rates were % (n = / ) and % (n = / ) in the gloucestershire and nottingham city ccgs, respectively. focus group discussion schedules were developed by the research group, including microbiologists, a patient, a psychologist, researchers and a gp, and were informed by the theoretical domains framework (tdf) ( table ) [ ] . topic areas included primary care staff attitudes and experiences of managing suspected and proven urinary tract infections, antimicrobial resistance and antibiotics, and a discussion with staff about their thoughts and opinions on the diagnostic process proposed in the draft uti diagnostic flowchart. the focus group discussion schedule for the practices was piloted, but there were no significant changes made following the pilot and findings from this group are included in the results. focus groups were facilitated and observed by trained qualitative researchers, held in general practices, and lasted from to min. discussions were audio-recorded, transcribed verbatim and checked for accuracy by a member of the research team. data was analysed inductively by phe researchers, lj and ra, using qsr nvivo [ , ] . themes were refined until redundant or infrequent codes were recoded. ten percent of transcripts were double coded by a second researcher (ng). codes were discussed by the researchers, and a consensus was reached. after this initial analysis, the results with representative participants' quotes were discussed by the research group and at an expert stakeholder workshop attended by gps, nurses, pharmacists, public representatives, microbiologists, and other medical professionals. the themes were then considered within the tdf framework. after each focus group, gp staff's opinions were used to tentatively modify a uti quick reference diagnostic tool for the next focus group. quotes specific to patients over the age of years were coded apart from those from the discussion about general patients and are presented elsewhere [ ] . though the general discussion did at times include discussion around men and a children, most of the focus was on younger women presenting at the practice as this was the focus of the uti diagnostic tool. quotations from the transcripts are used in the results table to illustrate the most prominent tdf domains (table ) and findings. the terms used to explain how many groups agreed on or discussed an issue or finding in the results include "most"-meaning that or more focus groups raised or discussed the issue; or "some" meaning that to groups raised or discussed the issue. the updated diagnostic tool: • links to latest national guidance on antimicrobial prescribing for utis; • lists the main at-risk groups and other risk factors to consider for antibiotic resistance, and • links to a uti leaflet for women under years that explains evidenced-based prevention and self-care recommendations. gp practices discussed frequent/recent use of antibiotics, long duration/high doses of antibiotics, recurrent uti, and positive lab results as risk factors for antibiotic resistance. "certainly, the people coming back, recurrent utis . . . you sometimes think are we actually missing something here are they having proper uti, the dipstick might show it but actually having an msu with a proven uti can help in the long term, so that's one group." (gp ) practice suggestions for prevention of uti focused on hydration, sachets/cranberry products, lemon barley water, and wiping front to back. some gp staff discussed conflicting information regarding the use of cystitis sachets and cranberry products for prevention or treatment of utis. "cranberry juice seems to have fallen out of fashion. the wording . . . in the guidance now . . . is that cranberry juice is effective for some women, but there is very limited research to back it up. the impression that we get is that the reason why cranberry juice is working is because they're drinking a lot of fluid." (gp ) some gp staff reported that phone consultations (sometimes with dipstick results) are being used to assess and treat patients at risk for a uti. " . . . we ask them relevant questions, how long they've had the symptoms for, have they tried any over the counter, what are their symptoms, whether it's dysuria, frequency, back pain, temperature, nausea, vomiting, that sort of thing, and it depends on the answers . . . particularly at our surgery, if they're under , we just, they give them a prescription over the phone." (gp ) the updated diagnostic tool: • clearly outlines how to clinically assess someone with suspected uti; • includes prompts/considerations around differential diagnosis, pyelonephritis, and sepsis; • clearly outlines the steps for clinical assessment of someone with suspected uti and when a urine dipstick test or culture is needed; • provides information on the sensitivity and specificity when using urine dipsticks to diagnose a uti for women under years; • has been developed as an update to previous guidance; • links to latest national guidance on antimicrobial prescribing for uti management (developed since this study was conducted); • links to uti leaflets and resources for women under years that explains evidenced-based prevention and self-care recommendations. some groups reported that they would prescribe antibiotics over the phone for a patient under the age of with - urinary symptoms. at the telephone consultation, some practice staff asked for a urine sample to be brought in but others considered this as unnecessary. "int: how would you diagnose a suspected uti over the phone versus in face to face consultation? f : well just do the same but not examine them or dip it . . . we tend to not ask for a sample unless there was something complicated about them." (gp ) some practice staff reported that patients 'drop and run', leaving urine samples at reception, often because they think they might have a uti. clinicians then ring the patient for a clinical history. "m : . . . we do end up with patients just turning up and leaving urine samples at the desk. int: so what determines whether they get sent for culture? m : well, well they get dipped but then we want to know a bit more of the clinical information so . . . the nurses comes and says, i've checked this urine. we need a bit more than that . . . i think commonly we'd just end up phoning the patient and saying look . . . why have you dropped it off?" (gp ) some gp staff feel that easy availability of urine samples influences their decision to use urine dipsticks as part of the diagnostic process. " . . . think for the vast majority we would test . . . even in females under who . . . you certainly don't need to send a culture for but if a urine is easily obtainable we'd normally get one." (gp ) most gp staff followed phe guidance for uti diagnosis and which focused on the key symptoms of dysuria, urgency and frequency as symptoms and would not include findings from the most recent literature. " . . . and i use the current guidance to decide whether to treat without dipping the urine or to just go ahead and treat. and i think it's if they have three symptoms, that you don't have to dip the urine and you just treat. if they're under and they're a woman then i would tend to use that . . . ." (gp ) most gp staff agreed that the exclusion of pyelonephritis and sepsis needed to be included in tools that are developed to diagnose uti. "i think sepsis has to be first, doesn't it? it's the trump card, is it?" (gp )" . . . and obviously, you've got to think about sepsis now." (gp ) some gp staff expressed the need for more national guidance specific to the management of utis. " . . . something on recurrent uti would be really helpful because . . . some guidance . . . just sort of says consider this, consider that . . . there's a lot more interpretation with recurrent uti." (gp ) some gp staff reported that lab specimen service pickups were not frequent enough to allow culture results to inform treatment, which leads to overcautious prescribing. " . . . i'm going to treat because i won't get the result of this msu, this is a thursday i'm not going to get it till tuesday so we tend to treat." (gp ) some gp staff reported that they did not have the option of using fosfomycin or pivmecillinam as second-line treatment. "f : but they didn't actually have fosfomycin or pivmecillinam on the (sensitivity reporting) list. m : no they don't have fosfomycin . . . ." (gp ) most gp staff indicated that more information or education for patients on uti was needed, including a uti leaflet and public health information/campaign that covers the prevention and treatment of uti in line with national guidance. " . . . like with coughs and colds everyone knows now that they're not going to get an antibiotic necessarily, they've braced themselves for the bad news, haven't they? but with uti they wee once and it stings and . . . they separate it and somehow it doesn't go under that hurt. it's literally they're right in, aren't they, really quickly." (gp ) some gp staff reported that receptionists in some surgeries ask patients who ring up to bring urine samples into the surgery and provide guidance on sample collection. "the receptionists actually, if anybody rings up and says, i think i've got a uti they, they say can you, next time you go can you make sure you keep a clean catch? so that we've already started a process of looking at having a . . . dip if needs be." (gp ) the updated diagnostic tool: some gp staff reported that nurses may be responsible for testing urine samples left at reception and referring to clinicians if they are concerned the patient has a uti. " . . . often, they've already had a urine dipped by our nurses by the time that they get to us . . . . if the other nurses see someone and they're suspecting a uti they'll . . . ask us to prescribe, but they'll tell us what they've found, examination wise and history. so run it by us." (gp ) some gp staff reported that nurse prescribers frequently see uncomplicated cases of uti independently. " . . . i (nurse prescriber) deal predominantly in the triage and assessment of acute illnesses and utis being probably quite an awful lot of it and it's part of a team where we prescribe quite regularly for it following national guidelines." (gp ) some gp staff reported that general practitioners will deal with utis but often focus on complicated cases or treatment failures. "i tend to be seeing people who either they've got complicated features or they've had treatment already, or there's something else . . . . i do quite a bit of telephone work, advice work." (gp ) some gp staff asked about vaginal discharge during a consultation, and one group reported this was done after using a urine dipstick to rule out a uti. " . . . you ask for certain symptoms . . . if it sounds like a uti and it seems like a uti on a dipstick you treat as such. it would only be if you weren't sure, if you needed to think about other symptoms then you would say have you got a vaginal discharge." (gp ) the updated diagnostic tool: • flags the need to assess for vaginal discharge early in the diagnostic process; • suggests when to use urine dipsticks; • states criteria for sending urine for culture; • links to a uti leaflet for women under years that provides evidenced-based recommendations for self-care, prevention, and safety netting. most groups said they would send a culture following treatment failure or for a recurrent uti but only some groups reported sending a urine for culture if the dipstick was negative but the patient symptomatic, if the patient was quite unwell, for male patients, pregnant women and for children. some groups indicated that they would not send a urine culture if the dipstick was negative or if the symptoms clearly indicated an uncomplicated uti. "with different things depending on the patient. so a pregnant or recurrent or, we're more likely to send a urine off. we don't send them off if it's an uncomplicated uti with typical symptoms." (gp ) most gp staff reported discussing non-medical advice with their patients. this was in the context of self-care for mild symptoms (especially with a negative dipstick), or preventing uti recurrence. "yeah, but if they've got relatively mild symptoms or few symptoms you can let them carry on flushing it out . . . " (gp ) some gp staff reported differences of opinion on interpretation/use of urine dipstick; especially when symptoms do not match urine dipstick results which challenge uti diagnosis. some gp staff feel that patient expectation influences their decision to use urine dipsticks as part of the diagnostic process. " . . . if they're young, fit, well, uncomplicated and got typical symptoms, technically you don't need to do a dipstick. but you often still do it because the patients have that expectation because they want to be told this is definitely a urine infection. if you just say, you've got typical symptoms here are antibiotics, they still feel as though they want to be told this is an infection, so they will ask for it to be dipped or expect it to be dipped." (gp ) the updated diagnostic tool: • links to a uti leaflet for women under years that provides support to a clinician when discussing with a patient about: o when a dipstick result should be used to diagnose a uti; o what a delayed prescription is and when to use it; o safety netting advice; o evidenced-based self-care and prevention advice for utis, including over-the-counter products. some practices generally felt that patients did not understand that a uti can clear on its own safely and expected treatment and believe that patients react differently to a no antibiotic decision with respiratory infections due to more consistent messaging/campaigns in this area. "almost never, usually, if it's for something like a sore throat or what have you, then . . . they're getting more receptive, because it's been a consistent message that they're not going to get antibiotics unless x, y, z, but in urinary tract infections almost never, they just want them." (gp ) some practices talked about how patients might obtain cystitis sachets from the community pharmacy and will only come for a consultation if symptoms don't improve. " . . . because we do get patients who have been to the pharmacist and i don't see the ones who don't come back, but i do see the ones who do, and . . . after week later they're now going their urine is painful and they need antibiotics . . . ." (gp ) some gp practices indicated that concern about issues like sepsis causes them to be overly cautious when diagnosing and treating utis. the updated diagnostic tool: • clearly outlines the steps for clinical assessment of someone with suspected uti; • includes prompts/considerations around differential diagnosis, pyelonephritis, and sepsis; • references national sepsis guidance; • references national guidelines on delayed and back-up prescribing for utis; • clarifies criteria and risk factors for antibiotic resistance; • references recent evidence; around hydration as a mechanism for preventing recurrent uti. most gp staff would not usually use a delayed/back-up prescription for utis. "usually not so much utis because by then they've already had the symptoms they're coming in and they're symptomatic, whereas a lot of people with sore throats come in and say it started yesterday. so, you can give them delayed, but i'm sure the percentage that cash in a delayed prescription is a lot higher" (gp ) most groups reported that they would discuss antibiotic resistance with some patients with an expected uti, especially if there were additional risk factors. "occasionally, gradually, particularly if they've got a recurrent uti or if they've had, say, side effects following antibiotics previously, like thrush. then you might have a conversation about the pros and cons." (gp ) hydration was discussed by most groups as a way to "flush out" the bladder/infection and was seen by some as the reason that cranberry juice is effective. "basically, just get as much fluid down you as you can and flush it out. because if the urine analysis is negative each time, . . . that's all you can advise them." (gp ) though most practice staff used national guidance to manage utis, some would not refer to it every time. "i intermittently look at the guideline and make sure what i think and i'm doing is correct, and then invariably i look and realise what i think i'm supposed to be doing is slightly changed over the couple of months since i last read it." (gp ) the updated diagnostic tool: • is developed to be integrated into gp systems so that it can be updated and referred to easily. some gp staff believe that day courses of antibiotics were not sufficient. this was driven by patient expectations and perceived efficacy of the dose and pressured them to lengthen the dose or use a different antibiotic. "m : . . . i still find it quite hard to prescribe in three days, (some agreement) because patients don't like three days. m : they don't do they, they don't think it's worth it . . . m : they do not think that you're giving them enough and that's quite tricky i think, i still find that, trying to convince them that three days will be enough." (gp ) "i never find that three days of antibiotic works. i get so many people coming back (with uti symptoms) that i don't prescribe three days any more actually." (gp ) the updated diagnostic tool: • references national prescribing guidelines for utis which clearly states risk factors and co-morbidities that need to be considered when treating a uti; • references national guidelines on delayed and back-up prescribing for utis; • clarifies criteria and risk factors for antibiotic resistance; • links to a uti leaflet for women under years that provides support to a clinician when discussing with a patient: o what a delayed prescription is and when to use it o risk related to antibiotic use and resistance. some gp staff would delay antibiotics when waiting for results from urine culture if symptoms were mild. "it depends on the day of the week, so if it's a thursday and the results aren't going to come back, i might give them a prescription and say let me send it, if you get worse whilst you're waiting for the results, that's the context that i would do that." (gp ) some gp staff would discuss completing the antibiotic course but were less inclined to discuss antibiotic resistance in relationship to utis than other infections, especially if they were confident in their diagnosis. "i think it also depends on how convinced i am they've got a wee infection. so, if i'm convinced they've got a wee infection, and they're quite systemically unwell with it, then i may not fight trying to give them the antibiotics as much as i might do if they're going: i've had a bit of dysuria and i don't know quite what's going on." (gp ) various factors that would influence the clinician's decision to provide an immediate antibiotic include renal function; co-morbidity; diabetes; immunosuppression; cost of treatment; pregnancy; severity of symptoms; age of patient; and time before the weekend. "egfr, their diabetes status, the recurrence of the symptoms, whether they're pregnant or not, that sort of thing, so there's quite a few other issues that i need to then take on board despite the guidance that's being given out." (gp ) one gp group was optimistic that the message about not receiving an antibiotic immediately was becoming widely more accepted. "people are starting to get that message now, with what's been in the press, . . . it's refreshing that you now come across more patients who will say . . . i don't want one if i don't have to have one. and if you say, let's give this a few days or let's wait for the culture to come back or whatever and see, they're ok with that." (gp ) the updated diagnostic tool: • links to a uti leaflet for women under years can be used by a clinician when discussing with a patient about the need for antibiotics and alternative options for uti management. the usefulness of a having an accurate point-of-care test was mentioned by some groups, but the perceived benefit was often to provide reassurance to the patient. " . . . oximetry, one thing i do with these people the ones who come with cold and cough, i put them on the machine, i say look, oxygen, pulse is level, temperature normal, you haven't got an infection and they love it, so that reassures them. if there was a something which we got, where we put the urine and say look, it says there's no infection. they will be happy." (gp ) the updated diagnostic tool: • links to the target antibiotics toolkit which provides tools to audit uti prescribing. some groups had audited their antibiotic prescribing recently and none had audited antibiotic prescribing for utis specifically. "different members of staff have audited different topics, haven't you? we're doing one at the moment . . . on copd antibiotics. we have our own internal audits and most of you do an audit for your appraisals and things as well don't you?" (gp ) most gp staff believed that patients expect to be prescribed an antibiotic if they have urinary symptoms "m : i think, as *** has said, it's patient expectations. f : so they have these symptoms and they've always had antibiotics. m : they've had the symptoms. f : so they need antibiotics again, or they've got the same, the same symptoms and don't often consider that there might be another, another cause." (gp ) the updated diagnostic tool: • links to a uti leaflet for women under years that provides support to a clinician when discussing with a patient about: o what a delayed prescription is and when to use it o risk related to antibiotic use. there were no significant findings that were more related the domains of goals, intentions, and emotions than others covered above. * the terms used to attribute group consensus in the results include "most"- or more focus groups agreed/discussed; or "some"- to groups agreed/discussed. data was triangulated through discussions during an expert stakeholder workshop discussed previously (january ), where experts discussed and applied the findings to recommendations for diagnostic tool development. findings indicated that management of uti in younger patients was shared by most staff within the surgery. receptionists in some surgeries asked patients who telephone with urinary symptoms to bring urine samples into the surgery and provided guidance on sample collection. nurses often tested urine samples left by patients at reception and referred the patients to clinicians if they were concerned the patient had a uti. nurse prescribers frequently managed patients with uncomplicated cases of uti, without any referral to other medical staff. gps reported having face to face consultations for utis and telephone consultations, managing complicated cases and treatment failure. almost all focus groups reported that they may use telephone consultations to manage patients who have a suspected uti. at the telephone consultation, some clinicians asked for a urine sample to be brought in but others considered this as unnecessary. patients dropping unrequested urine samples off at gp reception was reported by most groups as a challenge in diagnosing and managing utis, and some groups reported that they would then have to ring the patient for a clinical history. some groups reported that they would prescribe antibiotics over the phone for a patient with - urinary symptoms, only requesting clinical examination to rule out pyelonephritis if: the patient had recurrent utis, there were any risk factors for more severe infection, or the clinician was worried about the patient. three groups reported asking about vaginal discharge and considering other genitourinary causes during a consultation for suspected uti. some of these groups indicated that other genitourinary causes were considered later in the consultation after ruling out a uti (by using urine dipstick). there was a range of opinions on when to send a urine for culture and when to rely on urine dipsticks for patients. most groups said they would send a culture following treatment failure or for a recurrent uti. some groups reported sending a urine for culture if the dipstick was negative but the patient was symptomatic, if the patient was quite unwell, for male patients, for pregnant women, and for children. some groups indicated that they would not send a urine culture if the dipstick was negative or if the symptoms clearly indicated an uncomplicated uti. most groups indicated that urine would always be dipped if it was dropped at reception or brought in with the patient who had a suspected uti. sometimes, this was at the request of the nurse/receptionist and performed by the nurse. some groups felt that patients expected that a dipstick would be used as part of the diagnostic process. this expectation and readily available urine samples influenced their decision to use urine dipsticks as part of the diagnostic process, though some prescribers indicated that they would not ask for a sample if the patient was strongly symptomatic (with three symptoms, as per the phe uti diagnostic guidance) [ ] . participants also reported varying interpretation and use of urine dipsticks, especially when symptoms did not match the urine dipstick results. most groups reported using the phe uti diagnostic guidance or local guidance to guide decision making, though they might not refer to it every time [ ] participants reported that laboratory specimen collection services were not frequent enough to allow culture results to inform treatment. some groups suggested that an accurate point-of-care test to aid in the diagnosis of a uti would be very useful. this was often related to the clinician's desire to have a visible test with which to reassure the patient, or a result to reliably determine the need for antibiotics. some groups indicated that concern that they might miss sepsis/pyelonephritis caused them to be overly cautious when diagnosing and treating utis. when reviewing the ideas for the updated diagnostic tool, most agreed that the exclusion of pyelonephritis and sepsis needed to be included, as part of any updates. there was discussion about what stage pyelonephritis and sepsis should be considered in a uti consultation; some groups thought it should be excluded early on and others thought it should be ruled out after uti symptoms were discussed. some groups expressed the need for more or clearer national guidance advising about key areas of the management of utis. this included recurrent utis (three groups), catheterised patients (one group), and frank haematuria (one group). most groups expressed the belief that patients expect to be prescribed an antibiotic if they have urinary symptoms, especially if they have had them before or if the dipstick is positive. this expectation was reinforced by being given antibiotics at previous consultations for similar symptoms. most groups would not usually use a delayed/back-up prescription for utis. some considered this option when waiting for results from urine culture if symptoms were mild. practices generally reported that patients did not understand that a uti can safely clear on its own and they expected antibiotics. some groups felt that patients more readily accepted why they might not be given an antibiotic right away for a respiratory tract infection/flu because of the consistent messaging and campaigns in this area, but these patients did not know that this message can also apply to uti. one group was optimistic that the message about not receiving an antibiotic immediately was becoming more widely accepted. various factors that would influence the clinician's decision to provide an immediate antibiotic included renal function, co-morbidity, diabetes, immunosuppression, cost of treatment, pregnancy, severity of symptoms, age of patient, and duration of time before the weekend. most groups reported that they would discuss antibiotic resistance with some patients with a suspected uti, especially if there were additional risk factors such as multiple courses of antibiotics. some gp staff would discuss the need to complete the antibiotic course with patients, but they were less inclined to discuss antibiotic resistance in relationship to utis than other infections, especially if they were confident in their diagnosis. when indicating risk factors for antibiotic resistance, practices listed factors such as frequent/recent use of antibiotics, long duration or high doses of antibiotics, recurrent uti, and positive laboratory results. three focus groups reported challenges associated with only prescribing a day course of antibiotics. participants said these were often driven by patient expectations, since patients had received longer courses in the past and felt that the shorter dose would not be as effective, even though the cost is the same. some prescribers also felt that the day course was less effective than the longer one, with many patients returning with symptoms. this pressured them to lengthen the dose or use a different antibiotic. some groups reported that they did not know about or have the option of using pivmecillinam or fosfomycin as second-line treatment for acute uncomplicated uti and indicated this was because laboratories did not provide antibiotic susceptibility testing for these antibiotics. some groups had audited their antibiotic prescribing, but none had audited antibiotic prescribing for utis specifically. most practices reported discussing self-management advice with their patients for mild symptoms (especially with a negative dipstick) or for preventing uti recurrence. key themes for prevention focused on hydration, cystitis sachets, cranberry products, lemon barley water, wiping front to back, and sodium bicarbonate (one group). there was confusion regarding the evidence for effectiveness of cystitis sachets and cranberry products for prevention or treatment of utis and whether these should be recommended. hydration was discussed by most groups as a way to "flush out" the bladder or infection and was seen by some as the reason that cranberry juice is effective. some focus groups reported that patients might have received cystitis sachets from the community pharmacy and only came for a consultation if symptoms did not improve. most groups indicated that more information for patients was needed, including a uti leaflet with a public health campaign that covers the prevention and treatment of uti, in line with national guidance. this study revealed practice and clinician variation in the use of urine dipsticks, empirical antibiotic choice and course length, exclusion of genitourinary causes and pyelonephritis, use of back-up/delayed antibiotics, and a lack of knowledge about the effectiveness of over-the-counter products for the prevention and treatment of uti. there was also variation in the use of pivmecillinam and fosfomycin. many utis were managed by nurse practitioners or by telephone consultation. our study found that clinicians reported using telephone consultations for the management of uti. small studies evaluating the use of protocol-led telephone consultations to manage utis show general success; however, a significant proportion of patients in these studies required physical examination, referral, or the need for urine culture because of the risk of complications [ , ] . a recent study in the united states of america (usa) assessed clinicians' management of , telemedicine patients who were diagnosed with a uti [ ] . the study did not provide any guidance for clinicians regarding diagnosis and management of utis. although the authors concluded that telemedical management was generally successful, there was an increase in the use of quinolones (against the usa's national recommendations) in some groups and challenges with the management of patients with pyelonephritis, indicating that some clinicians would have benefited from simple decision-support tools. these studies and guidance highlight that face to face consultations are optimal, but if this is not possible there is a need to ensure that phone consultations follow an agreed diagnostic and management practice protocol that helps exclude other causes of urinary symptoms such as vaginal infection or atrophy, more severe infection like pyelonephritis, the initial signs of sepsis, and need for urine culture. remote consultations in england have increased during the covid pandemic and digital-first primary care is part of the nhs long-term plan [ , ] . future diagnostic and management tools need to include guidance that can be applied to various types of consultations, including those done using phone or using other remote technology. a recent uk study showed that overreliance on only urine dipsticks or clinical symptoms only may contribute to an under diagnosis of uti, due to the limited ability of both to rule out infection [ ] . decision tools that use a combination of diagnostic symptoms and urine dipstick results might improve diagnostic accuracy and are currently the most reliable and cost-effective tools for the diagnosis of uti [ ] [ ] [ ] [ ] [ ] . however, clinicians need support to consider individual signs and symptom and recommend treatment options such as delayed antibiotics. although many of the practice clinicians in our study followed national guidance to inform management, clinicians in our study still perceive pressure from patients to use urine dipsticks and prescribe based on their results. this patient expectation was perpetuated by ongoing use of urine dipsticks within the practice. future uti diagnostic guidance should include guidance on the role and effectiveness of urine dipsticks in detecting a uti in all age groups, how dipstick results should be used alongside history and physical examination, and tools for communicating information on the appropriate use of dipsticks across the care pathway and with patients. uti audits (that were not reported by any of our participants) with feedback and action planning may help embed good practice into daily practice care [ , ] . non-steroidal anti-inflammatory drugs for uti when used without back-up antibiotic prescribing for acute uncomplicated utis in women may lead to increased incidence of pyelonephritis [ ] . however, nsaids used with the provision of a patient lead back-up antibiotic are acceptable to patients, and reduce antibiotic use without increasing complications [ , , ] . current national guidance includes recommendations for providing back-up antibiotics in women with uncomplicated acute uti along with appropriate pain relief and advice about hydration [ ] . our findings indicated that gp staff felt that patients put pressure on clinicians to prescribe for a suspected uti, and that this is often driven by the dipstick result and previous management experiences. this perception is similar to other qualitative research and could be related to lack of communication skills and knowledge about the consequences of infection, symptom resolution and risks and benefits of nsaids versus antibiotics [ , ] . both patients and clinicians will need more information, evidence and discussion about consequences of overuse of antibiotics versus back-up antibiotics to motivate them to use back-up antibiotics more frequently for suspected uti [ , ] . to improve public awareness, antibiotic campaigns and patient-facing leaflets could use language more inclusive of non-respiratory infections such as utis and highlight the benefits of back-up antibiotics. continued effort should be put in to development of a more accurate point-of-care test that can more accurately guide the need for and choice of antibiotic [ ] . our findings, and others, show that at present, clinicians may not discuss non-pharmaceutical self-care and prevention of utis with women during a consultation and that some women do try over-the-counter products before seeking medical treatment [ ] . national institute for health and care excellence (nice) guidance now includes information as to the effectiveness of non-pharmaceutical products including cranberry, cystitis sachets and hydration for the prevention and management of uti for pharmacy and gp surgery staff [ ] . the nice evidence review found little robust research to recommend cranberry products or other non-pharmaceutical means for the treatment of lower uti, but did find that some non-liquid cranberry products could be helpful in the prevention of recurrent uti for women under [ , ] . a randomised control trial found that increasing water intake over a year could help reduce the number and frequency of cystitis episodes experienced by pre-menopausal women with recurrent uti who previously drank less than . l of fluid a day [ ] . however, there is little other robust evidence to demonstrate the effect of hydration on utis. given the many non-pharmacological and non-antibiotic management options that are applied to all types of uti, further research is needed to support recommendations and timing for non-pharmaceutical prevention of utis, hydration and "self-care" advice. there are few qualitative studies assessing uti management in primary care, with most focusing on treatment options, prescribing and antibiotic resistance rather than diagnosis of uti. qualitative data from an irish study from highlighted the need for local antibiotic resistance surveillance data to inform antibiotic choice [ ] . this irish study and another in england found that patients want to discuss their illness and treatment options with their gp and are willing to accept a back-up/delayed prescription if time has been taken to explain the rationale for it [ , ] . a uk-based study, using qualitative data from gps and female patients in , showed that how a clinician manages a uti depends on a complex mix of factors. internal factors include personality, knowledge, teaching, and experience and external factors include perceived severity of diagnosis, guidance and protocols, training, cost of treatment, and perceived patient expectations/feelings [ ] . a swedish study indicated that gps who most reliably follow treatment guidance for utis had a higher level of awareness and concern about increasing antibiotic resistance than less compliant gps [ ] . this study used stratification and random sampling techniques to select participants, which will have helped to limit bias. the sample size is also quite large when compared to other qualitative studies, allowing for a wider range of stakeholders with varying views. by using a known behavioural framework in the development of the focus group questions, we were able to ensure our interview schedule covered key discussion topics needed to understand behaviours around uti management. this study was conducted alongside a programme of work to inform interventions to improve management of utis. this included a uti flowchart and leaflet for older adults, which could have biased discussion to focus more on management in older adult patients, even when respondents were asked to provide feedback specific to younger age/all groups. to limit this, we asked for information about the general population or usual practice before prompting for information specific to older adults in the interview schedule. it is noted that more gp surgery staff from gloucestershire participated in group discussions than from nottingham ( vs. , respectively). gloucestershire ccg has almost twice the population of nottingham city ccg and the average surgery list size is about people higher in gloucestershire [ ] . because the strength of findings was based on consensus arising from group discussions (not comments from individuals), this should have limited any bias towards discussions with higher numbers of staff. surgeries that were not able to participate indicated time constraints (often related to lack of staff/illness or changes within the surgery) and "no research" policies as a barrier to participation. this could have meant that our sample was biased towards practices that were more knowledgeable and interested in research and clinical issues like antimicrobial stewardship. however, topics related to antimicrobial stewardship were discussed at the end of the general discussion so should not have biased the initial conversations about uti management in their practice. further, there was a broad range of roles represented from across the practices, and we did reach data saturation. this study highlighted variation in the care pathway for managing utis in adult women. findings indicate this process could be improved by ensuring that guidance and protocols are appropriate for face to face consultations, as well as those by phone or using other remote technology, providing clear guidance on the effectiveness of urine dipsticks in detecting a uti in all age groups. practices should be encouraged to implement audits with feedback on uti management. tools to discuss management decisions and antibiotics with patients should be available across the care pathway; public campaigns around antimicrobial stewardship should use language more inclusive of non-respiratory infections such as utis. further high-quality research is needed to provide additional guidance around non-pharmaceutical recommendations for "self-care" and prevention of utis. as this study is part of service development, ethical approval was not required according to the health research authority in england. however, this study was reviewed and approved by the public health england research ethics and governance group. laboratory surveillance of polymicrobial bacteraemia and fungaemia in england the e. coli bacteraemia sentinel surveillance group. epidemiology of escherichia coli bacteraemia in england: results of an enhanced sentinel surveillance programme english surveillance programme for antimicrobial utilisation and resistance (espaur estimating the incidence and -day all-cause mortality rate of escherichia coli bacteraemia in england by / thirty day all-cause mortality in patients with escherichia coli bacteraemia in england epidemiology of escherichia coli bloodstream infections in children escherichia coli bacteraemia papers incidence, risk factors and outcomes of escherichia coli bloodstream infections in a large canadian region exploring the relationship between primary care antibiotic prescribing for urinary tract infections, escherichia coli bacteraemia incidence and antimicrobial resistance: an ecological study antibiotic awareness day : general practitioners encouraged to target antibiotics through guidance, education and tools the impact of a national antimicrobial stewardship program on antibiotic prescribing in primary care: an interrupted time series analysis antibiotics in primary care in england: which antibiotics are prescribed and for which conditions? english surveillance programme for antimicrobial utilisation and resistance (espaur) why did some practices not implement new antibiotic prescribing guidelines on urinary tract infection? a cohort study and survey in nhs england primary care diagnosis of urinary tract infections: quick reference tool for primary care census aggregate data population profile: gloucestershire county council gloucestershire county health profile validation of the theoretical domains framework for use in behaviour change and implementation research using thematic analysis in psychology nvivo qualitative data analysis software; qsr international pty ltd development of an information leaflet and diagnostic flow chart to improve the management of urinary tract infections in older adults: a qualitative study using the theoretical domains framework a randomized controlled trial of telephone management of suspected urinary tract infections in women acute cystitis in women: experience with a telephone-based algorithm management of urinary tract infections in direct to consumer telemedicine millions of patients benefiting from remote consultations as family doctors respond to covid- dipsticks and diagnostic algorithms in urinary tract infection: development and validation, randomised trial, economic analysis, observational cohort and qualitative study predicting acute uncomplicated urinary tract infection in women: a systematic review of the diagnostic accuracy of symptoms and signs management of urinary tract infection in general practice: a cost-effectiveness analysis validation of a decision aid to assist physicians in reducing unnecessary antibiotic drug use for acute cystitis validating the prediction of lower urinary tract infection in primary care: sensitivity and specificity of urinary dipsticks and clinical scores in women target uti resource suite: uncomplicated uti audit for women under audit and feedback: effects on professional practice and healthcare outcomes symptomatic treatment of uncomplicated lower urinary tract infections in the ambulatory setting: randomised, double blind trial optimising management of utis in primary care: a qualitative study of patient and gp perspectives to inform the development of an evidence-based, shared decision-making resource effectiveness of five different approaches in management of urinary tract infection: randomised controlled trial urinary tract infection (lower): antimicrobial prescribing; national institute for health and care excellence urinary tract infection in women aged - : doctors', patients', and lay perceptions and understandings point-of-care urine culture for managing urinary tract infection in primary care: a randomised controlled trial of clinical and cost-effectiveness antimicrobial prescribing; national institute for health and care excellence effect of increased daily water intake in premenopausal women with recurrent urinary tract infections: a randomized clinical trial using qualitative insights to change practice: exploring the culture of antibiotic prescribing and consumption for urinary tract infections awareness of antibiotic resistance and antibiotic prescribing in uti treatment: a qualitative study among primary care physicians in sweden patients registered at a gp practice the authors declare no conflict of interest. key: cord- -nmjwzk e authors: bent, stephen; saint, sanjay; vittinghoff, eric; grady, deborah title: antibiotics in acute bronchitis: a meta-analysis date: - - journal: am j med doi: . /s - ( ) - sha: doc_id: cord_uid: nmjwzk e purpose: most patients with acute bronchitis who seek medical care are treated with antibiotics, although the effectiveness of this intervention is uncertain. we performed a meta-analysis of randomized, controlled trials to estimate the effectiveness of antibiotics in the treatment of acute bronchitis. subjects and methods: english-language studies published january to april were retrieved using medline, bibliographies, and consultation with experts. only randomized trials that enrolled otherwise healthy patients with a diagnosis of acute bronchitis, used an antibiotic in the treatment group and a placebo in the control group, and provided sufficient data to calculate an effect size were included. results: we identified eight randomized controlled trials that satisfied all inclusion criteria. these studies used one of three antibiotics (erythromycin, doxycycline, trimethoprim/sulfamethoxazole). the use of antibiotics decreased the duration of cough and sputum production by approximately one-half day (summary effect size . ; % ci, . to . ). for specific symptoms, there were nonsignificant trends favoring the use of antibiotics: a decrease of . days of purulent sputum ( % ci, − . to . ), a decrease of . days of cough ( % ci, − . to . ), and a decrease of . days lost from work ( % ci, − . to . ). conclusion: this meta-analysis suggests a small benefit from the use of the antibiotics erythromycin, doxycycline, or trimethoprim/sulfamethoxazole in the treatment of acute bronchitis in otherwise healthy patients. as this small benefit must be weighed against the risk of side effects and the societal cost of increasing antibiotic resistance, we believe that the use of antibiotics is not justified in these patients. stephen bent, md, sanjay saint, md, mph, eric vittinghoff, phd, deborah grady, md, mph purpose: most patients with acute bronchitis who seek medical care are treated with antibiotics, although the effectiveness of this intervention is uncertain. we performed a meta-analysis of randomized, controlled trials to estimate the effectiveness of antibiotics in the treatment of acute bronchitis. subjects and methods: english-language studies published january to april were retrieved using medline, bibliographies, and consultation with experts. only randomized trials that enrolled otherwise healthy patients with a diagnosis of acute bronchitis, used an antibiotic in the treatment group and a placebo in the control group, and provided sufficient data to calculate an effect size were included. results: we identified eight randomized controlled trials that satisfied all inclusion criteria. these studies used one of three antibiotics (erythromycin, doxycycline, trimethoprim/ sulfamethoxazole). the use of antibiotics decreased the dura-tion of cough and sputum production by approximately onehalf day (summary effect size . ; % ci, . to . ). for specific symptoms, there were nonsignificant trends favoring the use of antibiotics: a decrease of . days of purulent sputum ( % ci, Ϫ . to . ), a decrease of . days of cough ( % ci, Ϫ . to . ), and a decrease of . days lost from work ( % ci, Ϫ . to . ). conclusion: this meta-analysis suggests a small benefit from the use of the antibiotics erythromycin, doxycycline, or trimethoprim/sulfamethoxazole in the treatment of acute bronchitis in otherwise healthy patients. as this small benefit must be weighed against the risk of side effects and the societal cost of increasing antibiotic resistance, we believe that the use of antibiotics is not justified in these patients. am j med. ; : - . ᭧ by excerpta medica, inc. a cute bronchitis is a common clinical disorder characterized by the acute onset of cough and sputum production in a patient with no history of chronic pulmonary disease and no evidence of pneumonia or sinusitis. this definition excludes patients with acute exacerbation of underlying pulmonary disorders, in whom a previous meta-analysis found that antibiotic use led to a small, statistically significant benefit ( ) . the effectiveness of antibiotics in patients with acute bronchitis remains uncertain, although the disorder is the tenth most common diagnosis seen by physicians in the united states, accounting for million office visits annually ( ) . the etiology of acute bronchitis is unclear. most studies have identified viruses (adenovirus, rhinovirus, coronavirus, influenza, parainfluenza, respiratory syncytial virus, and coxsackievirus) as the cause in the majority of patients ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . atypical bacteria, including mycoplasma pneumoniae, chlamydia pneumoniae, and legionella species, have been reported to cause % to % of cases of acute bronchitis ( ) ( ) ( ) , and typical bacteria (streptococcus pneumoniae, haemophilus influenzae, branhamella catarrhalis) have been recovered from the sputum in % to % of patients ( , , ) . however, the importance of positive bacterial cultures from sputum is not known, because many of these pathogens are part of the oropharyngeal flora ( , , - ) . recent evidence suggests that some bronchitis in adults may be caused by bordetella pertussis and parapertussis, which are better known for their role in causing whooping cough in children ( ) . the majority of patients diagnosed with acute bronchitis in the united states are treated with antibiotics ( - ) . in a nationwide survey of Ͼ , physicians, gonzales et al ( ) found that two-thirds of patients without underlying lung disease who were diagnosed with acute bronchitis were treated with antibiotics. in another survey, % of children with a diagnosis of acute bronchitis were given a prescription for antibiotics ( ) . although antibiotics are often used in the treatment of acute bronchitis, their efficacy is uncertain. clinical trials examining this issue have yielded conflicting results ( - ) , and qualitative reviews are similarly inconclusive ( , , , , ) . widespread antibiotic use carries a substantial cost, puts patients at risk for medication side effects, and promotes antibiotic resistance. to clarify the optimal treatment of this disorder, we performed a meta-analysis to determine whether antibiotics were beneficial in patients with acute bronchitis. using explicit inclusion and exclusion criteria and accepted quantitative methods ( - ) , a meta-analysis provides summary estimates of effectiveness that may clarify the disparate results of previous trials ( ) . the literature review began with a computerized medline search using the subheading "bronchitis, drug therapy" and the term "xs acute disease," and included english-language articles published between january and april . the reference lists of all retrieved articles were scanned, and experts were consulted to identify potential trials not identified in the medline search. inclusion criteria consisted of the following: randomized trials using an antibiotic in the treatment group and a placebo in the control group; subjects with acute bronchitis, no history of chronic lung disease, and pneumonia excluded by chest radiograph or clinical exam; therapy for at least days; and the presentation of sufficient data to calculate the difference in efficacy between the treatment and the placebo as a continuous variable. studies were excluded if they were nonexperimental in design or if they compared one antibiotic with another without a placebo arm. for each study, two authors independently abstracted the author, journal title, year of publication, sample size, average age of subjects, antibiotic regimen used, major outcome measure(s), and the inclusion and exclusion criteria. discrepancies in the abstracted data were resolved by consensus. the eight eligible studies did not use a common outcome measure. when several outcomes were available from one study, we chose "days of sputum production" as the main outcome, because this symptom is most characteristic of the disease ( ) . for studies that did not include the outcome "days of sputum production," we chose the outcome in the study that was the most clinically similar (sputum production score, cough amount score). we transformed each outcome into units of standard deviation, thus giving a comparable effect size for different outcomes. the study-specific effect size was the difference in the mean outcome for the antibiotic and placebo groups, divided by the pooled standard deviation of the outcome measure in that study. the summary effect size across studies was calculated as a weighted average of the study-specific effect sizes, with weights equal to the inverse of the estimated variance. the significance of the summary effect size, standardized by its estimated variance, was assessed by comparing it with the standard normal distribution. a test for heterogeneity was calculated by comparing the weighted average of the squared differences between summary and study-specific effect sizes with an appropriate x distribution, with the same weights being used. these calculations used standard formulas ( ) , which assume that the outcomes are normally distributed and the sample sizes are approximately equal in the antibiotic and placebo groups. we also calculated summary mean differences for all outcomes reported by four or more studies. the summary measure was the weighted average of the difference between the antibiotic and placebo groups in the mean outcome measure for each study. weights were given by the inverse of the variance of each mean difference, estimated using the pooled standard deviation for each study. tests of the significance of the observed summary mean differences and of heterogeneity were also performed ( ) . we examined the potential for publication bias using the correlation between the number of subjects and the effect size in each study. if small studies with negative results were less likely to be published, then the correlation between number of subjects and effect size would be large. if there was not any publication bias, then there should not be a significant correlation between the number of subjects and the effect size. our search identified reports, including randomized, placebo-controlled trials of antibiotics for the treatment of acute bronchitis ( - ) . two ( , ) of these studies had to be excluded because insufficient data were presented in the original articles, and attempts to retrieve the necessary data from the authors were unsuccessful. the remaining eight trials, all of which used one of three antibiotics (erythromycin, doxycycline, trimethoprim/ sulfamethoxazole), were included in the meta-analysis. reasons for exclusion are listed in table . the characteristics of the randomized controlled trials, including the two that were excluded because of insufficient data, are shown in table . the overall summary effect size was . ( % ci, . to . ) indicating a small (about one-fifth of a standard deviation), statistically significant benefit from the use of antibiotics (figure) , equivalent to approximately one half day less of cough and sputum production. three outcomes were reported by at least four studies (table ) . although each of these results favor antibiotics, none was statistically significant. for days of purulent days lost from work. the effect of antibiotic treatment on days lost from work was very small, and unlike days of cough and sputum production, did not approach statistical significance. a test for heterogeneity was not significant for the overall summary effect size (p ϭ . ) or for days of sputum production (p ϭ . ), suggesting that these results are homogenous and can be combined. a test for heterogeneity was significant for the summary mean difference for days lost from work (p ϭ . ) and days of cough * result is the mean in the antibiotic group minus the mean in the placebo group for the main outcome measure. a positive result indicates a benefit from antibiotics. a negative result indicates a benefit from placebo. † effect size is the difference between the mean outcome in the antibiotic and placebo groups divided by the pooled standard deviation. ‡ these studies did not provide data that allowed calculation of a confidence interval or a continuous outcome measure, and therefore could not be included in the overall summary effect size. § cough amount score was a patient-reported score on a severity scale of to . ¶ sputum production score was a patient-reported score on a severity scale of to . # sputum production score was a patient-reported score on a severity scale of to . ci ϭ confidence interval. effect sizes and summary overall estimate. effect size is the difference between the mean outcome in the antibiotic and placebo groups divided by the pooled standard deviation. horizontal lines denote % confidence intervals. dots represent point estimates. randomized controlled trials evaluating the efficacy of antibiotics in acute bronchitis have had inconsistent results. of the eight trials included in our meta-analysis, four showed no benefit from the use of antibiotics ( ) ( ) ( ) ) , whereas four reported a benefit ( , , , ) . part of the discrepancy may be because studies used different outcome measures, some of which are of uncertain clinical importance. for example, the outcome measures in one trial that reported a statistically significant benefit from antibiotics included a reduction in mean temperature from . Њc to . Њc and a reduction in the use of antihistamines ( ) . because the published trials used several outcome measures, we used the standardized effect size, expressed in units of standard deviation, to quantitate the overall effect of antibiotic therapy. we chose the outcome that is most characteristic of acute bronchitis (days of sputum production) in the six studies where it was available, and we used the most similar outcome in the two other studies (cough amount score, sputum production score). we found a small, statistically significant benefit to the use of antibiotics in patients with acute bronchitis approximately equal to one-fifth of a standard deviation unit. to relate the observed benefit in the summary effect size to clinical variables, we also calculated summary mean differences for all outcomes that were reported by at least four trials (duration of sputum production, duration of cough, and days lost from work), all of which showed small, nonsignificant trends favoring the use of antibiotics. our meta-analysis suggests that patients with acute bronchitis who are treated with antibiotics have a reduction in the duration of cough and sputum production of approximately one half day. our results should be interpreted with caution. as with all meta-analyses, we assumed that the individual trials are sufficiently similar to provide a meaningful summary. the studies did have several important differences. they took place in different geographic locations, used three different antibiotics (erythromycin, doxycycline, trimethoprim/sulfamethoxazole), and were conducted during a -year period. however, despite these differences, statistical tests for heterogeneity did not show differences between studies for the main outcome, or for the outcome of sputum production. although different antibiotics were used, all groups were treated for at least days, and the spectrum of organisms covered by the various antibiotics was similar. we identified randomized controlled trials in our literature review. results from two of these trials could not be included because insufficient data were reported ( , ) . both of these trials showed no benefit from the use of antibiotics. thus, their exclusion tended to bias our results in favor of antibiotics. in addition, the summary effect size may have been overestimated if publication bias made it more likely that studies showing benefit were published, whereas those showing no benefit were not. if there was publication bias, small studies with negative findings should have been unlikely to be published, whereas small studies with positive findings should have been more likely to be published, leading to a correlation between study size and effect size. we found no such correlation. we used similar methodology to an earlier meta-analysis that examined the effect of antibiotics in patients with acute exacerbations of chronic obstructive pulmonary disease ( ) . that study reported a summary effect size of . ( % ci, . to . ), also indicating a small, statistically significant benefit from the use of antibiotics. patients who were treated with antibiotics had a modest improvement in peak expiratory flow of approximately l/min compared with those treated with placebo. although the magnitude of benefit from antibiotic treatment in that meta-analysis is similar to that in the current meta-analysis, such a benefit may be more important for a patient with underlying lung disease who has less functional reserve. the costs of widespread antibiotic use are great for both patients and society. they include prescription costs, medication side effects, and an increase in antibiotic resistance. several studies have shown that widespread antibiotic use leads to the development of resistant organisms ( ) ( ) ( ) . antibiotic use for acute bronchitis constitutes a substantial portion of all antibiotic use in the united states, accounting for % of all prescriptions written for children ( ) . furthermore, side effects of antibiotics used for acute bronchitis are common, occurring in % to % of patients ( - , , , ) . the practice of routinely giving antibiotics for acute bronchitis encourages patients to expect antibiotics for subsequent episodes ( ) , which adds to the cycle of medication costs, side effects, and antibiotic resistance. we believe that there should be a clear, substantial benefit to antibiotics to justify these costs. some authors have suggested that certain subgroups of patients with acute bronchitis may benefit from antibiotics ( , , ) . in a study of patients randomly assigned to treatment with doxycycline or placebo, verheij et al ( ) reported that doxycycline resulted in clinical benefit among patients older than years and in those who felt ill at study entry. however, approximately % of the patients in that study had abnormalities on lung auscultation and therefore may have had conditions such as pneumonia that would show a large benefit from antibiotic treatment ( ) . others have suggested treating patients who test positive for mycoplasma pneumoniae or chlamydia pneumoniae ( ) , although there is no evidence from randomized trials to support this practice. in a randomized trial using erythromycin to treat acute bronchitis, king et al ( ) found no difference in outcomes between patients who tested positive and those who tested negative for mycoplasma pneumoniae. more research is needed to determine if there are subgroups of patients who are likely to have a substantial benefit from treatment with antibiotics. the studies included in this meta-analysis examined the effect of one of three different antibiotics (erythromycin, doxycycline, trimethoprim/sulfamethoxazole). none of the studies used one of the newer macrolide or floroquinolone antibiotics. we are not aware of any randomized, placebo-controlled trials of these agents in adults with acute bronchitis. future studies should determine the risks and benefits associated with use of these newer antibiotics. in summary, we found a statistically significant benefit from the use of antibiotics in acute bronchitis. treatment reduced the duration of cough and sputum production by approximately one half day. the decision to use antibiotics for the treatment of adults with acute bronchitis must be weighed against the costs associated with widespread use of these agents. in healthy patients with acute bronchitis who have no evidence of chronic pulmonary disease, we believe that the small benefit associated with antibiotic treatment does not outweigh the risk of side effects and the increase in antibiotic resistance. note added in proof: after this paper was submitted, a meta-analysis on a similar topic was published: smucny jj, becker la, glazier rh, mcisaac w. are antibiotics effective treatment for acute bronchitis? a meta-analysis. j fam pract. ; : - . antibiotics in chronic obstructive pulmonary disease exacerbations: a meta-analysis national ambulatory medical care survey: 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choosing the best treatment randomized placebo-controlled trials of antibiotics for acute bronchitis: a critical review of the literature implications of overviews of randomized trials summing up: the science of reviewing research obtaining medically meaningful answers from an overview of randomized clinical trials meta-analyses of randomized controlled trials meta-analysis, decision analysis, and cost-effectiveness analysis: methods for quantitative synthesis in medicine effect of antimicrobial use and other risk factors on antimicrobial resistance in pneumococci the effect of changes in the consumption of macrolide antibiotics on erythromycin resistance in group a streptococci in finland production of beta-lactamase in respiratory tract bacteria in children: relationship to antibiotic use patient knowledge of upper respiratory infections: implications for antibiotic expectations and unnecessary utilization what will it take to stop physicians from prescribing antibiotics in acute bronchitis? antibiotics in acute bronchitis/bent et al key: cord- -s hdhh authors: zeimet, anthony; mcbride, david r.; basilan, richard; roland, william e.; mccrary, david; hoonmo, koo title: infectious diseases date: - - journal: textbook of family medicine doi: . /b - - - - . - sha: doc_id: cord_uid: s hdhh nan infections of the upper respiratory tract accounted for more than million ambulatory medical visits in , according to the national ambulatory medical care survey (cherry et al., ) . although a large percentage of these infections are viral in origin, antibiotics are still prescribed for more than % of patients with acute respiratory tract infection (arti). acute bronchitis, in the arti category, is defined as a respiratory infection in which cough is the predominant symptom and there is no evidence of pneumonia. antibiotics are often prescribed despite limited evidence that they shorten the duration of acute bronchitis. with increasing incidence of antibiotic resistance, bronchitis allows physicians to practice "prescriptive restraint" and to provide supportive therapy. consider using the phrase "chest cold" to help patients understand the viral and benign nature of this infection. chronic bronchitis is one of the manifestations of chronic obstructive pulmonary disease (copd) and is defined clinically as cough and sputum production on most days for months annually for years. chronic bronchitis is thought to be primarily inflammatory in origin, although infection may be associated with acute exacerbations; with increased sputum production and worsening dyspnea, antibiotics have proved effective in acute episodes. however, systemic corticosteroids are the mainstay of copd exacerbation management. the patient with acute bronchitis presents with cough, often productive. patients may report clear or colored mucus in association with the presumed diagnosis of acute bronchitis. despite what many patients believe, the color of sputum, even purulent sputum, is not predictive of bacterial infection. the cough of bronchitis can last up to weeks, sometimes even longer. typically, acute bronchitis is associated with other manifestations of infection, such as malaise and fever. respiratory viruses are thought to cause the majority of cases of acute bronchitis. influenza a and b, parainfluenza, respiratory syncytial virus (rsv), coronavirus, adenovirus, and rhinovirus are common pathogens in the viral category. clues to a specific virus may be found in the patient history; for example, rsv might be considered when there is household exposure to infected children. influenza typically presents with sudden onset of symptoms, including fever, myalgias, cough, and sore throat. neuraminidase inhibitors are modestly effective in shortening the duration of influenza in ambulatory and healthy patients (by about day), if initiated in the first hours of illness. the resistance patterns of influenza a and b have shifted in the last several years and may vary based on yearly viral strains. influenza b has remained, as of , sensitive to zanamivir (relenza) and oseltamivir (tamiflu). currently circulating strains of influenza a, both h n and h n , and influenza b have generally remained sensitive to both oseltamivir and zanamivir (fiore et al., ) . family physicians are advised to consider restraint in the prescribing of these agents, since resistance is of great concern. yearly influenza immunization and cough etiquette and hygiene are likely the most useful techniques for influenza management. studies have identified other pathogens, such as mycoplasma pneumoniae and chlamydophila pneumoniae, in a small minority of cases of clinical acute upper respiratory illness with cough as the predominant symptom. no significant benefit has been found in treating these infections with antibiotics. an exception in the treatment of acute bronchitis-like illness with antibiotics is when confirmed or probable bordetella pertussis is present. early treatment with a macrolide antibiotic and patient isolation will likely decrease coughing paroxysms and limit spread of disease (braman, ) . although common upper respiratory bacterial pathogens, such as moraxella (branhamella) catarrhalis, streptococcus pneumoniae, and haemophilus influenzae, may be isolated from patients with acute bronchitis, their relevance is questionable because these bacteria can be present in the respiratory tract of healthy individuals. obtaining sputum for culture when bronchitis is the diagnosis generally is not useful. antibiotics may offer a modest benefit in the treatment of acute bronchitis, with many studies showing no statistical significance in the outcome of treated versus not-treated groups. measures of function, such as duration of illness, loss of work, and limitation of activity, have not shown clinically significant improvement in those with acute bronchitis taking antibiotics. coupled with cost and the potential for side effects, the use of antibiotics for acute bronchitis is not recommended. if a provider decides to use an antibiotic in a specific patient situation, narrow-spectrum respiratory agents are preferred, such as a first-generation macrolide or doxycycline. treating the symptom of cough in acute bronchitis is an important concern for patients. in adults with acute bronchitis with signs of airway obstruction, evidenced by wheezing on examination or decreased peak expiratory flow rate, beta- agonists may be helpful in alleviating cough. these agents are not helpful for children with acute cough or adults with cough and no evidence of airway obstruction. side effects of tremor and an anxious feeling must be weighed against this benefit. patients often are primarily interested in alleviating symptoms caused by respiratory illness. unfortunately, there is mixed evidence for the use of over-the-counter (otc) and prescription cough medications. dextromethorphan and codeine may be somewhat effective, although they have not been evaluated in randomized, double-blinded, placebo-controlled trials for acute bronchitis. combination first-generation antihistamine-decongestant products may be effective for the cough associated with colds. naproxen showed efficacy against cough in one upper respiratory model study (sperber et al., ) . guaifenesin acts as an expectorant and may have some effect on cough by its mucus-thinning properties. community-acquired pneumonia (cap) is defined as an acute infection of the pulmonary parenchyma and, along with influenza, is the seventh leading cause of death in the united states. fever, cough, sputum production, pleuritic chest pain, and dyspnea are common symptoms of cap. nausea, vomiting, and diarrhea also may occur, and in elderly patients, cap may present with mental status changes. although its absence usually makes pneumonia less likely, fever can be absent in the elderly patient. other physical examination findings include an elevated respiratory rate, conversational dyspnea, tachycardia, and rales. egophony and dullness to percussion may be noted with focal consolidation. typical laboratory findings include leukocytosis. the diagnosis of pneumonia is based on the presence of symptoms and the presence of an infiltrate on chest radiograph. if infiltrate is not present, consider obtaining a chest tomography scan (which has higher sensitivity) to rule in or rule out cap. if negative, other diagnoses should be considered. the most common microbiologic agent of pneumonia is often not isolated (table - ). furthermore, studies have shown that bacteriologic causes of pneumonia cannot be determined by radiographic appearance (i.e., "typical" vs. "atypical"). in the proper clinical setting, certain clinical microbes should be considered because they can affect treatment considerations and epidemiologic studies. these include legionella spp., influenza a and b, and communityacquired methicillin-resistant staphylococcus aureus (mrsa). certain diagnostic tests are performed based on clinical setting. blood cultures are not routinely done in the outpatient setting but should always be done if the patient is being admitted to the hospital, ideally before antibiotics are given. the use of gram stain and sputum culture remains controversial but can provide more evidence of a bacterial cause (e.g., many pmns). if sputum cultures are being obtained, it is recommended that the physician have the patient expectorate directly into a specimen cup and have it sent immediately for processing. this can increase the yield of isolating streptococcus pneumoniae among antibiotics for the treatment of bronchitis is not recommended because of the cost, potential for side effects, and lack of clinical benefit (braman, ; smith et al., ) (sor: a). in the treatment of bordetella pertussis, early administration of a macrolide antibiotic and patient isolation will likely decrease coughing paroxysms and limit spread of disease (braman, ) (sor: a). in adults with acute bronchitis with signs of airway obstruction, as evidenced by wheezing on examination or decreased peak expiratory flow rate, beta- agonists may be helpful in alleviating cough (braman, ) (sor: b). for acute exacerbation of copd associated with purulent sputum and increased shortness of breath, treatment with antibiotics decreases mortality by % and treatment failure by % (ram et al., ) (sor: a). other respiratory pathogens. other tests include urine antigen tests for s. pneumoniae, legionella pneumophila serogroup , and nasal swab for influenza a and b. in young children, rsv, adenovirus, and parainfluenza in addition to influenza are common causes. nasal swab for rsv and influenza can be rapidly done, but the other causes can be determined with viral cultures, serology, enzyme-linked immunosorbent assay (elisa), and polymerase chain reaction (pcr), although results usually are received after resolution of the acute symptoms. perhaps the most important decision for clinicians is to determine the location of treatment. the american thoracic society (ats) and the infectious diseases society of america (idsa) recommend use of the pneumonia severity index (psi), which uses variables to risk-stratify the patient into five mortality classes, or the curb- , which measures five clinical variables in this decision making. the curb- may be the easiest and most convenient to use at the site of decision making. a score of or indicates treatment as an outpatient; a score of requires hospital admission to the general medical ward; and a score of or more indicates admission to an intensive care unit (icu) (box - ). treatment of cap should be targeted toward the most likely etiology (table - ). outpatient therapy for patients who have no comorbidities and have not received antibiotics within the last months includes doxycycline or a macrolide antibiotic. use of a fluoroquinolone antibiotic (levofloxacin or moxifloxacin) should be reserved for patients with more complicated pneumonia and those requiring hospitalization. patients who have comorbid conditions or recent antibiotic exposure, or who will be hospitalized, should receive a respiratory fluoroquinolone or combination therapy with a betalactam drug plus a macrolide, for to hours after fever abates (usually - days' total therapy). if an organism is isolated, therapy may be narrowed to cover the causative agent. the clinician should consider longer therapy and appropriate antibiotics to cover for infection by less common organisms such as staphylococcus aureus or pseudomonas aeruginosa. if the patient has no more than one abnormal value (temperature < . ° c, heart rate < , respiratory rate < , sbp > , o saturation > %, po > on room air) and the patient is able to maintain oral intake and has a normal mental status, the clinician can safely switch to oral therapy and discharge the patient from the hospital. unless the etiology of the pneumonia is known, the physician should switch to oral antibiotics in the same class as the intravenous antibiotics used. the u.s. preventive services task force (uspstf) along with idsa and ats recommend annual influenza vaccinations to those over years of age, those who are (or who reside with those who are) at high risk for influenza complications, and all health care workers. furthermore, the pneumococcal vaccine should be given to all those over age . smoking cessation is also important and should be discussed at each clinic visit. • concerns about development of resistant seasonal and h n swine-derived influenza virus should be considered in the decision to administer antiviral medications to healthy patients with these infections. • the abrupt onset of fever with chills, headache, malaise, myalgias, arthralgias, and rigors during "flu season" is sufficient to diagnose influenza. • prevention of influenza is generally with vaccination. influenza deserves special mention because it is an important cause of pneumonitis and can precede a bacterial pneumonia. influenza viruses are medium-sized enveloped ribonucleic acid (rna) viruses that consist of a lipid bilayer with matrix proteins with spiked surface projections of glycoproteins (hemagglutinins, neuraminidase) on the outer surface ( figure - ) . both influenza a and influenza b have eight segmented pieces of single-stranded rna. the only difference between influenza a and b is that b does not have an m ion channel. hemagglutinins, three types of which typically infect humans (h , h , h ), bind to respiratory epithelial cells and allow fusion with the host cell. neuraminidase, consisting of two types (n , n ), allows release of virus from the infected cells. a unique aspect of influenza is that antigenic variation occurs annually. antigenic shift is caused by a genetic reassortment between animal and human influenza strains, producing a novel virus that generally causes the worldwide pandemics. influenza viruses circulate mostly among humans, birds, and swine. sometimes; a human strain and an animal strain can intermingle and create a new, unique virus. this is what happened during spring , heralding the most recent pandemic and creating "novel h n influenza" (swine influenza). genotype analysis • score or : outpatient treatment • score : inpatient treatment on a general medical floor • score > : inpatient treatment in an intensive care unit bun, blood urea nitrogen. locally adapted guidelines should be implemented to improve the processing of care variables and relevant clinical outcomes in pneumonia (mandell et al., ) (sor: b) . objective criteria or scores should always be supplemented with physician determination of subjective factors, including the patient's ability to take oral medication safely and reliably and the availability of outpatient support resources (sor: b). for patients with curb- score of or higher, more intensive treatment (i.e., hospitalization or, where appropriate and available, intensive in-home health care services) is usually warranted (sor: c). of this strain determined that components came from an influenza virus circulating among swine herds in north america that combined with a virus circulating among ill swine in eurasia, creating a new influenza strain capable of causing disease in humans. because this virus had not previously infected humans, it had the potential to cause widespread morbidity and mortality worldwide. during pandemics, the u.s. centers for disease control and prevention (cdc) estimates an additional , to , deaths caused by influenza. although higher than in nonpandemic years, mortality was significantly less than initially predicted in . no recent antibiotic therapy a respiratory fluoroquinolone alone or an advanced macrolide plus a β-lactam † † an advanced macrolide plus a β-lactam, or a respiratory fluoroquinolone alone (regimen selected will depend on nature of recent antibiotic therapy) intensive care unit (icu) a β-lactam † † plus either an advanced macrolide or a respiratory fluoroquinolone pseudomonas infection is not an issue but patient has a β-lactam allergy a respiratory fluoroquinolone, with or without clindamycin pseudomonas infection is an issue ‡ ‡ (cystic fibrosis, impaired host defenses) either ( ) copd, chronic obstructive pulmonary disease; mrsa, methicillin-resistant staphylococcus aureus. * azithromycin or clarithromycin. † that is, the patient was given a course of antibiotic(s) for treatment of any infection within the past months, excluding the current episode of infection. such treatment is a risk factor for drug-resistant streptococcus pneumoniae and possibly for infection with gram-negative bacilli. depending on the class of antibiotics recently given, one or another of the suggested options may be selected. recent use of a fluoroquinolone should dictate selection of a nonfluoroquinolone regimen, and vice versa. ‡moxifloxacin, levofloxacin, or gemifloxacin. § dosage: g orally (po) three times daily (tid). ¶ dosage: g po twice daily (bid). ** high-dose amoxicillin ( g tid), high-dose amoxicillin-clavulanate ( g bid), cefpodoxime, cefprozil, or cefuroxime. † † cefotaxime, ceftriaxone, ampicillin-sulbactam, or ertapenem. ‡ ‡the antipseudomonal agents chosen reflect this concern. risk factors for pseudomonas infection include severe structural lung disease (e.g., bronchiectasis) and recent antibiotic therapy, health care-associated exposures or stay in hospital (especially in the icu). for patients with cap in the icu, coverage for s. pneumoniae and legionella species must always be considered. piperacillin-tazobactam, imipenem, meropenem, and cefepime are excellent β-lactams and are adequate for most s. pneumoniae and h. influenzae infections. they may be preferred when there is concern for relatively unusual cap pathogens, such as p. aeruginosa, klebsiella spp., and other gram-negative bacteria. § § piperacillin, piperacillin-tazobactam, imipenem, meropenem, or cefepime. ## data suggest that older adults receiving aminoglycosides have worse outcomes. ¶ ¶ dosage for hospitalized patients, mg/day. the abrupt onset of fever, along with chills, headache, malaise, myalgias, arthralgias, and rigors during "flu season," is sufficient to diagnose influenza. as the fever resolves, a dry cough and nasal discharge predominate. a rapid nasal swab or viral cultures can be used to confirm the diagnosis of influenza but is rarely needed. in fact, the sensitivity of these rapid tests can range from % to %, so a negative test does not rule out influenza. the primary care physician needs to determine if the patient has influenza or the common cold, because symptoms of both illnesses generally overlap (table - ) . treatment of influenza is generally not necessary because it is usually a self-limiting condition. treatment should be reserved for those with comorbidities who present within hours of symptom onset. neuraminidase inhibitors (zanamivir and oseltamivir) prevent the release of virus from the respiratory epithelium and are approved for both influenza a and influenza b. the m inhibitors (amantadine and rimantadine) are approved by the u.s. food and drug administration (fda) for the treatment of influenza a because these drugs block the m ion protein channel, preventing fusion of the virus to host cell membrane (influenza b has no m ion channel). the use of m inhibitors is limited because of increasing resistance among influenza a viruses, as well as causing central nervous system (cns) problems that are usually exacerbated in elderly persons, who are more likely to seek treatment for influenza (table - ). the major complication of influenza is a secondary bacterial pneumonia or exacerbation of underlying copd. initial improvement in clinical symptoms followed by deterioration usually suggests a secondary bacterial pneumonia, which can usually be confirmed with a chest radiograph showing an infiltrate. other, less common complications of influenza include myositis, myocarditis, pericarditis, transverse myelitis, encephalitis, and guillain-barré syndrome. prevention of influenza is generally with vaccination. box - outlines patients at risk for influenza complications who should be vaccinated yearly. although anyone wanting an influenza vaccine should be vaccinated, during periods of vaccine shortage, high-risk groups have priority. a well-matched vaccine can prevent influenza among % to % of adults and decrease work absenteeism. conversely, a poorly matched vaccine only prevents influenza in % of healthy adults. proper hand hygiene and covering one's cough are two additional important components in preventing the spread of influenza virus. • population-based vaccination programs have been highly effective in decreasing the incidence of many viral infections. • acyclovir can be used in adults and children with varicella to decrease symptoms if given in the first hours after rash onset, but its benefit must be weighed against its cost and the possibility of development of viral resistance. • antiviral medications should be considered to decrease the incidence of postherpetic neuralgia, particularly in older patients. early treatment (within hours of onset of symptoms) with oseltamivir or zanamivir is recommended for influenza a (jefferson et al., ) (sor: a). use of oseltamivir and zanamivir is not recommended for patients with uncomplicated influenza with symptoms for more than hours (kaiser and hayden, ) (sor: a). oseltamivir and zanamivir may be used to reduce viral shedding in hospitalized patients or to treat influenza pneumonia (sor: c). (from treanor jj: influenza viruses, including avian influenza and swine influenza. in mandell gl, bennett je, dolin rd (eds) . mandell, douglas, and bennett's principles and practices of infectious diseases, th ed. philadelphia, churchill livingstone, , p .) • measles has had a resurgence in recent years and should be suspected when a patient presents with cough, coryza, conjunctivitis, and head-to-toe rash. • epstein-barr virus and cytomegalovirus infections are generally not clinically distinguishable, and their treatment is primarily supportive. vaccinations have dramatically decreased the incidence of a number of historically common viral infections; smallpox has been eradicated through widespread vaccination. however, recent outbreaks of measles and mumps on college campuses underscore the need to remain vigilant in administering vaccines at the population level, even though no vaccine is available for many common viruses. varicella is one of the classic viral exanthems of childhood. before routine vaccination, having chickenpox was one of childhood's "rites of passage." the virus, a herpesvirus (human herpesvirus ), is effectively transmitted, causing outbreaks in schools and households. patients with primary varicella present with fever, headache, and sore throat. generally within to days of onset of symptoms, a papulovesicular rash erupts diffusely. the classic description of the chickenpox lesion is "a dewdrop on a rose petal," suggesting a central vesicle on an erythematous base. lesions continue to appear for to days. all lesions going from papule to vesicle to crusted lesion takes about weeks. patients are considered to be infectious, primarily through respiratory secretions, during the days before symptoms appear and until all lesions are crusted. treatment of varicella is generally supportive. control of spread may be a concern in group-living environments such as schools or residence halls. isolation of the infected patient away from those susceptible to varicella infection is standard practice. acyclovir can be started within the first hours after rash eruption to achieve an attenuation of the infectious course. in children, this means a decrease in the duration of fever by about day and a decrease in the number of lesions (swingler, ) . in adults, acyclovir decreases rash duration and the number of lesions, although the results are less significant than for children. adult dosing of acyclovir for varicella is mg five times daily. the marginal benefit must be weighed against the possible development of resistance at a population level and the cost of the medication. complications of varicella can include secondary infection of skin lesions, pneumonitis, encephalitis, and dehydration from vomiting and diarrhea. varicella is prevented primarily through administration of vaccine. the vaccine is highly effective in children, with recommended dosing at to months with a second dose at to years. varicella is now included in a measles-mumpsrubella (mmr) vaccine, which can be given between months and years of age. the varicella vaccine is a live, attenuated virus and should not be given to certain immunocompromised patients. the vaccine can also be administered to exposed immunocompetent contacts, although the benefit is clearer for children than adults. severely immunocompromised patients exposed to varicella (particularly those with advanced hiv disease) may be given high-dose acyclovir to prevent development of disease. herpes zoster is a reactivation of the neurotropic varicella virus, typically in a dermatomal distribution. this is more common in elderly or immunocompromised patients but can occur in healthy people as well. patients with zoster may note generalized malaise, hyperesthesia, numbness, tingling, and pain in the skin before development of a rash. the appearance of the rash is the same as for chickenpox, although most often isolated to a unilateral dermatome. the diagnosis of herpes zoster is clinical based on the history and the classic appearance of the rash. in immunocompromised patients, however, the rash may not be dermatomally isolated. when the diagnosis is unclear, viral culture can be obtained from the base of a lesion. antiviral medications are likely to decrease the incidence of postherpetic neuralgia and are recommended, particularly in elderly patients (wareham, ) . valacyclovir ( g three times daily) or famciclovir ( mg every hours) for days is likely more effective than acyclovir in achieving this result. either drug should be started as soon after the diagnosis as possible, preferably within to hours of rash onset. when patients have established postherpetic neuralgia, gabapentin and tricyclic antidepressants are helpful in alleviating the pain. the rash of zoster is infectious to the touch. patients should be advised to keep the rash covered until all the lesions have crusted. zoster of the trigeminal nerve can extend to the eye and warrants immediate ophthalmologic intervention. a vaccine to prevent herpes zoster in adults was released in . the zoster vaccine differs from the varicella vaccine in that the amount of attenuated virus is times higher in the zoster vaccine. the vaccine decreases the incidence of zoster by %. it is recommended for administration by the american academy of family physicians (aafp) to adults over age , regardless of prior varicella or zoster history. although generally well tolerated, the vaccine is somewhat costly. in , more measles cases were reported than in any other year since (cdc, ) . measles is the "first disease" of childhood from the history of medicine. in adults, measles infection may be acquired in the face of waning immunity from remote immunization. a booster dose of mmr vaccine is recommended before college entry. clinically, measles presents with cough, coryza (nasal irritation and congestion), and conjunctivitis. fever is common several days before the onset of the rash. the rash of measles typically spreads from head to toe and has an erythematous, papular appearance with a "sandpaper" feeling. koplik's spots are erythematous papules with a bluish center on the oral mucosa and appear early in measles. measles is highly contagious through droplets. lymphopenia and neutropenia are common laboratory findings with measles infection. complications of measles include primary infections such as pneumonia, gastroenteritis, encephalitis, and the rare subacute sclerosing panencephalitis. secondary infections such as otitis media, pneumonia, and adenitis may also occur. treatment is supportive, and the implications of measles infection are primarily in the public health realm. patients with measles should be isolated for at least days after the appearance of the rash. it is important to recognize that patients are contagious for days before the development of symptoms. careful verification of immunization status for close contacts is essential. clinical infectious mononucleosis is a common infection in adolescents and early adults. the clinical syndrome is most often caused by epstein-barr virus (ebv), although cytomegalovirus (cmv) may also be the source in this clinical syndrome, which includes fever, exudative tonsillitis, adenopathy (often including posterior cervical or occipital nodes), and fatigue. ebv is transmitted in oral secretions and may be transmitted sexually as well. b cells are infected with ebv either directly or after contact with epithelial cells, resulting in diffuse lymphoid enlargement. the diagnosis of infectious mononucleosis is made by recognizing the clinical symptoms of fever, pharyngitis, and adenopathy along with the laboratory findings of greater than % lymphocytes with % or more atypical lymphocytes (hoagland, ) . also, a positive serologic test for heterophile antibody assists the family physician in the diagnosis. to differentiate ebv from cmv mononucleosis, serology (igg and igm) may be obtained. results of these tests are generally not available in time to have a significant benefit clinically. splenic enlargement as part of this lymphoid hypertrophy can lead to splenic rupture ( . % risk) (dommerby et al., ) . athletes with infectious mononucleosis must be managed carefully to avoid their participation in sports that could result in abdominal trauma. other risks associated with infectious mononucleosis include upper airway obstruction, asymptomatic transaminase elevation, thrombocytopenia, and rash after the administration of ampicillin or amoxicillin. routinely obtaining transaminase levels in patients without clinical hepatitis is of little value and can increase the overall cost of management. treatment of infectious mononucleosis is largely supportive. patients should be instructed to treat fever with antipyretics, rest, and expect symptom duration of to weeks, although symptoms can last for several months. the use of steroids, such as prednisone, has shown limited benefit. data suggest an initial benefit hours after steroid administration, although this is lost within several days (candy and hotopf, ) . combination of steroid and an antiviral (valacyclovir) may have some positive effect on fatigue. • the most common presentation of tuberculosis is pulmonary disease. • tuberculosis is diagnosed by acid-fast bacilli smears and cultures. • standard first-line agents to treat tb are isoniazid, rifampin, pyrazinamide, and ethambutol. • high-risk patients with a positive purified protein derivative skin test or quantiferon-tb gold test should be treated for latent tb infection. • the current recommendation for first-line treatment for latent tb is months of oral isoniazid. tuberculosis skin testing should be interpreted without regard to bacille calmette-guérin (bcg) history, because bcg is administered in areas where tb is endemic and bcg does not provide complete protection from tb infection. tuberculosis (tb) is a disease that has plagued humans since antiquity, with evidence of spinal tb in neolithic and early egyptian remains. at present, tb affects approximately one third of the world's population. tb is the world's second most common cause of death from infectious disease after human immunodeficiency virus or acquired immunodeficiency syndrome (hiv/aids). tuberculosis is caused by mycobacterium tuberculosis, an acid-fast bacillus. tb is acquired by inhalation of respiratory droplets. these respiratory droplets are spread by coughing. brief contact carries little risk for acquiring tb, and infection generally does not occur in open air; open-air sanatoriums were the cornerstone of tb treatment before antimicrobial therapy. in the united states, tb incidence rates have been on the decline since , coinciding with the control of hivinduced aids by antiretroviral therapy. however, tb remains prevalent in certain high-risk groups (i.e. immigrants, iv drug use, homeless persons). most cases of tb are in people age to years. tb in elderly persons is generally caused by a reactivation of latent infection acquired in the remote past, whereas tb in young children indicates ongoing active transmission in the community. infection in children is more likely to progress to active tb and disseminated disease. persons with hiv infection have a disproportionately higher risk for acquiring tb than the general population. tuberculosis is most frequently manifested clinically as pulmonary disease, but it can involve any organ. extrapulmonary tb accounts for about % of disease in hiv-seronegative persons but is more common in hiv-seropositive persons. pulmonary tb typically manifest with fever, night sweats, chronic cough, sputum production, hemoptysis, anorexia, and weight loss. chest radiographs in patients with pulmonary tb typically reveal upper-lobe cavitary lesions and can reveal infiltrates or nodular lesions, as well as lymphadenopathy ( figure - ). tb in the setting of advanced hiv co-infection does not generally manifest in the typical manner (table - ) . acyclovir started within the first hours after varicella rash eruption can attenuate the infectious course, decreasing duration of fever by day and reducing the number of lesions (sor: a). administration of varicella vaccine to a susceptible child within days of exposure will likely modify or prevent disease (macartney and mcintyre, ) the diagnosis of pulmonary tb is made by the demonstration of acid-fast bacilli (afb) in sputum and the growth of m. tuberculosis in culture. these patients typically have an abnormal chest radiograph, as previously described. m. tuberculosis is a slow-growing bacterium, and cultures can take up to weeks to grow. a pcr assay developed for m. tuberculosis can be run on afb smear-positive sputum to hasten the diagnosis of pulmonary tb. a positive pcr on afb-positive sputum is diagnostic of pulmonary tb, but a negative test does not rule out the diagnosis. patients with afb positive smears from sputum samples should be started on anti-tb therapy while awaiting results of pcr and cultures. the treatment of tb always uses multiple agents with anti-tb activity. single agents should never be used. the standard first-line agents are isoniazid (inh), rifampin (rif), pyrazinamide (pza), and ethambutol (emb) (figure - and table - ). if administered, inh should be given with pyridoxine (vitamin b ; - mg orally daily) to prevent neuropathy. treatment of active pulmonary tb is generally for months regardless of hiv status, but treatment may need to be extended in certain situations. directly observed therapy (dot) is the preferred mechanism of administration to ensure compliance. many local county and state health departments have systems for dot. treatment of hiv-seropositive patients with tb who are receiving an antiretroviral (arv) regimen that contains a protease inhibitor is complicated by the latter's interaction with rifamycins (particularly rifampin). management of such patients should be coordinated with an infectious diseases specialist, who also should manage drug-resistant tb treatment. in the united states, latent tuberculosis infection (ltbi) is the most prevalent form of tuberculosis. ltbi is the term given to patients with a positive purified protein derivative (ppd) skin test without evidence of active tb. ppd has been used for more than years and relies on delayed-type hypersensitivity (dth) to m. tuberculosis cellular proteins. early late figure - treatment algorithm for tuberculosis. patients in whom tb is proved or strongly suspected should have treatment initiated with isoniazid, rifampin, pyrazinamide, and ethambutol for the initial months. a repeat smear and culture should be performed when months of treatment has been completed. if cavities were seen on the initial chest radiograph or the acid-fast smear is positive at completion of months of treatment, the continuation phase of treatment should consist of isoniazid and rifampin daily or twice weekly for months to complete a total of months of treatment. if cavitation was present on the initial chest radiograph and the culture at completion of months' therapy is positive, the continuation phase should be lengthened to months (total of months of treatment). if the patient has hiv infection and the cd + cell count is less than /mm , the continuation phase should consist of daily or three-times-weekly isoniazid and rifampin. in hiv-uninfected patients having no cavitation on chest radiograph and negative acid-fast smears at completion of months of treatment, the continuation phase may consist of either once-weekly isoniazid and rifapentine, or daily or twice-weekly isoniazid and rifampin, to complete a total of months (bottom). patients receiving isoniazid and rifapentine, and whose -month cultures are positive, should have treatment extended by an additional months (total of months). *emb may be discontinued when results of drug susceptibility testing indicate no drug resistance. †pza may be discontinued after it has been taken for months ( doses). ‡rpt should not be used in hiv-infected patients with tb or in patients with extrapulmonary tb. therapy should be extended to months if -month culture is positive. afb, acid-fast bacilli; cxr, chest radiograph (x-ray); emb, ethambutol; inh, isoniazid; pza, pyrazinamide; rif, rifampin; rpt, rifapentine. because ppd relies on dth, any factor that reduces the dth affects the host response to ppd. the most common clinical example is use of corticosteroids, which blunt the dth response and can complicate ppd interpretation. therefore, ppd testing should not be performed while a patient is taking corticosteroids. also, tb testing should be targeted to those with higher risk of infection and should not routinely be done in those with low risk (ats/cdc, ) . the ppd can also give false-positive results in patients with previous bacille calmette-guérin (bcg) vaccination or with infection by other mycobacterial infections. in the united states, this may cause difficulties in testing immigrants from countries who routinely use bcg vaccination programs. however, previous bcg vaccination should not change the interpretation of the ppd or willingness to treat such individuals accordingly. ‡when dot is used, drugs may be given days per week and the necessary number of doses adjusted accordingly. although there are no studies that compare five with seven daily doses, extensive experience indicates this would be an effective practice. § patients with cavitation on initial chest radiograph and positive cultures on completion of months of therapy should receive a -month ( weeks, either doses [daily] or doses [twice weekly]) continuation phase. ¶ five-days-a-week administration is always given by dot. rating for day per week regimens is aiii. ¶ ¶ not recommended for hiv-infected patients with cd + cell counts < cells/μl. ** options c and b should be used only in hiv-negative patients who have negative sputum smears at completion of months of therapy and who do not have cavitation on initial chest radiograph. for patients started on this regimen and found to have a positive culture from the -month specimen, treatment should be extended an extra months. the dth response can wane over time. to overcome this problem, nonreacting patients may undergo repeat ppd week after their initial ppd. the diagnosis of ltbi is made by interpretation of a ppd and by ascertaining the patient's risk factors for progression to active tb if left untreated . interpretation of the ppd should be based on the area of induration and not the area of surrounding erythema. persons whose ppds have converted from negative to positive within years are presumed to have been infected recently. the decision to use ppd means treating the patient for ltbi if the ppd test is positive. patients at increased risk for progression to active tb include those who have been recently infected (recent ppd converters); patients who are hiv seropositive; patients who have silicosis, diabetes, or chronic renal failure (including those receiving hemodialysis); solid-organ transplant recipients; patients with gastrectomy or jejunoileal bypass or head and neck cancer; injection drug users; patients with chest radiograph evidence of prior tb; and patients who weigh at least % less than ideal body weight. patients taking chronic corticosteroid therapy and those who are to receive tumor necrosis factor alpha (tnf-α) blockers (e.g., infliximab) are also at risk. patients taking corticosteroids also have higher risk of progression to active tb with larger doses and longer courses of corticosteroids. standard therapy for ltbi is inh, mg orally daily for months, regardless of hiv status. again, inh should always be administered with pyridoxine to prevent neuropathy. to overcome the false-positive results and confusion of ppd testing in certain populations, newer interferon-gamma (ifn-γ) release assays such as the quantiferon-tb gold (qft-g) test have been developed to detect latent m. tuberculosis. qft-g quantifies the release of ifn-γ from lymphocytes of the host's blood in response to three m. tuberculosis target antigens that are absent from bcg and most other nontuberculous mycobacterium spp. the advantages of using qft-g include one-time blood testing without the need for followup visit, no triggering of amnestic responses, and possibly more specific response to m. tuberculosis. however, qtf-g use in immunocompromised or anergic patients is limited, with indeterminate results. some studies also show discordant results in individuals tested with both ppd and qtf-g. in general, qtf-g may be used in all circumstances in which the ppd is used. however, whether the qtf-g is truly more specific or sensitive than the ppd in latent or active tb is yet to be determined. • the u.s. preventive services task force recommends "highintensity" behavioral counseling to at-risk adults and adolescents to prevent sexually transmitted infections. • be specific in addressing patients' sexual practices so as to provide appropriate prevention advice. hiv-positive persons recent contacts of tuberculosis patients fibrotic changes on chest radiography consistent with prior tuberculosis patients with organ transplants and other immunosuppressed patients (receiving equivalent of ≥ mg/day of prednisone for at least month) development in the primary prevention of stis is immunization against human papillomavirus (hpv). the vaccine can prevent infection with certain strains of hpv that cause cervical cancer and genital warts. trials are ongoing to determine the effectiveness of daily arv therapy in preventing transmission of hiv. vaccination investigation is ongoing for herpes simplex, chlamydia trachomatis, and hiv. this breadth of research effort holds promise for the future in the prevention of stis. the uspstf recommends "high-intensity" behavioral counseling to at-risk adults and adolescents to prevent stis. highintensity counseling involves multiple sessions and often is delivered to groups of patients. unfortunately, this type of intervention has limitations in its practicality for population-based delivery. no risk of harm was discovered in the delivery of counseling for sti prevention. vaccination is the most important form of primary prevention of common infectious diseases. two vaccines are currently on the market for hpv prevention-one that protects against four viral subtypes ( , , , ) and is licensed for use in males and females to years of age, and the other against two subtypes ( , ), licensed for females to years of age. hepatitis b is a sexually transmitted infection, and immunization is recommended for adolescents who have not been previously inoculated. this is a requirement in many states for school entry. hepatitis a can be transmitted by oro-anal sexual contact, and vaccination should be offered to patients who are contemplating engaging in this sexual practice. recommendations surrounding the use of barrier methods for sti prevention should be tailored to the sex practices of the client. for example, a percentage of women use anal sex as a method of birth control but may not consider the need for condom use with this practice. the question, "do you regularly use condoms?" has little relevance to infection control for many sexual practices. evidence supports the advice to use barrier methods of latex or other approved material in a manner that prevents the exchange of blood and body fluids in decreasing stis. condoms confer a % risk reduction for herpes simplex and up to an % risk reduction for hiv, when used correctly (weller and davis-beaty, ; martin et al., ) . the secondary prevention of stis is achieved through direct and nonjudgmental patient assessment and screening and avoiding assumptions about patient sexual practices. screening is a tool to prevent the inadvertent spread of infection as well as the sequelae of undetected disease. infectious genital ulcers are associated with herpes simplex virus (hsv), syphilis, chancroid, lymphogranuloma venereum, and granuloma inguinale. hsv is by far the most common, affecting million people in the united states. hsv- and hsv- are chronic, neurotropic viral infections that enter through epithelium and come to rest in the dorsal root ganglia. therefore, infection leads to lifetime presence of the virus, but the clinical manifestation of this condition is variable. a small percentage of those with serologic evidence of hsv- ( %- %) have had symptoms of clinical herpes infection. in addition, patients with hsv infection can shed the virus in the absence of symptoms, creating a prime opportunity for spread. herpes simplex outbreak may be followed by a prodrome of malaise, fever, and regional lymphadenopathy before the appearance of grouped vesicles on an erythematous base. the vesicles are typically quickly broken and become ulcerated in appearance, with each vesicle usually less than several millimeters in size. true first-time infections tend to present more severely than secondary presentations of previously infected individuals, with a prodrome present in % of cases. the lesions can be in any location around the genitals or rectum, on the proximal thighs and buttocks, inside the vagina, and in and around the mouth. the lesions are most who to screen? often painful, particularly when on mucosal surfaces, or itchy. in women, herpes simplex can present with cervicitislike symptoms with bleeding and discharge and cervical ulcerations on examination, or simply mucopurulent cervicitis. herpetic lesions around the urethra tend to be extremely painful and can make urination difficult. rectal hsv can be confused with irritation, perianal fissure, and even candidiasis because of its often beefy-red appearance and itching. vesicles typically appear days after infection and can last up to weeks in an initial infection. subsequent outbreaks tend to have a shorter duration and to be less uncomfortable for patients. confirmation of infection is helpful, but the diagnosis can be made primarily on the clinical appearance of the exanthema. vigorous sample collection from an ulcer (which the patient may not appreciate) to be sent for pcr identification and typing is the most readily available method of laboratory diagnosis. serum antibody testing is not useful in the initial hsv diagnosis because antibody levels will not be appreciable early in infection. the appearance of convalescent immunoglobulin g (igg) and igm levels several weeks after a suspected outbreak might help to support the diagnosis of hsv infection. the value of screening for hsv immunity is debatable and should generally not be recommended for asymptomatic individuals. in addition, the uspstf recommends against screening asymptomatic pregnant women for hsv to prevent transmission to the newborn. given that many patients with hsv infection never manifest symptoms, the value of knowing that one is hsv seropositive is questionable. in addition, hsv- and hsv- , although classically oral and genital, respectively, can "mix and match" based on sexual practices. it is often confusing for asymptomatic individuals to know that they have hsv antibody (do i have cold sores? do i have genital herpes? how should this change the way i live my life?). in monogamous couples with one partner known to be hsv positive and the other with unknown status, testing of the latter may indicate suppressive therapy in the seropositive partner if the other is found to be negative. regular barrier method use decreases transmission of herpes in both men and women, with patients using condoms % of the time having a % reduction in hsv acquisition from those who never use condoms (martin et al., ) . serodiscordant couples may also decrease transmission through antiviral suppressive therapy to the hsv-positive partner (table - ) . syphilis is a spirochetal infection that has resurged since , the nadir year since . syphilis infection rates are highest in men who have sex with men. syphilis is much less common than the other stis, with an infection rate of . per , population in the united states (vs. per , for chlamydia). syphilis presents in several stages. the primary phase of syphilis is a painless ulcer called a chancre (figure - ) . the chancre may be visible on the genitals, although it can also be inside the vagina, mouth, or rectum, making it difficult to find. this lesion will appear within weeks of transmission and will last for several weeks untreated. the secondary phase of infection is disseminated and involves a diffuse macular rash, typically with palm and sole lesions, generalized lymphadenopathy, fever, and condyloma latum (smooth, moist lesions on genitals without cauliflower appearance of condyloma acuminatum). tertiary syphilis is often asymptomatic but affects the heart, eyes, and auditory system and can be associated with gumma formation. gummas are soft, granulomatous growths in organs that can cause mechanical obstruction and weakening of blood vessel walls. latent infection often involves the cns. diagnosis of primary syphilis is challenging. the test of choice is darkfield microscopy, which is not readily available. direct fluorescent (monoclonal) antibody (dfa) testing may be available. antibody tests for syphilis, such as the rapid plasma reagin (rpr) and the less frequently used venereal disease research laboratories (vdrl), are often not positive early in infection and thus cannot be used to rule out primary syphilis based on a single reading. treponemal antigen testing (eia) may be available in some laboratories. the fluorescent treponemal antibody absorption (fta-abs) test may also be negative in the early infection. direct pcr for primary syphilis lesions has been tested but is not yet fda approved. a physician may choose to treat presumptively if a painless chancre and risk factors are present and may then do a convalescent rpr test in to weeks to confirm the infection by the appearance of a positive reaction. one would expect a fourfold change in titer of either test to indicate the presence of disease. primary and secondary syphilis are treated with a single injection of penicillin g, . million units. other regimens do not have proven effectiveness but can be used in the penicillin-allergic patient, including doxycycline, mg twice daily for days; ceftriaxone, mg to g intramuscularly (im) daily for to days; or azithromycin, g as a single oral dose, although resistance to azithromycin has been observed. patients treated for primary syphilis should have periodic clinical follow-up and serologic testing to determine a fourfold decrease in rpr reactivity within months. latent syphilis can be either early, meaning infection within the last year, or late, meaning infection beyond a year. early latent syphilis is treated with a single injection of penicillin g, . million units. syphilis of late latency or unknown duration is treated with three injections of penicillin g, . million units, in consecutive weeks. for penicillin-allergic patients, doxycycline, mg twice daily for days, is required. those with latent syphilis should have ophthalmic examination as well as evaluation for vascular gumma formation. suspected neurologic involvement of latent syphilis must be evaluated with cerebrospinal fluid (csf) examination and treatment with aqueous penicillin g, - million units intravenously (iv) every hours for to days. partners of patients with newly diagnosed syphilis are at risk for infection. partners within days of a diagnosis of primary syphilis should be tested, but treated presumptively even if serologic testing is negative. for partners prior to days before diagnosis, serology is generally reliable in detecting presence of infection and may guide treatment. patients with secondary syphilis should inform partners within months before diagnosis, or months for those diagnosed with tertiary syphilis (table - ). chancroid may occur in regional outbreaks and presents with a painful genital ulcer and suppurative regional adenopathy. herpes and syphilis should both be ruled out in the patient suspected of having chancroid infection. chancroid is caused by haemophilus ducreyi and there is currently no fda approved test to directly detect this organism. treatment with azithromycin ( g as single dose), ceftriaxone ( mg im as a single dose), ciprofloxacin ( mg twice daily for days), or erythromycin ( mg three times daily for days) are all alternatives (table - ). it may be necessary to perform incision and drainage on fluctuant inguinal nodes. patients should be reexamined in to weeks to ensure healing of the primary ulcer(s) and resolution of the adenopathy. partners who had contact with the infected patient starting days before development of the patient's symptoms should be treated, regardless of the presence of symptoms. less common ulcerating stis include lymphogranuloma venereum (lgv) and granuloma inguinale ( figure - ). lgv causes regional adenopathy and often an ulcer at the point of entry. rectal lgv may cause a proctocolitis with anal pain, discharge, bleeding, and diarrhea. lgv is caused by chlamydia trachomatis serotypes and can be detected by testing swabbed material from open lesions or aspirates from lymph nodes with culture, dfa, or nucleic acid detection. treatment is noted above (table - ) . granuloma inguinale, caused by klebsiella granulomatis, is rare in the united states and causes progressive ulcerative disease of the genitals. a second sti category includes those causing the clinical presentation of vaginal discharge, pelvic pain, dyspareunia, and dysuria in women and penile discharge and dysuria in men, as well as possible rectal pain and discharge in men and women. of this group, chlamydia trachomatis is the most common, causing . million infections in the united states in (cdc, ). in fact, chlamydia is the most frequently reported reportable infection. the majority of women with chlamydia infection are without symptoms. many men are asymptomatic as well. regular screening for chlamydia, as recommended by the uspstf, can significantly reduce the incidence of pelvic inflammatory disease (pid), one of the most serious sequelae of untreated infection. in women with untreated chlamydia infection, in addition to pid, tubo-ovarian abscess, tubal scarring and ectopic pregnancy, and infertility can all result. as previously mentioned, regular screening is currently recommended for all sexually active women under age , all pregnant women under , and at-risk pregnant and nonpregnant women over . chlamydia testing can be performed on several liquid-based papanicolaou (pap) tests. endocervical swabs for nucleic acid amplification are acceptable when a conventional pap smear is being used. given the recent liberalization of recommendations about pap testing for women under years of age, urine nucleic acid amplification is a readily available alternative for chlamydia testing. this can easily be done at a contraceptive counseling clinic. urine testing is also an acceptable method of testing for men, in addition to a urethral swab. rectal chlamydia infection can occur in individuals who practice receptive anal intercourse. an fda-approved method of testing should be used for screening and diagnosis of this infection. asymptomatic chlamydia infection is treated with either a single dose of azithromycin, g orally, the drug of choice, or doxycycline, mg twice daily, for days (table - ) . patient-delivered partner therapy (pdpt), the practice of dispensing treatment to diagnosed patients to treat their partner(s), has proved effective in reducing reinfection rates and further spread of infection. ept is legally allowable in states and potentially allowable in another . chlamydia infection may present symptomatically in men or women with symptoms of dysuria and with discharge and with pelvic pain and dyspareunia in women. the discharge of c. trachomatis, versus that of neisseria gonorrhoeae, is said to be more mucoid than purulent, although this characteristic is not specific enough to provide diagnostic accuracy. symptomatic chlamydia, without evidence of pid, is treated the same as asymptomatic infection. many practitioners will treat presumptively for chlamydia and gonorrhea in patients who present with the symptoms previously mentioned while they wait for confirmatory testing. neisseria gonorrhoeae infection may be asymptomatic in both men and women. the current uspstf recommendation is for screening women at risk. men with penile gonorrhea typically present with purulent penile discharge and dysuria with n. gonorrhoeae infection. mucopurulent discharge, dysuria, pelvic pain, and dyspareunia are typical symptoms in women. in patients who engage in anal intercourse, anal discharge, rectal pain, and bleeding can be presenting symptoms. gonococcal pharyngitis is within the differential of exudative pharyngitis in sexually active patients. when symptomatic, throat pain, tonsillar exudates, and anterior cervical adenopathy may be present. testing for gonorrhea can be done using liquid-based pap technologies, cervical or urethral swabs, or urine for nucleic acid amplification. in men with visible discharge, a gram stain with white blood cells (wbcs) and gram-positive intracellular diplococci has a high degree of sensitivity. culture testing may be preferred for suspected pharyngeal and rectal specimens pending fda approval of other methods. again, physicians may opt to treat patients with mucopurulent cervicitis or urethritis presumptively for gonorrhea and chlamydia while waiting for confirmatory testing. fluoroquinolone therapy is no longer recommended because of widespread resistance (table - ) . because reinfection with gonorrhea is common for several months after treatment, it may be advisable to retest patients with confirmed gonorrhea in the months after treatment. similarly, stis may be an indicator of risk behavior, and a complete risk history and testing for other stis is advisable if not completed at the initial visit. in male patients with symptomatic urethritis, a causative agent may not be identified, a situation often referred to as nongonococcal urethritis (ngu). technically, chlamydia is included in this category. organisms such as ureaplasma urealyticum and mycoplasma genitalium may be the cause and may be difficult to detect. treatment for these infections is the same as for symptomatic chlamydia, with azithromycin or doxycycline (table - ). it is recommended that partners of patients with ngu should be evaluated and treated. in some cases, testing of partners may detect a specific organism as the cause of infection (e.g., chlamydia). trichomonas vaginalis causes vaginitis in women, who may have a stereotypic frothy, green, and foul-smelling discharge. many women are asymptomatic with trichomoniasis. in addition to causing asymptomatic infection in men, t. vaginalis may cause urethritis. this organism may be suspected in men when patients have repeated treatment failures and no other explanation for symptoms. microscopic examination of vaginal discharge is % to % sensitive in women. a first voided urine specimen or urethral swab for microscopic exam may be helpful in identifying the protozoa. culture for trichomonas, which requires a special medium, may be necessary to identify this infection accurately in men. trichomonas is effectively treated with a single -g dose of metronidazole (table - ) . for non-sti causes of vaginal discharge, see the online discussion at www.expertconsult.com. pelvic inflammatory disease can be caused by a number of organisms, including chlamydia, and presents with pelvic pain and discharge. findings that contribute to the diagnosis of pid include fever greater than ° f, cervical or vaginal mucopurulent discharge, abundant wbcs on saline preparation of vaginal discharge, elevated erythrocyte sedimentation rate (esr), elevated c-reactive protein (crp), and evidence of n. gonorrhoeae or c. trachomatis infection. hospitalization with parenteral antibiotics may be necessary in pregnant patients, patients in whom surgical emergency cannot be ruled out, those who do not respond to oral treatment, those who cannot tolerate oral treatment, and patients who have severe illness or tubo-ovarian abscess. when treating pid parenterally, improvement of symptoms for hours may prompt a change to oral therapy (table - ) . conversely, if oral therapy is not producing significant improvement within to days, admission for parenteral therapy may be necessary. patient awareness of human papillomavirus infection has greatly increased in recent years, in large part related to the patient-directed advertising of the hpv vaccine. hpv is likely the most common sti. thirty types of hpv can infect the genital area, some causing genital warts, some causing malignancies of the genital organs, and most being asymptomatic. the gross categories most often used are "high risk" (most often types and ) and "low risk" (types and ) hpv infection, the former more often associated with genital cancer. prevention of hpv infection and cervical cancer was revolutionized with the release of the hpv vaccine, which is effective in reducing the incidence of hpv-associated disease. currently, two vaccines are licensed in the united states. gardasil (merck), released in , includes protection against viral types , , , and . it is approved for the prevention of vulvar and vaginal cancer and for the prevention of cervical cancer, cervical dysplasia, and genital warts in females age to . the vaccine was recently approved for males of the same age range for the prevention of genital warts. more recently, cervarix (glaxosmithkline) was approved for the prevention of cervical cancer and cervical dysplasia from hpv types and in women age to . ideally, the vaccine should be administered before initiation of sexual activity to prevent initial acquisition of these hpv types. patients who are already sexually active may also receive the vaccine. the transmission of hpv to men decreases with consistent condom use, from . % in men who never use condoms to . % in men who "always" use them. unfortunately, hpv can infect skin that is not covered by the use of traditional barrier methods (nielson et al., ) . male circumcision may decrease the transmission of hpv. patients have many questions about hpv, in particular about screening for asymptomatic infection. hpv infection occurs with high frequency in the sexually active population; up to % or more of sexually active individuals have hpv at some point in their life. in addition, hpv is effectively transmitted, even if contact does not involve genital-togenital touching (i.e., manual stimulation can transmit the virus). again, most hpv infections are without symptoms and resolve spontaneously through eradication by the intact immune system. for all these reasons, screening for the mere presence of hpv infection has minimal utility. there is no treatment for asymptomatic hpv infection. the most common presentation of hpv infection is in the context of an abnormal pap smear. hpv is directly linked to cervical dysplasia. for women over age and under , hpv testing with high-risk viral detection is common. the presence of high-risk hpv informs further management of the pap result. it is currently recommended that women over be automatically tested for high-risk hpv infection at the pap smear. patients may present with visible warts, or these may be detected at routine or sti screening. genital warts are often cosmetically unacceptable to patients, even though they are infrequently functionally problematic. in some circumstances, wart burden can be high enough to cause physical discomfort or relative obstruction of the vagina or rectum. vulvovaginal candidiasis and bacterial vaginosis are generally not thought to be sexually transmitted, although they are often in the differential diagnosis of sexually transmitted infection (sti). both these infections likely are related to changes in the vaginal ph and the normal flora distribution. it is not always clear which of these factors is primary and which is secondary, because at diagnosis, both ph and normal vaginal flora will often be abnormal. vulvovaginal candidiasis is a common infection causing typically white, curdlike discharge, itching, and sometimes dysuria. the causative organism is usually candida albicans but can be other candida spp. antibiotics can alter normal vaginal flora, so the recent use of antibiotics may predispose women to candidiasis. physical examination may reveal erythematous external genitalia as well as external and internal white, clumping discharge. usually, no distinctive odor is associated with vaginal yeast. wet preparation of vaginal specimen or treatment with potassium hydroxide (koh) may reveal branching pseudohyphae and yeast. when ph is performed, it should be directly on the vaginal discharge and not on the saline-diluted specimen because the saline will alter the ph of the specimen. typically, the ph of yeast discharge is less than . (normal vaginal ph, . - . ). bacterial vaginosis (bv) is the most common cause of infectious vaginal discharge (spence and melville, ) . many different organisms are associated with the diagnosis of bv, including gardnerella vaginalis and mycoplasma hominis. women with bv may report discharge, vaginal irritation, vaginal odor, and at times, dysuria. findings of bv are often detected during a normal screening pap smear or pelvic examination. physical findings may reveal signs of vaginal irritation. the discharge is usually thin and gray. an amine (fishy) odor may be produced with the application of koh. the finding of clue cells, or epithelial cells with adherent bacteria, under saline preparation microscopy and a decrease in normal lactobacilli are common findings. the amsel criteria are useful in bv diagnosis; other scoring systems (e.g., nugent criteria) have been used but require gram staining. the specific amsel criteria are ( ) milky, homogeneous, adherent discharge; ( ) discharge ph greater than . ; ( ) positive whiff test (fishy smell with addition of koh); and ( ) at least % clue cells on microscopic examination. if three of the four criteria are present, the likelihood of bv is %. in routine vaginal examination and bimanual examination for patients with vaginal discharge, signs and symptoms of vaginitis are poor predictors of the microbiologic cause of infection (schaaf et al., ) . the clinical examination and office testing, in fact, are fair predictors of the true cause of infection (lowe et al., ). many patients with vaginal discharge will use over-the-counter preparations before consulting a physician, which can delay correct diagnosis of the etiology of symptoms. patient-collected, low vaginal swabs may be as useful as provider-collected specimen in making a diagnosis for the patient with vaginal discharge. the purpose of bimanual examination is to evaluate for signs of pelvic inflammatory disease and is not necessary in the low-risk patient with vaginal discharge. treatment of asymptomatic bv or vaginal yeast is not necessary in the nonpregnant patient or usually is not needed to test or treat partners of patients with isolated yeast or bv. when infection is recurrent, particularly when a woman's male partner is uncircumcised, treatment of the male partner for carriage of either infection may be warranted. options for treatment of recurrent infections are presented in etable - . the treatment of warts is destructive and may serve to stimulate an immune response to the hpv-infected cells, which are typically "above" the surveillance mechanisms of the immune system in the epidermis. office methods of treatment include cryotherapy and trichloroacetic acid or podophyllin resin application. patients may apply podofilox . % solution or gel or imiquimod % cream (table - ) . for more extensive cases of warts or intra-anal or intravaginal infections that are difficult to treat using the previous methods, surgical techniques may be necessary to achieve resolution. untreated, warts may resolve spontaneously, remain the same, or worsen. patients with pediculosis pubis, or pubic lice, most often present with pruritus or with visible nits. pubic lice are visible on inspection of the pubic area, as are nits, which are adherent to the hair shaft. partners of patients with pubic lice should also be treated to prevent reinfection. linens and clothing should be laundered or dry-cleaned or kept in a closed plastic container or bag for hours. scabies diagnosis can be challenging. again, patients present with itching that can be anywhere on the body, although often in the genital area or on the buttocks when infection is sexual in origin. the pruritus associated with sarcoptes scabiei is a result of sensitization to the mite droppings underneath the skin as the mite burrows. the classic "burrow" or linear papular eruption is not always present. scraping of lesions with microscopic examination may be performed to identify the mite. as with pediculosis, close contacts should be treated. linens and clothing should be laundered or dry-cleaned or isolated in plastic containers for hours. the pruritus-associated with scabies can take several weeks to resolve after treatment. patients living in group settings (dormitories or apartments) may reinfect one another as a result of inadequate primary treatment of all contacts ( cryotherapy trichloroacetic acid (tca): small amount applied until wart whitens podophyllin resin, % to % all these may be repeated every to weeks until warts are resolved. podofilox . % solution or gel applied twice daily for days, followed by days of no therapy. imiquimod % cream applied once daily at bedtime three times a week for up to weeks; washed off to hours after application. urinary tract infection (uti) is defined as significant bacteriuria in the presence of symptoms. uti accounts for a significant number of emergency department visits; an estimated % of women experience a uti in their lifetime. the urinary tract is normally sterile. uncomplicated uti involves the urinary bladder in a host without underlying renal or neurologic disease. the bladder mucosa is invaded, most often by enteric coliform bacteria (e.g., e. coli) that ascend into the bladder via the urethra. sexual intercourse can promote this migration, and cystitis is common in otherwise healthy young women. frequent and complete voiding has been associated with a reduction in the incidence of uti. complicated uti occurs in the setting of underlying structural, medical, or neurologic disease. signs and symptoms of a uti include dysuria, frequency, urgency, nocturia, enuresis, incontinence, urethral pain, suprapubic pain, low back pain, and hematuria. fever is unusual. up to % of patients with symptoms of cystitis have a smoldering pyelonephritis, especially when symptoms have been present for more than week. a patient with pyelonephritis usually appears ill, with fever, sweating, and prostration, along with costovertebral angle (flank) tenderness in most cases. the differential diagnosis of uncomplicated uti includes use of diuretics or caffeine, interstitial cystitis, vaginitis, pregnancy, pelvic mass, pid, and benign prostatic hypertrophy (bph). if a uti is suspected, the initial test of choice is urinalysis, although with classic signs and symptoms of infection in women, this test is not always necessary. pyuria, as indicated by a positive result on the leukocyte esterase dip test, is found in the majority of patients with uti. the presence of urinary nitrites is fairly specific for uti. the combination of positive leukocyte esterase and nitrites improves sensitivity. on urine microscopy, levels of pyuria as low as two to five leukocytes per high-power field ( - wbcs/hpf) in a centrifuged specimen are significant in the female patient with appropriate symptoms, as is the presence of bacteriuria. urine culture and sensitivity are not needed in simple utis. cultures should be done in patients with recurrent utis, patients with pyelonephritis, and pregnant patients. antibiotic therapy can be given in a -day regimen for young, sexually active women. a -to -day course of antibiotics should be used in pregnant patients and patients with complicated utis. all the drugs listed in table - can be used in a -day or -to -day course. clinical practice guidelines that include telephone assessment and treatment have shown a decrease in unnecessary laboratory utilization while maintaining quality of care (saint et al., ) . trimethoprim-sulfamethoxazole (tmp-smx) has been a mainstay of uti therapy, but in some localities, resistance of e. coli to tmp-smx is % (mehnert-kay, ) . if a urine culture is done and the organism is resistant to the drug prescribed, a change in antibiotics is indicated only if the patient is still symptomatic. for symptomatic treatment, a bladder anesthetic can be used, such as phenazopyridine (pyridium), mg three times daily for days. patients should be warned that this produces an orange tinge in tears and urine. patients should also be instructed to increase fluid intake. pyelonephritis is suggested by a failure of a short course of antibiotics. signs and symptoms of pyelonephritis include shaking chills and fever higher than . ° c ( . ° f), flank pain, malaise, urinary frequency and burning, and costover-tebral angle tenderness. the infection can produce septic shock. a patient who is unable to tolerate oral intake should be hospitalized and given empiric iv antibiotics aimed at broad-spectrum gram-negative coverage, such as third-generation cephalosporins, fluoroquinolones, or aminoglycosides, while awaiting results of blood and urine cultures. a -day course of antibiotic therapy (iv or po) is recommended. although the most common bacterial infection during pregnancy, the incidence of uti in pregnancy is similar to that reported in sexually active nonpregnant women of childbearing age. up to % of pregnant women with tmp-smx, / mg q h trimethoprim, mg q h fluoroquinolones ‡ ciprofloxacin, - mg q h ciprofloxacin xr, mg qd gatifloxacin, mg qd levofloxacin, mg qd nitrofurantoin monohydrate/macrocrystals, mg q h nitrofurantoin macrocrystals, - mg qid amoxicillin, mg q h or mg q h cephalexin, mg q h, or other cephalosporin consider -day regimen. amoxicillin, mg q h or mg q h nitrofurantoin monohydrate/macrocrystals, mg q h nitrofurantoin macrocrystals, - mg qid cephalexin, mg q h, or other cephalosporin tmp-smx, / mg q h male gender, diabetes, symptoms for days, recent antimicrobial use, age > tmp-smx, § / mg q h fluoroquinolones, as per -day regimens cephalexin, mg q h, or other cephalosporin consider -day regimen. from hooton tm, stamm we. diagnosis and treatment of uncomplicated urinary tract infection. infect dis north am ; : . tmp-smx, trimethoprim-sulfamethoxazole; qd, every day; q h, every hours; q h, every hours; q h, every hours; qid; four times daily. * treatments listed to be prescribed before etiologic agent is known (gram stain may help); therapy can be modified when cause is identified. † characteristic pathogens are escherichia coli ( %- %) and staphylococcus saprophyticus ( %- %); other organisms account for less than % of cases and include proteus mirabilis, klebsiella pneumoniae, and enterococcus spp. ‡fluoroquinolones should not be used in pregnancy. § although classified as pregnancy category c, tmp-smx is widely used; however, avoid its use in the first and second trimesters. untreated bacteriuria in the first trimester develop acute pyelonephritis later in pregnancy. premature births and perinatal mortality are increased in pregnancies complicated by uti. therefore, in pregnant women, asymptomatic bacteriuria should be actively sought and aggressively treated with at least one urinalysis, preferably toward the end of the first trimester. nitrofurantoin, ampicillin, and the cephalosporins have been used most extensively in pregnancy and are the regimens of choice for treating asymptomatic or minimally symptomatic uti. tmp-smx should be avoided in the first trimester because of possible teratogenic effects and should be avoided near term because of a possible role in the development of kernicterus. fluoroquinolones are avoided because of possible adverse effects on fetal cartilage development. for pregnant women with overt pyelonephritis, admission to the hospital for parenteral therapy should be the standard of care; beta-lactam agents with or without aminoglycosides are the cornerstone of therapy. prevention of uti, including pyelonephritis, can be accomplished during pregnancy with nitrofurantoin or cephalexin taken prophylactically after coitus or at bedtime without relation to coitus. such prophylaxis should be considered for patients who have had acute pyelonephritis during pregnancy, patients with bacteriuria during pregnancy who have had a recurrence after a course of treatment, and patients who had recurrent uti before pregnancy that required prophylaxis. catheter-associated utis are associated with increased mortality and costs. risk factors for catheter-associated utis include the duration of catheterization, lack of systemic antibiotic therapy, female gender, age older than years, and azotemia. to help prevent infection, urinary catheters should be avoided when possible and used only as long as needed. the catheter should be inserted with strict aseptic technique by trained persons, and a closed system should be used at all times. treatment of catheter-associated uti depends on the clinical circumstances. symptomatic patients (e.g., those with fever, chills, dyspnea, and hypotension) require immediate antibiotic therapy along with removal and replacement of the urinary catheter if it has been in place for a week or longer. in an asymptomatic patient, therapy should be postponed until the catheter can be removed. patients with long-term indwelling catheters seldom become symptomatic unless the catheter is obstructed or is eroding through the bladder mucosa. in patients who do become symptomatic, appropriate antibiotics should be administered and the catheter changed. therapy for asymptomatic catheterized patients leads to the selection of increasingly antibiotic-resistant bacteria. recurrence of uncomplicated cystitis in reproductive-age women is common, and some form of preventive strategy is indicated if three or more symptomatic episodes occur in year. however, risk factors specific to women with recurrent cystitis have received little study (sen, ) . several antimicrobial strategies are available, but before initiating therapy, the patient should try such simple interventions as voiding immediately after sexual intercourse and using a contraceptive method other than a diaphragm and spermicide. ingestion of cranberry juice has been shown to be effective in decreasing bacteriuria with pyuria, but not bacteriuria alone or symptomatic uti, in an elderly population. cranberry juice may be effective for preventing uti in young, otherwise healthy women. if simple nondrug measures are ineffective, continuous or postcoital-if the infections are temporally related to intercourse-low-dose antimicrobial prophylaxis with tmp-smx, a fluoroquinolone, or nitrofurantoin should be considered. typically, a prophylactic regimen is initially prescribed for months and then discontinued. if the infections recur, the prophylactic program can be instituted for a longer period. an alternative approach to antimicrobial prophylaxis for women with less frequent recurrences (< a year) is to supply tmp-smx or a fluoroquinolone and allow the patient to self-medicate with short-course therapy at the first symptoms of infection. a minority of patients have relapsing uti, as evidenced by finding the same bacterial strain within weeks after completion of antimicrobial therapy. two factors can contribute to the pathogenesis of relapsing infection in women: ( ) deep tissue infection of the kidney that is suppressed but not eradicated by a -day course of antibiotics and ( ) structural abnormality of the urinary tract, particularly calculi. patients with true relapsing utis should undergo renal ultrasound, intravenous pyelogram (ivp), or voiding cystourethrogram, and longer-term therapy should be considered. urinary tract infection is one of the most common infections of childhood. factors predisposing to uti include taking broad-spectrum antibiotics (e.g., amoxicillin, cephalexin), which are likely to alter gastrointestinal and periurethral flora; incomplete bladder emptying or infrequent voiding; voiding dysfunction; and constipation. uti in young children serves as a marker for abnormalities of the urinary tract. imaging of the urinary tract is recommended in every febrile infant or young child with a first uti to identify children with abnormalities that predispose to renal damage. imaging should consist of urinary tract ultrasonography to detect dilation of the renal parenchyma. voiding cystourethrography is often ordered but does not appear to improve clinical outcomes in uncomplicated utis (alper and curry, ) . a common complication of uti in men is prostatitis. bacterial prostatitis is usually caused by the same gram-negative bacilli that cause uti in female patients; % or more of such infections are caused by escherichia coli. the pathogenesis of this condition is poorly understood. antibacterial substances in prostatic secretions probably protect against such infections. a national institutes of health (nih) expert consensus panel has recommended classifying prostatitis into three syndromes: acute bacterial prostatitis, chronic bacterial prostatitis, and chronic pelvic pain syndrome (cpps). acute bacterial prostatitis is a febrile illness characterized by chills, dysuria, urinary frequency and urgency, and pain in the perineum, back, or pelvis. the bladder outlet can be obstructed. on physical examination, the prostate is found to be enlarged, tender, and indurated. pyuria is present, and urine cultures generally grow e. coli or another typical uropathogen. chronic bacterial prostatitis is a clinically more occult disease and may be manifested only as recurrent bacteriuria or variable low-grade fever with back or pelvic discomfort. urinary symptoms usually relate to the reintroduction of infection into the bladder, with both pyuria and bacteriuria. a chronic prostatic focus is the most common cause of recurrent uti in men. cpps is the diagnosis for the large group of men who present with minimal signs on physical examination but have a variety of irritative or obstructive voiding symptoms; perineal, pelvic, or back pain; and sexual dysfunction. these men can be divided into those with and those without inflammation (defined as > wbcs/hpf in expressed prostatic secretions). the etiology and appropriate management in these patients, regardless of inflammatory status, is unknown. • laboratory findings in acute tick-borne infection often include a normal or low wbc count, thrombocytopenia, hyponatremia, and elevated liver enzymes. • doxycycline is the drug of choice for patients with rmsf. • appropriate antibiotic treatment should be initiated immediately with strong suspicion of ehrlichiosis. • if left untreated, lyme disease can progress to cognitive disorders, sleep disturbance, fatigue, and personality changes. in the united states, more vector-borne diseases are transmitted by ticks than by any other agent. tick-borne diseases can result from infection with pathogens that include bacteria, rickettsiae, viruses, and protozoa. most tick-borne diseases are transmitted during the spring and summer months when ticks are active. a knowledge of which species of tick is endemic in an area can help narrow the diagnosis (table - ) . rocky mountain spotted fever (rmsf) is the most severe and most often reported rickettsial illness in the united states. it is caused by rickettsia rickettsii, a species of bacteria that is spread to humans by ixodid (hard) ticks (figure - ) . initial signs and symptoms include sudden onset of fever, headache, and muscle pain, followed by development of rash. the disease can be difficult to diagnose in the early stage. rmsf is most common among males and children. risk factors are frequent exposure to dogs and living near wooded areas or areas with high grass. the presentation of rsmf is nonspecific, following an incubation of about to days after a tick bite. initial symptoms can include fever, nausea, vomiting, severe headache, muscle pain, and lack of appetite. later signs and symptoms include rash, abdominal pain, joint pain, and diarrhea. the rash first appears to days after the onset of fever. most often it begins as small, flat, pink, nonitchy spots on the wrists, forearms, and ankles. the characteristic red spotted rash of rmsf is usually not seen until the sixth day or later after onset of symptoms. as many as % to % of patients never develop a rash (figure - ) . no widely available laboratory assay provides rapid confirmation of early rmsf, although commercial pcr testing is available. therefore, treatment decisions should be based on epidemiologic and clinical clues. treatment should never be delayed while waiting for confirmation by laboratory results. routine clinical laboratory findings suggestive of rmsf include normal wbc count, thrombocytopenia, hyponatremia, and elevated liver enzyme levels. serologic assays are the most often used methods for confirming cases of rmsf. doxycycline is the drug of choice for patients with rmsf. therapy is continued for at least days after fever subsides and until there is unequivocal evidence of clinical improvement, generally for a minimum total course of to days. tetracyclines are usually not the preferred drug for use in pregnant women. whereas chloramphenicol is typically the preferred treatment for rmsf during pregnancy, care must be used when administering chloramphenicol late during the third trimester of pregnancy because of risks associated with gray baby syndrome. three species of ehrlichia in the united states are known to cause disease in humans. ehrlichia chaffeensis, the cause of human monocytic ehrlichiosis, occurs primarily in southeastern and south-central regions and is primarily transmitted by the lone star tick, amblyomma americanum ( figure - ) . human granulocytic ehrlichiosis is caused by anaplasma phagocytophila or anaplasma equi and is transmitted by ixodes ticks. ehrlichia ewingii is the most recently recognized human pathogen, with cases reported in immunocompromised patients in missouri, oklahoma, and tennessee. after an incubation period of about to days following the tick bite, initial symptoms generally include fever, pregnant women should be screened for asymptomatic bacteriuria in the first trimester of pregnancy (wadland and plante, ) (sor: a). pregnant women who have asymptomatic bacteriuria should be treated with antimicrobial therapy for to days (nicolle et al., ) (sor: b) . pyuria accompanying asymptomatic bacteriuria should not be treated with antimicrobial therapy (nicolle, ) (sor: c ). a -day course of tmp-smx (bactrim, septra) is recommended as empiric therapy of uncomplicated utis in women, in regions where the rate of resistant e. coli is less than % (warren et al., ) (sor: c). fluoroquinolones are not recommended as first-line treatment of uncomplicated utis, to preserve their effectiveness for complicated utis (warren et al., ) (sor: c). a randomized, placebo-controlled trial of women over months found that cranberry juice and cranberry extract tablets significantly decreased the number of patients having at least one symptomatic uti per year (stothers, ) appropriate antibiotic treatment should be initiated immediately when there is a strong suspicion of ehrlichiosis on the basis of clinical and epidemiologic findings. the treatment recommendations are the same as for rocky mountain spotted fever. rifampin has been used successfully in a limited number of pregnant women with documented ehrlichiosis. babesiosis is caused by hemoprotozoan parasites of the genus babesia. the white-footed deer mouse is the main reservoir in the united states, and the vector is ixodes ticks. most infections are probably asymptomatic. manifestations of disease include fever, chills, sweating, myalgias, fatigue, hepatosplenomegaly, and hemolytic anemia. symptoms typically occur after an incubation period of to weeks and can last several weeks. the disease is more severe in immunosuppressed, splenectomized, or elderly patients. diagnosis can be made by microscopic examination of thick and thin blood smears stained with giemsa, looking for the parasite in red blood cells (rbcs). options for treatment include clindamycin plus quinine or atovaquone plus azithromycin. lyme disease is caused by the spirochetal bacterium borrelia burgdorferi. ixodes ticks are responsible for transmitting lyme disease bacteria to humans. in the united states, lyme disease is mostly localized to states in the northeastern, mid-atlantic, and upper north-central regions, as well as northwestern california. lyme disease most often manifests with a characteristic bull's-eye rash (erythema migrans) accompanied by nonspecific symptoms such as fever, malaise, fatigue, headache, muscle aches, and joint aches (figure - ) . lyme disease spirochetes disseminate from the site of the tick bite, causing multiple (secondary) erythema migrans lesions. other manifestations of dissemination include lymphocytic meningitis, cranial neuropathy (especially facial nerve palsy), radiculoneuritis, migratory joint and muscle pains, myocarditis, and transient atrioventricular blocks of varying degree. if left untreated, the disease can progress to intermittent swelling and pain of one or a few joints (usually large weight-bearing joints such as the knee), cognitive disorders, sleep disturbance, fatigue, and personality changes. the diagnosis is based primarily on clinical findings, and it is often appropriate to treat patients with early disease solely on the basis of objective signs and a known exposure. serologic testing may provide valuable supportive diagnostic information in patients with endemic exposure and objective clinical findings that suggest later-stage disseminated lyme disease. treatment for to weeks with doxycycline or amoxicillin is generally effective in early disease. cefuroxime axetil or erythromycin can be used for persons allergic to penicillin or who cannot take tetracyclines. later disease, particularly with objective neurologic manifestations, can require treatment with intravenous ceftriaxone or penicillin for weeks or more, depending on disease severity. tularemia is caused by francisella tularensis, one of the most infectious pathogenic bacteria known. most cases in the united states occur in south-central and western states. humans can become infected through diverse environmental exposures, including bites by infected arthropods; handling infectious animal tissues or fluids; direct contact with or ingestion of contaminated food, water, or soil; and inhalation of infective aerosols. inhaled f. tularensis causes pleuropneumonitis. some exposures contaminate the eye, resulting in ocular tularemia; penetrate broken skin, result- ing in ulceroglandular or glandular disease; or cause oropharyngeal disease with cervical lymphadenitis. untreated, bacilli inoculated into skin or mucous membranes multiply, spread to regional lymph nodes, multiply further, and then can disseminate to organs throughout the body. the onset of tularemia is usually abrupt, with fever, headache, chills and rigors, generalized body aches, coryza, and sore throat. a dry or slightly productive cough and substernal pain or tightness often occur with or without objective signs of pneumonia. nausea, vomiting, and diarrhea can occur. sweats, fever, chills, progressive weakness, malaise, anorexia, and weight loss characterize continuing illness. rapid diagnostic testing for tularemia is not widely available. respiratory secretions and blood for culture should be collected in suspected patients and the laboratory alerted to the need for special diagnostic and safety procedures. streptomycin ( g im bid for days) is the drug of choice, and gentamicin is an acceptable alternative. tetracyclines and chloramphenicol can also be used. colorado tick fever is an acute viral infection transmitted by the bite of the dermacentor andersoni tick (figure - ) . the disease is limited to the western united states and is most prevalent from march to september. symptoms start about to days after the tick bite. fever continues for days, stops, and then recurs to days later for another few days. other symptoms include excessive sweating, muscle aches, joint stiffness, headache, photophobia, nausea, vomiting, weakness, and an occasional faint rash. routine blood tests might show a low wbc count, mildly elevated liver function, and mildly elevated creatine phosphokinase (cpk). diagnosis is confirmed by testing blood for complement fixation immunofluorescent antibody staining to colorado tick virus. treatment is removal of the tick and treatment of symptoms. physicians should advise patients who walk or hike in tickinfested areas to tuck long pants into socks to protect the legs and wear shoes and long-sleeved shirts. ticks show up on white or light colors better than dark colors, making them easier to remove from clothing. if attached, ticks should be removed immediately by using a tweezers, pulling carefully and steadily. insect repellents such as deet, alone or in combination with permethrin, may be helpful. • most cases of cellulitis are caused by staphylococci or streptococci, but other causes should be considered by clinical situation. • physicians must rule out more ominous causes of skin inflammation, such as necrotizing fasciitis and pyomyositis, when considering cellulitis. • edema-associated cellulitis is best treated by mobilizing edema fluid. cellulitis is an acute, spreading inflammation of the derma and subcutaneous issue. patients complain of tenderness, warmth, swelling, and spreading erythema. in contrast to erysipelas, cellulitis usually lacks sharp demarcation at the border. factors that predispose to cellulitis include trauma, an underlying skin lesion (furuncle, ulcer), or a complication arising from a wound, ulcer, or dermatosis. occasionally, cellulitis results from a blood-borne infection that metastasizes to the skin. pain and erythema usually develop within several days and are often associated with malaise, fever, and chills. the area involved is often extensive, red, hot, and swollen. patchy involvement with skip lesions can be seen. regional lymphadenopathy is common, and bacteremia can occur. several clinical entities resemble cellulitis, including pyoderma gangrenosum, gout, and insect bites. necrotizing fasciitis and gas gangrene are surgical emergencies. given that the predominant organism involved in most cases of cellulitis is a grampositive coccus, clinical history and morphology on physical examination usually suffice in the diagnosis and treatment of cellulitis. a history of freshwater exposure may implicate aeromonas hydrophila as the causative organism; saltwater appropriate antibiotic therapy should be initiated immediately when there is suspicion of rocky mountain spotted fever, ehrlichiosis, or relapsing fever rather than waiting for laboratory confirmation (bratton and corey, ; spach et al., ) (sor: c). treatment with doxycycline (vibramycin) or tetracycline is recommended for rmsf, lyme disease, ehrlichiosis, and relapsing fever (bratton and corey, ; spach et al., ) (sor: c). recommended actions to prevent tick-borne disease include avoidance of tick-infested areas; wearing long pants and tucking the pant legs into socks; applying diethyltoluamide (deet) insect repellents; using bed nets when camping; and carefully inspecting oneself frequently while in an at-risk area (bratton and corey, ; spach et al., ) (sor: c). antibiotic prophylaxis is not routinely recommended for a tick bite to prevent lyme disease, unless the risk of infection is high (wormser et al., ) (sor: b). recommended treatment for suspected tularemia is streptomycin or gentamicin given empirically before evidence of laboratory confirmation (bratton and corey, ; spach et al., ) (sor: c). exposure suggests vibrio spp. cellulitis in a patient with liver disease and shellfish ingestion moves vibrio vulnificans to the top of the differential. patients with soft tissue infection should have blood drawn for laboratory testing if signs and symptoms of systemic toxicity are present (e.g., fever or hypothermia, tachycardia, hypotension). laboratory testing should include blood culture and drug susceptibility tests; wbc count with differential; and measurement of creatinine, bicarbonate, cpk, and crp levels. hospitalization should be considered for patients with hypotension or an elevated creatinine level, low serum bicarbonate level, elevated cpk level (i.e., - times upper limit of normal), marked left shift, or crp level greater than mg/l ( . nmol/l). gram stain with culture and culture of needle aspiration or punch biopsy specimens should be performed to determine a definitive etiology, and a surgical consult should be considered for inspection, exploration, and drainage. findings that may signal potentially severe, deep, soft tissue infection and that may require emergent surgical evaluation include cutaneous hemorrhage, gas in the tissue, pain disproportionate to physical findings, rapid progression, skin anesthesia, skin sloughing, and violaceous bullae. radiologic studies may be helpful if abscess or osteomyelitis is a possibility. ultrasonography is helpful in detecting a subcutaneous collection of fluid. magnetic resonance imaging (mri) is also useful in differentiating cellulitis from necrotizing fasciitis. the diagnosis of necrotizing cellulitis is by direct surgical examination or by frozen pathology sections. empiric antibiotics for immunocompetent patients with cellulitis should be targeted toward gram-positive cocci (table - ) . broader coverage should be initiated for diabetic patients to include gram-positive aerobes, gram-negative aerobes, and anaerobes. patients who present with severe infection or whose infection is progressing despite empiric antibiotic therapy should be treated more aggressively; the treatment strategy should be based on results of appropriate gram stain, culture, and drug susceptibility analysis. in the case of staphylococcus aureus, the physician should assume that the organism is resistant, and agents effective against mrsa, such as vancomycin, linezolid (zyvox), or daptomycin (cubicin), should be used. the antibiotic may be switched from an intravenous drug to an oral drug when fever has subsided and the skin lesion begins to resolve, usually in to days. the total duration of therapy should be to days. longer duration may be required if the response is slow or is associated with abscess, tissue necrosis, or underlying skin processes (infected ulcers or wounds). treatment of cellulitis should include elevation and immobilization to decrease swelling. patients with interdigital dermatophytic infections should be treated with a concomitant topical antifungal applied once or twice daily. topical antifungals can also help reduce the risk of recurrence of the cellulitis. support stockings, good skin hygiene, and prompt treatment of tinea pedis helps with prevention of cellulitis in patients with peripheral edema, who are predisposed to recurrence. in patients who continue to have frequent episodes of cellulitis or erysipelas, prophylactic treatment with penicillin v, mg or mg orally twice daily, or erythromycin, mg once or twice daily (for penicillin-allergic patients), may be indicated. • the majority of furuncles and carbuncles are caused by staphylococcus spp., increasingly, community-acquired methicillin-resistant s. aureus. • drainage of pus is of primary importance in treating skin and soft tissue infections. • culture of sstis is important in guiding antibiotic treatment when initial measures of drainage are not effective. • for recurrent boils, consider referral to infectious disease specialist, possibly to eradicate carriage state. furuncles, or boils, are infections of the skin and soft tissue usually associated with a hair follicle. carbuncles are an extension of this skin and soft tissue infection continuum and involve more of the surrounding and subcutaneous tissue. the broad category skin and soft tissue infections (sstis) is used to describe this continuum that includes furuncles and carbuncles. sstis are common in both healthy and immunocompromised patients and likely initiate with some breach of the skin integrity, such as irritation of hair follicles from friction or microscopic trauma to the skin. up to % of furuncles and carbuncles are caused by community-acquired methicillin-resistant staphylococcus aureus (ca-mrsa) (cdc, ). other potential causative organisms include nonresistant staphylococcus spp. and streptococcus spp. it has become increasingly important to obtain culture of a lesion to direct antibiotic coverage given the increase in ca-mrsa. there is no reliable historical or examination element that will distinguish a ca-mrsa from a methicillin-sensitive staphylococcal skin lesion. stereotypically, patients report ca-mrsa lesions starting like a spider bite. furuncles and carbuncles can occur anywhere on the body, although the axillae, groin, and buttocks are particularly common sites. in addition, practices that cause skin trauma (e.g., shaving, waxing) are often noted in patients with these sstis. fever and malaise are uncommon with milder lesions but become more frequent with the increasing scope of localized infection. of primary importance in the management of carbuncles and furuncles is facilitation of drainage of any purulent material. with smaller lesions, this may be accomplished by heat application by the patient at home. as lesions increase in size and fluctuance, surgical drainage is essential to facilitate resolution of an ssti. it is important to consider culture penicillin, given parenterally or orally depending on clinical severity, is the treatment of choice for erysipelas (sor: a). for cellulitis, a penicillinase-resistant semisynthetic penicillin (amoxicillin/clavulanate) or a first-generation cephalosporin should be selected, unless streptococci or staphylococci resistant to these agents are common in the community (sor: a). for suspected mrsa skin infections, oral treatment options include trimethoprim-sulfamethoxazole, clindamycin, and doxycycline of purulent material when performing incision and drainage in the event that the patient fails to improve and antibiotic coverage becomes necessary. cure rates of lesions with drainage alone exceed %. careful follow-up after drainage is essential to ensure clinical improvement; daily dressing changes in the office after surgical drainage is effective. the addition of postdrainage antibiotics has not shown much added benefit. to prevent the spread of infection to others who come into contact with the patient recovering from an ssti, an occlusive dressing to prevent leakage of lesion fluid and careful hygiene are indicated. there is no evidence that extensive cleaning of common spaces (e.g., locker rooms) prevents the spread of ssti-causing bacteria more than routine cleaning measures. towels and soiled clothing should be laundered in hot water, and any common equipment should be cleaned per manufacturer recommendations. when lesions do not respond to heat, or when lesions are larger yet not amenable to drainage, antibiotics may be used. reasonable first-line antibiotic coverage for nonfluctuant lesions may include dicloxacillin, first-or secondgeneration cephalosporins, macrolides, or clindamycin. in patients with suspected ca-mrsa, better choices include tmp-smx, tetracycline, or clindamycin. it is important to note that up to % of ca-mrsa species will be resistant to clindamycin, particularly if the patient has been treated with other antibiotics in the previous weeks to months . oral administration of these antibiotics is acceptable in the nontoxic patient. patient signs and symptoms that would warrant hospital admission include fever or hypothermia, tachycardia, or hypotension as signs of sepsis and lesions greater than cm in size (table - ) . for patients with recurrent sstis, evaluation for the presence of nasal carriage with a nasal culture is indicated. the value of eradication of bacterial carriage is unclear. referral for infectious disease specialist evaluation may be indicated to guide decision making in the patient with recurrent furuncles and carbuncles. • the existence, severity, and extent of infection, as well as vascular status, neuropathy, and glycemic control, should be assessed in patients with a diabetic foot infection. • visible bone and palpable bone on probing suggest underlying osteomyelitis in patients with a diabetic foot infection. • before an infected wound of a diabetic foot infection is cultured, any overlying necrotic debris should be removed to eliminate surface contamination and to provide more accurate results. patients with diabetes are prone to skin ulcers caused by neuropathy, vascular insufficiency, and diminished neutrophil function. minor wounds can be secondarily infected, leading to ulcer formation. these ulcers often have extensive undermining with necrotic tissues and are often close to the anus, thus promoting an environment suitable for multiple species of microorganisms, including anaerobes. diabetic foot infections range in severity from superficial paronychia to deep infection involving bone. non-limb-threatening infections involve superficial ulcers with minimal cellulitis (< cm from portal of entry), no signs of systemic toxicity, and no significant ischemia in the limb. cure rates of fluctuant skin lesions with drainage alone is over %. postdrainage antibiotics do not significantly improve outcomes rajendran et al., ) (sor: a). trimethoprim-sulfamethoxazole (tmp-smx), clindamycin, and tetracycline are first-choice antibiotics when ca-mrsa is suspected. up to % of ca-mrsa species will be resistant to clindamycin, particularly in the patient previously treated with other antibiotics (sor: c). subcutaneous tissues, and prominent ischemia. infection in patients who have recently received antibiotics or who have deep, limb-threatening infection or chronic wounds are usually caused by a mixture of aerobic gram-positive, aerobic gram-negative (e.g., escherichia coli, proteus spp., klebsiella spp.), and anaerobic organisms (e.g., bacteroides, clostridium, peptococcus, and peptostreptococcus spp.) . surgery is necessary to unroof encrusted areas, and the wounds need to be examined and probed to determine the extent of the infection and check for bone involvement (dinh et al., ) . debridement or drainage should be promptly performed. deep wound cultures should be obtained if possible. if deep culture is not feasible, gram stain and culture from the curettage of the base of the ulcer or from purulent exudates may be needed to guide antibiotic therapy (figure - ) . plain radiography of the foot is indicated for detection of osteomyelitis, foreign bodies, and soft tissue gas. when plain radiography is negative but osteomyelitis is clinically suspected, radionuclide scan or mri should be performed. mri provides more accurate information regarding the extent of the infectious process. the presence of peripheral artery disease and neuropathy should be assessed. the antibiotic regimen should be based on meaningful bacteriologic data. however, the initial regimen for a previously untreated patient with non-limb-threatening infection should focus on s. aureus and streptococci. mild infections may be treated with dicloxacillin or cephalexin for weeks. amoxicillin/clavulanate may be used if polymicrobial infection is suspected. if msra is suspected, oral treatment options include tmp-smx or doxycycline. for limb-threatening infections, broad-spectrum antibiotics are recommended for coverage of group b streptococci, other streptococci, enterobacteriaceae, anaerobic gram-positive cocci, and bacteroides spp. treatment regimens include ampicillin-sulbactam or ertapenem (invanz), clindamycin plus a third-generation cephalosporin, and clindamycin plus ciprofloxacin. intravenous vancomycin should be added if mrsa infection is suspected. ciprofloxacin as a single agent is not recommended. in addition to antibiotic treatment, good glycemic control should be obtained and open wounds gently packed with sterile gauze moistened with ¼-strength povidone-iodine (betadine) solution. edema should be reduced by bed rest, elevation, and diuretic therapy as indicated. for prevention of diabetic foot ulcers, all patients with diabetes should have an annual foot examination that includes assessment for anatomic deformities, skin breaks, nail disorders, loss of protection sensation, diminished arterial supply, and inappropriate footwear. • the use of prophylactic antibiotics may be necessary in the initial management of bite wounds, particularly if the bite is on the hand or face or from a cat. • first-generation cephalosporins (e.g., cephalexin) are not effective as monotherapy for bite wounds because of resistance issues. • avoid primary wound closure in the management of bite wounds. it is estimated that bites account for , medical visits annually in the united states, making up % of emergency department visits. bite wounds consist of lacerations, evulsions, punctures, and scratches. the microbiology of bite wounds is generally polymicrobial, with an array of potential bacteria from the environment, the victim's skin flora, and the biter's oral flora. dog bites account for approximately % of all animal bites requiring medical attention, in which % are provoked attacks. most dog bites occur on the distal extremities, but children tend to sustain facial bites. patients who present for medical attention are often concerned about the care of disfiguring wounds or the need for appropriate vaccination (i.e., tetanus, rabies). however, up to % of medically treated wounds may become infected. these wounds are often contaminated with multiple strains of aerobic and anaerobic bacteria. local signs of infection with erythema, edema, pain, and purulent drainage are common with animal bite wounds. although the most frequently isolated pathogen related to dog and cat bite wounds is pasteurella multocida, the array of potential organisms is much greater. anaerobes such as bacteroides tectum, prevotella spp., fusobacteria, and peptostreptococci can be isolated from animal bite wounds % of the time, mostly from wounds with abscess formation. capnocytophaga canimorsus has also been associated with fatal infection from fulminant sepsis in asplenic patients. wounds inflicted by cats are often scratches or tiny punctures located on the extremity and are likely to become infected and lead to abscess formation. in the united states, venomous snakes bite approximately people yearly. envenomation in such snakebites account for the majority of morbidity and mortality associated with such bites. however, infection of soft tissue structures may also occur as a result of oral flora from the snake, which tends to be fecal in nature because live prey usually defecate in the snake's mouth with their ingestion. human bites are not uncommon, especially in children. human bites have a higher complication and infection rate than do animal bites. human bite wounds most often affect the hand and fingers and in some cases may present as "love routine wound swabs and cultures of material from sinus tracts are unreliable and strongly discouraged in the management of diabetic foot infection (pellizzer et al., ; senneville et al., ) nips" to the breast and genital areas. self-inflicted bites often include wounds of the lip and tissues surrounding the nail, such as paronychia. also included in this are clenched-fist injuries or "fight bites," which result in small lacerations to the knuckles when striking a person in the mouth. normal human oral flora, rather than skin flora, is the source of most bacteria isolated from human bite wound cultures (viridans streptococci, eikenella corrodens). management of bite wounds is the same as for any other wound: good wound care in the form of adequate irrigation and debridement of nonviable tissue as needed (table - ) . bite wounds in general do not require primary closure, but after adequate irrigation and debridement, wounds may be approximated and closed by delayed primary or secondary intention. an exception to this rule may include bite wounds to the face. general wound management measures such as tetanus toxoid administration should also be employed. bite wounds involving the hands should be evaluated by a hand surgeon, given the risk of adjacent tendon sheath, bone, or joint involvement and the dire consequences if such structures are involved. the transmission of rabies through the bites of domestic pets in the united states and developed countries is rare. in fact, the dog strain of rabies is considered eliminated in the u.s. dog population, and cat bites are often managed through observation of the animal, without the immediate need for rabies postexposure treatment (pet). however, wild mammal exposure, especially bat, skunk, or raccoon, often warrants pet, which involves thorough cleaning of the bite wound, ideally with povidone-iodine solution, along with rabies immune globulin given at the wound site and rabies vaccine given on days , , , and . bite wounds should be considered contaminated wounds from presentation, given the oral microbial flora of humans and animals, and most patients should probably receive antibiotics early. empiric antibiotics are used to eradicate oral flora inoculated from the mouth of the biter, whether human or animal, into the wound. all moderate to severe animal bite wounds, or wounds that have an associated crush injury or that are close to a bone or joint, should be considered contaminated with potential pathogens, and these patients should receive to days of "prophylactic" antimicrobial therapy. gram stains with culture of bite wounds are specific but not sensitive indicators of bacterial growth. nonetheless, gram stain can be used to help guide initial empiric antibiotic therapy. amoxicillin-clavulanic acid (amoxicillin-clavulanate; augmentin) or penicillin plus a penicillinase-resistant penicillin are normally first-line agents for empiric therapy directed at bite wounds. first-generation cephalosporins (e.g., cephalexin) are not effective as monotherapy because of resistance of some anaerobic bacteria and e. corrodens. a -to -day course of antibiotics is usually adequate for infections limited to the soft tissue, and a minimum of weeks of therapy is required for infections involving joints or bones. close follow-up is required in all bites to ensure adequate healing. of special consideration in human bite wounds is the potential for spread of viral pathogens, most notably hepatitis b virus (hbv) and hiv, if the source person is positive. hbv exposure in this setting should be handled in the same manner as other exposures, with administration of hbig and hbv vaccination. with regard to hiv, cdc guidelines for managing nonoccupational hiv exposure recommend handling each case individually in consultation with an infectious diseases specialist. • the diagnosis of osteomyelitis is based on radiographic findings (plain radiograph or mri) showing bony destruction along with histologic analysis and culture results. • chronic osteomyelitis is not an emergency, and antibiotics can be safely withheld until an etiologic diagnosis is established. • diabetic foot infections require a careful evaluation to assess perfusion and vascular supply, and corrective measures should be undertaken to reestablish adequate perfusion if necessary. • in diabetic foot ulcers, if one can probe to bone, the patient most likely has osteomyelitis. • orthopedic hardware infections are best managed in conjunction with an infectious diseases specialist and orthopedic surgeon. osteomyelitis is defined as progressive, inflammation leading to destruction of the bone, usually secondary to an infectious agent. bacteria can enter bone through hematogenous seeding or a contiguous focus after trauma, implantation of a foreign device, or a local soft tissue infection. acute osteomyelitis is defined as infection that evolves over a few weeks. chronic osteomyelitis implies persistent infection of several weeks to months. hematogenous osteomyelitis occurs primarily in children within the metaphyses of long bones (tibia and femur) and vertebrae in adults. in addition to local signs of inflammation and infection, patients generally have various systemic signs, including fever, irritability, and lethargy. physical findings include tenderness over involved area and decreased range of motion in adjacent joints. chronic osteomyelitis usually occurs in adults, caused by an open injury to bone and surrounding soft tissue. erythema, drainage around area, and bone pain are usually present on physical examination. systemic symptoms occur less frequently. the diagnosis of osteomyelitis is based on the clinical picture and supporting laboratory and radiologic findings. leukocytosis and elevations in crp and esr may use of antibiotic prophylactic after bites of the hand reduces the incidence of infection (medeiros and saconato, ) (sor: b) . antibiotic prophylaxis after bites by humans reduces incidence of infection (sor: c). animal bite: ascertain the type of animal, whether the bite was provoked or unprovoked, and the situation/environment in which the bite occurred. if the species can be rabid, locate the animal for days' observation or sacrifice. patient: obtain information on antimicrobial allergies, current medications, splenectomy, mastectomy, liver disease, and immunosuppression. record a diagram of the wound with the location, type, and depth of injury; range of motion; possibility of joint penetration; presence of edema or crush injury; nerve and tendon function; signs of infection; and odor of exudate. infected wounds should be cultured and a gram stain performed. anaerobic cultures should be obtained in the presence of abscesses, sepsis, serious cellulitis, devitalized tissue, or foul odor of the exudate. small tears and infected punctures should be cultured with a minitipped (nasopharyngeal) swab. copious amounts of normal saline should be used for irrigation. puncture wounds should be irrigated with a "high-pressure jet" from a -ml syringe and an -gauge needle or catheter tip. devitalized or necrotic tissue should be cautiously debrided. debris and foreign bodies should be removed. radiographs should be obtained if fracture or bone penetration is possible to provide a baseline for future osteomyelitis. wound closure may be necessary for selected, fresh, uninfected wounds, especially facial wounds, but primary wound closure is not usually indicated. wound edges should be approximated with adhesive strips in selected cases. prophylaxis: consider prophylaxis ( ) for moderate to severe injury less than hours old, especially if edema or crush injury is present; ( ) if bone or joint penetration is possible; ( ) for hand wounds; ( ) for immunocompromised patients (including those with mastectomy, liver disease, or steroid therapy); ( ) if the wound is adjacent to prosthetic joint; and ( ) if the wound is in the genital area. coverage should include pasteurella multocida, staphylococcus aureus, and anaerobes. treatment: cover p. multocida, s. aureus, and anaerobes. use oral medication if the patient is seen early after a bite and only mild to moderate signs of infection are present. the following can be considered for cat or dog bites in adults: • first choice: amoxicillin/clavulanic acid, / mg bid or / mg tid with food. • penicillin allergy: no alternative treatment for animal bites has been established for penicillin-allergic patients. the following regimens can be considered for adults: . clindamycin ( mg po qid) plus either levofloxacin ( mg po daily) or trimethoprim-sulfamethoxazole ( double-strength tablets po bid). . doxycycline, mg po bid. . moxifloxacin, mg po daily. . in the highly penicillin-allergic pregnant patient, macrolides have been used, but the wounds must be watched carefully. on emergency department discharge, a single starting dose of parenteral antibiotic, such as ertapenem ( g), may be useful in selected cases. if hospitalization or closely monitored outpatient follow-up is required, intravenous agents should be used. current choices include ampicillin/sulbactam and cefoxitin. the rising incidence of community-acquired s. aureus isolates that are methicillin resistant and therefore resistant to the drugs recommended here emphasizes the importance of susceptibility-testing any s. aureus isolates. indications include fever, sepsis, spread of cellulitis, significant edema or crush injury, loss of function, a compromised host, and patient noncompliance. give tetanus booster (td; tetanus and diphtheria toxoids for adults) if original three-dose series has been given but none in the past years. adults who have not received acellular pertussis vaccine (tdap), should be given this instead of td. give a primary series and tetanus immune globulin if the patient was never immunized. rabies vaccine (on days , , , , and ) with hyperimmune globulin may be required, depending on the type of animal, ability to observe the animal, and locality. elevation may be required if any edema is present. lack of elevation is a common cause of therapeutic failure. be seen but can also be normal. blood cultures may be positive in up to half of children with acute osteomyelitis. if plain radiographs show bone destruction and inflammation; the diagnosis of osteomyelitis is confirmed. typical findings on plain-radiographs will include osteolysis, periosteal reaction, and sequestra (segments of necrotic bone separated from living bone by granulation tissue). findings seen on plain radiographs usually denote a process that has been ongoing for at least weeks. bone scintigraphy (bone scan) is often performed on patients with suspected osteomyelitis; however, sensitivity is quite low, and a negative result can offer false reassurance to the physician, so its routine use is not recommended. if the plain-radiographs are negative but the suspicion for osteomyelitis is still high, an mri scan should be considered. once the diagnosis of osteomyelitis has been made, the next step is to obtain an etiologic diagnosis. histopathologic and microbiologic examination of bone is the "gold standard." cultures of sinus tracts are not reliable for identifying the causative organism. common causative bacteriologic organisms in neonates include staphylococcus aureus, group b streptococci, and escherichia coli. later in life, s. aureus is most common, and in elderly persons, gram-negative organisms such as pseudomonas aeruginosa and serratia spp. have increased incidence. empiric antibiotics are rarely required for chronic disease but are often necessary for acute osteomyelitis. ideally, surgical debridement of all necrotic tissue and inflammatory debris (pus) should be undertaken and multiple surgical cultures with bone histology samples obtained. antimicrobial therapy will be dictated by test results. generally, treatment is for to weeks. with the exception of the fluoroquinolone class of antibiotics, which achieve high serum levels with oral administration, bone antibiotic levels cannot exceed the minimum inhibitory concentration (mic) for the infecting organism; therefore, antibiotics must be given intravenously. this underscores the importance in obtaining a bacterial diagnosis so that the appropriate antibiotic can be used for the duration of treatment. acute osteomyelitis is usually readily curable; however, chronic osteomyelitis is generally more refractory to therapy and requires repeat debridement and antibiotic courses. patients with uncontrolled diabetes are at increased risk for development of osteomyelitis, especially in the presence of neuropathy or venous or arterial insufficiency. s. aureus and beta-hemolytic streptococci are the predominant organisms, although other gram-positive or gram-negative aerobic or anaerobic bacteria may also be seen. plain radiographs should be the initial test to evaluate for the presence of osteomyelitis, followed by mri if negative. if there is a draining sinus, the "probe to bone" test should be performed with a sterile probe; if bone is palpated, the diagnosis of osteomyelitis is highly likely. further evaluation of the diabetic patient should be to assess for vascular insufficiency with the use of ankle-brachial indices and transcutaneous oximetry. if significant compromise is found, arteriography followed by revascularization should be undertaken. surgical debridement is again the cornerstone of treatment, along with antibiotics directed toward the causative microorganism. infections secondary to orthopedic hardware devices have become common problems with the increasing incidence of hip, knee, and shoulder replacement surgeries. also, patients with traumatic injury resulting in a fracture often have hardware implanted to stabilize the bone. these patients present in one of the three following ways: . early: symptoms develop less than months after surgery and have an acute presentation with pain, erythema, and warmth, usually caused by s. aureus and gram-negative bacilli. . delayed: symptoms develop to months after surgery, generally with subtle signs of infection, including implant loosening and persistent pain, and usually caused by less virulent organisms such as coagulasenegative staphylococci and propionibacterium acnes. . late: symptoms develop months after surgery and are usually caused by hematogenous seeding from skin, dental, respiratory, and urinary infections. treatment requires debridement of the surrounding tissue and hardware removal, although this cannot always be done in patients with bone instability. it is recommended that treatment follow-up should occur at hours and perhaps hours for outpatients. reporting the incident to a local health department may be required. from goldstein ejc. bites. in mandell gl, bennett je, dolin rd (eds). mandell, douglas, and bennett's principles and practice of infectious diseases, th ed. philadelphia, churchill livingstone--elsevier, . po, orally; bid, twice daily; tid, three times daily; qid, four times daily. of these infections be done in conjunction with an infectious diseases specialist working with the orthopedic surgeon. septic arthritis is defined as infection within the joint space of two bones. the major causative organisms include s. aureus and in the sexually promiscuous individual, neisseria gonorrhoeae. intravenous drug users are likely to develop septic arthritis within unusual joints (e.g., sternoclavicular, sacroiliac). rheumatoid arthritis, presence of joint prostheses, and steroid use are predisposing factors for development of septic arthritis. diagnosis is usually based on clinical presentation of a warm, swollen joint with limitation in range of motion. a joint aspiration should be completed and the synovial fluid sent for gram stain with culture, wbc count with differential, and crystal analysis to rule out gout and pseudogout. blood cultures should also be drawn before initiation of antibiotics. gonococcal arthritis usually presents as an acute arthritis involving one or more joints in a sexually active individual. two thirds of patients have dermatitis with one or multiple, usually asymptomatic, lesions that progress from macular to papular and finally vesicular or pustular. joint fluid, urethral, and rectal cultures should also be obtained. treatment is generally with a third-generation cephalosporin intravenously until improvement, followed by oral therapy to complete a -week course of therapy. treatment of nongonococcal arthritis requires proper draining of the infected joint. this is often done surgically, although repeat needle drainage may also be successful if the joint is easily accessible. treatment generally depends on the gram stain and includes a third-generation cephalosporin, with the addition of vancomycin if gram-positive cocci in clusters are seen. duration of therapy is to weeks. • a comprehensive history and physical examination with laboratory and radiologic evaluation are important in the workup for fever of unknown origin (fuo). • if routine information is unrevealing, more specific testing for fuo is undertaken based on the patient's age, travel history, and disease process to develop a differential diagnosis. • the serum ferritin level (often elevated with malignancy) and naproxen test (reduces fever with malignancy) may be helpful in determining an underlying malignant process. • initiation of empiric antibiotics should be done only in specific fuo situations to prevent skewing culture results, thus maximizing isolation of the causative organism. patients who have a persistent fever despite workup are generally classified as having a "fever of unknown origin" (fuo). in , petersdorf and beeson described patients with persistent fever, otherwise known as fever of unknown origin. they introduced the standard, classic definition of fuo: fever higher than . ° c ( ° f) on several occasions, persisting without diagnosis for at least weeks, with week of investigational study in the hospital setting. with advancing technology, this definition has been revised to allow for more than two outpatient visits, or days if investigation is in the hospital setting. most patients with fuo have chronic or subacute symptoms and can be safely evaluated in the outpatient setting, with a median time to diagnosis of days. the differential diagnosis of fuo is quite broad and extensive. determining an etiologic diagnosis of an fuo depends on generating a differential diagnosis compatible with the patient's history and physical examination. the principal disease categories for fuo include infection ( % overall), neoplasms ( %), collagen vascular diseases ( %), and miscellaneous ( %) (box - ). because of this broad differential, a newer classification system divides fuo into four groups: classic, nosocomial, neutropenic, and hiv associated, which helps narrow the differential diagnosis. furthermore, classic fuo can be broken down into three subgroups: infants and children, elderly, and travelers. despite an extensive workup, the etiologic diagnosis usually remains elusive in % to % of patients (box - ) . the diagnostic workup of fuo should begin with a thorough history and physical examination, including documentation of the fever. the patient may provide a diary noting the date and time of fever. routine noninvasive investigations are recommended in all patients before diagnosing fuo (box - ). acute febrile illness is never called an fuo. the patient's medication profile is reviewed because numerous drugs can be the cause. if unrevealing, a workup is initiated based on the differential diagnosis for the patient's age, travel history, geographic location, and disease process. dukes criteria for infective endocarditis have % specificity in patients with fuo. when the initial investigations are not helpful in identifying a cause, imaging should be considered, such as computed tomography (ct) scans of the chest, abdomen, and pelvis; ct may reveal an abscess or suggest an underlying malignancy. an elevated serum ferritin level can suggest a neoplasm or myeloproliferative disorder and, if normal, greatly decreases the chance that the patient has an underlying malignancy. lower-extremity doppler ultrasound should be considered in the sedentary or obese patient to rule out deep venous thrombosis. a temporal artery biopsy should be considered in the elderly patient to rule out temporal arteritis. liver biopsy has a high diagnostic yield with minimal toxicity, whereas bone marrow cultures usually have a low yield and should be considered only in special situations. empiric therapy with antibiotics is rarely appropriate for the patient with fuo. a diagnosis is essential to guide treatment of osteomyelitis requires surgical debridement followed by a -to -week course of intravenous antibiotic therapy (sor: c). septic arthritis is usually caused by a gonococcus in a sexually active adult, and use of a third-generation cephalosporin is the mainstay of therapy (sor: a). nongonococcal arthritis should be treated with surgical debridement or repeated needle aspirations, with a third-generation cephalosporin and vancomycin if gram-positive cocci are seen (goldenberg, ) (sor: b). treatment, and use of antibiotics may delay determining a causative infectious agent. the naproxen test (naprosyn; mg po every hours for days) is helpful in determining if the fever is secondary to infection or malignancy. a dramatic decrease in the patient's temperature during the test generally indicates a malignant focus, whereas minimal or no response indicates an infectious etiology. the prognosis of fuo depends on the etiologic category. undiagnosed fuo has a very favorable outcome. patients in whom diagnostic investigations fail to identify an etiology should be followed clinically with serial history reviews and physical examinations until the fever resolves or new diagnostic clues are found. connective tissue diseases are more prominent. infections: malaria, hepatitis, pneumonia/bronchitis, uti/pyelonephritis, dysentery, dengue fever, enteric fever, tb, rickettsial infection, acute human immunodeficiency virus (hiv) infection, amebic liver abscess. postoperative urinary and respiratory tract instrumentation; use of intravascular devices; drug therapy; immobilization. septic thrombophlebitis, pulmonary embolus, clostridium difficile colitis, drug fever. fungal: % susceptible to empiric antifungals, % will be resistant to empiric therapy. bacterial: % not responding to empiric antimicrobial therapy and usually with cryptic focus. unusual pathogens: % will be toxoplasmosis (toxoplasma gondii) reactivation, atypical mycobacterial, tb, fastidious pathogens (legionella, mycoplasma, chlamydophila). viral: % of causes (hsv, cmv, ebv, hhv- , vzv, rsv, influenza, parainfluenza). other: % will be transplant related (e.g., gvhd) following stem cell transplant, % will be undefined. infections: mycobacterium avium complex (mac), pneumocystis carinii pneumonia (pcp), cytomegalovirus (cmv), histoplasmosis, viral (hcv, hbv, adenovirus, hsv esophagitis, vzv encephalitis), tb, other fungi, cerebral toxoplasmosis, disseminated cryptosporidiosis. neoplasms: lymphoma, kaposi's sarcoma. other: drug fever, castleman's disease. hsv, herpes simplex virus; ebv, epstein-barr virus; hhv, human herpesvirus; vzv, varicella-zoster virus; rsv, respiratory syncytial virus; gvhd, graft-versus-host disease; hcv, hepatitis c virus; hbv, hepatitis b virus. abscesses: hepatic, subhepatic, gallbladder, subphrenic, splenic, periappendiceal, perinephric, pelvic, and other sites. granulomatous: extrapulmonary and miliary tuberculosis, atypical mycobacterial infection, fungal infection. intravascular: catheter-related endocarditis, meningococcemia, gonococcemia, listeria, brucella, rat-bite fever, relapsing fever. viral, rickettsial, and chlamydial: infectious mononucleosis, cytomegalovirus, human immunodeficiency virus, hepatitis, q fever, psittacosis. parasitic: extraintestinal amebiasis, malaria, toxoplasmosis. collagen vascular diseases: rheumatic fever, systemic lupus erythematosus, rheumatoid arthritis (particularly still's disease), vasculitis (all types). granulomatous: sarcoidosis, granulomatous hepatitis, crohn's disease. tissue injury: pulmonary emboli, sickle cell disease, hemolytic anemia. familial mediterranean fever fabry's disease cyclic neutropenia intra-abdominal infections may either be uncomplicated (limited to the gut lumen, such as gastroenteritis or colitis) or complicated (extending through to the peritoneum) . the clinical presentation of complicated intra-abdominal infections can range from mild symptoms such as nausea, mild abdominal pain, and cramping to lifethreatening septic shock. clinical findings result from local or diffuse inflammation with or without abscess formation. fever and abdominal pain are typically present, with additional symptoms depending on the organ involved. elderly and immunocompromised patients present with atypical, usually milder symptoms. imaging studies form an important adjunct to diagnosis. management involves empiric antibiotic coverage for bowel flora-mainly streptococci, enterococci, enteric gram-negative rods, and anaerobes-as well as controlling the source of infection, usually through surgery. • spontaneous bacterial peritonitis usually occurs in the setting of ascites and chronic liver disease. • spontaneous bacterial peritonitis is a diagnosis of exclusion. • ascitic fluid culture yield improves with inoculation into blood culture bottles at bedside. spontaneous bacterial peritonitis (sbp) is a form of infectious peritonitis without a surgically correctable cause and is therefore a diagnosis of exclusion. the route of infection in sbp is usually not apparent and is often presumed to be hematogenous, lymphogenous, by transmural migration through an intact gut wall from the intestinal lumen, or in women, from the vagina via the fallopian tubes (levison and bush, ) . sbp occurs in the setting of ascites in most cases, and it is particularly common in patients with cirrhosis. in pediatric populations, those with postnecrotic cirrhosis or nephrotic syndrome are more often affected. in adults, almost % of patients who develop sbp have child-pugh class c liver disease, and % to % of hospitalized patients with cirrhosis and ascites have sbp (mowat and stanley, ) . sbp is almost always caused by a single organism, typically enteric gram-negative rods, most often e. coli, followed by klebsiella pneumoniae. gram-positive cocci account for about % of episodes of sbp, and streptococci are isolated most often. sbp caused by anaerobes is rare. growth of more than one organism should raise the suspicion of secondary peritonitis. signs and symptoms of sbp are subtle and require a high index of suspicion. fever greater than ° f ( ° c) is the most common presenting sign, occurring in % to % of cases. abdominal pain, nausea, vomiting, and diarrhea are usually present. peritoneal signs (abdominal tenderness or rebound tenderness) are common but may be absent in patients with ascites. in adults, mental status changes may also occur. sbp is often confused with acute appendicitis in children. in adults, sbp should be suspected in any patient with previously stable chronic liver disease who undergoes acute decompensation in clinical status. spontaneous bacterial peritonitis is diagnosed by analysis of ascitic fluid obtained by abdominal paracentesis. infection has been typically defined as an ascitic fluid wbc count higher than cells/mm , which is considered diagnostic even when the culture of the ascitic fluid is negative. in cases where bloody fluid is obtained ("traumatic paracentesis"), the wbc count should be corrected by wbc per rbcs/mm . the use of bedside dipstick for leukocyte esterase has a high false-negative rate and is not recommended (nguyen-khac et al., ) . ascitic fluid culture yield can be increased by inoculating blood culture bottles with ml of ascitic fluid at the bedside. blood cultures should also be obtained as part of the workup. after the diagnosis of peritonitis is established, secondary peritonitis should be ruled out. ct of the abdomen with oral and intravenous contrast can help direct the surgeon to a particular source of infection, as opposed to doing a full exploratory laparotomy. a high ascitic fluid total protein (> g/dl) or amylase level is suggestive of secondary peritonitis. the treatment of choice is generally a third-generation cephalosporin such as cefotaxime ( g iv every - hours) or ceftriaxone ( g iv once daily). patients who have an ascitic fluid wbc count higher than cells/mm should be given empiric intravenous antibiotics without delay. oral amoxicillin-clavulanic acid can be used for mild, uncomplicated cases (navasa et al., ) . duration of treatment varies diagnosis of fuo may be assisted by the dukes criteria for endocarditis, ct scan of the abdomen, nuclear scanning with a technetiumbased isotope, and liver biopsy (mourad et al., ) (sor: b) . routine bone marrow cultures are not recommended in the fuo workup (mourad et al., ) (sor: b) . empiric antibiotics should be initiated only in specific situations, to avoid skewing culture results and thus maximizing potential isolation of the causative organism (mourad et al., ) (sor: b). from to days depending on clinical response. patients usually respond to appropriate antibiotic therapy within to hours; otherwise, a repeat paracentesis should be performed. if the ascitic fluid wbc count does not decrease by more than %, alternative diagnoses should be considered. prophylaxis with a fluoroquinolone or trimethoprim-sulfamethoxazole should be considered, particularly in high-risk patients (garcia-tsao and lim, • bacterial meningitis is life threatening and requires urgent medical attention and treatment. • viral encephalitis should be treated with acyclovir until herpes simplex virus is ruled out. • most brain abscesses are caused by streptococci and staphylococcus aureus. • the cns infections most likely to be encountered in clinical practice include meningitis, encephalitis, and abscess. • all cns infections can be difficult to diagnose, and a high index of suspicion by the health care provider is sometimes indicated to ensure patient survival. • mri is the most sensitive neuroimaging test for encephalitis. • acyclovir should be started immediately and continued until hsv pcr testing is obtained. meningitis can be acute, subacute, or chronic. in otherwise healthy children, the three most common organisms causing acute bacterial meningitis are streptococcus pneumoniae, neisseria meningitidis, and haemophilus influenzae type b (hib). isolation of an organism other than these three organisms from the csf of a child older than months always requires an explanation or evaluation for unusual host susceptibility. children with cochlear implants, asplenia, hiv infection, or csf leak from basilar skull or cribriform fracture are at greater risk for pneumococcal meningitis. deficiencies in terminal components of complement lead to greater risk for meningococcal infection (saez-llorens and mccracken, ) . in adults, the common etiologic agents of acute meningitis include s. pneumoniae, n. meningitidis, and listeria monocytogenes. patients with acute meningitis most often present with fever, headache, meningismus, and altered mental status. infants can present with nonspecific symptoms such as inconsolable crying, irritability, nausea, vomiting, and diarrhea. lethargy, anorexia, and grunting respirations indicate a critically ill infant. older children may complain of headache, vomiting, back pain, myalgia, and photophobia; may be confused or disoriented; and may verbalize specifically that the neck is stiff or sore. seizures are noted in up to % to % of children before hospital admission or early in the course of the illness. in contrast, patients with subacute or chronic meningitis may have the same symptoms with a much more gradual onset, lower fever, and associated lethargy and disability. mycobacterium tuberculosis, treponema pallidum (syphilis), borrelia burgdorferi (lyme disease), and fungi (e.g., cryptococcus neoformans, coccidioides spp.) are the most common agents (tunkel et al., ) . physical examination should look for papilledema, middle ear and sinus infections, petechiae (common with n. meningitidis), nuchal rigidity, and in infants, a bulging fontanel. blood cultures should be taken. a lumbar puncture (lp) for csf analysis should be done as soon as possible. a brain ct scan before lp is not necessary if the patient has no evidence of immunocompromise, cns disease, new seizure, papilledema, altered consciousness, or focal neurologic deficit, and if a subarachnoid hemorrhage is not suspected. if neuroimaging is necessary, blood cultures should be taken and antibiotics given before the study; a delay in administration of antibiotics leads to a worse outcome. csf should be sent for cell count, wbc differential, glucose, protein, and gram stain with culture. acid-fast bacilli stain and cryptococcal antigen may be obtained when indicated. empiric antibiotics for the initial treatment of bacterial meningitis are listed in table - , but these should be tailored to the isolated organisms whenever possible. adjunctive dexamethasone is recommended for children and infants with hib meningitis, but not if they have already received antibiotics. in adults, adjunctive dexamethasone is recommended for pneumococcal meningitis (tunkel et al., ) . close contacts of patients with n. meningitidis should receive rifampin, mg/kg (not to exceed mg) twice daily for days, or ciprofloxacin, mg as a single dose, or ceftriaxone, mg im as a single dose. unimmunized persons exposed to h. influenzae meningitis should receive rifampin (turkel et al., ) . pregnant women should not receive rifampin or doxycycline. a repeat lp should be done if no clinical response is seen after hours of appropriate antibiotic therapy, particularly for patients with resistant pneumococcal disease and those who received dexamethasone. neonates with gram-negative bacilli and patients with ventriculoperitoneal (vp) shunts require documentation of csf sterility. the duration of antimicrobial therapy is days for patients with n. meningitidis or hib, to days for pneumococcal meningitis, and to days for streptococcus agalactiae. spontaneous bacterial peritonitis is treated with third-generation cephalosporins (cefotaxime or ceftriaxone), with ampicillin-sulbactam, fluoroquinolones, or carbapenems as alternative agents (solomkin et al., ) (sor: b) . patients with diffuse peritonitis should undergo an emergency surgical procedure as soon as possible, even if ongoing measures to restore physiologic stability need to be continued during the procedure (sor: b). viral meningitis viral meningitis manifests similar to bacterial meningitis, although its course is rarely aggressive. the diagnostic process and examination are similar to those for bacterial meningitis. viral meningitis is usually caused by enteroviruses, hsv, mumps virus, and hiv. along with the signs of meningitis, signs that suggest a viral etiology include genital lesions (hsv- ), diarrhea, or a maculopapular rash (enteroviruses). diagnosis is made by the history, examination, and csf results. early in the course, the csf might show predominantly neutrophils that can resemble bacterial meningitis. treatment is symptomatic. suppressive therapy should be offered to patients with recurrent hsv meningitis. although encephalitis can also be caused by bacteria and fungi, the great majority of cases are caused by viruses. herpes simplex accounts for % of cases. patients present with fever, acute decreased level of consciousness, and occasionally, seizures and language, memory, or behavior disturbances. mri is the most sensitive neuroimaging test for encephalitis and might show temporal lobe inflammation in early hsv encephalitis. csf studies and electroencephalography (eeg) are also recommended for all patients with encephalitis. herpes simplex pcr should be done, and acyclovir should be given immediately until hsv encephalitis is ruled out. during late summer and early fall, doxycycline should be considered to cover for tick-borne illnesses, and testing should include the mosquito-borne encephalitides such as west nile, st. louis, eastern equine, and western equine. treatment depends on the suspected etiologic agent but is generally supportive (tunkel et al., ) . a brain abscess is a focal, intracerebral infection that develops into a collection of pus surrounded by a well-vascularized capsule. although fungi and protozoa (particularly toxoplasma) can also cause brain abscesses, bacterial causes are much more common. streptococci are found in % of bacterial abscesses and are usually from oropharyngeal infection or infective endocarditis, whereas staphylococcus aureus accounts for % to % of isolates and is more often found after trauma. community-associated mrsa strains have been increasing. enteric gram-negative bacilli (e.g., e. coli; proteus, klebsiella, and pseudomonas spp.) are isolated in % to % of patients, often in patients with ear infection, septicemia, or immunocompromise and those who have had neurosurgical procedures. most clinical symptoms are caused by the size and location of the abscess rather than the systemic signs of an infection. headache is the most common complaint and may be accompanied by fever, mental status changes, evidence of increased intracranial pressure (nausea, vomiting, papilledema), or focal neurologic deficits. diagnosis is usually made by ct scan with iv contrast showing the characteristic hypodense center with a peripheral uniform ring enhancement, with or without a surrounding area of brain edema. mri is becoming the preferred imaging modality because of increased sensitivity, particularly for detecting satellite lesions. additional testing depends on risk factors and the likely underlying source of infection and may include blood cultures, chest imaging, testing for hiv and antibodies to toxoplasma, and transesophageal echogram. empiric therapy typically involves vancomycin, ceftriaxone, and metronidazole. optimal management also includes surgical drainage for most abscesses, both to find an etiologic microorganism and to improve chances of cure (turkel, ) . • most acute diarrheal illness is viral and can be managed symptomatically and with appropriate attention to hydration. • travelers' diarrhea is usually caused by diarrheogenic escherichia coli. • the infection in travelers' diarrhea is usually self-limited. • antibiotics may shorten the duration of diarrhea by to days. • the most common cause of antibiotic-associated diarrhea is clostridium difficile. • treatment of antibiotic-associated diarrhea involves discontinuing the offending agent, if possible. adjunctive dexamethasone is recommended for children and infants with h. influenzae type b meningitis, but not if they have already received antibiotics (tunkel et al., ) (sor: a). in adults, adjunctive dexamethasone is recommended for pneumococcal meningitis (tunkel et al., ) (sor: b). diarrhea is a common presenting complaint in the primary care physician's office. not all causes of diarrhea are infectious, and not all infectious causes of diarrhea require specific antibiotic therapy. diarrhea remains a major cause of morbidity and mortality, particularly for children in the developing world. diarrhea is an alteration of normal bowel function, characterized by an increase in the water content, volume, or frequency of stools. acute diarrhea is typically defined as present less than days, and diarrhea is considered chronic when symptoms persist longer than days (figure - ). infectious diarrhea seen in the primary care physician's office is most frequently caused by viruses. a number of viral agents can cause diarrheal illness (box - ). rotaviruses are the principal enteric pathogens in children less than years of age and the most important cause of hospitalization and infant mortality related to diarrheal illnesses. noroviruses evaluate severity and duration obtain history and physical examination [ ] [ ] [ ] [ ] [ ] treat dehydration report suspected outbreaks check all that apply: are the most common cause of food-borne disease worldwide. viral gastroenteritis is usually an acute self-limited illness, referred to as the "stomach flu." enteric viruses are easily spread by fecal-oral transmission, through contamination of food and water, fomites, and person-to-person spread. secondary attack rates can be high. nausea and vomiting are the most prominent symptoms of viral gastroenteritis. diarrhea, fever, headache, and constitutional symptoms may also be experienced. these viral infections can occur at any time during the year, but tend to occur more often in the winter. there is no specific therapy. treatment is supportive, with particular emphasis on adequate replacement of fluids and electrolytes. if rehydration can be accomplished enterally, it is preferred. both the pentavalent bovine-human reassortment (rv ) and the oral, live-attenuated monovalent (rv ) rotavirus vaccines are effective for prevention of severe gastroenteritis. the rv vaccine series is recommended for children at ages , , and months, whereas the rv vaccine should be administered to children and months of age. approximately % of travelers to developing regions of the world will develop diarrhea. bacteria are responsible for approximately % of diarrhea acquired by travelers. other important causes include viruses and parasites. the onset of the majority of cases of travelers' diarrhea is usually within to days after arrival. the presentation is typically a noninflammatory, nonbloody diarrhea associated with abdominal discomfort, fever, nausea, or vomiting. the duration is usually to days. enterotoxigenic e. coli is responsible for approximately % of travelers' diarrhea. enteroaggregative e. coli is the second most common bacterial agent and causes % of cases. salmonella, shigella, and campylobacter spp. are less often detected but are important causes of dysentery, particularly in asia and africa. dysentery is severe inflammatory diarrhea manifested by fever and bloody stools. most cases of travelers' diarrhea are self-limited, but chronic postinfectious irritable bowel syndrome may occur in up to % of those who experience diarrhea. prevention of travelers' diarrhea is an important component of pretravel counseling for high-risk countries. food should be boiled, cooked, or peeled and water boiled to avoid consumption of fecal contamination. if a person develops travelers' diarrhea, a short course of antibiotics with rifaximin, ciprofloxacin, or azithromycin can shorten the duration of illness by to days. antibiotic therapy is recommended for persons with bloody diarrhea or fever. rifaximin, a nonabsorbed antibiotic, is not effective against invasive pathogens and should not be administered for dysentery. ciprofloxacin or azithromycin should be used for dysenteric symptoms based on local antimicrobial susceptibilities. antibiotics are frequently prescribed in the primary care physician's office for a variety of infections. unfortunately, antibiotics can alter the normal host microflora that can be protective against other infections. antibiotic effects on the normal gastrointestinal tract microbiome can lead to antibiotic-associated diarrhea, which causes significant morbidity and mortality. administration of antibiotics usually precedes symptoms of antibiotic-associated diarrhea by about week but can be as distant as or months. strong associations with clindamycin (cleocin), cephalosporins, penicillins, and fluoroquinolones have been demonstrated, but any antibiotic can lead to antibiotic-associated diarrhea. the most important cause of antibiotic-associated diarrhea is clostridium difficile, an anaerobic, gram-positive, spore-forming rod. c. difficile is implicated as the cause in up to % of antibiotic-associated diarrhea cases, in % to % of antibiotic-associated colitis cases, and in more than % of antibiotic-associated pseudomembranous colitis cases. risk factors for c. difficile diarrhea include antibiotics, health care exposure (recent stay in hospitals or long-term care facilities), older age (> ), and comorbid conditions. the clinical presentation of c. difficile colitis is usually diarrhea, abdominal pain or cramping, and fever in a patient who recently received antibiotics. leukocytosis is common and may be profound; levels can be consistent with leukemoid reaction. a rare but potentially fatal complication is toxic megacolon. toxic megacolon manifests as acute colonic dilation to a diameter greater than cm, associated with systemic toxicity and the absence of mechanical obstruction. with its high associated mortality, any patient who develops toxic megacolon requires immediate surgical evaluation for possible colectomy. diagnosis of c. difficile diarrhea is achieved by demonstration of c. difficile toxin a or b in the stool by enzyme immunoassay (eia) or cell culture cytotoxicity assay in a symptomatic patient with a previous history of antibiotic use. asymptomatic patients should not be tested. with the improved sensitivities of these diagnostic assays, one stool sample is usually sufficient to test for c. difficile, unless symptoms recur. test of cure after therapy with repeat stool for c. difficile toxin is not recommended because stools may remain positive for c. difficile toxin despite clinical resolution. endoscopy can demonstrate pseudomembranes in the colon. pseudomembranes are diagnostic of c. difficile infection, but are often not present. endoscopy may only reveal the presence of nonspecific colitis. clostridium difficile colitis is treated by discontinuing the offending agent(s) if possible and initiating antibiotic therapy (box - ). antimotility agents should be avoided. oral metronidazole (flagyl), mg three times daily for to days, is recommended for mild-moderate c. difficile diarrhea. severe diarrhea should be treated with oral vancomycin. oral vancomycin is currently not recommended for all patients with c. difficile diarrhea because of concerns for the promotion of vancomycin-resistant enterococci (vre) and its expense. about % to % of patients experience relapse in travelers' diarrhea, in which enterotoxigenic e. coli or other bacterial pathogens are likely causes, prompt treatment with a fluoroquinolone, azithromycin, or rifaximin or, in children, azithromycin mg/kg/day once daily can reduce the duration of an illness from to days to to days (dupont, ) (sor: a). after therapy. for relapse, a repeat course of the original c. difficile treatment should be administered. patients who have mild to moderate cases without volume depletion or systemic toxicity can be treated as outpatients. discussions of the following infections can be found online at www.expertconsult.com: • infectious viral hepatitis • endocarditis treat mild-moderate c. difficile diarrhea with metronidazole (zar et al., ) evidence-based reviews of the diagnosis and treatment of many common clinical problems. www.mdcalc.com/curb- -severity-score-community-acquired-pneumonia curb- score calculator to determine the severity of communityacquired pneumonia and need for hospitalization. the complete reference list is available online at www.expertconsult.com. anthony zeimet hepatitis is defined as inflammation of the liver that is commonly induced by viruses that include the hepatitis viruses a through e, which will be the focus of this discussion. other viruses that can induce hepatitis include epstein-barr virus (ebv), cytomegalovirus (cmv), herpes simplex virus (hsv), varicella zoster virus (vzv), adenovirus, and coxsackievirus. various medications and alcohol abuse are two important nonviral causes. most infectious causes of hepatitis are self-limiting; however, hepatitis b and c viruses can cause a chronic infection that may lead to cirrhosis and eventual liver failure, as well as hepatocellular carcinoma. hepatitis a virus (hav) and hepatitis e virus (hev) are spread by the fecal-oral route and only cause an acute infection. hepatitis b, c, and d viruses (hbv, hcv, hdv) are spread through the blood and have an acute form of disease that sometimes can become chronic. the clinical presentation of hepatitis is clinically indistinguishable. asymptomatic infections are more common than symptomatic infection. symptoms generally include right upper quadrant (ruq) abdominal pain, anorexia, nausea, vomiting, diarrhea, dark-colored urine, pale stools, and generalized malaise; patients may notice a yellow hue to their skin or eyes. pruritus is common, caused by deposition of bilirubin in the skin. the physical examination generally reveals jaundice and sclera icterus in addition to ruq pain. hepatomegaly is seen in % and splenomegaly in % of patients with hepatitis. liver function tests reveal elevated levels of aspartate transaminase (ast), alanine transaminase (alt), and bilirubin, and to a lesser extent, alkaline phosphatase (alp). hepatitis a virus is the most common cause of viral hepatitis worldwide. poor hygiene practices in both the industrial and the developing world account for its prevalence. in the united states, hav is common among lower socioeconomic groups, daycare attendants and workers, men who have sex with men (msm), and illicit drug users. hepatitis a is often acquired by travelers to endemic areas. the incubation period is to days (mean, days). hav is highly contagious, and peak fecal shedding generally occurs at the onset of illness in most infected patients. viremia averages to days. hav infection manifests as an acute, self-limited illness, with the prodromal symptoms lasting about a week before the onset of jaundice. jaundice generally resolves after weeks, and most patients recover. fulminant hepatic failure is possible but extremely rare. diagnosis of acute hav infection is made by demonstration of anti-hav immunoglobulin m (igm) in the patient's serum. this may be negative if the patient presents early, and repeat testing may be necessary if hav is strongly suspected. anti-hav igg in the serum indicates remote infection or immunization (efig - ). treatment is primarily supportive, except in patients with fulminant liver failure, who may require a liver transplant. vaccination should be administered to all patients who are seronegative and to persons at increased risk for acquiring hav, including those about to travel to endemic areas, patients with chronic liver disease or receiving clotting factor concentrates, msm, hiv-positive patients, and illicit drug users. certain areas of the united states now require mandatory vaccination of children as well as those who work in the restaurant industry. the vaccine is safe and highly efficacious and is given as a two-dose series at and at to months. passive immunization with immune globulin is recommended for those exposed to the virus by a known contact, including household and sexual contacts, and those who are traveling to an endemic area for less than weeks but never vaccinated. any person who receives immune globulin should also start the vaccination series. hepatitis b virus infection can be acute or chronic. about , people die from acute hbv infection annually, and , die of cirrhosis and hepatocellular carcinoma caused by chronic infection. about million people worldwide are living with chronic hbv infection. in the united states, an estimated . million residents have chronic hbv infection, with to deaths each year. significant burdens of disease are seen in asia, pacific islands, sub-saharan africa, amazon basin, and eastern europe. most adults with acute hbv will clear the virus, with less than % progressing to chronic infection. chronic infection will develop in almost all children infected perinatally and in % of those who become infected at to years of age. hbv is transmitted through exchange of body fluids, sexually and perinatally. in the united states, most hbv cases are acquired during adolescence and early adulthood with onset of sexual activity, experimentation with drug use, and sometimes occupational exposure. fever, polyarthralgia, rash, and a serum sickness-like illness are features of hbv infection in addition to jaundice and may be seen in association with polyarteritis nodosa. clinicians have the most difficulty in interpreting the various serologic tests for diagnosis of hepatitis b (etable - ) . the mean incubation period is to days, with a range of of days after infection. diagnosis of acute infection can be detected by obtaining hbv surface antigen (hbsag), which can appear as early as week after exposure but generally by day . in a patient strongly suspected to have hbv infection, the clinician can consider checking the hbv dna viral load; which can be detected as early as week after exposure. eventually the patient will develop an anti-hbv surface antibody, which indicates recovery from the illness. the other viral serologies for hbv are rarely obtained in acute illness. in chronic hbv infection, there are three major phases of infection: . immune tolerant. active viral replication in the liver with high levels of hbv dna levels but essentially normal or minimal elevation of ast and alt. most patients eventually progress to the next stage. . immune active. more robust liver inflammation with alt elevation, and liver biopsy shows inflammation with or without fibrosis. hbv early antigen (hbeag) is detected along with hbsag. . inactive carrier state. as patients enter this phase, they clear the hbeag and develop anti-hbe antibody and have undetectable or low levels of hbv dna, with normalization of alt and liver inflammation. if patients become hbsag negative, they then develop anti-hbs and have resolved their infection; otherwise, they are considered a chronic carrier. treatment of acute hbv is primarily supportive. in the last decade, however, there have been significant advances in the treatment of chronic hbv infection. the use of interferon has long been the mainstay of treatment and has a defined, limited course but is generally poorly tolerated. with the advent of the hiv/aids epidemic and research into treatment of hiv disease, antiviral medications are now starting to replace interferon as the preferred treatment option for hbv patients. nucleoside/nucleotide analogs such as lamivudine, adefovir, entecavir, tenofovir, and telbivudine are generally given for long-term, indefinite therapy to prevent progression of liver disease and development of hepatocellular carcinoma. any patient with chronic hbv infection should be referred to an infectious diseases specialist or a hepatologist to determine the appropriate treatment course. universal vaccination of newborns and infants is routine in the united states since , and the incidence of hbv infection has declined. during primary care visits, the vaccination status of any adult or adolescent born before should be reviewed and the vaccine offered. the vaccine requires three doses given at , , and months. an unvaccinated person or neonate who is exposed to the body fluids of a hbv-infected individual should start the vaccination series in addition to receiving the hepatitis b immune globulin (hbig). hepatitis c virus infection is the most common cause of chronic viral hepatitis in the united states. hcv does have an acute form of infection but is usually subclinical and rarely diagnosed. the cdc estimates that there are more than . million people with hcv infection. hcv is generally transmitted parenterally, as in injection drug users who share needles. before , those who received a blood transfusion may have contracted hcv. sexual transmission acute hbv has been reported in monogamous couples, with one partner who has hcv infection and the other without infection who eventually acquires the virus. this occurs in % to % of couples and represents a rare mode of transmission. because the most common mode of acquisition is sharing needles, any patient who is hcv positive should be screened for hiv because these two infections often occur together (ebox - ). the diagnosis of acute hcv infection can be made by obtaining a hcv rna viral load; although this is rarely done because the initial infection is subclinical. chronic disease is generally discovered by a positive anti-hcv antibody along with an elevated hcv rna viral load. hcv genotype should also be obtained in any positive individual, because this has important prognostic factors with regard to therapy, with genotype a and b the predominant type in the united states and unfortunately having a poor response to therapy. as with hbv, chronic hcv infection can lead to cirrhosis and the development of hepatocellular carcinoma. treatment consists of to weeks of interferon and ribavirin therapy. any patient being considered for therapy should be referred to an infectious diseases specialist or hepatologist. a liver biopsy is often needed to determine appropriate treatment candidates. also known as the hepatitis delta antigen virus, hdv is a defective virus that requires the presence of hbv to be infectious. hdv should be suspected in any patient with chronic hbv who develops acute hepatitis. hepatitis d is endemic in the mediterranean, balkans, africa, middle east, and amazon basin. diagnosis is made through an anti-hdv antibody in the presence of someone with positive hbsag or anti-hb core antibody igm or igg. treatment is supportive. any person vaccinated against hbv cannot become infected with hdv. similar to hav infection, hev is spread by the fecal-oral route. hev only has an acute form and does not progress to chronic infection. most reported epidemics have been related to consumption of contaminated drinking water. hev is endemic to southeast and central asia, north africa, middle east, mexico, brazil, venezuela, and cuba. hepatitis e can be considered a cause of infectious hepatitis in the united states in the traveler returning from an endemic area. the incubation period is days. infection is of major concern during pregnancy, which can cause death in late pregnancy. diagnosis is made by demonstration of anti-hev antibody in serum. treatment is supportive. • endocarditis prophylaxis is now recommended solely for patients at high risk of a complicated course with a more narrow range of cardiac conditions. • routine prophylaxis for gi and gu procedures is no longer recommended. • the duke criteria represent a reliable scoring system for diagnosing endocarditis. • echocardiography is indicated to confirm suspected endocarditis. bacterial endocarditis is one of the most feared infections; although uncommon, it carries high morbidity and mortality. increase in antibiotic resistance among bacteria causing this infection has created challenges for effective treatment. the fundamental view of the american heart association (aha) in preventing infective endocarditis has shifted in recent years. views on pathophysiology have not changed substantially, but it is now recognized ebox - persons for whom hepatitis c virus (hcv) screening is recommended persons who have injected illicit drugs in the recent and remote past, including those who injected only once and do not consider themselves to be drug users. persons with conditions associated with a high prevalence of hcv infection, including: persons with human immunodeficiency virus (hiv) infection persons with hemophilia who received clotting factor concentrates before persons who have ever received hemodialysis persons with unexplained abnormal transaminase (aminotransferase) levels prior recipients of transfusions or organ transplants before july , including: persons who were notified that they had received blood from a donor who later tested positive for hcv infection persons who received a transfusion of blood or blood products persons who received an organ transplant children born to hcv-infected mothers health care, emergency medical, and public safety workers after a needle stick injury or mucosal exposure to hcv-positive blood current sexual partners of hcv-infected persons * modified from centers for disease control and prevention. recommendations for prevention and control of hepatitis c virus (hcv) infection and hcv-related chronic disease. mmwr ; (rr): - . *although the prevalence of infection is low, a negative test in the partner provides reassurance, making testing of sexual partners of benefit in clinical practice. • universal vaccination of infants with hepatitis b vaccine reduces the risk of acute hepatitis, chronic carrier state, and complications of chronic infection and may be more effective than selective vaccination of high-risk individuals (lee et al., ) (sor: a). • as part of a comprehensive health evaluation, all persons should be screened for behaviors that place them at high risk for hepatitis c infection (ghany et al., ) (sor: b). • liver biopsy may be considered in patients with chronic hcv infection to determine fibrosis stage for prognostic purposes or to make a treatment decision (ghany et al., ) (sor: b). that cumulative daily episodes of bacteremia likely carry more risk than the transient bacteremia caused by dental procedures. infective endocarditis likely begins with turbulent flow and damaged endothelium around heart valves, which allow platelet aggregation and thrombus formation, causing a "nonbacterial thrombotic endocarditis" (wilson et al., ) . the presence of bacteremia then allows this vegetation to become seeded with infection. bacterial "adhesins" are present to a greater degree in some species and allow for more effective attachment to the injured area of endothelium. with high concentrations of bacteria in the mouth, vagina, gi tract, and perhaps gu system, antibiotic prophylaxis was initiated when these anatomic locations were manipulated. recommendations for infective endocarditis prevention changed in - , with aha recognizing more likely benefit from providing adequate population-based dental care and good oral hygiene, and thus less significant ongoing bacteremia at home in brushing, flossing, and "toothpicking," than in providing antibiotic prophylaxis to patients undergoing a dental procedure. no prospective rct has shown that dental prophylaxis prevents infective endocarditis. with recognition of the risk associated with administration of antibiotics (gi upset, diarrhea, rash, anaphylaxis) and the risk of contributing to increasing antibiotic resistance, versus the likely negligible benefit, aha has substantially changed its advice on this long-held practice. a preexisting cardiac condition produces a predisposition to the development of infective endocarditis (ebox - ). for example, those who have valve replacement for infection of an infected native valve carry a lifetime risk of per , patient-years. the risk in the general population without known heart disease is per , patient-years. more concerning, however, is the risk to a given patient of poor outcome if the patient develops endocarditis, which drives current aha recommendations. those with an infected mechanical valve have a mortality rate of about %, versus % or less for patients with an infected native valve (wilson et al., ) . a summary of current recommendations for endocarditis prophylaxis is provided in etable - . of note, gi and gu procedures have been removed from those for which antibiotics are recommended, unless those systems are actively infected at the time of the procedure. the same is true for skin and soft tissue procedures, in that only infected tissue would warrant antibiotics to prevent infective endocarditis. it is still recommended to provide prophylaxis for respiratory tract procedures, if the respiratory wall will be invaded through biopsy or the procedure. in addition, respiratory procedures to treat infections (e.g., empyema) should be combined with antibiotic administration (nishimura et al., ) . antibiotic regimens for prophylaxis for dental procedures are still based primarily on synthetic penicillins as their cornerstone. this is with recognition that streptococcus viridans is both a mouth floral inhabitant and a common agent causing infective endocarditis. with other procedures, antibiotics should be targeted to bacterial pathogens causing any active infection in the system being manipulated. ebox - cardiac conditions associated with the highest risk of adverse outcome from endocarditis for which prophylaxis with dental procedures is reasonable prosthetic cardiac valve or prosthetic material used for cardiac valve repair previous ie congenital heart disease (chd) * unrepaired cyanotic chd, including palliative shunts and conduits completely repaired congenital heart defect with prosthetic material or device, whether placed by surgery or by catheter intervention, during the first months of the procedure † repaired congenital heart defect with residual defects at the site or adjacent to the site of a prosthetic patch or prosthetic device (which inhibit endothelialization) cardiac transplantation recipients who develop cardiac valvulopathy *except for the conditions listed above, antibiotic prophylaxis is no longer recommended for any other form of chd. †prophylaxis is reasonable because endothelialization of prosthetic material occurs within months after the procedure oral antibiotic william osler discussed "malignant endocarditis" in and its great diagnostic challenge. in the modified duke criteria remains a reliable tool for assessing patients with endocarditis. endocarditis is suspected in febrile patients without an obvious source, in those with recent bacteremia (including iv drug use), in those with underlying cardiac predisposition, and perhaps in patients with the clinical finding of a new cardiac murmur. in establishing a diagnosis of infective endocarditis, a patient is considered to have definite disease if two major or one major and three minor or five minor criteria are present. possible disease is defined as one major and one minor or three minor criteria (ebox - ). pathologic specimens showing changes consistent with endocarditis would make a definitive diagnosis. echocardiography is indicated in making the diagnosis of infective endocarditis. transthoracic echocardiography (tte) is helpful if vegetations are seen, although size of the patient and other disease (e.g., copd) may limit the ability of tte to view the cardiac valves adequately. if tte is negative and suspicion remains, transesophageal echocardiography (tee) is indicated. tte may be more widely available, depending on regional and institutional variation, and should be used rather than delaying this diagnostic test. bacteria present within valvular vegetations are often less metabolically active, which partly explains the requirement for longer courses of antibiotics for this type of infection. clearly, therapy for endocarditis should be targeted at the organism identified on blood culture, if any. the counting of antibiotic days should begin when the blood culture becomes negative and not at the start of the particular agent. recommendations for antibiotic use in infectious endocarditis are highly variable and based on the presence or absence of synthetic valvular material and the infectious agent (etable - ). generally speaking, a minimum of weeks of iv antibiotics is indicated. in cases of resistant organisms, up to weeks may be required. in either case, synergistic use of agents such as gentamicin may be indicated for the first several weeks of treatment, which then can be discontinued. the ability of a given patient to complete this course at home versus in a health care facility is dependent on the dosing frequency of the antibiotic, availability of inhome nursing services, and the type of intravenous access through which the antibiotic will be delivered. at the completion of endocarditis therapy, echocardiography should be repeated to re-assess the function of the valve(s) in question. valvular dysfunction at the completion of therapy is a good indication that the patient will need valve replacement in the future. there are circumstances, like the development of congestive heart failure in the face of endocarditis, in which primary surgery is indicated. typical microorganisms consistent with ie from separate blood cultures: viridans streptococci, streptococcus bovis, hacek group, staphylococcus aureus; or community-acquired enterococci in the absence of a primary focus; or microorganisms consistent with ie from persistently positive blood cultures, defined as follows: at least positive cultures of blood samples drawn > hours apart; or all of or a majority of ≥ separate cultures of blood (with first and last sample drawn at least hour apart). single positive blood culture for coxiella burnetii or anti-phase igg antibody titer > : echocardiogram positive for ie (tee recommended for patients with prosthetic valves, rated at least "possible ie" by clinical criteria, or complicated ie [paravalvular abscess]; tte as first test in other patients) defined as follows: oscillating intracardiac mass on valve or supporting structures, in the path of regurgitant jets, or on implanted material in the absence of an alternative anatomic explanation; or abscess; or new partial dehiscence of prosthetic valve; new valvular regurgitation (worsening or changing or preexisting murmur not sufficient) predisposition, predisposing heart condition, or idu fever, temperature > ° c vascular phenomena, major arterial emboli, septic pulmonary infarcts, mycotic aneurysm, intracranial hemorrhage, conjunctival hemorrhages, and janeway's lesions immunologic phenomena: glomerulonephritis, osler's nodes, roth's spots, and rheumatoid factor microbiologic evidence: positive blood culture but does not meet a major criterion as noted above * or serological evidence of active infection with organism consistent with ie echocardiographic minor criteria eliminated echocardiography should be performed in all patients with suspected infective endocarditis (baddour et al., ) there is no evidence that antibiotic prophylaxis is effective or ineffective for preventing infectious endocarditis after dental procedures in patients at risk (chung, ) (sor: c). regimen dosage * and route duration (wk) chronic cough due to acute bronchitis: accp evidencebased clinical practice guidelines interim recommendations for the use of influenza antiviral medications in the setting of oseltamivir resistance among circulating influenza a (h n ) viruses, - influenza season national ambulatory medical 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management of community-acquired pneumonia in adults influenza viruses, including avian influenza and swine influenza steroids for symptom control in infectious mononucleosis hepatosplenomegaly in infectious mononucleosis, assessed by ultrasonic scanning infectious mononucleosis vaccines for post-exposure prophylaxis against varicella (chickenpox) in children and adults centers for disease control and prevention (ats/cdc). targeted tuberculin testing and treatment of latent tuberculosis infection centers for disease control and prevention. extensively drug-resistant tuber culosis-united states short-course therapy with rifampin plus isoniazid, compared with standard therapy with isoniazid, for latent tuberculosis infection: a meta-analysis genital warts expedited partner therapy in the management of sexually transmitted diseases. atlanta: us department of health and human services center for disease control and prevention. sexually transmitted disease surveillance. division of std 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disease society of america acute meningitis guidelines on acute infectious diarrhea in adults. the practice parameters committee of the american college of gastroenterology a comparison of vancomycin and metronidazole for the treatment of clostridium difficileassociated diarrhea, stratified by disease severity acute cholecystitis nett's principles and practices of infectious diseases diagnosis and management of complicated intra-abdominal infection in adults and children: guidelines by the surgical infection society and the infectious diseases society of america infectious viral hepatitis national institutes of health consensus development conference statement: management of hepatitis b acute viral hepatitis hepatitis b virus infection chronic viral hepatitis chronic hepatitis diagnosis, management and treatment of hepatitis c: an update acute viral hepatitis hepatitis c virus infection effect of hepatitis b immunisation in newborn infants of mothers positive for hepatitis b surface antigen: systematic review and meta-analysis chronic hepatitis b: update infective endocarditis: diagnosis, antimicrobial therapy, and complications prescription of antibiotics for prophylaxis to prevent bacterial endocarditis experience with a oncedaily aminoglycoside program administered to adult patients acc/aha guideline update on valvular heart disease: focused update on infective endocarditis prevention of infective endocarditis: guidelines from the american health association. circulation key: cord- -rs cz lq authors: wordley, v.; shah, s.; thompson, w. title: increased antibiotics use date: - - journal: br dent j doi: . /s - - -z sha: doc_id: cord_uid: rs cz lq nan nhs dentistry in england in and . the number of antibiotics dispensed each month by community pharmacists in england relating to nhs dental prescription forms from january to may is given in figure . this shows antibiotic use in may was a clear outlier compared to the previous months being . % higher than in may (n = , and , respectively). interestingly, antibiotic use in april was slightly higher than the previous april but still within the normal range for the period of study. this is despite the significantly poorer access to dentistry (only around , patients were seen at designated urgent dental centres [udcs] across england) compared to may when the capacity of these centres increased and saw over , patients. a range of non-clinical factors are known to be associated with dentists' decision-making about antibiotics prescription for acute conditions. antibiotics may have been used: • as a 'quick fix' to avoid the life-time impact of an unnecessary extraction, in anticipation that agps might soon be permissible in general dental practices • because dentists felt pressured by some patients for antibiotics, irrespective of their efficacy or appropriateness for treating toothache • because of difficulties diagnosing a patient's condition remotely prompting a 'just in case' approach through concerns of life-threatening deterioration without treatment • as some udcs were requiring patients to have tried antibiotics before accepting referral for face-to-face care, highlighting system and process impact on antibiotic prescribing. finally, the nhs may have seen an influx in patients who might otherwise receive care privately, resulting in an increase in nhs dental prescriptions as, anecdotally, not all practices were open for telephone triage during april and may . examination of figures for the remainder of will reveal any enduring impact that covid interventions may have on dental antibiotic prescribing and in identifying optimisation of future dental antibiotic stewardship. v sir, pre-covid, dentists were responsible for about % of all antibiotic prescribing worldwide. at the onset of the pandemic most dental practices were restricted to giving advice, analgesia and antibiotics (aaa). reduced access to dental care and an inability for dentists to provide dental procedures increases dental antibiotic prescribing. a large increase in dental antibiotic use in england during april and may was widely anticipated and so we undertook a rapid analysis comparing antibiotic use across sir, the pre-visit triage, which practices are advised to do, will preclude any proven or probable covid- patients from attending a practice, leaving only the possible, undiagnosed cases as posing a risk of bringing this infection into a practice. our city council produces weekly updates of new cases, which gives a good indication of the level of infection in the population which our practice serves. when this figure is combined with the average number of patients that we have seen each week, since lockdown was eased, and the local population, this enables us to quantify the risk of us seeing an undiagnosed covid- patient in the practice. last week, this indicated that the average risk of seeing such a patient was one every , weeks, or one every . years. there are plenty of generalisations used in that calculation but it is certainly food for thought. povidone iodine covid- : povidone-iodine intranasal prophylaxis in front-line healthcare personnel and inpatients (piippi). clinicaltrials.gov practical use of povidone-iodine antiseptic in the maintenance of oral health and in the prevention and treatment of common oropharyngeal infections stable compositions of uncomplexed iodine and methods of use references . fdi. antibiotic stewardship in dentistry -fdi policy statement: fdi world dental federation factors associated with prescribing of systemic antibacterial drugs to adult patients in urgent primary health care, especially dentistry personal communication re: dr re: request for information key: cord- -pzjj wxc authors: smith, geof title: antimicrobial decision making for enteric diseases of cattle date: - - journal: vet clin north am food anim pract doi: . /j.cvfa. . . sha: doc_id: cord_uid: pzjj wxc diarrhea in neonatal and adult cattle is common and can be caused by several etiologic agents. as diagnostic testing is not always readily available, practitioners must often decide on a course of treatment based on knowledge of the likely pathogen and their own clinical experience. antimicrobials have long been used to treat diarrhea in adults and neonates; however, there is increased pressure to prevent unnecessary use of antibiotics in food animal species. this article reviews existing data on the use of antibiotics given to cattle with enteric diseases to decide when they are necessary and which antimicrobials should be used. antibiotics to calves to prevent diarrhea cannot be recommended. however, the use of certain antimicrobials to treat select cases of calf diarrhea may be effective in reducing mortality and decreasing the severity and duration of diarrhea. unfortunately, it is unlikely that any of the antibiotics that are currently approved for the treatment of diarrhea in the united states would be effective. instead of mass medicating large numbers of animals, antimicrobial therapy should be targeted to specific animals that are likely to develop septicemia or have systemic signs of disease. there are many causes of diarrhea in adult cattle, and the vast majority of these do not warrant antimicrobial therapy. common enteric diseases of cattle include simple indigestion, rumen acidosis, parasites, coccidiosis, bovine viral diarrhea (bvd), winter dysentery, salmonella, paratuberculosis (johne disease), molybdenosis (copper deficiency), and malignant catarrhal fever (mcf), along with a wide range of toxicities including a host of poisonous plants. the only disease on this list that is likely to truly benefit from antimicrobial therapy is salmonella enteritis; however, an argument could be made for bvd and mcf. both these diseases suppress normal immune function and can lead to an increased occurrence of secondary bacterial infections. it is well understood that bvd is associated with the bovine respiratory disease complex and can lead to higher rates of bacterial pneumonia. however, cases of severe salmonella enteritis have also been reported after bvd infection in cattle causing significant mortality. therefore, it would not be inappropriate to administer a broad-spectrum antimicrobial to cattle suspected of having bvd or mcf, likely one that is labeled for metaphylactic use in cattle at high risk for developing respiratory disease. it is also important to note that many toxic cows with severe mastitis, metritis, or peritonitis often have diarrhea that is a direct result of endotoxemia. the mechanism of endotoxin-induced diarrhea is not completely understood; however, it seems to involve both prostaglandins and nitric oxide. the administration of endotoxin leads to abundant accumulation of fluid inside the small intestines of animals, which is thought to be prostaglandin mediated. endotoxin also increases the enzyme activities of nitric oxide synthase in intestinal smooth muscle, which changes the propagation of jejunal contractions resulting in rapid intestinal transit. the diarrhea observed during endotoxemia in cattle is not profuse but is generally described as low volume. in these cases, choosing to use an antimicrobial would likely not benefit the diarrhea or enteric disease present in the cows but would almost certainly be indicated from the standpoint of treating the primary disease condition. despite the limited number of enteric diseases in adult cattle that would benefit from antimicrobial therapy, surveys indicate that diarrhea is a relatively common reason for the use of antibiotics. in the national animal health monitoring survey (nahms) dairy study, mastitis was the most common reason for antimicrobial use on dairy farms followed by lameness, reproductive diseases (metritis), respiratory disease, and then diarrhea or other enteric disease. results of the survey showed that about % of cattle on dairy farms from the survey population had been treated with an antimicrobial for diarrhea in the preceding -month period and % of farms said they routinely had cows that received antimicrobial drugs because of diarrhea. data from the nahms feedlot study indicated that % of feedlots reported diarrhea or other enteric disease in calves after arrival with . % of calves showing evidence of diarrhea. further data from the study indicated that % of calves with diarrhea received treatment upon arrival. when the survey looked into what specific therapy was administered, % of calves received an injectable antimicrobial, while % of the cattle received an oral antibiotic. when reviewing the data of both the nahms dairy and feedlot studies, it becomes clear that enteric disease is not the primary reason for antimicrobial use in adult cattle. however, it is also apparent that diarrhea is one of the top or reasons cattle receive antimicrobials and that at least half of the cattle diagnosed with diarrhea receive either a parenteral and/or an oral antibiotic. most of the time dairy or beef cattle have diarrhea, it is not clear what the cause is, and therefore they are empirically treated with antibiotics. the assumption in many cases is that the animal has salmonellosis or some other bacterial enteritis. although this is certainly true in some cases, it is very likely that most cases of diarrhea are because of simple indigestion caused by an abrupt diet change, moldy feed, spoiled feed, or perhaps a mild grain overload (rumen acidosis). however, simple indigestion is often difficult or impossible to diagnose definitively and therefore cattle are treated empirically with antimicrobials. if salmonella are the main target of antimicrobial therapy in adult cattle with diarrhea, drug selection should ideally be based on the results of susceptibility testing using bacterial strains recovered from that particular dairy or feedlot. broad-spectrum antimicrobials are usually used pending the availability of susceptibility test results. salmonella show variable resistance patterns to ampicillin, amoxicillin, ceftiofur, florfenicol, neomycin, streptomycin, sulfonamides, tetracycline, and trimethoprim-sulfa and general resistance to penicillin, erythromycin, and tylosin. [ ] [ ] [ ] the most recently published data indicated that salmonella isolates from cattle were most commonly resistant to streptomycin, ampicillin, and sulfonamides, whereas resistance to ceftiofur was extremely low. as salmonella are facultative intracellular pathogens, selecting an antimicrobial with good tissue penetration and the ability to attain intracellular therapeutic drug concentrations within macrophages is desirable. in summary, antimicrobials for the treatment of diarrhea in adult cattle are likely being overused at present in the cattle industry. although diarrhea occurs fairly commonly, most causes are unlikely to respond to antimicrobials. treatment should be primarily supportive care, including fluid therapy, anthelmintics if needed, and provision of good-quality pasture or other forages. mortality rates in most cases of diarrhea in mature cattle are low, and the diarrhea generally resolves within a few days. diseases such as paratuberculosis would have a higher mortality but would still not be likely to respond to antimicrobial therapy. however, when cattle have signs of systemic infection such as pyrexia or bloody diarrhea, it may be rational to begin antimicrobial therapy, particularly on farms that have a history of salmonellosis. when examining an adult ruminant with enteric disease, the practitioner should consider the age of the animal; the onset, severity, and duration of diarrhea (acute vs chronic); the number of cattle affected (is this an individual animal or a herd problem); clinical signs in the animal other than diarrhea (does the animal show systemic signs of disease); nutritional history (especially recent changes in the diet), and whether there has been an introduction of new animals (bvd). all these help to determine a list of possible causes for the diarrhea and may help reduce the use of antimicrobial drugs in cattle that are unlikely to benefit from therapy. prudent use of antimicrobial drugs is recommended with an emphasis on establishing a herd diagnosis and conducting susceptibility testing for the specific salmonella serotype or other bacterial pathogen present and choosing an appropriate antibiotic. calf health should be a priority on both beef and dairy farms. despite this importance, the united states department of agriculture dairy study shows a preweaned antimicrobial decision making heifer calf mortality rate of . % and reports that only % of farms can supply an adequate number of replacements from their own herd. although mortality is slightly less in beef calves, % to % still die before weaning. in both beef and dairy calves, diarrhea represents the most common reason for loss due to death before weaning. therefore, practitioners and producers spend a significant amount of time trying to prevent diarrhea and also making sure good treatment programs are in place when diarrhea does occur. the main principles of diarrhea prevention in both beef and dairy cattle include ( ) using a vaccine in late gestation cattle containing enterotoxigenic escherichia coli, rotavirus, and coronavirus; ( ) making sure a good colostrum program is in place ensuring adequate intake of immunoglobulins by the calf; and ( ) decreasing the load of enteric pathogens in the environment through sanitation, hygiene, housing, and pasture management. historically, many producers (particularly in the dairy and veal industries) have used feeding of oral antibiotics to prevent diarrhea and hopefully decrease mortality in newborn calves. however, the practice of continually feeding antibiotics to calves is now prohibited in many countries, and the efficacy of feeding antibiotics to calves as a method of diarrhea prevention has not proven to be effective in recent studies. almost years ago, a thorough review was published on the efficacy of antibiotics for preventing diarrhea and improving weight gain in dairy calves. the investigator concluded that the addition of chlortetracycline and oxytetracycline to milk replacer in the first weeks of life decreased the incidence and severity of diarrhea. the minimum daily doses necessary for efficacy in this study were . to . mg/lb, which led to the routine inclusion of these antibiotics in milk replacers throughout the united states. unfortunately, this study did not look at critical factors such as mortality rate in calves or incidence of diarrhea. the primary benefits of oral antibiotics were found to be higher weight gain and decreased severity and duration of diarrhea. as discussed in a previous review article, there were several studies done in the s and the s using various antibiotics (including ampicillin, chlortetracycline, furazolidone, neomycin, oxytetracycline, and streptomycin) to prevent diarrhea in calves. although the results of these studies varied, only study documented a decrease in mortality rate from diarrhea due to prophylactic oral administration of chlortetracycline. a few studies did find a decrease in the total number of days of diarrhea associated with antibiotics ; however, other studies (particularly with neomycin) found increased rates of diarrhea in antibiotic-treated calves. , quite a few of these older studies found that oral administration of various antibiotics did not change the incidence of diarrhea in calves when compared with untreated controls. more recent studies have found that either oral antibiotics had no effect on decreasing calf diarrhea or in some cases diarrhea rates actually increased in calves fed antibiotics. for example, a study in california fed group of holstein heifers monensin in the starter ration, whereas another group was fed lasalocid and chlortetracycline (aureomycin) for the first weeks of life (in addition to nonmedicated milk replacer or whole milk). antibiotic-treated calves had no difference in average daily gain, feed efficiency, or the proportion of calves treated for diarrhea. in another study, holstein heifers were fed milk replacer medicated with oxytetracycline and neomycin or an unmedicated milk replacer that contained a probiotic (enteroguard-no longer commercially available). once again, body weight gain, feed efficiency, and the incidence and severity of diarrhea were similar between groups. in a third study, dairy calves were divided into groups: medicated milk replacer (neomycin and tetracycline for the first days of life) plus the administration of trimethoprim-sulfamethoxazole, spectinomycin, penicillin, and bismuth pectin for the treatment of diarrhea (referred to as conventional therapy); medicated milk replacer for the first days of life, bismuth pectin for diarrhea, and other antibiotics only in cases of fever or depressed attitude (targeted therapy); nonmedicated milk replacer with antimicrobial treatment of diarrhea (same treatments as the conventional therapy group above); and nonmedicated milk replacer with targeted therapy. calves fed a medicated milk replacer had % more days with diarrhea when compared with calves fed nonmedicated milk replacer. in a survey, about % of dairy farms in the united states fed medicated milk replacers to preweaned heifer calves, most commonly a combination of oxytetracycline and neomycin. however, a new federal regulation that began in restricts the feeding of medicated milk replacers to a period of to days. thus continuous feeding of antibiotics in the milk from birth to weaning is no longer permitted, and this is meant to transition the use of oral antibiotics in calves from prophylactic to therapeutic. medicated milk replacers should now be reserved for the treatment of bacterial enteritis (diarrhea) and bacterial pneumonia in dairy calves and not for prophylactic prevention. since the late s, the european union has prohibited the sale of milk replacers and other animal feeds containing antibiotics. all the feed and milk replacers for dairy cattle must be sold as nonmedicated, and then antibiotics can be added only for therapeutic use (for example, in calves with diarrhea). australia and new zealand also have strict laws regarding the importation of any animal feed, and these products are generally nonmedicated as well. overall, the conventional practice of adding antibiotics to milk or milk replacers for prophylactic use is being discouraged worldwide. most modern studies fail to find any benefit of using antibiotics as a prevention for diarrhea, and their use in this manner should be discouraged. the use of antibiotics as a treatment in calves with diarrhea is a controversial topic with strong opinions on both sides. several articles have been published indicating that antibiotics are contraindicated in calves with diarrhea or that they serve no beneficial purpose. , in contrast, other studies have indicated that antibiotics are effective in reducing mortality rate and speeding recovery in calves with diarrhea. , to begin the discussion, it is important to establish a reason to use antibiotics in calves with diarrhea. the primary treatment goals of an antibiotic in calves with diarrhea would be ( ) to prevent bacteremia and ( ) to decrease the number of coliform bacteria in the small intestine. several studies have reported that a significant number of calves with diarrhea subsequently develop bacteremia. an initial study in the early s reported that colostrum-deprived calves with diarrhea were frequently bacteremic ( / calves or %). in contrast, none of the diarrheic calves in this study that had received colostrum were bacteremic ( . or %). a study conducted on a large calf-rearing facility in california examined dairy calves with severe diarrhea ; of the calves ( %) had failure of passive transfer and ( %) calves were bacteremic (predominantly e coli). another study done in prince edward island, canada, looked at the prevalence of bacteremia in calves with diarrhea ; of the ( %) calves in this study were bacteremic (predominantly e coli). as noted previously, the percentage of calves with bacteremia was significantly higher in the failure of passive transfer group ( / or %) than in adequate passive transfer group ( / or %). taken together these studies indicate that it can be assumed that one-third of the calves with severe diarrhea are bacteremic and that the percentage is likely significantly higher in calves with failure of passive transfer. although some have argued that antibiotic use in calves with diarrhea is inappropriate and leads to the emergence antimicrobial decision making of resistant bacteria, a case can be made that the use of antibiotics to prevent and/or treat bacteremia in calves with diarrhea and systemic signs of disease is warranted. withholding effective treatment (antibiotics) for a life-threatening disease (such as bacteremia in calves with diarrhea) should not be condoned on animal welfare grounds. another potential reason for antibiotic therapy in calves with diarrhea is coliform overgrowth of the small intestine (fig. ) . research conducted in the s documented increased numbers of e coli in the abomasum, duodenum, and jejunum of calves with diarrhea. , more recent studies have consistently found increased numbers of intestinal e coli in calves with naturally acquired diarrhea regardless of the age of the calf or the cause of the diarrhea. , specifically, the numbers of e coli bacteria increase from -to , -fold in the duodenum, jejunum, and ileum of calves with scours, even when rotavirus or coronavirus is identified as the cause of diarrhea. this small intestinal overgrowth of the intestines with coliform bacteria can persist after the pathogen causing the diarrhea is gone. the increased numbers of coliform bacteria in the small intestine of calves with diarrhea is associated with altered small intestinal function, morphologic damage, and increased susceptibility to bacteremia. therefore there is some logic to the use of antimicrobials in scouring calves to decrease the number of intestinal coliform bacteria. this use could potentially prevent the development of bacteremia, decrease calf mortality, and decrease damage to the small intestine, facilitating digestion and absorption and increasing growth rate. several of which would be illegal to use in the united states (ie, chloramphenicol, furazolidone, or marbofloxacin). the results indicated that specific antibiotics were effective in reducing mortality and increasing growth rate when administered to calves with diarrhea. several studies provided evidence that even calves with simple diarrhea (without systemic signs of disease) seemed to recover faster with antibiotics as opposed to calves that did not receive antibiotics. some veterinarians feel that oral or parenteral administration of antibiotics to calves with diarrhea is contraindicated. the arguments most commonly used to support this approach include: ( ) oral antibiotics alter intestinal flora and thereby induce diarrhea or exacerbate existing diarrhea, ( ) antibiotics harm good intestinal bacteria more than bad bacteria, ( ) antimicrobial use in calves with diarrhea is not effective, and ( ) the use of antibiotics provides a selection pressure on the enteric bacterial population likely leading to increased antimicrobial resistance. there is solid evidence to indicate that the use of antimicrobial drugs can decrease mortality in calves and there is no evidence to support the argument that antimicrobials harm good bacteria more than the bad. however, the emergence of resistant bacteria is certainly serious and is something the veterinarian must take into account before treating calves with diarrhea. table contains a list of antimicrobials currently approved for the treatment or prevention of diarrhea in the united states. at present, oxytetracycline administered parenterally and chlortetracycline, neomycin, oxytetracycline, sulfamethazine, and tetracycline administered orally are the only antimicrobials labeled in the united states for the treatment of calf diarrhea. of these, none have been shown to be consistently efficacious in peer-reviewed studies. as discussed above, when treating calves with diarrhea the primary goals of therapy are to ( ) decrease the number of e coli bacteria in the small intestine and ( ) treat potential e coli bacteremia. with these goals in mind, the target of antimicrobial therapy in calves with diarrhea should be coliform bacteria both in the blood and in the small intestine. as none of the approved drugs for treating diarrhea in the united states are likely to be effective, extralabel use is likely justified. some efficacy has been described for oral amoxicillin in the treatment of calves with experimentally induced diarrhea, , but was not effective in the treatment of naturally acquired diarrhea in beef calves. amoxicillin trihydrate ( mg/kg administered orally every h) or amoxicillin trihydrate-clavulanate ( . mg combined drug/kg administered orally every h) for at least days is one antimicrobial approach that likely has some efficacy for calves with diarrhea. amoxicillin is partially absorbed from the calf small intestine with absorption being similar in both milk-fed and fasted calves. high amoxicillin concentrations are found in bile and intestinal contents after oral administration, with lower concentrations in serum. oral ampicillin could also be used, and its efficacy in one study was shown to be equivalent to that of amoxicillin. although very popular in the united states, oral sulfonamides cannot be recommended for treating calves with diarrhea because of the lack of efficacy studies. most antimicrobial susceptibility studies done in the past years indicate that sulfamethazine (and other sulfonamide drugs) would have poor sensitivity against coliform bacteria in the blood or small intestine. the most logical antimicrobial for parenteral treatment of calf diarrhea in the united states is ceftiofur ( . mg/kg given intramuscularly [im] every h) for at least days. ceftiofur is a broad-spectrum antibiotic that is resistant to b-lactamase. the labeled dose maintains plasma concentrations of ceftiofur above the minimum concentration required to inhibit the growth of % of e coli (mic ) in young calves ( . mg/ml). furthermore, % of the active metabolite (desfuroylceftiofur) is excreted into the intestinal tract of cattle providing activity in both the blood and the small intestine. parenteral ampicillin ( mg/kg im every h) is another antibiotic that would be likely to have efficacy in calves with diarrhea. in europe, parenteral enrofloxacin is labeled for the treatment of calf diarrhea, and several studies have documented efficacy with using fluoroquinolone antibiotics in calves with diarrhea. [ ] [ ] [ ] however, it must be emphasized that the extralabel use of fluoroquinolone antibiotics in the united states is illegal and obviously not recommended. historically, gentamicin was also considered an appropriate treatment for use in calves with diarrhea. however, parenteral administration of aminoglycosides cannot be recommended in calves with diarrhea because of the lack of published efficacy studies, prolonged slaughter withdrawal times ( months), potential for nephrotoxicity in dehydrated calves, and availability of other drugs likely to be equally successful (ceftiofur, amoxicillin, and ampicillin). the issue of whether or not to use antibiotics in a calf with simple diarrhea (without systemic signs of disease) is a little more controversial. although there have been studies to show that these calves gain more weight and recover faster than calves not given antibiotics, there are other studies that indicate no benefit to using antibiotics in these cases. , the clinician must weigh any potential benefit of antimicrobial therapy against the possibility of increasing the population of resistant bacteria on the farm. a fairly recent study demonstrated that individual treatment of sick calves with antibiotics increased the level of resistance to e coli isolates; however, the change in antimicrobial susceptibility was only transient. the next logical question is whether or not antimicrobial susceptibility testing should play a role in determining which drug is used to treat calves with diarrhea. historically, culture and susceptibility results from fecal culture have been routinely used to guide treatment decisions; however, it is not clear whether or not this has any clinical relevance. research validating susceptibility testing as being predictive of treatment outcome for calves with diarrhea is currently not available. part of the problem is that our target is coliform bacteria in the blood and small intestine, which are likely different from fecal bacterial flora. older studies have demonstrated that the predominant strain of e coli in the manure of calves with diarrhea usually changes several times during the course of disease. , these studies also show that about % of calves have different e coli strains isolated from the upper and lower parts of small intestine. so it is logical to conclude that fecal coliform isolates are not representative of what is happening in the intestine. another potential problem with using susceptibility testing to guide antimicrobial selection in cases of diarrhea is that most of the bacterial cultures submitted usually come from dead animals, which represent treatment failures and may have already received antibiotics. preferential growth of resistant bacterial strains can start within a few hours after antibiotic administration, and therefore culture results from dead calves may not be representative of the actual clinical problem. to the author's knowledge, the only study that has tried to assess the predictive ability of fecal antimicrobial susceptibility testing found that it was an inaccurate predictor of clinical outcome. in a large group of experiments evaluating the efficacy of amoxicillin for treating calf diarrhea, calves were divided into groups that either received amoxicillin or did not. diarrhea was experimentally induced using enterotoxigenic e coli and smith rectal swab culture, and susceptibility testing was done. most calves ( %) developed diarrhea after challenge; however, in only about % of cases did calves shed the actual challenge strain of e coli. recovery or treatment success in these studies was defined as normal feces within days after the start of treatment, while treatment failure was defined as death or scouring for more than days. among calves in which the e coli cultured from rectal swabs were susceptible to amoxicillin, % died and % recovered with . as the mean number of days scouring. outcomes were not different in calves that had amoxicillin-resistant strains of e coli cultured from rectal swabs with % death loss, % recovery rates, and . scouring days. in calves given a placebo instead of amoxicillin, mortality was significantly increased ( %), recovery rates were decreased ( %), and the number of scouring days was longer ( . ). the investigators concluded that amoxicillin had a significant effect on disease by decreasing mortality and number of scouring days; however, treatment success could not be predicted by whether the e coli cultured from rectal swabs was susceptible or resistant to the antimicrobial being used. two studies have concluded that there was a good correlation between in vitro antimicrobial susceptibility of fecal e coli isolates and clinical response to treatment; however, neither study had data to statistically analyze this association. , in contrast, other studies reported no correlation between in vitro susceptibility results for coliform isolates and response to antimicrobial treatment. , however, these studies did not differentiate enterotoxigenic and nonenterotoxigenic strains of e coli and also failed to do any statistical analysis of the data. there is a significant need for antimicrobial susceptibility data from e coli and salmonella isolates collected from the small intestine of untreated calves with diarrhea. minimum inhibitory concentrations (mic) could then be compared with free antimicrobial concentrations that are actually achievable in the intestinal tract of calves to determine the best drug to use along with the optimal dosing interval. however, it should be emphasized that antimicrobial concentrations can be altered by multiple variables, such as intestinal ph, which may be quite different between healthy calves and those with diarrhea. therefore even after establishing mic values and setting appropriate breakpoints, these need to be validated through clinical trials examining the use of specific antimicrobial drugs in calves with diarrhea as compared to the pathogen isolated and disease outcome. until then the use of fecal culture and susceptibility testing to guide antimicrobial selection for treating calf diarrhea is probably of little value. drug selection is based on knowledge of the likely pathogen (e coli in the blood and small intestine), pharmacokinetics of the drug (can it achieve therapeutic concentrations at the site of infection), and evaluation of the response to treatment (does the animal get better). on farms in which salmonella or e coli septicemia is a problem, looking at susceptibility results from blood cultures is likely much more appropriate than fecal culture. certainly the overuse of antibiotics is a concern, and the overall philosophy in veterinary medicine is to use antibiotics conservatively to preserve the efficacy of these drugs in both animals and humans. based on the need to minimize the use of antibiotics and because of the lack of any demonstrated recent efficacy, the feeding of antimicrobials to calves as a method of diarrhea prevention is not recommended. however, calves with diarrhea and systemic signs of illness should receive antibiotics targeted toward coliform bacteria in the blood (because of likelihood of bacteremia) and the small intestine (because of bacterial overgrowth). a clinical sepsis scoring system to predict bacteremia based on physical examination does not seem to be sufficiently accurate to guide antimicrobial decision making, and therefore the clinician should assume that calves are bacteremic when they exhibit inappetence, coinfection with bovine viral diarrhea virus and mycoplasma bovis in feedlot cattle with chronic pneumonia outbreak of salmonella enterica serotype newport in a beef cow-calf herd associated with exposure to bovine viral diarrhea virus supportive therapy of the toxic cow effect of lipopolysaccharide on diarrhea and gastrointestinal transit in mice: roles of nitric oxide and prostaglandin e effects of endotoxin on regulation of intestinal smooth muscle nitric oxide synthase and intestinal transit united states department of agriculture animal plant health inspection service (usda aphis) feedlot part iv: health and health management on u.s. feedlots with a capacity of , or more head salmonella in calves antimicrobial susceptibility of salmonella isolates recovered from calves with diarrhea in australia prevalence of antimicrobial resistance among salmonella on midwest and northeast usa dairy farms antibiotics as growth stimulants for dairy cattle: a review use of antibiotics to prevent calf diarrhea and septicemia antibiotics and calf diarrhea diarrhea and malabsorption in calves associated with therapeutic doses of antibiotics: absorptive and clinical changes adverse effect of oral antibacterial prophylaxis and therapy on incidence of neonatal calf diarrhea evaluation of an oral glucose-glycine-electrolyte formulation and amoxicillin for the treatment of diarrhea in calves a field trial comparing the effects of supplementation with aureomycin plus lasalocid or monensin on the health and production performance of dairy calves growth and health of holstein calves fed milk replacers supplemented with antibiotics or enteroguard targeting therapy to minimize antimicrobial use in preweaned calves: effects on health, growth, and treatment costs no effect of a homeopathic preparation on neonatal calf diarrhea in a randomized double-blind, placebo-controlled clinical trial a rational approach to treatment of calf diarrhea antimicrobial use in the treatment of calf diarrhea treatment of calf diarrhea: antimicrobial and ancillary treatments observations on the etiology of neonatal diarrhea (scours) in calves bacteriological culture of blood from critically ill neonatal calves model to predict septicemia in diarrheic calves the distribution of the colon-aerogenes group of bacteria in the alimentary tract of calves the bacteriology of the intestinal tract of young calves with special reference to early diarrhea distribution and virulence of escherichia coli in the small intestine of calves with and without diarrhea changes in small intestinal morphology and flora associated with decreased energy digestibility in calves with naturally occurring diarrhea pathogenesis and prevention of infectious diarrhea (scours) of newborn calves amoxycillin: distribution and clinical efficacy in calves a clinical evaluation of antimicrobial agents and temporary starvation in the treatment of acute undifferentiated diarrhea in newborn calves oral absorption and bioavailability of ampicillin derivatives in calves clinical efficacy of amoxicillin in calves with colibacillosis field evaluation of efficacy of marbofloxacin bolus in the treatment of naturally occurring diarrhea in the new born calf comparison of danofloxacin with baquiloprim/sulphadimidine for the treatment of experimentally induced escherichia coli diarrhea in calves efficacy of danofloxacin % injectable solution in the treatment of escherichia coli diarrhoea in young calves in europe field trial evaluating the influence of prophylactic and therapeutic antimicrobial administration on antimicrobial resistance of fecal escherichia coli in dairy calves the typing of e. coli by bacteriophage, its application to the study of e. coli populations of the intestinal tract of healthy calves and of calves suffering from white scours passage of antibiotics through the digestive tract of normal and scouring calves and their effect upon the bacterial flora discrepancy between antibiotic (amoxycillin) resistance in vitro and efficacy in calf diarrhea further observations on the effect of chemotherapy on the presence of drug-resistant bacterium coli in the intestinal tract of calves the sensitivity to chemotherapeutic agents of a further series of strains of bacterium coli from cases of white scours: the relationship between sensitivity tests and response to treatment neonatal diarrhea in calves escherichia coli and salmonella newport in calves: efficacy of prophylactic and therapeutic treatment dehydration, lethargy, or fever. in calves with diarrhea and no systemic signs of illness (normal appetite for milk, no fever), evidence suggests that the clinician continue to monitor the health of the calf and not administer antibiotics unless the calf's condition deteriorates. key: cord- - pr oae authors: riad, a.; yilmaz, g.; boccuzzi, m. title: molecular iodine date: - - journal: br dent j doi: . /s - - - sha: doc_id: cord_uid: pr oae nan sir, i write with my thoughts on three recent items published in the bdj. , , in relation to fit testing for ffp respirators, an additional consideration is that the occupational safety and health administration have advised that prescription glasses, or where required safety goggles, must be worn during the fit test. the author cited reasons for undergoing a fit test, one of which was facial change since the previous test. it would be interesting to note that major dental work such as new dentures would fall under this category. secondly, in relation to thermal screening the cdc in its guidelines for dental settings recommends that a patient should not be deferred treatment for the sole reason of being febrile ie a clinical correlation of the fever must be made. the same guidelines recommend that the definition of fever be updated to either a measured reading of ≥ . °f or subjective fever. if a patient is found to be febrile with a strongly associated diagnosis of dental origin such as the presence of intra-oral swelling and pulpal/ periapical dental pain with the absence of symptoms suggestive of covid- , dental care may be provided following routine protocol. finally, in relation to orthodontic treatment this author mentions the use of self-etch primers (sep) to avoid an agp, however the technique of applying sep involves gentle air drying according to some manufacturers, making it a potential agp. there is also a mention of utilising light cured resin modified gic, but this material does not require a dry field and in fact, the surface of the enamel should be moist during bonding to ensure success. the author suggests hand trimming of excess composite/flash with a scalpel. an alternative to this would be to utilise either: band removing pliers (posterior teeth), hand scalers/mitchell's trimmers (incisors) or adhesive removing pliers. minimal remnants of residual material on the enamel surface can be lost with time as a result of toothbrushing. v. sahni, new delhi, india https://doi.org/ . /s - - - workers. the mechanism of action of pvp-i relies primarily on the free iodine component, which is bound to a large polyvinylpyrrolidone molecule (pvp) acting as a carrier to deliver i to target cells. however, the viricidal activity of pvp-i is highly associated with its i content: the commonly used % pvp-i can only deliver - ppm of i in a compound of more than , ppm of total iodine atoms. the high percentage of bounded 'non-active' iodine contributes to all the undesirable toxicological and staining properties of pvp-i. a new generation of iodine-based antiseptics 'super iodine' was initiated recently to overcome the compositional side effects of pvp-i. therefore, iotech international (boca raton, fl) produced a patented aqueous solution of i that contains over times more i than pvp-i and comes in various forms ready for prophylactic use including mouthwash, nasal spray, and hand cleanser. moreover, the non-bioactive iodine content was reduced from , ppm in pvp-i to several hundred in the new formula thus accelerating its effect, increasing its shelf-life, and minimising its potential irritancy and mucosal staining. in comparison to several antiseptic mouthwashes, the new i formulas showed higher viricidal efficacy against coronaviruses and took as short as seconds to inactivate alpha coronaviruses ( e) completely. the same was observed in rhinovirus which was totally inactivated above the cytotoxicity level after exposure to the new i formula for seconds. to the best of our knowledge, there is an ongoing randomised control trial at st. joseph's hospital university (paterson, nj) to evaluate the efficacy of i mouthwashes and nasal sprays in protecting frontline healthcare workers by reducing their susceptibility of getting infected by sars-cov- . therefore, sir, we have read with great interest the correspondence of challacombe et al. on the antiseptic efficacy of povidone-iodine (pvp-i) against sars-cov- ; we aim to demonstrate the potential prophylactic capacity of the new generation of uncomplexed molecular iodine (i ) mouthwashes. pvp-i has been a gold standard antiseptic for decades with proven efficacy against the previously identified beta coronaviruses; it was one of the first candidates for the emergency trials attempting to establish an additional layer of protection for frontline healthcare comment letters to the editor send your letters to the editor, british dental journal, wimpole street, london, w g ys. email bdj@bda.org. priority will be given to letters less than words long. authors must sign the letter, which may be edited for reasons of space.  we suggest more controlled trials to be initiated using i products to benefit from their potential superiority over conventional pvp-i mouthwashes. a. riad, brno, czech republic; g. yilmaz, istanbul, turkey; m. boccuzzi, pisa, italy nhs dentistry in england in and . the number of antibiotics dispensed each month by community pharmacists in england relating to nhs dental prescription forms from january to may is given in figure . this shows antibiotic use in may was a clear outlier compared to the previous months being . % higher than in may (n = , and , respectively). interestingly, antibiotic use in april was slightly higher than the previous april but still within the normal range for the period of study. this is despite the significantly poorer access to dentistry (only around , patients were seen at designated urgent dental centres [udcs] across england) compared to may when the capacity of these centres increased and saw over , patients. a range of non-clinical factors are known to be associated with dentists' decision-making about antibiotics prescription for acute conditions. antibiotics may have been used: • as a 'quick fix' to avoid the life-time impact of an unnecessary extraction, in anticipation that agps might soon be permissible in general dental practices • because dentists felt pressured by some patients for antibiotics, irrespective of their efficacy or appropriateness for treating toothache • because of difficulties diagnosing a patient's condition remotely prompting a 'just in case' approach through concerns of life-threatening deterioration without treatment • as some udcs were requiring patients to have tried antibiotics before accepting referral for face-to-face care, highlighting system and process impact on antibiotic prescribing. finally, the nhs may have seen an influx in patients who might otherwise receive care privately, resulting in an increase in nhs dental prescriptions as, anecdotally, not all practices were open for telephone triage during april and may . examination of figures for the remainder of will reveal any enduring impact that covid interventions may have on dental antibiotic prescribing and in identifying optimisation of future dental antibiotic stewardship. v sir, pre-covid, dentists were responsible for about % of all antibiotic prescribing worldwide. at the onset of the pandemic most dental practices were restricted to giving advice, analgesia and antibiotics (aaa). reduced access to dental care and an inability for dentists to provide dental procedures increases dental antibiotic prescribing. a large increase in dental antibiotic use in england during april and may was widely anticipated and so we undertook a rapid analysis comparing antibiotic use across sir, the pre-visit triage, which practices are advised to do, will preclude any proven or probable covid- patients from attending a practice, leaving only the possible, undiagnosed cases as posing a risk of bringing this infection into a practice. our city council produces weekly updates of new cases, which gives a good indication of the level of infection in the population which our practice serves. when this figure is combined with the average number of patients that we have seen each week, since lockdown was eased, and the local population, this enables us to quantify the risk of us seeing an undiagnosed covid- patient in the practice. last week, this indicated that the average risk of seeing such a patient was one every , weeks, or one every . years. there are plenty of generalisations used in that calculation but it is certainly food for thought. ffp respirator face fit testing -what is it all about? thermal screening agps and orthodontics transcript for the osha training video entitled respirator fit testing the agp question: implications for orthodontics povidone iodine covid- : povidone-iodine intranasal prophylaxis in front-line healthcare personnel and inpatients (piippi). clinicaltrials.gov practical use of povidone-iodine antiseptic in the maintenance of oral health and in the prevention and treatment of common oropharyngeal infections stable compositions of uncomplexed iodine and methods of use references . fdi. antibiotic stewardship in dentistry -fdi policy statement: fdi world dental federation factors associated with prescribing of systemic antibacterial drugs to adult patients in urgent primary health care, especially dentistry personal communication re: dr re: request for information key: cord- -la vi j authors: brower, jennifer l. title: the threat and response to infectious diseases (revised) date: - - journal: microb ecol doi: . /s - - - sha: doc_id: cord_uid: la vi j the threat from microorganisms is complex, and the approaches for reducing the challenges the world is facing are also multifaceted, but a combination approach including several simple steps can make a difference and reduce morbidity and mortality and the economic cost of fighting infectious diseases. this paper discusses the continually evolving infectious disease landscape, contributing factors in the rise of the threat, reasons for optimism, and the policies, technologies, actions, and institutions that might be harnessed to further reduce the dangers introduced by pathogens. it builds upon and updates the work of other authors that have recognized the dangers of emerging and re-emerging pathogens and have explored and documented potential solutions. in just the past year, the united states has been bombarded with headlines on the dangers of infectious diseases: "hiv 'epidemic' triggered by needle-sharing hits scott county, indiana [ ] ;" "american with ebola now in critical condition [ ] ;" "seasonal flu vaccine even less effective than thought: cdc [ ] ;" "'superbug' outbreak at california hospital, more than exposed [ ] ;" "deadly cre bugs linked to hard to clean medical scopes [ ] ;" "painful virus [chikungunya] sweeps central america, gains a toehold in u.s. [ ] . " the ebola outbreak that began in and the measles outbreak initiated at disney world in particular brought the threat of "exotic" infectious diseases back to the american and global consciousness. this coupled with the fact that the most commonly circulating strains of the influenza a virus h n drifted [ ] from that used in the - influenza vaccines serve as reminders that the threat from microorganisms is continuously evolving and is persistent. the threat of emerging and re-emerging pathogens has been discussed in the scientific literature, the medical community, by policy makers, and the general public over the past years, but much of the discussion was among directly affected populations and their caregivers. general interest flourished after a series of events in the s and early s. in , a report by russian general kuntsevich followed by boris yelstin's decree in april of that year to end all offensive biological weapons programs revealed that the former soviet union had an extensive biowarfare program and that facilities and expertise still existed which would enable russia to unleash deadly pathogens on the world [ ] . in when shoko asahara, the spiritual leader of a japanese religious cult, was arraigned, the magnitude of the organization's attempts to deploy anthrax in was exposed [ ] . in october , the united states was transfixed by the first bioterrorism attacks on its own soil: envelopes containing bacillus anthracis spores were sent through the mail to targets ranging from media companies to government officials [ ] . five people died and thousands were treated with prophylactic antibiotics. the attacks and other attempted and planned attacks, along with widely publicized outbreaks such as west nile virus in [ ] and severe acute respiratory syndrome (sars) in [ ] , brought the topic of infectious disease to the forefront. in addition, more incessant threats such as influenza and lower respiratory infections continue to kill and cause economic harm through lost productivity and hospitalizations. furthermore, zoonotic diseases such as salmonella and listeria, which represent more than two-thirds of emerging and re-emerging diseases [ ] , raise the visibility of the economic and human and animal health issues caused by pathogens. in april , the sabra dipping company voluntarily recalled about , cases of hummus potentially contaminated with listeria monocytogenes. at the same time, blue bell recalled nearly products also similarly contaminated. while there were no known casualties as a result of the sabra contamination, authorities in kansas and texas reported that three deaths in each state might be attributed to the blue bell incident [ ] . the threat from microorganisms is complex, and the approaches for lowering the challenges the world is facing are also multifaceted, but several simple steps can make a difference. this paper will discuss the emerging infectious disease landscape, contributing factors in rise of the threat, reasons for optimism, and the actions, policies, technology, and institutions that might be harnessed to further reduce the dangers introduced by pathogens. it builds upon the work of other authors who have recognized the dangers of emerging and re-emerging pathogens and have explored and documented potential solutions [ ] [ ] [ ] . microorganisms pose health and economic threats and may pose a strategic threat if a large percentage of the population is overcome or if the potential transmission of infectious diseases across borders causes an increase in tension among state allies or enemies. one organism alone, clostridium difficile, is estimated to cost the united states between $ and $ billion per year [ ] , with its primary impact on american children [ ] . initially identified in the early s as a commensal organism in the digestive tract, c. difficile infection (cdi) has only been recognized as a significant threat to pediatric health over the last decade [ ] . the threat to both children and adults is global. infections since have become more common, more acute, less treatable by standard therapy, and more likely to reoccur [ ] . initially, the c. difficile infections were associated with the use of the antibiotic clindamycin, but fluoroquinolones and cephalosporins are currently the more likely cause of disturbed gut microbiota, which increasingly lead to colonization with ribotype , a severe variant of c. difficile [ ] . according to the centers for disease control and prevention (cdc), emerging infectious diseases are those "whose incidence in humans has increased in the past two decades or threatens to increase in the near future [ ] ." while there may be debate about the specifics, for the purposes of this article, re-emerging and emerging diseases are distinguished as follows: re-emerging diseases are those that were known to impact humans or animals in the past and were thought to be brought under control with zero or few infections in the past several decades. these include infections resulting from changes or evolution of existing organisms and changes in the geographic distribution of an organism or populations affected by the organisms. previously unrecognized (in the past several decades) infections are considered emerging. according to this definition, c. difficile would be considered an emerging pathogen as its dangers were not recognized when it was first identified. other outbreaks and trends of concern include the following: tuberculosis (tb), while no longer among the leading causes of death in , was still among the leading causes, killing over , people in [ ] . in the united states, while overall tb incidence is decreasing, it is still a large problem for foreign-born residents and for the homeless population at a cost of nearly $ million per year [ ] . lyme disease caused by the spirochete borrelia burgdorferi was recently recognized as an epidemic. the disease is difficult to diagnose, causes long-term disability if untreated, and may impact as many as , people in the united states [ ] . more than % of lyme disease patients continued to exhibit symptoms after six months, and for % of infected people, symptoms continued for more than three years [ ] . the spread of diseases such as multidrug resistance acinetobacter in at-risk populations is also of increasing concern. "within the last years, members of the bacterial genus acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. the driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use [ ] ." acinetobacter resistance to drugs such as imipenem and ampicillin/sulbactam increased % from to [ ] . leptospirosis, one of the most widely distributed zoonotic diseases worldwide, is an emerging public health concern particularly in large urban centers of developing countries [ ] . it is also important in the united states in humans, pets, and wildlife. experts believe incidence in humans is underreported, but the cdc estimates that - leptospirosis cases occur annually with approximately half of those in hawaii [ ] . in , triathletes in illinois were exposed to leptospirosis of which became symptomatic [ ] , representing the largest human outbreak in the united states. recently, cases in pets have caused concern in california [ ], michigan [ ], and florida [ ] . more than a quarter of the tested deer population in michigan was infected with the disease [ ] . west nile virus (wnv) is another zoonotic disease of concern, and the us population and health practitioners have become more aware of this disease over the past decade. birds carry the virus, which is then transmitted by mosquitoes to humans, horses, and other mammals. disease symptoms range from fever to neurological complications, such as encephalitis or meningitis. mortality is observed mostly in older and immunocompromised individuals. in , wnv was introduced to the united states, and its range soon extended across north america [ ] . not only is the number of wnv outbreaks increasing but also novel strains are emerging, which display higher virulence. wnv has also developed sophisticated avoidance mechanisms to avoid its elimination [ ] . noroviruses are the leading cause of foodborne disease outbreaks worldwide and may soon eclipse rotaviruses as the most common cause of severe childhood gastroenteritis, because rotavirus vaccine use is becoming more prevalent [ ] . norovirus rapidly undergoes genetic mutations and recombinations so that new epidemic strains are constantly evolving. although norovirus infection is generally not fatal, infections in children, the elderly, and the immunocompromised can cause morbidity and even death. research into a vaccine or treatment has been impeded by the lack of a cell culture or small animal model. however, vaccines based on norovirus capsid protein virus-like particles show potential and may become broadly available through transgenic expression in plants [ ] . vibrio vulnificus, a common gram-negative bacterium in warm coastal waters globally, is an emerging pathogen [ , ] . up to million vulnerable americans are at risk when consuming raw or improperly prepared seafood tainted with v. vulnificus which can cause primary septicemia [ ] . additionally, all individuals are at risk of serious wound infection that may lead to secondary septicemia [ , ] . even with antibiotic treatment, half of patients may die from primary septicemia and a quarter from secondary [ , ] . other environmental organisms of concern include the waterborne pathogen that causes legionnaires' disease, legionella bacterium; naegleria fowleri, which causes amebic meningoencephalitis; other mycobacterium (hospital environment) such as mycobacterium abscessus and m.massiliense in lung disease; the mosquitoborne chikungunya virus and the tickborne bourbon virus. in addition to causing acute illness, research has uncovered links between infectious diseases and cancer. in one study by wu et al. [ ] , researchers found measurable differences in fecal microbiota between healthy individuals and those with colorectal cancer as determined by pyrosequencing of the s rrna gene v region. as early as , researchers found that hepatitis b surface antigen (hbsag) carriers had a greater incidence of primary hepatocellular carcinoma (phc) than among non-carriers [ ] . the list of emerging and re-emerging pathogens could fill up a tome. these organisms vary in virulence and distribution, but all of them share common characteristics in that the incidence or virulence or both are increasing and humans must find methods of preventing, detecting, and treating them. to combat infectious disease, it is important to understand the factors that are working to increase the occurrence and severity of infections. human behavior has a large impact on the creation of environments where microorganism can evolve and mutate. these changes can sometimes make organisms more infectious and/ or virulent. examples include the following: antibiotics in the environment through overuse and misuse; changes in sexual norms; patterns of drug use and incarceration; global climate change; human incursion into new environments; and changing patterns of human interactions with wild and domesticated animals; expanding travel patterns; vaccination avoidance; and population concentrations in large cities. recent cases are used to illustrate how differences in human behavior have modified the threat from bacteria and viruses. the problem of antibiotic resistance is threefold: there has been a rise in the number or identification of resistant bacterial strains; the pipeline for the development of new medicines to treat infection dried up significantly over the past years; and the most significant problem is the lack of stewardship of existing antimicrobials. these issues have led to a reduction in the efficacy and number of responses available to physicians and their patients. the biological processes that lead to resistance are extremely complicated and not fully understood, resulting in sometimes limited progress in the control and treatment of resistant microorganisms and the diseases they cause [ ] despite recognition of the problem nearly a century ago. davies and davies [ ] compiled a list of "suberbugs," which have increased pathogenicity and are more impervious to treatment. their list includes the following: multidrug-resistant (mdr) m. tuberculosis; nosocomial (hospital-linked) infections with acinetobacter baumannii, burkholderia cepacia, campylobacter jejuni, citrobacter freundii, clostridium difficile, enterobacter spp., enterococcus faecium, enterococcus faecalis, escherichia coli, haemophilus influenzae, klebsiella pneumoniae, proteus mirabilis, pseudomonas aeruginosa, salmonella spp., serratia spp., staphylococcus aureus, staphylococcus epidermidis, stenotrophomonas maltophilia, and streptococcus pneumoniae. their list does not include the new delhi metallo-beta-lactamase- (ndm- ) resistant strains discussed below. as the authors point out, in addition to the direct human toll, treatment is often more costly [ ] when resistant organisms are involved. in fact, the issue has become so acute that new terms have developed over the past decades: microorganisms that are pan-drug resistant (pdr) or extremely drug resistant (xdr). one of the most widely dispersed antibiotic resistant organisms is m. tuberculosis. worldwide, this organism is often resistant to multiple drugs, and in , completely drug-resistant forms of tuberculosis were reported in citizens of four countries: afghanistan, azerbaijan, iraq, and iran [ ] . in many organisms, such as enteric bacteria which are acquired both in community and hospital settings, resistance (often to β-lactam antibiotics in this case) spreads through horizontal gene transfer on plasmids; however, there have been no documented cases of this in tuberculosis, where all resistance occurs by spontaneous mutation [ ] . multidrug resistant pseudomnas aeruginosa is also of concern as it is deadly and widespread [ , ] . m. tuberculosis is one example of the multitudes of resistant organisms. other widespread and dangerous bugs include staphylococcus aureus ( . per inpatient prevalence rate in [ ] ) and c. difficile (in us hospitals in , c. difficile was the most commonly reported pathogen causing . % of health careassociated infections and staphylococcus aureus caused the second highest percentage, . %. klebsiella pneumoniae and klebsiella oxytoca . % and escherichia coli . % followed closely behind [ ] ). at a single hospital in and , resistant acinetobacter baumannii infected . % of patients who were not previously infected [ ] . infections with resistant organisms are harder to control; standard treatments are less effective; illness and hospital stays are longer; and mortality is higher. gram-positive organisms resistant to antibiotics were the first concern, but resistance in gramnegative organisms emerged: gram-negative bacteria resistance increases faster than in gram-positive bacteria [ ] , and there are fewer antibiotics in the pipeline that work against gram-negative bacteria [ ] . cosgrove et al. [ ] performed a meta-analysis of studies published between and on the impact of methicillin resistance on mortality. these studies included nearly patients, a third of whom were infected with methicillin resistant staphylococcus aureus (mrsa). mortality was significantly lower in the group infected with susceptible bacteria. in another study, cosgrove's group found that mrsa bacteremia also increased median length of hospital stay by almost % and not surprisingly (given the longer stay), increased hospital charges from an average of $ , to $ , [ ] . a prospective study found similar results in hemodialysis patients at the duke university hospital [ ] as did a study on orthopedic patients [ ] . vancomycin-resistant enterococci (vre) [ ] and enterobacter species resistant to third generation cephalosporins [ ] showed a similar trend; however, penicillin-and cephalosporin-resistant streptococcus pneumonia results were dissimilar, and the authors surmised that this might be due to the specific use of vancomycin [ ] . chemicals in daily use may also change microorganism susceptibility to antimicrobial agents. for instance, it has been regularly demonstrated in the laboratory that resistance to triclosan, an antimicrobial agent used in many household products including hand sanitizer, and crossresistance to antimicrobials increases with use of triclosan containing products; however these results have not yet been observed in the community. based on the available evidence, the risk of potential antimicrobial resistance outweighs the benefit of widespread triclosan use in antimicrobial soaps [ ] . resistance is not something that can be conquered: bacteria with their relatively short lifespans can mutate quickly; however, with knowledge of the , resistance genes of types [ ] , it may be possible to stay one step ahead of resistance and find new ways to treat bacterial infections. other changes that have impacted infectious disease distribution and prevalence are changes in sexual norms, drug use, and incarceration. needle sharing itself can spread infections, and the use of drugs can affect sexual and risk taking behavior which can put people in jeopardy [ ] . while homophobia is decreasing in the united states and worldwide, homophobia has been one of the major social determinants of infection particularly with hiv/ aids and other sexually transmitted diseases. for example, men sleeping with men accounted for % of new hiv infections in [ ] . historical legal restrictions, which are now being relaxed in this decade, had ostracized gay people, limiting their self-identification and therefore efforts to target gay communities for education and prevention as well as diagnosis and treatment efforts. injecting drug users account for % of new hiv infections often due to inadequate access to sterile needles and syringes and addiction treatment programs [ ] . as noted below, drug use also changes behavior which also leads to increased transmission. drug use and incarceration patterns go largely hand-in-hand. in part because of the united states hard line on drug use, united states incarceration rates are the highest in the world with minorities accounting for a disproportionate percent of the prison population. incarceration rates disrupt community and sexual relationships and compound poverty issues, amplifying the exposure of communities and individuals to hiv infection and other infections [ ] . in a second example, methamphetamine use has been shown to affect a person's judgment and may lead to unsafe behaviors such as reduced condom use, multiple partners, and increased drug injection. methamphetamines also increase physical susceptibility because their use dries mucosa intensifying chafing and abrasions, which, in turn, allow microorganisms to enter the body during sexual and other activity [ , ] . aquaculture contributes to the pollution of rivers, bays, and even our oceans with antibiotics and antibiotic resistance genes (args). from china to the united states, antibiotics and args have been found in surface water of all types. for example, in the coastal water of the bohai bay, china, fluoroquinolones, macrolides, sulfonamides, tetracyclines and chloramphenicoles, and polypeptides were found at concentrations up to several micrograms per liter with higher concentrations where human activity was concentrated [ ] . in a review, comparing aquaculture and land animal production with the respect to type, mechanism, and quantity of antibiotic resistance, done, venkatesan, and halden [ ] found that aquaculture was similar to terrestrial agriculture in terms of the resistance mechanisms, that antibiotics used in aquaculture are important in human health, and that pathogens isolated from the farmed fish were resistant to multiple antibiotics. due to improper use and disposal of antibiotics, the presence of antibiotic-resistant organisms and genes in natural waterbodies, wastewater, and treated municipal water has been widely demonstrated and reviewed [ ] [ ] [ ] [ ] . without additional treatment, this water is commonly used on crops; humans and animals then consume the products, and serious outbreaks have occurred that are difficult to treat because the microorganisms do not respond to commonly used antibiotics [ ] [ ] [ ] [ ] . pruden et al. [ ] found concerning levels of args in colorado (united states) dairy lagoon water, irrigation ditch water, river sediments, treated drinking water, and recycled wastewater. ramsden et al. [ ] similarly found antibacterial resistance in municipal wastewater treatment plants. zuccato et al. [ ] discovered that the concentrations of atenolol, bezafibrate, clofibric acid, cyclophosphamide, diazepam, erythromycin, furosemide, lincomycin, oleandomycin, ranitidine, salbutamol, spiramycin, and tylosin were in the nanogram per liter range in river or drinking water or river sediments in several sites in italy. munir et al. [ ] examined the presence of antibiotic-resistant genes and bacteria in several types of wastewater effluents in michigan and found that advanced water treatment systems such as membrane bioreactors were significantly more effective than conventional wastewater treatment at removing the tetracycline-resistant gene teto and sulfonamide-resistant gene (sul-i) as well as tetracycline and sulfonamide-resistant bacteria. anaerobic digestion and lime stabilization treatment of wastewater was more effective than the conventional dewatering and gravity thickening methods for removing antibiotic-resistant genes and bacteria [ ] . burch et al. [ ] were able to significantly reduce the concentrations of the args tet(a), tet(w), and erm(b) using conventional wastewater treatment (aerobic); however, removal of inti required batch treatment, while the others required relatively long-term semi-continuous treatment. tet(x) increased in concentration. according to the world bank, nearly million travelers visited the united states and approximately one billion people traveled globally in [ ] . the incidence of tuberculosis in the united states is largely due to foreign visitors and citizens and residents born in other countries [ ] . another, travel related resistance threat emerged in the united states in when three patients were reported to have the gene for new delhi metallo-beta-lactamase (ndm- ), an enzyme that destroys beta-lactam antibiotics including commonly used penicillins, cephalosporins, and carbapenems. the first case was reported in india in [ ] , and to date, india and pakistan have reported the most instances of ndm- , but the gene is spreading globally, and cases have now been detected in many countries, including great britain, canada, sweden, australia, japan, and the united states. antibiotics are widely used in india and some researchers [ ] have demonstrated that overuse of carbapenems led to the development of ndm- [ ] . research also points to medical tourism as a cause [ ] [ ] [ ] [ ] . ndm- is a newly identified problem, only recognized since about december in the medical literature, but it is only one example of diseases transmitted through medical tourism which is defined as travel to a country to get medical care that is not available or is more expensive in one's own country. precise data on the economic value and the number of patients seeking medical procedures are not easily available. in , smith et al. [ ] estimated that approximately four million patients crossed borders seeking treatment. in , guidelines to unify definitions of medical tourism and methodologies for reporting its extent were published and accuracy of the types and amounts of medical tourism may improve in the near future [ ] . a greater potential threat is related to the increasing travel of immunocompromised patients. lortholary et al. [ ] illuminated the fact that as more and more people are living with hiv, having organ transplants, using immunodilators, or suffering from diabetes, more individuals are infected when traveling. the authors suggested preparations and responses to prevent severe illnesses when traveling. infections spread within the united states from travel as well. for example, during the period from through , cryptococcus gattii infections were reported to the cdc. c. gattii, an environmental fungus typically prevalent in tropical and sub-tropical regions, can cause an uncommon infection of the lungs and/or the central nervous system in those who inhale the fungus. more than % of the cryptococcosis cases occurred in people who had traveled to the pacific northwest. the infection was fatal for % of the patients [ ] . many factors have reduced the number of new antibiotics approved in the united states each year as well as reduced domestic production including demanding food and drug administration (fda) regulations, the cost and time to market of development, the consolidation in the pharmaceutical industry, and the lack of financial impetus to produce and distribute antibiotics, which are generally used on a one-off basis versus drugs used to treat chronic conditions such as statins, viagra, and allergy medications. in a may speech, janet woodcock, the director of the center for drug evaluation and research (cder), acknowledged that new antibiotics were not sufficient to address growing antibiotic resistance and that fda's approach to approval was a significant factor [ ] . the fda introduced new regulations for clinical trials at the beginning of the twenty-first century, which led to a cooling of antimicrobial development in the pharmaceutical industry [ ] . first, the newly required approach doubled the cost of phase iii clinical trials, already a substantial barrier for development. in phase iii, it is expected that testing will include pairs of relatively large (usually > total subjects per study) groups of people conducted for the selected pathogen at the relevant body location(s). this has become challenging as new antibiotics focus on particular pathogens including resistant pathogens, making it difficult to enroll large numbers of patients [ ] . in part because of the cost of the new regulations, eli lilly, bristol-myer squib, glaxo smithkline, proctor and gamble, roche, and wyeth left the development business [ , ] . in addition, while the amount of antibiotics prescribed has continued to grow, the market value has not changed and was estimated at $ billion in [ ] as compared to a $ . billion market in for statins alone [ ] . companies are getting out of the market because the regulatory burden is high, antimicrobials are typically used for short periods of time, public pressure is building to lower use, and the medicines are often subject to price controls outside of the united states [ , ] . while development has slowed, in the past years, new antibiotics have been brought to market. two approved more recently, fidaxomicin and bedaquiline, have new modes of action. fidaxomicin was shown to effectively treat c. difficile [ ] . because the financial incentives are few, much antibiotic production has been outsourced from the united states to india, china, and other countries where labor, raw material, and energy costs are lower [ ] . in fact, it has been more than years since the active ingredient for penicillin was last manufactured in the united states. this presents a significant strategic problem for the united states in the case of an outbreak, particularly during times of conflict or worldwide scarcity. global climate change is increasingly accepted as causing extreme, unusual weather patterns [ ] . changing weather patterns can impact the presence of infectious agents in many ways. for instance, in may and june , an initially unidentified disease killed ten people in the four corners region of arizona and new mexico. at the outset, % of the patients died of the infection, and after the medical staff developed enhanced protocols, the death rate was only reduced to %. scientists isolated a hantavirus [ ] , and later, researchers determined that an unusually wet spring led to increased rodent carrier density which in turn impacted human infection rates; however, these factors alone are not enough to explain persistent hantavirus infection in the southwestern united states [ ] . ecosystem changes and human interactions with the environment may increase the transmission of infectious disease [ ] . for instance, three studies found robust correlations between the threat to humans from west nile virus and low bird diversity in the united states [ ] [ ] [ ] . the spread of emerging infectious diseases among animals has significant human health and economic costs. zoonotic diseases kill more than two million people per year and transmission occurs from both wild and domesticated animals [ ] . halsby et al. [ ] reviewed the english literature with respect to infectious diseases caused by pet store animals and found discussions of infections related to pet shops. the most commonly observed diseases were salmonellosis and psittacosis: other diseases such as tularemia were also identified. the human animal interaction has impacted civilization throughout history. according to daszak et al. [ ] , "parallels between human and wildlife emerging infectious diseases (eids) extend to early human colonization of the globe and the dissemination of exotic pathogens. in the same way that spanish conquistadors introduced smallpox and measles to the americas, the movement of domestic and other animals during colonization introduced their own suite of pathogens. the african rinderpest panzootic of the late s and s is a paradigm for the introduction, spread, and impact of virulent exotic pathogens on wildlife populations. this highly pathogenic morbillivirus disease, enzootic to asia, was introduced into africa in . the panzootic front traveled km in years, reaching the cape of good hope by , extirpating more than % of kenya's buffalo population and causing secondary effects on predator populations and local extinctions of the tsetse fly." more recently, bovine tuberculosis, while responsible for only cases of human tuberculosis in the uk, prompted the slaughter of tens of thousands of cattle in the first decade of the twenty-first century [ ] . in , throughout the united states, domestic poultry and wild birds have been suffering from a highly pathogenic strain of avian influenza (hpai) h [ ] . through june , , more than million birds were put to death. the cost of the government response is tagged at $ million primarily to fund the work of staffers and contractors [ ] . on the commercial side, analysts used economic models and found that for a million dollars in direct losses there are $ . million in overall economic losses. in mid-may direct losses in poultry production were estimated at $ million leading to overall losses of more than $ million [ ] . transmission to humans in the united states has not been detected, although related viruses have caused serious illness and death around the world [ ] . typically, people have focused on wildlife diseases that affect human health and agriculture. recently, researchers, policy makers, and others have begun to pay attention to wildlife infectious diseases, because a number of endangered species including birds, amphibians, and invertebrates [ ] are impacted [ ] . human's changing relationship with the environment "deforestation and ensuing changes in land use, human settlement, commercial development, road construction, water control systems (dams, canals, irrigation systems, reservoirs), and climate, singly, and in combination have been accompanied by global increases in morbidity and mortality from emergent parasitic disease [ ] ." lyme disease is a prime example of how human destruction of the environment (forests) can lead directly to increased risk for disease exposure. allan, keesing, and ostfeld [ ] found that as forest patch size decreased ioxdes nymphal infection prevalence and nymphal density with increased, resulting in a noticeable rise in the density of infected nymphs and concluded that habitat fragmentation affects human health. as humans change or destroy the local environment, they tend to interact with or disturb wildlife populations, creating further instances for exposure to infectious diseases. goldberg et al. [ ] found increased rates of interspecific gastrointestinal bacterial exchange between people and nonhuman primates when humans visited chimpanzee and ape habitats. chimpanzees carried antibiotic-resistant bacteria although there had never been treatment with antibiotics. many of the factors discussed above coexist to increase the threat from microorganisms. the antivaccine lobby, especially in the united states, has led to a significant decline in the vaccination rates of infants and children, particularly among specific demographics despite the overwhelming success of vaccines in the fight against vaccine-preventable diseases. for instance, in (pre-vaccine), , cases of measles were reported with mortalities. in , there were cases of measles but no deaths. similarly in , cases of diphtheria were reported resulting in deaths. in , there were no reported cases of diphtheria [ ] . up to two % of parents in the united states refuse vaccination completely for their children with up to % more who are cautious or elect to delay vaccination [ ] . the reduction in vaccination coverage is typically attributed to the lack of perceived threat due to the success of vaccination, combined with false medical research and media reporting [ ] . the reduction in vaccination rates has resulted in the highest number of cases of measles in the united states since it was declared eliminated in [ ] . while native measles has been eliminated in canada, several measles cases are imported each year by international travelers and due to inadequate vaccination, these cases often lead to secondary spread. in the first five months of , cases in five provinces from known importations occurred through infected travelers arrived from the philippines, india, the united states, thailand, pakistan, italy, and the netherlands [ ] . travel patterns in canada are exemplary of much of the world. in years, international travel (excluding travel to the united states) more than doubled from . million to million trips [ , ] . if the antivaccine trend does not abate, and in conjunction with widespread global travel, the threat from diseases once thought under control may pose a significant threat to the population. influenza outbreaks kill and hospitalize more than , americans each year. the predominant strategy in the united states is to encourage all eligible populations to get vaccinated; however, for the - flu season, more than half of influenza a (h n ) viruses had drifted from the h n vaccine virus. this mismatch leads to decreased vaccine effectiveness [ ] . it may also discourage individuals from getting the flu vaccine in the future. population growth, urbanization, and travel along with deterioration in public health infrastructure have contributed to the resurgence of infectious diseases. dengue fever provides a prime example of the intersection of the triad. while dengue viruses were dispersed throughout the tropics in the first half of the twentieth century, epidemics were infrequent because urban populations were comparatively small, and the viruses and mosquito vectors were transported on ships versus the air transport of today. the travel of both goods and people during world war ii set the stage for the spread of dengue fever. in the post war era with unparalleled urban growth and travel, serious epidemics occurred more frequently. scarcely years later, dengue hemorrhagic fever became a principal cause of hospitalization and mortality in the pediatric population throughout southeast asia [ ] . with respect to the intentional use of microorganisms as a weapon, the united states and the world have an outmoded threat-view focused on soviet era biological weapons, but travel, medicine abuse, and the lack of a us capability to approve and manufacture new antimicrobial and antiviral agents have changed many dimensions of the threat as discussed above. with the dissolution of the soviet union, the fact that the us biological weapons program ended decades ago, and the intellectual, medical, manufacturing, and weaponization knowledge needed to start a bioweapons program, the threat from naturally occurring organisms is far greater than the threat of bioterrorism or biowarfare in . the threats of infectious diseases dwarf that of terrorism and other asymmetric threats to human life. approximately three million people died in due to lower respiratory infections [ ] , and infectious diseases are the major cause of death of children under five. "the most important pathogens are rotavirus for diarrhea and pneumococcus for lower respiratory infections [ ] ." however, there is hope that new antibiotics will be identified and developed. recent research such as that performed by ling et al. [ ] found new ways to identify antibiotics [ ] in the environment and companies are beginning to invest again. under the direction of dr. kim lewis, ling and colleagues identified teixobactin. to do this, the team used the novel screening method to examine , strains. in both in vitro and in vivo tests, teixobactin was demonstrated to be operative, without major side effects, against the organisms that cause common illnesses such as pneumonia, tuberculosis, and staph infection, diseases which sicken more one million americans yearly. while teixobactin was effective against diseases of public health concern, it was ineffective against gram-negative bacteria. teixobactin binds on several targets triggering cell wall break down. the ability to bind on multiple sites lessens the chance of early teixobactin resistance. in addition to developing the new antibiotic, the researchers commercialized the screening technology, which can examine organisms that cannot typically be cultured in the lab [ ] . researchers are also developing techniques to enhance the impact of probiotics in fighting infections and other diseases such as cancer [ ] . while recent events bring the threat of microorganisms to the forefront of the public mind, the work of doctors, researchers, public health professionals, and other experts have continued unabated for decades. these attempts include scientific, technological, policy, and commercial attempts to reduce or eliminate the deaths and other losses caused by pathogens. to a large extent, these efforts have succeeded. in , the average lifespan in the united states was . for men and . for women, and one of the predominant causes of death was infectious disease. by the end of the century, lifespan had increased to . for men and . for women [ ] . in , infectious diseases accounted for more than half of all deaths: in , this percentage was reduced tenfold [ ] . the increases in life expectancy have been distributed across the world, although some areas have benefitted more than others from breakthroughs in sanitation, nutrition, and medical advances. one of the primary contributors to the reduction in the death rate was the reduction of infant deaths due to infectious diseases. prior to the mid- s, infectious disease played the predominant role in infant mortality with half of the (out of ) infant deaths due to pathogens [ , ] . by , the united states infant mortality rate had decreased to . per live births [ ] . also in the united states, in the midnineteenth century, foodborne and waterborne diseases such as typhoid, cholera, and dysentery resulted in deaths per , . these diseases were eliminated in the united states by the early s [ ] . one noteworthy exception to the steady progress in increased life expectancy is due to an infectious disease: hiv/aids decreased life expectancy dramatically in parts of africa over the past years [ ] . the leading causes of death and illness have shifted from infectious and parasitic diseases to noncommunicable diseases and chronic conditions. with the introduction of widespread antibiotics [ , ] in the s and antivirals in the late s [ ] , a new era of public health was ushered in, and the death rate due to infectious diseases accounted for less than % of mortality worldwide [ ] ; however, the optimism was short lived. even before there was prevalent proof that bacteria could quickly evolve to thwart antibiotics, evidence indicates that bacteria exhibit resistance in nature even without human pressure [ ] ; however, mechanisms of resistance impacting disease treatment were first noticed in the late s with regards to the use of sulfonamides [ ] . due to overuse, underuse, and incorrect disposal, antibiotic resistance has become a worldwide threat to public health [ ] . in addition, the cost and difficulty in developing new antibiotics has stunted the pipeline. finally, environmental [ ] , behavioral, and other physical and cultural changes have fostered situations where new pathogens can emerge and old enemies reemerge or spread to new locations. global climate change is altering where species thrive, and more localized or temporary changes modify infectious disease risk to humans as well. while ndm- strains are difficult to treat, many of them remain sensitive to an older, seldom used antibiotic, colistin, or aztreonam [ , ] years, clinical trial number n c t ; a n d s a f e t y, to l e r a b i l i t y, a n d immunogenicity study of a clostridium difficile toxoid vaccine in healthy adult volunteers, clinical trial number nct (a total of studies were found on www. clinicaltrials.gov when searching for 'c. difficile vaccine [ ] .' improvements are needed in dosage and timing to achieve high level immunity, however the investment required is large with estimates ranging from $ , , to $ , , [ ] to take a vaccine or antibody, respectively, through clinical trials. until a vaccine is developed, antibiotics will be used to treat infections. fidaxomicin, the first new antibiotic approved by the fda to treat cdi was approved in may . it was shown to be as effective as oral vancomycin, previously the only fdaapproved therapy for mild-to-moderately severe cdi. vancomycin is expensive and resistance in enterococci is a concern. oral metronidazole has been used by the medical community off label (it was approved for the treatment of certain anaerobic bacteria and parasites); however, relapse was observed in a quarter of patients within a month following treatment. fidaxomicin, in addition to being as effective as standard treatment, is a narrow spectrum antibiotic, allowing patients to maintain healthy native gut microbiota [ , ] . on a larger scale, according to the world health organization (who), hiv mortality was reduced from . million in to . million in , and diarrhea fell from one of the top five causes of death to number seven, with a similar number of deaths to hiv/aid in [ ] . tuberculosis distribution has declined since the turn of the century, in part because of the reach of the who's directly observed therapy short-course strategy and the implementation of the stop tb partnership plan [ ] . malaria cases and mortality has been meaningfully reduced by over cases and four million people respectively over the years between and through the use of artemisinin-based drugs, distribution of insecticide-treated bed nets, and indoor residual spraying of insecticide [ ] . this demonstrates that research, infrastructure, and other health-based investments have improved prevention and response to infectious diseases. all of this comes at a cost: between and governments including the united states, the uk, australia, canada, france, and germany and large non-profits and international institutions such as the gates foundation and the global fund contributed more than $ billion to the fight against hiv/ aids and nearly $ billion for international maternal and child health, which is in large part funding for vaccination [ ] . in addition, president obama has recognized that infectious diseases pose a national security threat. on september , , in his weekly address [ ] , the president stated, "so this is an epidemic that is not just a threat to regional security-it's a potential threat to global security if these countries break down, if their economies break down, if people panic. that has profound effects on all of us, even if we are not directly contracting the disease. and that's why, two months ago, i directed my team to make this a national security priority." because the challenges of new and re-emerging infections are complicated, a combination of science and technological advances, policy initiatives, and cooperative institutions are required. to make a significant difference, the united states and other countries must invest in technology and have systems capable of making these advancements available to those who need them, build technology development, and public health infrastructure; put in place policies and institutions that encourage these investments both in the public and private sectors. the success of programs such as the malaria initiative that combine these approaches is self-evident, but more needs to be done. an illustrative, but not complete, discussion of recent and additional proposals/initiatives is below. the united states, other countries, states, and international institutions have taken many steps to combat the threat. below are many of the important efforts and characteristics needed for resilience to the microbial threat. most importantly, it is critical to have a well-defined leader who is responsible for directing and monitoring progress as well as communicating risks. in president obama's september executive order [ ] , he directed the "national security council staff, in collaboration with the office of science and technology policy, the domestic policy council, and the office of management and budget to coordinate the development and implementation of federal government policies to combat antibiotic-resistant bacteria [ ] ." the president also created both a task force and an advisory council; however, he did not put a single individual in charge. identifying and developing a central, qualified, trusted person in charge of coordinating the investments in research, infrastructure and outreach; policies to incentivize behaviors to improve medicine development, infection control in medical and community settings; and communicate risks and responses in a directed and trusted manner at the federal government level, will enhance accountability and the likelihood of success. during times of low or chronic threat (e.g., flu season), the named person can develop a trusted relationship with the public, the medical and public health communities, the pharmaceutical industry, the defense department, international peers, and others involved in infectious disease response and defense. this is particularly difficult in diverse countries with divided political parties. a history of purposeful and innocent ethical lapses and scientific mistakes have contributed to a lack of trust such as the inaccurate flu vaccine in the - season and the confusing messages from the texas hospital and the cdc on ebola in . when a man traveled from africa and came down with a high fever and other symptoms, he was sent home by the hospital with antibiotics for two days [ ]: ebola was not well diagnosed in texas. one of the last trusted public health officials was the surgeon general under ronald reagan, dr. c. edward koop. by the time he stepped down in , he had become a household name, a rare distinction for a public health administrator. "dr. koop issued emphatic warnings about the dangers of smoking, and he almost single-handedly pushed the government into taking a more aggressive stand against aids [ ] ." dr. anthony fauci, director of the united states national institutes for allergy and infectious disease, has been a source of trusted and accurate infectious disease related information recently with regards to the ebola outbreak of . fauci is a natural leader for the us infectious disease/public health message, "he is someone who is really trusted by all the different organizations and people surrounding the aids challenge, ranging from the scientific community, the academic community and the activist community," according to louis sullivan, m.d., secretary of health and human services during the first bush administration and president emeritus of morehouse school of medicine in atlanta. "i don't know of anyone as broadly accepted by all those disparate groups [ ] ." the head of the cdc can also be a valuable spokesperson, but the cdc may have lost some of the public's trust during the ebola crisis [ ] . to centralize response, president obama appointed rob klain as the ebola coordinator. he was neither a doctor nor a scientist, and he left the job after six months, while ebola was still spreading in africa. while additional capability was developed at medical centers in the united states under klain's tenure, there were few noticeable signs of progress; he was not open to the media [ ] ; and likely as a result, was not embraced by the public. if the president chose a well-respected individual with healthcare and pharmaceutical industry expertise to serve in the white house to coordinate policies, funding and messages from nih, the cdc, the department of defense, the state department, state public health agencies, and other national and international institutions involved in the chain of prevention, detection, and treatment of infectious disease, it would be optimal. critical manufacturing capabilities have moved overseas, particularly to india and china. the us government could provide tax and other incentives and clear policies for approval for drugs, biologics, and manufacturing facilities to get manufacturing of key ingredients back to the united states. this would allow a faster and more certain response in times of emergency and the allow the government to initiate emergency medicine production under president obama's march executive order [ ] -national defense resources preparedness for manufacturing and distribution of medicines during times of crisis and the defense production act of as amended [ ] . international institutions are making significant efforts in preventing, detecting and responding to infectious diseases, and the continued work and support through the who, un, nato, the pan american health organization, the g , the cdc global health initiative, and other domestic and international bodies will improve international surveillance, reporting, prevention, and response. mechanisms for early reporting would avoid punishment such as travel bans for acknowledgement of dangerous infectious diseases within countries' borders. in addition, leaders in the united states would work to develop trusted relationships with peers in other countries. with more us foreign aid directed towards building public health infrastructure, the funds would have the primary impact of bolstering response and reducing transmission and casualties from infectious diseases within a country and secondary impacts of stabilizing societies (studies have shown that countries with healthy populations are more stable [ ] ). these outcomes would result in a safer and more secure world as there would be reduced disease transmission across borders. there are many existing global and domestic health initiatives such as the following: [ ] . lessons learned from this work can be utilized to further the goals of improving prevention and response to infectious disease. a research and response focus on diseases we encounter in the modern era as opposed to an emphasis on old soviet threats (unless the intelligence community identifies specific threats in the areas of bioterrorism and biowarfare) would enhance prevention and response capacities and funnel limited resources to current health and disease issues. preparations for naturally occurring outbreaks will not only prevent deaths year to year, but will also help exercise countries to fight intentionally introduced diseases by developing policies, procedures, infrastructure, and new technologies that foster quick innovation and therefore response to any microorganism, natural or manmade. each day, there are technological advances for preventing and combatting infectious diseases in addition to the progress specifically in medical research. for instance, adoption of advanced wastewater treatment systems can reduce exposure to antibiotics and args. this can be accomplished by tax incentives and partial payment by the federal government when wastewater treatment systems are replaced and advanced systems are used. in , $ billion federal dollars were spent on water utilities (water supply or treatment) accounting for approximately one quarter of public infrastructure spending [ ] . state and local governments spent $ billion for the operation and maintenance of infrastructure double the spending on capital improvements ($ billion). "although state and local governments rely primarily on their own revenues to purchase capital, federal grants also are an important source of funds. since , federal grants have accounted for one-third or more of the capital spending on infrastructure by states and localities. that share was considerably larger from the mid- s through the mid- s as a result of federal support for water utilities after passage of the clean water act in [ ] ." a renewal of this investment, with a focus on improving water treatment to remove antibiotics, args and other pollutants and destroying resistant organisms, would expand the positive results. regulations limiting the concentrations of antibiotics and args in treated municipal water, if enacted, in concert with meaningful financial penalties for those violating these standards, may significantly reduce the risk of population exposure. this can be difficult because the source of the contamination is often hard to identify. current antiviral drugs have several disadvantages including their specificity, toxicity and expense. researchers at the charles draper stark laboratories developed draco (double-stranded rna activated caspase oligomerizer). in lab-grown cells, draco killed different viruses, including ones that cause the common cold, influenza, polio and dengue fever with minimal effects on healthy cells [ ] ; however, there is still much work to be done before this drug can be fda approved and used by the general public. vectored vaccines use a live-vaccine made with a partial pathogen. they have been developed against sars-cov and demonstrated in mice, but the safety of vesicular stomatitis virus vaccine (vsv) in humans requires further research. newcastle disease virus, a host range-restricted virus, has been developed as a vaccine vector for intranasal immunization against emerging pathogens [ ] . science informs advances in drug development. for instance, authors reviewed a variety of genome sequence and gene knockout data for acinetobacter spp., with a focus on the critical systems to find the most appropriate sequences to target for therapies [ ] . this is just one early example in the explosive field of bioinformatics. in , in recognition of the importance of bioinformatics as a tool to diagnose and develop therapeutics for infectious diseases, the national institute of allergy and infectious diseases established four bioinformatics resource centers (brcs) to collect, store, and share bioinformatics information on bacteria, viruses, eukaryotic pathogens, and invertebrate vectors of human pathogens. as with the factors involved in the rise of the threat the responses are interrelated. the fda is, and must continue to, evolve its policies and regulations in the approval process so that research can proceed to the stage where drugs and biologics are ready for human use. this is discussed in more detail in the policies section below. because infectious diseases do not respect borders, it is in the strategic interest of the united states, the european union, and other countries with developed public health systems to invest in global public health infrastructure. this requires both a long-term investment as well as an acute response capability. president obama recognized both of these in the fall of . first on september , at the global health summit, president obama discussed long-term capacity building: "we, collectively, have not invested adequately in the public health capacity of developing countries." "this speaks to a central question of our global age-whether we will solve our problems together, in a spirit of mutual interest and mutual respect, or whether we descend into the destructive rivalries of the past. when nations find common ground, not simply based on power, but on principle, then we can make enormous progress. [ ] " a few weeks later, president obama discussed the acute strategic needs, "as i have said from the start of this [ebola] outbreak, i consider this a top national security priority. this is not a matter of charity-although obviously the humanitarian toll in countries that are affected in west africa is extraordinarily significant. this is an issue about our safety [ ] ." the president also signed the executive order on combating antibiotic-resistant bacteria in september of [ ] . recent outbreaks of diseases thought banished from the united states demonstrate the need for full vaccination. several communities resist vaccination, and incentives to vaccinate will increase population safety and prevent those who cannot be vaccinated from coming down with vaccinepreventable diseases. one common incentive is the requirement to be vaccinated to enter public school. waivers can be sought, but to boost the vaccination rates, state and local governments can reduce the numbers of exemptions provided. mississippi has already followed this course, and it has the highest vaccination rates in the united states. other potential policies include requiring exemption forms to be filed yearly; requiring parents to complete an education component; and requiring private as well as public school children to be vaccinated [ ] . several states are implementing one or more related measures. while only four states do not recognize a religious exemption from vaccinations, states do not allow exemptions for personal reasons (all states allow exemptions for medical reasons). in part due to the measles outbreak, on july of california will eliminate all non-medical vaccine exemptions. pennsylvania is also pondering eliminating personal exemptions. colorado has made the exemption process more burdensome [ ] . dina fine maron of scientific american [ ] suggested the following common sense approach: improved education and communication, sustain and enhance immunization outreach, maintain vigilance and rapidly contain imported infections. anthony fauci proposed partnerships, among government, industry, and academia to develop additional timely solutions to the threat of new and resurgent infectious diseases [ ] . one example of a successful academia-industry partnership is the response to the hiv/aids epidemic. aids was first recognized in the early s and the death rate steadily increased through the mid- s when it was recognized as a worldwide epidemic. research at and collaboration among academic institutions (including wayne state university) and investment by the public and private sectors (burroughs wellcome which later became glaxosmithkline) led to the development of the antiretroviral treatments used today. the partnerships transformed a deadly infection into a principally chronic disease within two decades [ ] [ ] [ ] . partnerships now work to ensure prevention, testing, distribution of anti-hiv/aids drugs and treatment worldwide. over the years fda has introduced innovations for the development and approval of pharmaceuticals including fast track, parallel track, orphan drugs, surrogate endpoints, noninferiority [ ] . according to the fda guidance [ ] , a non-inferiority (ni) study is used to demonstrate that the degree of inferiority of the drug being tested as compared to the control (an already approved drug) is less than the noninferiority margin. recently, to facilitate the development of biopharmaceuticals, a cross-industry group, including members from astra zeneca, university of texas medical school houston and smaller pharmaceutical companies, proposed a tiered evidence-based regulatory approach. in this approach tier a is the typical large phase iil approach and tier d is equivalent to the animal rule, which states that "for drugs developed to ameliorate or prevent serious or life threatening conditions caused by exposure to lethal or permanently disabling toxic substances, when human efficacy studies are not ethical and field trials are not feasible, fda may grant marketing approval based on adequate and well-controlled animal efficacy studies when the results of those studies establish that the drug is reasonably likely to produce clinical benefit in humans [ ] ." tiers b and c rely heavily on preclinical data and combined animal and human pharmacokinetic and pharmacodynamic (pk-pd) data fully integrated into a limited clinical program [ ] . in the c. difficile study discussed above, suggestions for prevention include: limit contact, limit inappropriate antibiotic usage, and increase surface cleaning. handwashing with soap from dispensers with sealed refills instead of open refillable dispensers can lower the risk of infection [ ] and is just one example of a common sense technique to prevent the spread of many bacterial infections. another common sense response is increased monitoring. cryptosporidium parvum did not appear to pose a risk until , people became ill, and approximately people died of cryptosporidiosis in milwaukee's water service area in . today, regulators and public health scientists are trying to identify microbes that pose a similar risk in the future. if these microbial contaminants occur in raw water supplies, they may need monitoring and treatment prior to these waters entering the potable water distribution system. the contaminant candidate list (ccl) developed by the united states environmental protection agency outlines a series of biological contaminants of concern that are not currently regulated but may pose a threat. should these contaminants move from the ccl to a regulatory framework, water supply utilities will incur added monitoring and testing of their water supply sources, and potentially added monitoring and treatment costs in their operations, but safety will likely increase as a result of these expenditures. the article discusses many of the problems and solutions due to emerging pathogens with a focus on the impact and response in the united states. these challenges are exacerbated in less well-off countries with poor sanitation, lack of access to preventative health care, unstable governments, or weak public health infrastructure. awareness is key, and this and other articles are working to spread the message. the threat from emerging diseases is continuously evolving as evidenced by the recent appearance of the zika virus. while the virus itself was isolated from the zika forest in uganda in the first half of the twentieth century, it did not begin to take a serious human toll until when it traveled from the pacific islands to brazil [ ] : it is now considered a global threat, with its vector, the aedes species mosquito living on all continents [ ] . there have been more than one million cases in brazil, and researchers noticed a surge in fetal microcephaly, a small head size for gestational age and sex indicating issues with brain growth, in zika-prone locations [ ] . it is now widely accepted that maternal infection with zika can lead to serious consequences for a fetus. for most infected, the effects will be minimal, but in addition to the fetal effects guillain-barre increases have been associated with zika infections. reliable diagnosis is not yet widely available, but reverse-transcriptase polymerase chain reaction (rt-pcr) testing of serum in the first seven days after symptom onset or igm-capture enzyme-linked immunosorbent assay (mac-elisa) analysis of samples are the most promising methods [ ] . animal models for further research, therapeutics and vaccines are required [ ] to stop the negative impacts of the disease since the vector is widespread and difficult if not impossible to eradicate. the general growing awareness of the threat posed by infectious disease because of travel, urbanization and all of the other factors described above combined with the serious consequences, primarily for pregnant mothers and their fetuses led to one of the fastest global responses to an infectious disease in the history of humankind. on april , , president obama announced that he would direct $ million in federal dollars remaining from the fund to fight ebola to fight the zika virus. the money will primarily be used for cdc and nih research on the virus, its role in birth defects, and vaccines for prevention. funds will also go to the formation of cdc response teams. this funding falls short of the $ . billion in emergency money president obama initially requested, and the shortfall is likely to delay a complete, effective response. internationally, the who designed and disseminated a global strategic response framework and joint operations plan, which can be accessed at http://www.who. int/emergencies/zika-virus/response/en/ . compare this to the response to polio, an enterovirus that causes few symptoms in the vast majority of cases, but can cause paralysis and even death in - % of cases. though poliovirus circulated in the population for hundreds of years, it did not reach epidemic propositions until the early s. it took nearly years to develop a vaccine and implement widespread vaccination so that in polio was eradicated in the western hemisphere. polio is now endemic in only three countries: afghanistan, nigeria, and pakistan. more recently effective prevention and treatment options for hiv/aids did not take hold for decades. this timeline is now significantly reduced. research is already underway on vaccines for zika as well as prevention through vector control. we do not know exactly which microorganism will become the next virulent threat, but surveillance and monitoring, robust public health and research infrastructures, policies to encourage the approval of treatments and vaccines, and openness and communication will allow for the quickest responses possible to any emerging, currently unknown threat. hiv 'epidemic' triggered by needle-sharing hits scott county american who contracted ebola now in critical condition flu vaccine less effective than 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bulk-soap-refillable dispensers zika virus the global distribution of the arbovirus vectors aedes aegypti and ae albopictus acknowledgments dr. ralph mitchell inspired me to look at the world in a new way, from the perspective of the tiny organisms that make the world what it is, but also threaten that world. key: cord- -zq huaoz authors: rørtveit, guri; simonsen, gunnar skov title: the primary care perspective on the norwegian national strategy against antimicrobial resistance date: - - journal: antibiotics (basel) doi: . /antibiotics sha: doc_id: cord_uid: zq huaoz a national strategy to combat antimicrobial resistance (amr) has been subject to cyclic processes in norway since . in , a renewed process cycle was launched. here, we describe the process and the approach of the process. in addition, we describe two concepts from philosophy of science that may help to frame the process: amr is an example of a super wicked problem, and post-normal science provides tools to analyze the problem from a new angle. the international struggle against antimicrobial resistance (amr) is a matter of huge importance, with no simple solutions in sight [ , ] . over the years, since the usefulness of antibiotics was discovered and large-scale production was developed, antibiotics have been used in healthcare, veterinary medicine, agriculture, fish farming, and other areas. although amr is a naturally occurring phenomenon, the wide use of antibiotics is known to drive and spread amr, which is a problem at the ecologic as well as individual level [ , ] . the need for antibiotics in healthcare cannot be overestimated [ ] . they are used to treat deadly infections as well as prevent serious complications after surgery. however, they are also used for less severe infections and even viral infections, where they should not play a role. the increasing challenge with resistant microbes can reasonably be compared with the climate change problem. although the scientific basis and the political implications of amr and climate change are different, there are many commonalities in terms of complexity, the difficulties finding solutions, and the acuteness of the problem. furthermore, like climate change, amr is a global problem that cannot be solved by individual countries alone. still, initiatives and actions at the national level are needed, and engagement from governmental bodies is part of the solution. within human medicine the general current approach is to prevent infections, improve appropriateness of antimicrobial use through antibiotic stewardship, and improve sanitation and hygiene. in countries with a strong primary healthcare sector, most infections are managed at that level. hence, a substantial proportion of antibiotic prescriptions are issued by primary care physicians, implying that this part of the healthcare sector needs to be heavily involved in any strategy to reduce amr. in , norwegian governmental institutions started a national strategy process to combat amr, with revision and renewal every five year. currently, such a revision process is ongoing; hence, the content of the new strategy is not yet ready to be published. the aim of the current paper is to describe the strategy process with emphasis on the relevance for the primary healthcare sector. we also analyze the process by use of two concepts from philosophy of science; wicked problems and post-normal science. one of the first steps towards a national strategy was taken in , when the norwegian ministry of health and social affairs appointed a project group with the mandate to establish a coordinating plan to fight amr. the group delivered its report including an action plan in . the action plan resulted in the establishment of the norwegian surveillance system for antibiotics resistance in microbes in and the norwegian prescription database with data available from . since then, norwegian health authorities and government have hosted a cyclic strategic process against amr, directed at the national and international level. the current strategy is based on a report from a multidisciplinary expert group, published in [ ] . the national strategy against antimicrobial resistance ( - ) was then released by four ministries of the national government [ ] . the four ministries involved (health and care services; trade, industry and fisheries; agriculture and food; climate and environment) reflected the multidisciplinary competence needed in this effort. the strategy relates to the aims of the world health organization's global action plan on amr from [ ] . the norwegian document introduced four overarching goals for the -year period (box ). the specific goals for the health sector are presented in box . following up on the strategy, the ministry of health presented the national action plan in [ ] , which launched concrete advice to achieve the goals of the strategy, structured and directed towards national health authorities, the population, primary care (including physicians, dentists and institutions), and secondary healthcare. box . the overarching goals of the current national strategy to reduce amr ( - ) [ ] . reduction of total use of antibiotics . more correct use of antibiotics . increase knowledge about driving forces and spread of amr resistance . engage in international collaboration to strengthen access, correct use and development of new antibiotics, vaccines, and better diagnostic tools box . the specific goals for the healthcare sector in the current national strategy to reduce amr ( - ) [ ] . antibiotics use in the population reduced by % (defined daily dose (ddd)/ inhabitants/day) compared to the level . norway among the three lowest prescribing countries in europe . average prescription of antibiotics reduced from to per inhabitants per year . prescriptions of antibiotics for respiratory infections reduced by % compared to the level . conduct studies of amr burden of disease, consequences of too little use of antibiotics and effects of infection control in , a new multidisciplinary expert group was appointed by the national government, again with the mandate to lay the basis for a renewed strategy against amr. the group is specifically asked to update relevant knowledge from , with emphasis on knowledge of strategic relevance. the current group has expertise from the healthcare sector (including primary and secondary levels), microbiology, veterinary medicine, ocean, agriculture, and the wildlife/environment sector. the strategy process has consistently aimed to apply a one health perspective, which implies a collaborative effort to attain optimal health for people, domestic animals, wildlife, plants and the environment [ ] . the group is working to submit our report in the fall of , with an expected follow-up process resulting in a renewed strategy and action plan from the norwegian government. norway is organized with a strong primary care sector based on general practitioners (gps) who also run out-of-hours services, a home care system and municipal care institutions for fragile elderly people. generally, all norwegian citizens are registered with a gp, who is their primary contact for any medical encounter. the prescription rate for antibiotics is generally low, and amr is still a relatively minor concern, although increasing [ ] . three of the specific goals for the healthcare sector in the current strategy are directly relevant for primary healthcare (box ), including reducing antibiotics use by %, reducing the number of prescriptions from to per inhabitants, and reducing prescriptions for respiratory infections by %-all compared to the level. by , these goals were completely or nearly reached, and norwegian primary care physicians should be proud of their contribution. the achievement is even more impressive as the antibiotic prescribing rate always has been low in norway. whether this success may be ascribed to the national strategy alone is debatable. there was a trend towards less prescribing before the strategy was launched, and this is part of an international trend in comparable countries such as nordic countries and the uk [ ] [ ] [ ] . however, the strategy has undoubtedly supported, and likely also enhanced, this positive ongoing trend. two aspects for further reduction of antibiotics prescribing rates should be thoroughly discussed in the upcoming process: firstly, avoiding so-called unnecessary prescribing, and secondly, the balance between low prescribing rate and risk for adverse patient outcomes [ ] [ ] [ ] . these aspects are particularly relevant for primary care physicians, who generally manage less severe infections, often of viral origin. current diagnostic tools are not sufficiently precise and safe to decide a priori which patients will develop a severe condition. hence, prescriptions which turn out to be "unnecessary" are a matter of hindsight not available at the time of the consultation. the acceptable level of uncertainty is a verbal and non-verbal negotiation between doctor, patient, relatives and society at large [ ] . a low prescription rate will inherently lead to more cases with adverse outcomes. this must not be a responsibility for the individual doctor to bear but part of a common understanding that some suffering in patients today will result in less suffering for future patients if we can keep antibiotics effective. an important question for the current expert group is what strategies are purposeful for norwegian primary care in a situation with an already low prescription rate. there is room for improvement in terms of reducing the number of frequent prescribers, increasing the proportion of narrow spectrum antibiotics, reducing the duration of courses etc. [ , ] . however, applying new targets merely amplifying current targets (box ) will probably be neither useful nor achievable. both primary care physicians and the general population may question the safety and legitimacy of "ever lower antibiotic prescription" and thus jeopardize the strong alliance between healthcare providers, public health authorities and the population, which has been a key success factor in the present strategy. the amr problem has been described as an example of a "super wicked problem" [ ] . "wicked problems" is a term which was first coined by rittel and webber [ ] to denote social problems that are so multi-faceted and refractory to solutions that we can only hope to minimize their negative effects. in addition to the original ten criteria of rittel and webber, amr has been suggested to also demonstrate the characteristics of a so-called "super wicked" problem [ ] : ( ) the time to solve the problem is running out; ( ) those who are responsible for solving the problem are also partly creating the problem; ( ) the mandate for responsible agencies to act is weak; ( ) political acts are not consistent with the need for response. although, from a legal perspective, the government could assign agencies with a mandate, it is still unclear as to how this could be executed. societal problems within this category are so complex and have so many different causes that we cannot expect to solve them, but we should nevertheless do our best to minimize their negative effects. the concept of a problem being "super wicked" should not be confused with any problem which is serious or difficult to solve. one may argue that, e.g., the present covid- pandemic is a dramatic example of a very serious global health challenge; still, the emergence and handling of a novel virus and the possible development of a vaccine represent a relatively simple conceptual framework. the scientific approach to most problems is consequently necessary and useful; however, it is not sufficient to address super wicked problems. although it does not provide a solution, a useful way of thinking in situations with fundamental uncertainty and an urgent need to act has been developed by funtowicz and ravetz [ , ] : the concept of "post-normal science" provides a tool to analyze complex problems in the interface between science and policy, of which amr is an example. in such situations, facts are uncertain, the stakes are high, values are under dispute, and decisions are urgent. that facts are uncertain implies acknowledging that there is a real difference between questions that can be solved by more research and inherent (clinical) uncertainty, where reliable predictions cannot be made now or in the future [ ] . for primary care physicians, the latter is the case in many consultations, typically in encounters with elderly patients with respiratory infections. who will and will not develop deadly complications may be unpredictable in the early phase of any infection. stakes are high means that the outcomes may be successful or devastating depending on the decisions made, and this is difficult to judge beforehand. we do not know how severe the amr consequences will be in the future, whether we act this way or the other [ , ] . in the primary care context, substantially reducing antibiotics prescriptions may severely harm many people for the potential benefit of future patients, but we do not know the full consequences of our choices, neither good nor harmful. values under dispute may be of political, moral or economic character, implying that two people may view the same situation differently: for a patient, the possibility of relief of symptoms will probably outcompete the consideration for consequences of amr for the rest of the society. on the other hand, this may be a constant worry for the primary care physician. countries with different sets of cultural dimensions have been shown to struggle differently with inappropriate antibiotic prescriptions [ ] . finally, and maybe most importantly, decisions are urgent, and we cannot wait for science to establish the facts before we act. professor peter gluckman, the former chief science adviser in new zealand, has launched a set of principles for science advice to the government, based on a post-normal science strategy [ ] . these may apply to the work with national and international amr strategies as well. neither politicians nor scientists have the solutions, and we must work together and negotiate acceptable steps along the way to reduce the negative impact of amr. we believe that for an amr strategy to achieve bold goals, collaboration and respectful interaction between policy makers, political leaders, clinical providers and the scientific community are necessary. the one health perspective on the amr problem is internationally accepted, and this implies the need for a broad, multidisciplinary approach both within and among nations. the norwegian national strategy against amr is funded on this understanding. the process has been successful this far, in terms of reaching set goals. however, further national reduction of antibiotic prescriptions is not a solution to the global amr problem and maybe not even to the amr problem within our own borders. in conclusion, perceiving amr as a super wicked problem may help in understanding its scope. applying post-normal science analytic tools may be useful to address the specific challenges that primary care is faced with internationally within the amr context. traditional strategies must be accompanied by new approaches and perspectives. although the norwegian strategy so far has been a success in terms of reducing antibiotic prescriptions, this is only a surrogate endpoint. to reach the real goal of reducing amr, we need a global, multidisciplinary, innovative approach involving all stakeholders. there is no simple solution, and the struggle will be endless, but we still cannot give up. author contributions: conceptualization, g.r. and g.s.s.; writing-original draft preparation, g.r.; writing-review and editing, g.r. and g.s.s. all authors have read and agreed to the published version of the manuscript. funding: this research received no external funding. guri rørtveit and gunnar skov simonsen are member and leader of the expert group for the norwegian amr strategy, respectively. understanding the mechanisms and drivers of antimicrobial resistance public health burden of antimicrobial resistance in europe effect of 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in tackling a crisis for the health and wealth of nations national cultural dimensions as drivers of inappropriate ambulatory care consumption of antibiotics in europe and their relevance to awareness campaigns the art of science advice to government antibiotics , , key: cord- - iv qt t authors: tan, glorijoy shi en; tay, hui lin; tan, sock hoon; lee, tau hong; ng, tat ming; lye, david chien title: gut microbiota modulation: implications for infection control and antimicrobial stewardship date: - - journal: adv ther doi: . /s - - -z sha: doc_id: cord_uid: iv qt t the human microbiome comprises a complex ecosystem of microbial communities that exist within the human body, the largest and most diverse of which are found within the human intestine. it has been increasingly implicated in human health and diseases, demonstrably playing a critical role in influencing host immune response, protection against pathogen overgrowth, biosynthesis, and metabolism. as our understanding of the links between the gut microbiota with host immunity and infectious diseases deepens, there is a greater need to incorporate methods of modulating it as a means of therapy or infection prevention in daily clinical practice. traditional antimicrobial stewardship principles have been evaluated to assess their impact on the gut microbiota diversity and the consequent repercussions, taking into consideration antibiotic pharmacokinetic and pharmacodynamic properties. novel strategies of selective digestive decontamination and fecal microbiota transplantation to regulate the gut microbiota have also been tested in different conditions with variable results. this review seeks to provide an overview of the available literature on the modulation of the gut microbiota and its implications for infection control and antimicrobial stewardship. with increased understanding, gut microbiota profiling through metataxonomic analysis may provide further insight into modulating microbial communities in the context of infection prevention and control. diseases deepens, there is a greater need to incorporate methods of modulating it as a means of therapy or infection prevention in daily clinical practice. traditional antimicrobial stewardship principles have been evaluated to assess their impact on the gut microbiota diversity and the consequent repercussions, taking into consideration antibiotic pharmacokinetic and pharmacodynamic properties. novel strategies of selective digestive decontamination and fecal microbiota transplantation to regulate the gut microbiota have also been tested in different conditions with variable results. this review seeks to provide an overview of the available literature on the modulation of the gut microbiota and its implications for infection control and antimicrobial stewardship. with increased understanding, gut microbiota profiling through metataxonomic analysis may provide further insight into modulating microbial communities in the context of infection prevention and control. our knowledge of the human microbiome has increased over the past decade. it comprises a complex ecosystem of microbial communities that exist within the human body. the largest and most diverse of these exists within the human intestine. collectively known as the gut microbiota, they have increasingly been found to play a significant role in the maintenance of human health and the development of diseases [ ] . the human microbiome was first characterized by the human microbiome project sponsored by the national institutes of health [ ] . using high-throughput sequencing, the human lower intestinal microbiota has been estimated to contain at least - microorganisms per gram of content, comprising mainly anaerobes, more than % of which belong to the phyla firmicutes and bacteroidetes [ , ] . its composition is highly variable, changing with age, diet, and geographic distribution [ ] . in recent years, increased understanding and analysis of the gut microbiota have shed light on the impact of alterations in it on human health. it plays a critical role in influencing host immune response, protection against pathogen overgrowth, biosynthesis, and metabolism [ ] . there are implications for health and diseases even from birth [ ] . additionally, the gut microbiota serves as an important reservoir of antibiotic resistant genes, also known as the ''resistome'', which can become an amplifier of antimicrobial resistance [ ] . as our understanding of the link between the gut microbiota with host immunity and infectious diseases increases, there is a greater need to incorporate methods of modulating it as a means of therapy or infection prevention in daily clinical practice. however, much of the available data are in the realm of in vitro data or animal studies. this review seeks to provide an overview of the available literature on the modulation of the gut microbiota, and its implications for infection control and antimicrobial stewardship. this article is based on previously conducted studies and does not contain any studies with human participants or animals performed by any of the authors. in this section, we review antimicrobial stewardship strategies and evaluate their impact on the gut microbiota and the development of antibiotic resistance. antibiotic use reduces the diversity of the gut microbiota through the elimination of susceptible strains that make up normal flora. this can subsequently lead to the overgrowth of resistant or potentially pathogenic bacteria, increasing the risk of infection, especially with multidrug-resistant organisms (mdro) [ , ] . the degree to which the microbiota is affected varies with the type and duration of the antibiotic used [ ] . anti-anaerobic antibiotics have a great impact on the gut microbiota as anaerobes form a significant proportion of it [ , ] . it has been shown that just - days of piperacillin-tazobactam for intra-abdominal infections resulted in a substantial decrease in anaerobic commensals [ ] . a study by hecker et al. reported that anaerobic cover accounted for about % of the unnecessary antimicrobial days of therapy [ ] . inappropriate use of anti-anaerobic antibiotics can increase the likelihood of colonization by resistant organisms [ ] . in a randomized clinical study comparing the use of piperacillin-tazobactam versus ertapenem, the resistance of enterobacterales to piperacillin-tazobactam developed at a significantly higher rate compared with ertapenem [ ] . several studies have demonstrated that newer fluoroquinolones such as levofloxacin and moxifloxacin had greater ecological effects on gram-positive organisms than ciprofloxacin [ ] [ ] [ ] . logically, advocating the prescription of narrower spectrum antibiotics whenever appropriate should reduce disruption of the microbiota and resultant opportunistic infections, such as clostridiodes difficile infection (cdi) and fungal infections. benefits were demonstrated in the comparison of vancomycin and fidaxomicin in the management of c. difficile diarrhea. fidaxomicin exposure had a smaller impact on microbiota composition in mice and conferred higher colonization resistance to c. difficile spores compared with vancomycin [ ] . consequently, this was associated with a lower recurrence rate in patients treated with fidaxomicin compared with vancomycin [ ] . a study by lew et al. suggested that classical antimicrobial stewardship strategies, specifically switching to narrower spectrum antibiotics, antibiotic cessation once treatment is completed, or when there is no bacterial infection, can reduce rates of antibiotic resistance and cdi [ ]. this concurred with tay et al. who reported the usage of carbapenem as a risk factor for severe cdi [ ] . excessively prolonged antibiotic use is a global concern [ , , ] , and can lead to significant alteration in the gut microbiota, restoration of which can take months to years [ , ] . conversely, shorter antibiotic duration results in less collateral damage to the gut microbiota, and allows for earlier restoration. late-preterm infants who received longer courses of antibiotics had more prolonged alterations in their gut microbiota compared with those who received a shorter duration [ ] . there is increasing evidence that a shorter duration of antibiotics of less than days for commonly encountered infections, such as skin and soft tissue infection [ ] and male urinary tract infections [ ], are not associated with increased treatment failures. antibiotic stewardship principles of making an accurate diagnosis of infection, appropriate antibiotics, and a shorter duration of antibiotic treatment or prophylaxis, would reduce unnecessary antibiotic exposure to the gut microbiota without compromising patient outcomes [ ] . the route, dose, and excretion of antibiotics affect the gut microbiota differently. zhang et al. compared oral versus intravenous tetracycline and ampicillin using murine models, and recovered higher copies of resistant genes in mice fed with oral antibiotics compared with those which received intravenous antibiotics [ ] . lower tetracycline doses were associated with slower resistance development with fewer copies of resistant genes being isolated [ ] . when clindamycin was administered via the oral route, a higher concentration of clindamycin were found in feces compared to when administered via an intravenous route. this resulted in a greater reduction of anaerobic colonic flora, leading to an overgrowth of clindamycin-resistant bacteria, such as enterococci and c. difficile [ ] . however, compared with oral agents that are highly absorbed and excreted minimally through the bile or feces, intravenous antibiotics that undergo enterohepatic re-circulation or are excreted through bile, feces, or secreted into the intestinal tract may have a greater impact on the gut microbiota [ ] . various studies have found that imipenem and meropenem are excreted minimally in fecal samples after administration, and minor changes to the gut microbiota when administered for a limited duration ( - days) have been observed [ , ] . oral penicillin was also reported to have a low fecal concentration, with almost no change in microflora [ ] . in contrast, ceftriaxone, a broad-spectrum cephalosporin with high biliary excretion, effectively suppressed enterobacterales [ ]. among macrolides, erythromycin has lower absorption from intestines compared with clarithromycin. about % of erythromycin versus - % of clarithromycin is metabolized in the liver and excreted in bile as its active form [ ] . this explains the higher impact of erythromycin on intestinal microflora [ ] . in light of the above, antibiotic prescribers should firstly, only start antibiotics in the presence of a clear indication. secondly, prescribers should choose the narrowest spectrum antibiotic available for treatment to reduce the impact on the gut microbiota (e.g., the omission of anaerobic cover if not indicated). thirdly, antibiotics should be prescribed for the shortest duration to allow the recovery of the gut microbiota as soon as possible, and finally, oral antibiotics should be used if possible to reduce line-related infections and reduce hospitalization days. oral agents that are highly absorbed and excreted minimally through the bile or intestinal tract are preferred. prescribers will also need to consider the resistance potential of antibiotics. although carbapenems are excreted minimally through the gut with a smaller impact on the gut microbiota, antibiotic prescribers should be aware of the association between carbapenem use and the increase in carbapenem resistance, which should limit its use [ , ] . additionally, other factors, such as side effects, allergies, and penetration to the site of infection, will also need to be considered during prescribing, in addition to the impact of antibiotics on the gut microbiota. the use of non-systemic antibiotics for localized infections may help to minimize the impact on the gut microbiota and the development of antibiotic resistance. getting the drug to only where it is needed in high concentrations is a concept that has been used in some infections. inhaled antibiotics have been used for respiratory infections in patients with cystic fibrosis [ ] . studies have been conducted for other respiratory infections, such as pneumonia, infective exacerbation of chronic obstructive pulmonary disease, and non-cystic fibrosis bronchiectasis, but there has been a paucity of good quality studies and the outcomes have colonization resistance is the ability of the healthy microbiota to prevent expansion of potential pathogenic bacteria [ ] . maintaining or re-establishing colonization resistance by modulating the gut microbiota to prevent infection have been evaluated. the next section discusses how this can be achieved. the intestine is a reservoir for mdro that can be opportunistic pathogens selected for by antibiotic pressure, especially in critically ill and hospitalized patients [ ] . studies have shown that patients colonized with mdro are at risk of developing infections that arise endogenously, or may transmit them to other individuals [ , ] . these pathogens may translocate across a damaged intestinal barrier, or result in contamination to cause infections at other sites, such as central line infections or catheter-related urinary tract infections. the gut microbiome thus serves as a prime target for infection prevention strategies, giving rise to increased interest for use of fecal microbiota transplant (fmt) and selective digestive decontamination as infection control strategies to reduce carriage of mdro. fmt has been found to be one of the most effective ways to regulate the gut microbiota. it was first described in [ ] and has since gained increased acceptance as a medical intervention in recent decades. eiseman et al. observed that the administration of fecal enemas resulted in dramatic responses in critically ill patients with pseudomembranous colitis [ ] . it usually involves the transfer of processed stool from a healthy donor into the colon of a recipient, and is delivered enterally either endoscopically or via oral capsule preparations. this presumably allows the donor's microbiome to repopulate the gut with a healthy microbiome to restore gut dysbiosis. at present, recurrent cdi is the only indication for which fmt has been proven to be efficacious, and it is recommended when appropriate antibiotic therapies have failed [ ] . cure rates in this group of patients were up to % with repeated fmt in randomized controlled trials [ ] [ ] [ ] . engraftment of specific bacteria and viruses with physiologic effects within the gut was thought to play a significant role in reversing dysbiosis [ ] . cheng et al. demonstrated in a piglet model that fmt had several effects on metabolic pathways that occurred within the gut to improve gut mucosal barrier integrity [ ] . a number of case reports and case series have described successful decolonization of mdro as a primary outcome among patients treated with fmt [ ] . these reports included both immunocompetent and immunocompromised patients colonized with carbapenemase-producing enterobacterales [ , ] , vancomycinresistant enterococci (vre) [ ] and extended spectrum ß-lactamase-producing enterobacterales [ ] . unfortunately, these studies were often uncontrolled with high levels of heterogeneity and short follow-up periods, resulting in no conclusive evidence to support the safety and efficacy of fmt in this regard. in addition to the clinical implications on patient outcome, the successful decolonization of mdro via fmt may have several infection control implications. it reduces the burden on healthcare facilities to provide isolation rooms for such patients who require contact precautions and allows re-entry into long-term care facilities that would otherwise not have the adequate infection control resources to care for these patients [ ] (see table ). selective oropharyngeal decontamination (sod) has gained interest as an infection prevention strategy in critically ill patients in the intensive care unit (icu). in the s, johanson et al. observed that the prevalence of gramnegative bacteria in the pharyngeal flora increased markedly within a few days of hospitalization [ ] . it was postulated that, since the pathogenesis of bacterial pneumonia began with the aspiration of the oropharyngeal contents into the lung, altering the pharyngeal flora in ill patients may be important to prevent pneumonia secondary to gram-negative bacilli. in the s, stoutenbeek et al. introduced the concept of selective digestive decontamination (sdd) in the icu population [ ] . given that most infections in the icu are primary endogenous infections, reducing bacterial load within the gastrointestinal tract, in particular potentially pathogenic microorganisms, would theoretically reduce infection risks. in sdd, enteral antibiotics are selected for their inability to be absorbed into the systemic circulation, and are active against the most common nosocomial pathogens within the gut (e.g., escherichia coli, klebsiella pneumoniae, and pseudomonas aeruginosa). unfortunately, a randomized trial conducted in european icus among patients receiving mechanical ventilation found that sod and sdd were not associated with reductions in icu-acquired bloodstream infections caused by multidrug-resistant gram-negative organisms compared with standard care [ ] . in addition, a study conducted in icus in the netherlands demonstrated the ''rebound phenomenon'' that sod and sdd had on the gut microbiota, with increased rates of ceftazidime resistance in the intestinal tract after discontinuation of sdd. a combination of both interventions has been considered. a randomized trial reported no significant reduction in extended-spectrum b-lactamase or carbapenemase-producing enterobacterales intestinal carriage between patients who received a -day course of oral antibiotics followed by frozen fmt obtained from unrelated healthy donors and controls [ ] . in view of the lack of conclusive evidence of the efficacy of fmt and sdd, the european clinical guidelines do not recommend routine decolonization of third-generation cephalosporin-resistant and carbapenem-resistant enterobacterales carriers [ ] . antimicrobial stewardship broad-spectrum antibiotics can cause significant alteration to the gut microbiota diversity, in particular those with anti-anaerobic activity [ , ] alterations to the gut microbiota by antibiotics take months to years to restore [ , ] shorter duration of antibiotic is equally effective than prolonged use and can reduce alterations to the gut microbiota fecal microbiota transplant has been found to be one of the most effective ways to regulate the gut microbiota dysbiosis in the setting of cdi [ ] fecal microbiota transplant has been studied in gut decolonization of mdro, but has not conclusively been found to be effective [ , , ] selective oral decontamination and selective digestive decontamination with oral antibiotics has been evaluated as a means of reducing infections caused by endogenous mdro, but has not been found to be efficacious [ ] [ ] [ ] restoration of the gut microbiota diversity through probiotics and prebiotics have some role in restoring gut diversity in specific diseases, such as necrotizing enterocolitis, acute infectious diarrhea and antibiotic-associated diarrhea [ ] [ ] [ ] [ ] [ ] [ ] extrapolating the principles of sdd, the role of the gut microbiota in the development of surgical site infections (ssi) has been considered in colorectal surgery where surgeons operate in a cleancontaminated field. oral antibiotic preparation (oap) with variable combinations of aminoglycoside, macrolide, and metronidazole have been used to evaluate if they reduced rates of ssi, surgical complications of anastomotic leak, and length of hospital stay [ ] . a network metaanalysis of randomized controlled trials revealed that oap alone was not associated with a statistically significant reduction in ssi [ ] . koskenvuo et al. similarly reported no reduction in ssi or overall morbidity in colon surgery when mechanical and oral antibiotic bowel preparations were used compared with no bowel preparation [ ] . there is no strong evidence to suggest that oap as pre-operative prophylaxis is effective in reducing ssi. probiotics are ''living microorganisms which when administered in adequate amounts confer a health benefit on the host'' [ ] . prebiotics are non-viable substrates that are selectively utilized as nutrients by beneficial microorganisms, both indigenous and exogenously administered strains, thereby conferring a health benefit [ ] . current literature shows effective reduction of colonization by gram-positive organisms through the use of probiotics. manley et al. and szachta et al. both reported that vre in the gut can be significantly reduced even to the point of eradication through oral consumption of lactobacillus rhamnosus gg [ , ] . gut colonization of s. aureus including methicillin-resistant s. aureus was reduced after weeks of oral lactobacillus rhamnosus hn in a recent clinical trial [ ] . however, this beneficial effect of probiotics was not in gram-negative mdro in hospitalized patients and residents in long-term healthcare facilities [ , ] . randomized controlled trials have shown positive effects on gut health by probiotics in a myriad of conditions, such as infectious and antibiotic-associated diarrhea (aad), irritable bowel syndrome, and enterocolitis [ ] . lactic-acid bacteria, such as lactobacillus and yeast-based saccharomyces boulardii (cerevisiae) probiotics, are the commonest choices for treatment of gastrointestinal conditions [ ] [ ] [ ] . our knowledge of the effects of prebiotics are evolving. human studies which used-high throughput sequencing demonstrated stimulation of bifidobacteria in response to prebiotic use [ , ] . in these studies, there were variations in other microorganisms, with increased faecalibacterium prausnitzii [ ] and anaerostipes spp, whereas bilophila spp. decreased [ ] . although proof of causality is difficult to determine, the beneficial effects of prebiotics have been evidenced through numerous randomized controlled trials, albeit variable as a result of both environmental and host factors [ ] . necrotizing enterocolitis (nec) is a debilitating gastrointestinal disorder in neonates characterized by transmural inflammation and bowel necrosis. bacterial invasion of the bowel walls can occur, and empirical treatment with broadspectrum antibiotics forms part of the backbone of management [ ] . morbidity and mortality are high [ ] . nec most frequently occurs in neonates who are preterm or have very low birth weight [ , ] . they are inherently at a higher likelihood of receiving antibiotics due to their susceptibility to infections, and prolonged antibiotic use is a known risk factor for nec [ ] . the growth of gut-friendly commensal bifidobacteria is greatly compromised [ , ] . consistent benefits of probiotics in the prevention of nec have been extensively described in systematic reviews and meta-analyses [ ] [ ] [ ] . sawh et al. reported that, when compared with placebo, probiotics reduced the incidence of severe nec in trials ( , patients) [rr . , % ci ( . - . )] [ ] . the incidence of all-cause mortality was significantly reduced with probiotics in trials ( patients) [rr . , % ci ( . - . )] [ ] . as such, probiotics may have a role in reducing the occurrence of nec, and thus antibiotic usage and potential negative outcomes caused by nec. acute infectious diarrhea is one of the leading reasons for antibiotic prescription. reduction in diarrheal incidence, severity, and duration through probiotic use may reinforce antimicrobial stewardship principles of reducing antibiotic prescriptions. probiotics have been heavily studied in patients with acute infectious diarrhea and evidence of its benefits is well described [ , ] . a cochrane review of studies, mainly in infants and young children, reported an average reduction of day in the duration of diarrhea, reduction in the likelihood of diarrheal episodes lasting more than days, and stool frequency on day of illness [ ] . aad affects approximately % of patients and is frequently associated with broad-spectrum antibiotic use [ , ] . aad can outlast the period of antibiotic use and makes the patient more vulnerable to infections and other diseases [ , ] . positive associations between probiotics and a decrease in aad have been reported [ , , ] . however, studies were consistently limited as they were underpowered and used varying probiotic strains, formulations, and doses. the studied population had differences such as age, health conditions, and genetic factors. these factors resulted in the heterogeneity of the studies. therefore, the extent of purported benefits remains unknown [ ] . probiotics for c. difficile-associated diarrhea up to % of aad are secondary to cdi. it is the commonest cause of infectious diarrhea in healthcare settings [ , ] . the care of such patients requires intensive infection control measures of isolation, contact precautions, and terminal cleaning to limit nosocomial transmission. the clinical practice guidelines for cdi in adults and children by the society for healthcare epidemiology of america and the idsa make no recommendation with regard to the administration of probiotics for the treatment and prevention of primary or recurrent cdi [ ] . meta-analyses have shown that probiotics may be effective at preventing cdi with up to % risk reduction [ , ] . however, in post hoc analysis, it was demonstrated that this large risk reduction was significant only in patients who had a higher baseline cdi risk of [ % ( . % in the robiotic group vs. . % in the control group). risk of cdi recurrence is approximately %, and attempts have been made to lower the recurrence rate. a randomized placebo-controlled trial showed that patients with cdi treated with s. boulardii plus standard antibiotics had a significantly lower relative risk of cdi recurrence than placebo plus standard antibiotics [ ] . while there was a trend that s. boulardii could reduce cdi recurrence in patients with initial cdi and recurrent cdi, significance was demonstrated only in the latter [ ] . in a double-blind, placebocontrolled trial, among patients who received high-dose enteral vancomycin ( g/day), surawiez et al. demonstrated a significant reduction ( . % vs. . %) in cdi recurrence when s. boulardii was administered [ ] . however, the high-dose vancomycin arm only had subjects, and most were severely ill with cdi complications such as pseudomembranous colitis. in the low dose ( g/day) vancomycin and metronidazole arms (n = and , respectively), co-administration of s. boulardii was not associated with reductions in cdi recurrence. the efficacy of probiotics in preventing cdi recurrence is promising, but studies are still limited by small sample sizes and the lack of consistently reproducible data [ , ] . few clinical trials have addressed the safety profile of probiotics because of the lack of safety documentation. often, they are underpowered for this purpose [ ] . however, rare events such as bacteremia and fungemia have been reported, especially in vulnerable populations such as immunocompromised patients [ ] . lastly, there have been reports where commercial probiotic strains carried antibiotic resistance genes [ ] . this is a threat, especially when lateral transfer of these undesirable genes to pathogens and commensal the gut microbiota is possible. the maintenance of a healthy and diverse gut microbiota plays an important role in the prevention and acquisition of mdro, and strategies that modulate its composition have great potential in impacting human health. this serves to reinforce antibiotic stewardship principles that limit the negative effects of antibiotics on the gut microbiota. specific strategies include developing models for assessing the impact of various antimicrobial combinations on the gut microbiota, and promoting the development and use of such therapies with demonstrable reduced impact. novel interventions, such as microbiota auto-banking and transplantation to perform studies for reducing colonization by mdro, as well as developing more advanced probiotics that are reflective of the complexity of the native gut microbiota, can serve to restore gut microbiota diversity in the face of dysbiosis. as we discover more about the host protective mechanism afforded by an intact microbiota, further research should be invested in promoting the development of molecular therapeutics to mimic normal host-microbiota interactions. the vitora (nct ) and effect-cpe (nct ) trials are ongoing clinical trials that have been publicly registered to assess the effectiveness of the manipulation of the gut microbiota for the eradication of mdro carriage. a trial conducted by the memorial sloan kettering cancer center to see how different antibiotics affect the commensal bacteria existing in the intestinal tract is currently underway. with increased understanding, gut microbiota profiling through metataxonomic analysis may provide further insight into modulating microbial communities in the context of infection prevention and control. funding. no funding or sponsorship was received for this study or publication of this article. authorship. all named authors meet the international committee of medical journal editors (icmje) criteria for authorship for this article, take responsibility for the integrity of the work as a whole, and have given their approval for this version to be published. compliance with ethics guidelines. this article is based on previously conducted studies and does not contain any studies with human participants or animals performed by any of the authors. commons attribution-non-commercial . international license, which permits any non-commercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http:// creativecommons.org/licenses/by-nc/ . /. the human intestinal microbiome in health and disease the nih human microbiome project the human microbiota and infection prevention 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stewart williams, jennifer; wertheim, heiman; khan, wasif ali; matin, abdul; kinsman, john title: rural community perceptions of antibiotic access and understanding of antimicrobial resistance: qualitative evidence from the health and demographic surveillance system site in matlab, bangladesh date: - - journal: global health action doi: . / . . sha: doc_id: cord_uid: li ng v background: the use of large quantities of antimicrobial drugs for human health and agriculture is advancing the predominance of drug resistant pathogens in the environment. antimicrobial resistance is now a major public health threat posing significant challenges for achieving the sustainable development goals. in bangladesh, where over one third of the population is below the poverty line, the achievement of safe and effective antibiotic medication use for human health is challenging. objective: to explore factors and practices around access and use of antibiotics and understanding of antimicrobial resistance in rural communities in bangladesh from a socio-cultural perspective. methods: this qualitative study comprises the second phase of the multi-country abacus (antibiotic access and use) project in matlab, bangladesh. information was collected through six focus group discussions and in-depth interviews. informants were selected from ten villages in four geographic locations using the health and demographic surveillance system database. the access to healthcare framework guided the interpretation and framing of the findings in terms of individuals’ abilities to: perceive, seek, reach, pay and engage with healthcare. results: village pharmacies were the preferred and trusted source of antibiotics for self-treatment. cultural and religious beliefs informed the use of herbal and other complementary medicines. advice on antibiotic use was also sourced from trusted friends and family members. access to government-run facilities required travel on poorly maintained roads. reports of structural corruption, stock-outs and patient safety risks eroded trust in the public sector. some expressed a willingness to learn about antibiotic resistance. conclusion: antimicrobial resistance is both a health and development issue. social and economic contexts shape medicine seeking, use and behaviours. multi-sectoral action is needed to confront the underlying social, economic, cultural and political drivers that impact on the access and use of antibiotic medicines in bangladesh. antimicrobial drugs include antibiotics, antifungals, antivirals and antimalarials. their use in medical and veterinary practice, animal husbandry and agriculture has reduced infectious agents by killing bacteria, fungi, viruses and parasites [ ] [ ] [ ] . exposure to antimicrobials is causing drug resistance. factors thought to account for this include the suboptimal use of drugs in hospitals, the community, veterinary practice and agriculture. the leakage of compounds into the environment creates pathways for antimicrobial resistance (amr) although evidence of their relative importance and contribution has not been established [ ] [ ] [ ] . amr presents significant challenges for achieving sustainable development goals (sdgs) such as sdg (poverty), sdg (good health and well-being), sdg (clean water and sanitation) and sdg (responsible consumption and production) [ ] . amr is both a health and development issue. tackling amr requires an 'adaptive approach' that acknowledges how and why antimicrobial use has become entrenched in the way of life in both rich and poor countries [ ] . the world bank estimates that by up to million people could be forced into extreme poverty due to amr [ ] . addressing amr requires acknowledgement of how and why antimicrobials are embedded in societies and economies [ ] . the covid- pandemic will further exacerbate this trend which is impacting disproportionately on low-and middle-income countries (lmics) [ ] . the drivers of antimicrobial use in human health are complex and multifaceted [ ] . individual behaviours that promote amr result from limited knowledge and understanding of potential consequences [ ] . a systematic review of studies on amr showed that addressing the social determinants of poverty is an essential yet neglected step in addressing amr [ ] . in lmics structural, social, political and economic barriers impede access to prescription medicines, and health system development challenges compromise intervention efforts [ , , ] . in a qualitative study among human and animal healthcare professionals in ethiopia, nigeria, sierra leone, india, vietnam and the philippines, amr awareness raising did not reduce prescribing [ ] . a study of amr in rural thailand concluded that the results of educational programs in high-income countries cannot be generalised to lmics where impoverished populations endure precarious existence under fragmented under-resourced health and social support systems [ ] . in many countries antibiotics are a 'quick fix' medicine [ , ] . balancing access and excess in lmics poses precarious ethical questions about the roles and responsibilities of users and prescribers [ ] . discussion in the literature has focused on measured 'use' and 'misuse' of antimicrobials. researchers in the social sciences remind us of the dangers of injecting subjective bias and unfair judgement into scientific debate [ , ] . anthropological studies of antibiotic use in sub-saharan africa and south-east asia used the 'drug bag' method to address conceptual and semantic issues [ ] . by 'appropriate' use we mean that if a medicine is used appropriately (in a clinical sense) it is safe and effective in treating the disease. conversely, 'inappropriate' use occurs when the medicine is not clinically effective in treating the disease. yet it is important to acknowledge that what is considered 'appropriate' from a biomedical perspective, may not be 'appropriate' from a socio-cultural perspective [ ] . each country's 'risk profile' for amr is contextually determined [ ] . bangladesh is a lower-middle-income economy in south-asia with a population of million https:// www.unfpa.org/data/world-population/bd. more than two thirds of the population live in rural areas where social and economic disadvantage and poverty is widespread [ , [ ] [ ] [ ] . despite the government's national drug policy, access to formal healthcare and medical prescribing is limited, and antibiotics are commonly purchased, without prescription, from vendors in pharmacies [ , , , ] . a systematic review of amr studies ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) in bangladesh identified a high prevalence of resistance to most antibiotics and major gaps in surveillance [ ] . in a country where sixty seven percent of total healthcare expenses are out of pocket and thirty five percent of the population is below the poverty line, achieving safe and appropriate medication use for human health is challenging [ , ] . the access to healthcare framework articulated by levesque, harris and russell [ ] is used to guide the interpretation and framing of the findings in this study. the framework provides a theoretical underpinning because it offers a patient-centred perspective. it goes beyond conceptualising access in a one-dimensional space by presenting and articulating five interdependent dimensions and their corresponding abilities at the interface between the population and the health system. the same approach has been undertaken in other similarly designed studies of abr in lowresource settings [ ] . levesque et. al. [ ] propose five dimensions of access: ) approachability (transparency, outreach, information screening); ) acceptability (professional values, norms, culture, gender); ) availability (geographic location, accommodation, hours of opening, appointment mechanisms); ) affordability (direct costs, indirect costs, opportunity costs) and ) appropriateness (technical and interpersonal quality, adequacy, coordination, continuity). levesque et. al. [ ] proposed five corresponding conceptualisations of the ways in which peoples' abilities to interact with each of these dimensions are generated: ) ability to perceive (health literacy, health beliefs, trust, expectations); ) ability to seek (personal and social values, culture, gender, autonomy); ) ability to reach (living environments, transport, mobility, social support); ) ability to pay (income, assets, social capital, health insurance) and ) ability to engage (empowerment, information adherence, caregiver support). see figure . the objective of this study is to explore factors and practices around access and use of antibiotics and understanding of antimicrobial resistance in rural communities in bangladesh from a socio-cultural perspective. the study was conducted in the matlab site of the health and demographic surveillance system (hdss) in the chandpur district of bangladesh. the matlab hdss is an economically deprived rural area in southern bangladesh with an estimated population of , people in , households across villages. further information about matlab hdss is published elsewhere [ , [ ] [ ] [ ] [ ] http://ghdx. healthdata.org/record/bangladesh-matlab-health-anddemographic-surveillance-system. this qualitative exploratory cross-sectional study is one component in a larger multi-country research project abacus (antibiotic access and use) [ ] which assessed and compared community-based antibiotic access and use in bangladesh, south africa, ghana, vietnam, thailand and mozambique. http://www. indepth-network.org/projects/abacus. abacus was conducted in the six countries in two phases ( - ). the first phase involved identifying antibiotic resources by mapping suppliers and implementing inventories. in the second phase, factors that affect antibiotic access and use were explored using in-depth interviews (idis) and focus group discussions (fgds) with community members in each of the sites. this study reports the results of idis and six fgds conducted in the bangladesh matlab site in the second phase of the abacus project. supplementary file (sf) includes the preparatory in-depth interview guide, sf the in-depth questionnaire and sf the preparatory focus group guide. sampling and recruitment followed the abacus study protocol under the direction of the third author (hw) [ ] . fourth and fifth authors (wak and am respectively) were abacus study investigators in the matlab site. wak is a senior public health scientist and am is an anthropologist. in line with abacus protocols [ , , ] residents were 'randomly sampled' from different age and gender categories in ten villages across four different geographic areas identified in the matlab hdss database [ , ] . the same method applied in both idis and fgds. antibiotic suppliers and healthcare workers were not invited to participate. the sixteen idis (four men and women) and six fgds ( men and women) were conducted between march and april . four people (two men in the idis and one woman and one man in the fgds) declined to join the study. there were no drop-outs. see results section for details. the themes for the qualitative data collection instruments were informed by a review of the literature and developed by jk under the guidance of the abacus principal investigator (hw). local support was provided by wk and am. the interview and focus group questions were developed in english and translated into the bangla language by wak and am. the questions were divided into sections ) accessing treatment, ) the supplier/seller of medicines, ) the medicines. see sfs , and . references to specific medicines were made using international brand names which are commonly recognised both in clinical and community settings in bangladesh. all participants were familiar with the terms, concepts and brand names. the field workers ensured that there were no ambiguities. the fifth author (am) conducted all the interviews and discussions with the support of a trained field assistant. neither were known personally to the informants. all interviews and discussions were taperecorded. on average, the duration of the idis was minutes and the fgds minutes. the idis and fgds each had a different purpose. the idis were conducted in private homes. interviewees were encouraged to speak openly about their experiences and give personal opinions. in the fgds (held in community spaces in villages) there were many opinions being expressed on the same topic. participants interacted with one another and shared views and insights. both sets of data were analysed in the same manner. transcripts were recorded in bangla and translated to english for coding and analysis by the first author (mc) with input from the last author (jk). transcripts were not shared with the informants. data were analysed using a combined thematic approach. by this we mean that the approach was broadly inductive with the concept of access being central and a priori themes derived from the questions used in the fgds and idis. both sets of data (idis and fgds) were analysed in the same manner. we used braun and clarke's six thematic steps to: become familiar with the data; generate initial codes; search for themes; review potential themes; define themes, and produce a report [ , ] . codes were generated, assessed and clustered into emergent themes consistent with the access framework dimensions [ ] . atlas ti . software was used in coding all transcripts. we were critically aware of the importance of reflexivity during the collection and interpretation of data. the multidisciplinary nature of our team meant that we were cognisant of how different value systems can influence judgement and lead to biased processes and outcomes. the informants were fully informed about the backgrounds of the field workers with whom they had contact. all study informants were fully informed about the purpose of this study, the processes used to collect qualitative information, and the matlab study's relationship with the abacus project. informed written consent was a requirement for participation in the idis and fgds. approval for all abacus project sites was granted by the oxford university tropical research ethics committee, and the ethical review committee of the international centre for diarrhoeal disease research, bangladesh [ ] . over % of people in matlab live below the poverty line [ ] . according to the most recent ( ) matlab hdss household socio-economic census [ ] one in six households did not have access to improved water sources, most had mud flooring and tin was the predominant building material. the bicycle was the most common form of transportation. most men aged - years were working; the highest proportion of working women ( %) was in the age group - years. remittance payments were the main source of income for one third of households. twenty nine percent of females and % of males had not had any formal schooling. medical pluralism is an important characteristic of healthcare in matlab. residents access formal and informal services for both conventional and alternative medical care and advice. treatment seeking is influenced by social and cultural beliefs, previous experience and perceptions about the approachability, acceptability, availability, affordability and appropriateness of care [ ] . government-run services charge nominal fees [ ] . the most common reported acute illnesses are fever, diarrhoea/dysentery and aches/pains for which self-treatment is common. matlab's morbidity and mortality profile is changing from acute, infectious, and parasitic diseases to non-communicable conditions including cardiovascular and cerebrovascular diseases. longer duration illnesses are managed in government hospitals [ , ] . there were informants ( female and male) from different villages. the age range spanned - years. the average age of interviewees was years and the average age of focus group participants was . most of the men were employed and most of the women were engaged in full time home duties. islam was the dominant religious faith. none of the informants held health insurance (see tables and ). data are presented under the five thematic dimensions proposed by the access framework developed by levesque et. al. [ ] . as there were no substantial differences in the results of the idis and fgds, the findings are grouped togther. approachability/ability to perceive 'approachability' relates to how individuals perceive the existence of services they need. village pharmacies were directly approachable for primary treatment. young women sought treatment based on what they believed had worked well in the past. we usually go to the nearby pharmacies for primary treatment. if anything is serious then we travel to the upazilla (approximately nine kilometres). the treatment at the pharmacy works fine, that's why i barely go to the hospital. moreover, i get medicines in credit sometimes'. (idi -female, age , secondary education, homemaker). a mother commented that she used medications she could trust to provide a 'quick-fix'. if there is any trouble i take an extra dose of antibiotic. if i am having stomach-ache today, i will need a pill. so if i take one dose extra, then there will be no pain (idi -mother of child under five years, age , secondary education, homemaker). men referred to serious issues of structural violence in public sector facilities. in contrast, village pharmacies offered a safer trusted alternative. ' we go to private facilities because of the poor service in the public ones. even though the treatment is free in public facilities, they do not treat well without bribe or connection. moreover, often we do not even get free medicines. they just sell them outside. we are treated with negligence. if we go to the public healthcare centres, we might end up dying without treatment.' (fgd -male, age , secondary education, agriculture). women mentioned limited medicine supply as a further impediment. ' we do not have any government health facility in our area. there is one in our neighbouring village but the government ones do not always have a sufficient supply of medicines'. (fgd -female, age , primary education, homemaker). informants self-medicated with antibiotics for: wound healing, headache, lethargy, blood pressure control, urinary tract infection and stomach ache. commonly recognised brand names were: fimoxyl, zthrin, zmax, cephrad and cef- . health literacy and trust was built on familiar trusted brand names. there were several choices to make regarding where to seek acceptable healthcare. non-medical spiritual practices are important healing methods in the local belief system. these methods included 'jharfuk' (sorcery involving blowing holy verses), 'kabiraji' (treatment with herbal extracts), 'tabij' (an amulet containing verses from holy books believed to be protective and curative against diseases) and 'pani pora' (water with spell from the religious pastor which is believed to be curative). 'kabirajs do not give medicines, they give "tabij" instead, and people recover there. as we believe in religion, we believe that allah can cure us without medicines if he wants, he can save us without treatment'. (fgd -male, age , higher secondary education, service sector employment). younger people were aware of religious discrimination in government healthcare. this influenced their ability to seek healthcare. 'the hospital is in mnd which is a hindu area. so people from our area do not really prefer going there.' (fgd -male, , higher secondary education, business sector employment). medicines were obtained (free of charge) from friends, relatives and neighbours. having personal contacts with hospital or pharmacy experience enhanced self-efficacy. 'i do not need to visit doctors mostly as my neighbour works in the hospital and gets free medicines from there. i take antibiotics from her, even for my family members. she tells me how to take it'. (idimother of child under five years, age , undergraduate education, homemaker). a young wife had full confidence in her husband's advice because of his village pharmacy experience. ' in my family, my husband suggests which antibiotic is to be taken as he has a good knowledge about the ability to reach healthcare is related to the ability to seek healthcare. men aired complaints regarding the distance to hospitals. village based services were available and easy to reach. 'there is only a community clinic in our village. the nearest government hospital is there in ml (another village kilometers away from the village) and then matlab (sub-district centre kilometres from the village)'. (fgd -male, age , primary education, agriculture). public infrastructure was inadequate on multiple fronts -roads, facilities and the medical workforce. ' we do not have sufficient physicians in our area. for primary care, we need to go to dk (around kilometres away from his village). they are really far, moreover, look at the condition of the roads. we need more doctors and better facilities for treatment for our people'. (fgd -male, age , primary education, service sector employment). at the very least it was important to ensure that village residents could reach medical facilities to obtain treatment when needed. another male focus group informant made the following comment. 'government health facilities are far from here, also look at the condition of the roads. this is hard to travel. we need doctors and better treatment for our people'. (fgd -male, age , higher secondary education, business sector employment). even though most medicines are free of charge in government-run facilities, informants preferred to use trusted nearby village pharmacies where they could purchase medicines quickly over the counter. yet personal economic circumstances influenced ability to pay. men shared personal accounts of their healthcare expenditure and monthly earnings in the focus group. you have to accept the reality. if you earn bdt/ month ($us ) you cannot afford to pay healthcare costs at all if the problem is more than just a cold or a fever. many people in the village struggle with expenses for treatments. some people borrow money and others end up selling all their lands and properties to afford to pay treatment costs'. (fgd -male, age , higher secondary education, unemployed) pharmacy healthcare was appropriate. village residents were comfortable engaging with local salespersons in pharmacies. 'frankly speaking, our healthcare system is totally pharmacy-based.' (fgd -male, age , higher secondary education, service sector employment). pharmacy salespersons hold a level of authority and accountability with regard to medication advice. they are trusted and respected by both men and women. salespersons typically cut slits in the boxes to help those unable to read. three cuts, for example, can mean one pill three times a day. 'they (pharmacy salespersons) tell us how to take the medicines and we depend on this advice. if they give something wrong, they will be in trouble. they might not be mbbs doctors but they are from our area, so we trust their management.' (idi -mother of child under five years, age , secondary education, homemaker). antibiotics were perceived as being useful for treating infections. but there was also a belief that antibiotics could be used to treat non-infectious conditions such as hypertension and lethargy. some male and female focus group participants volunteered views on resistance. 'antibiotic resistance? i heard that antibiotics will be banned or something, on the tv news. it said around hundred companies were banned or something. i cannot remember correctly.' (fgd -male, age , postgraduate education, business sector employment). there was curiosity about correct dosages. 'yes, we have that habit. if we take antibiotics for two days and get well, we stop taking it. this causes the problem and the disease recurs. who knows? frequent use of antibiotics might turn out to be another disease.' (fgd -female, age , higher secondary education, homemaker). awareness raising activities were discussed. examples include audio-bulletins in villages, neighbourhood discussions, door-to-door promotions by community health workers, counselling by physicians and advertising in the media (television, radio and newspapers). treatment seeking was women's responsibility and their role was important in raising awareness about antibiotics and amr. 'i think the females of the community should be focused to educate about the issue as the males are usually busy. the female members of the family can teach them later'. (idi -female, age , primary education, unemployed). the findings of this qualitative study highlight multiple factors and practices around the access and use of antibiotics and the understanding of abr in matlab, bangladesh. healthcare seeking is embedded in social, economic, political and institutional structures and belief systems. individuals in resource-poor settings have limited capacity to make the same evidence-based choices that are available in more advantaged populations [ , , ] . 'structural violence' in government facilities inhibits access to the public sector for antibiotic medicines [ ] . local retail pharmacies and clinics are the accepted primary healthcare choice. advice regarding antibiotic medicines is based on common practice and reinforced by trust built on personal communication and local knowledge [ , , ] . according to the access to healthcare framework [ ] impediments to accessing prescription antibiotic medicines result from: the low density of facilities and the financial burden of purchasing antibiotics (availability/ability to reach and affordability/ability to pay); sociocultural factors and trust (acceptability/ability to seek and approachability/ability to perceive) and the abundance of unregulated services (appropriateness/ability to engage). enablers capture the willingness to learn (appropriateness/ability to engage). see figure . most were unaware of the term 'antibiotic resistance' or 'abr' although some understood the link between 'inappropriate' use and 'effectiveness'. many reported a willingness to engage in learning about amr. health literacy was built from past experience. 'trusted' brands that had provided a 'quick-fix' in the past were preferred. over sixty percent of patients' total healthcare expenditure is for pharmaceuticals, and over sixty percent of this is borne out of pocket [ ] . the average gross income per capita in bangladesh is only $us per day http://povertydata.worldbank.org/poverty/home/, the price per capsule of the three most popular antibiotics zithrin, (azithromycin), zmax (azithromycin) and cef- (cefixime) is about $us . . a standard course of any of these medicines costs between two and six $us. when medication costs impact on ability to pay there is an incentive to under-dose if this saves money. as is the case in most lmics, the informal sector in bangladesh provides the bulk of healthcare for the poor [ ] . a systematic review of the role of informal providers in developing counties cited convenience, affordability and social and cultural norms as the main reasons for their popularity [ ] . references to the informal sector, whether in housing, the labour market or healthcare are often made in a normative context, imposing unfair judgment and discrimination on disadvantaged and marginalised populations for whom these services offer the most affordable and suitable option [ ] . in this study, informants reported selfmedicating with antibiotics because they believed, in good faith, that these medicines would alleviate symptoms and lead to recovery [ ] . our findings illustrate how the acceptability of village pharmacies as providers of antibiotic medicines is embedded within the social and cultural fabric. people valued the accessibility of local stores and were reassured by the approachability and familiarity of trusted pharmacy salespersons. care seeking behaviours were motivated by good intent to remedy immediate health concerns in an expedient affordable manner [ ] . family budgets were constrained. healthcare was covered after providing food and shelter. even though antibiotics were nominally 'free of charge' when purchased from government facilities, there were service charges to consider. poorly maintained roads made people reluctant to travel to hospitals located several kilometres away when they could purchase medications and obtain healthcare advice locally. trust plays an important role in healthcare approachability [ ] . trust in government run services was eroded by perceptions of bribery, corruption, negligence and the scarcity of medicine supplies. some perceived patient safety to be at risk. informants therefore trusted pharmacy sales persons more than medical practitioners. it is essential for policy-makers to understand the underlying reasons for this trust imbalance. health sector reforms need to accommodate the roles played by both providers and seekers within a fractured pluralistic healthcare system [ ] . the availability and affordability of quality-assured medicines is an essential requirement for the delivery of primary healthcare [ ] . the commonly accepted purchasing of medicines from village pharmacies must be understood in context. the vulnerability of individuals due to circumstances such as hardship, poverty, and stress impacts on access to healthcare and medicines in ways that are often not well understood by policy-makers and regulators operating from positions of relative advantage and prosperity. the study was conducted in matlab, an hdss site since and home to numerous significant public health interventions in bangladesh [ , ] . the abacus project provides an empirical basis for understanding antibiotic use and informing context specific interventions in six lmics [ , , , , ] . the research infrastructure is well established, and we are confident that all ethical and scientific protocols were followed correctly over the course of this study. the data collection methods were standardised across the six-country study sites in the abacus project [ ] . although there were opportunities for some probing questions we followed the pre-defined topics. see sf , sf and sf . this study in matlab provides rich contextual insights into how and why people's medicine behaviours are as they are. however we do acknowledge that there may be a degree of fatigue due to the area being well-researched by the dhss over several decades. moreover, residents across matlab may be more astute about the issues discussed here than people in other rural parts of bangladesh. the findings are not intended to be representative, generalizable or comprehensive. antibiotic use in matlab villages reflects a fractured public healthcare system that remains out of touch with the issues that determine health seeking behaviours and oblivious to the erosion of trust in public infrastructure and services. future research in matlab might include ethnographic methods such as participant observation to explore further lines of enquiry regarding the way underlying social, economic and political determinants underpin behaviours [ ] . the focus on individual behaviour change needs to be complemented by attention to the dynamic complex processes responsible for knowledge acquisition. we need to understand more about the ways in which social, cultural and economic factors impact on the knowledge, attitudes, beliefs and behaviours of patients, health professionals and the broader public in regard to the use of antimicrobials in human health and agriculture [ , ] . cross discipline research, using mixed methods, is needed to focus on the dynamic interplay between contextual constraints, communication and behaviour change among the various agents involved in care seeking. informal providers are a neglected yet important group in amr research. there is a need for research to unpack the issues from the perspective of informal providers to help inform strategies to build community trust in government-run health services [ ] . awareness raising campaigns have had limited success in lmics because they have tended to focus on, and also judge, knowledge deficits [ , ] . yet mainstream public health education messages are not appropriate for those experiencing hardship and abject poverty on a daily basis [ ] . educational campaigns need to be complemented by upstream drivers of amr such as poverty and unemployment and structural violence [ , ] . at the national level, the implementation and enforcement of the bangladesh government's national drug policy must be strengthened [ , , , ] . the world health organization acknowledges the need to increase awareness and knowledge about antibiotic medicines and abr more broadly in society. specifically this means developing surveillance and research, enhancing infection control, optimizing the use of antimicrobials in human and animal health, and building sustainable investment in new medicines, diagnostic tools, and vaccines [ ] . progress will only be achieved by understanding human behaviours and actions in relation to norms, assumptions, beliefs and attitudes at the intersection between social and economic circumstances and political power structures. interventions aimed at mitigating amr must address the entrenched social, economic, political and cultural conditions in which people live, work and seek care [ , ] . sustainable solutions will require multi-sector national action plans with clear targets and lines of accountability to ensure that political will translates to effective action [ ] . accountability for amr lies with governments and global authorities both within and beyond the health sector [ , ] . developing a much stronger manuscript we learnt a lot from their feedback. the themes for the qualitative interviews were developed by jk under the guidance of hw and with support from wk and am. fieldwork was conducted by wak and am under the direction of hm as principal investigator for the abacus project. data analysis was undertaken by mc with assistance from wak, am and jsw and guidance from jk. the first draft was prepared by mc. jsw developed and finalised the draft, undertook the literature review and provided critical input for the submission and subsequent revision. all authors read and approved the final version. no potential conflict of interest was reported by the authors. the procedures followed in this study were approved by the oxford university tropical research ethics committee and the ethical review committee of the international centre for diarrhoeal disease research, bangladesh. the abacus project was funded by the wellcome trust [ ] major overseas programme; uk through indepth network. this paper is based on a master of public health thesis funded by the swedish institute. antimicrobial drugs (antifungals, antivirals and antimalarials) are public goods. inappropriate use promotes the spread of resistant pathogens and reduces treatment efficacy, thereby impacting on public health. in bangladesh, over sixty percent of patients' total healthcare expenditure is for pharmaceuticals, over sixty percent of which is borne through out-of-pocket purchasing of antibiotics from unregulated vendors without medical prescription or advice. this study found that people in rural communities in matlab were either not informed or knew little about appropriate access and use of antibiotic medicines. the principle means through which knowledge was available was village pharmacies. antimicrobial drug discovery: lessons of history and future strategies animal husbandry practices in rural bangladesh: potential risk factors for antimicrobial drug resistance and emerging diseases the threat of antimicrobial resistance in developing countries: causes and control strategies addressing the unknowns of antimicrobial resistance: quantifying and mapping the drivers of burden antimicrobial resistance -moving forward? the importance of an integrating framework for achieving the sustainable development goals: the example of health and well-being pulling together to beat superbugs: knowledge and implementation gaps 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drug policy - and recommendations in policy aspects antibiotic resistance in bangladesh: a systematic review paying out of pocket for healthcare in bangladesh -a burden on poor? evaluation of antibiotic susceptibility in wound infections: a pilot study from bangladesh patient-centred access to health care: conceptualising access at the interface of health systems and populations changing health-seeking behaviour in matlab, bangladesh: do development interventions matter? health and demographic surveillance system -matlab household socio-economic census . bangladesh: international centre for diarrhoeal disease research epidemiological transition in rural bangladesh health & demographic surveillance system profile. health and demographic surveillance system (hdss) in matlab community-level antibiotic access and use (abacus) in low-and middle-income countries: finding targets for social interventions to improve appropriate antimicrobial use -an observational multi-centre study [version ; peer review: . wellcome open res to sell or not to sell; the differences between regulatory and community demands regarding access to antibiotics in rural ghana community knowledge and practices regarding antibiotic use in rural mozambique: where is the starting point for prevention of antibiotic resistance? thematic analysis what can "thematic analysis" offer health and wellbeing researchers? antimicrobial resistance as a problem of values? views from three continents the spectre of superbugs: waste, structural violence and antimicrobial resistance in india what influences antibiotic sales in rural bangladesh? a drug dispensers' perspective informal allopathic provider knowledge and practice regarding hypertension in urban and rural bangladesh what is the role of informal healthcare providers in developing countries? a systematic review toward an epistemology of planning united nations children's fund. a vision for primary health care in the st century: towards universal health coverage and the sustainable development goal determinants of inappropriate antibiotics use in rural central ghana using a mixed methods approach. front public health antimicrobial resistance, inflammatory responses: a comparative analysis of pathogenicities, knowledge hybrids and the semantics of antibiotic use help seeking for antibiotics; is the influence of a personal social network relevant? prevention of antibiotic resistance -an epidemiological scoping review to identify research categories and knowledge gaps we are most grateful to the abacus team and the all of the informants who freely gave of their time to participate in the fgds and idis. we express our gratitude to the reviewers for their extensive commentaries. apart from key: cord- -u dhbmht authors: keske, Şiran; ergönül, Önder; tutucu, faik; karaaslan, doruk; palaoğlu, erhan; can, füsun title: the rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs date: - - journal: eur j clin microbiol infect dis doi: . /s - - - sha: doc_id: cord_uid: u dhbmht we aimed to describe the potential benefit of new rapid molecular respiratory tests (mrt) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ili). we included patients from inpatient and outpatient departments who had ili and performed mrt between january and december in a -bed private hospital in istanbul. at the end of , we implemented antimicrobial stewardship including systematic use of mrt. then, we compared our observations between the year and the year . we designed the study according to the strengthening the reporting of observational studies in epidemiology (strobe) tool. a u.s. food and drug administration (fda)-cleared multiplexed polymerase chain reaction (pcr) system (biofire filmarray, idaho technology, salt lake city, ut) which detects viruses and three bacteria was used for diagnosis. in total, patients were included; ( %) were inpatients and ( %) were older than years of age. at least one virus was detected in ( %) patients. rhinovirus/enterovirus, influenza virus, and adenovirus were the most commonly detected. among hospitalized patients, in children, a significant decrease in antibiotic use ( . % in and . % in , p = . ) was observed, but in adults, the decrease was not statistically significant ( % in and % in , p = . ). the duration of antibiotic use after the detection of virus was significantly decreased in both children and adults (p < . and p = . , respectively). by using mrt, inappropriate antibiotic use and, also, duration of inappropriate antibiotic use after the detection of virus was significantly decreased. it is time to increase the awareness about the viral etiology in respiratory tract infections (rtis) and implement mrt in clinical practice. respiratory tract infections (rtis) are the most common reasons for admission to healthcare facilities and one of the leading causes of hospitalization [ , ] . the viral pathogens in the etiology of rtis became more detectable along with the improvement in molecular diagnostic methods in recent years. in adults, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus (rsv), human coronavirus, and parainfluenza virus cause infections with considerable morbidity and mortality [ , ] , and in infants, rsv is the most common reason for rtis among hospitalized patients [ ] . the antibiotic prescription rate was reported to be more than % despite the high proportion of viral etiology [ ] [ ] [ ] [ ] . unnecessary antibiotic administration in viral infections and antimicrobial resistance prompted the implementation of antimicrobial stewardship (ams) programs. the bimplementing an antibiotic stewardship program^guideline by the infectious diseases society of america (idsa) suggested rapid viral testing for respiratory pathogens to decrease inappropriate antibiotic use [ ] . in this study, we aimed to describe the viral etiology in influenza-like illness (ili) in children and adults and to show the benefit of new rapid molecular respiratory tests (mrt) in decreasing inappropriate antibiotic use. we designed the study according to the strengthening the reporting of observational studies in epidemiology (strobe) tool [ ] . we included consequent patients from inpatient and outpatient departments, who had moderate to severe ili, and, therefore, needed further diagnostic evaluation between january and december in a -bed private hospital in istanbul. only the patients whom mrt was implemented for diagnosis were included in this study. mrt was introduced in our hospital in , and the demand for mrt increased over the years. at the end of , we enhanced our training on antimicrobial stewardship (ams). the intervention consists of training physicians to increase awareness about mrt, highlighting antimicrobial resistance because of unnecessary antibiotic consumption at ad hoc meetings in each related department. then, we compared our observations between the year and the year . this was a retrospective study performed by reviewing the patient charts. clinical features of the patients, demographic characteristics, chronic diseases including malignant disorders, diabetes mellitus, chronic kidney and liver diseases, and detailed information about antibiotic and antiviral drugs during hospitalization were collected by the chart review. complete blood count, c-reactive protein, and liver and kidney function tests were studied among all patients. bacterial cultures (throat, sputum, blood, and urine) were obtained, and procalcitonin (pct) was studied in all patients with suspicion of bacterial infection and/or in critical patients. chest x-ray and lung computed tomography was done if lower respiratory tract infection (lrti) was suspected. ili was defined according to the world health organization (who) and explained as an acute respiratory infection with fever of ≥ °c and cough and with onset within the last days [ ] . inappropriate antibiotic use was defined as antibiotic use despite detection of virus without documented and/or suspicious bacterial infection. antibiotic use duration was calculated as the duration of antibiotic use after the detection of virus in patients with inappropriate antibiotic use. for molecular detection and identification of respiratory viral pathogens, a u.s. food and drug administration (fda)cleared multiplexed respiratory polymerase chain reaction (pcr) system (mrt), biofire filmarray (idaho technology, salt lake city, ut) which detects viral respiratory pathogens (adenovirus, coronavirus hku , coronavirus nl , coronavirus e, coronavirus oc , hmpv, rhinovirus/enterovirus, influenza a, influenza a/h , influenza a/h - , influenza a/h , influenza b, parainfluenza , parainfluenza , parainfluenza , parainfluenza , and rsv) and three bacteria (bordetella pertussis, chlamydophila pneumoniae, and mycoplasma pneumoniae) was used according to the manufacturer's instructions. mrt yielded results within a few hours and the results were immediately reported to the physician of the patients by laboratory staff. in the statistical analysis, the t-test for continuous variables and the chi-square test for comparison of categorical variables were used. in the analysis, stata (statacorp, college station, tx) was used and a p-value < . was set as being in total, patients whom mrt was implemented were included; ( %) were inpatients and ( %) were older than years of age. at least one virus was detected in ( %) patients and ( %) of them were inpatients (fig. (fig. ) . in patients out of ( . %), multiple viral pathogens were detected. the overall rate of lrtis was % among inpatients. among inpatients infected with rsv, the rate of lrti was % in adults and % in children. similarly, in hmpv infections, the rate of lrti was % in adults and % in children (table ) . in total, among hospitalized patients, antibiotics were continued inappropriately in % ( table ). in children, the antibiotic continuation rate was . % in and decreased to . % in (p = . ); in adults, there was a decrease towards but this was not significant ( table ). the mean duration of inappropriate antibiotic use after the detection of virus decreased in both adults and children in when compared with . the most commonly inappropriately used antibiotics were third-generation cephalosporins, quinolones, and second-generation cephalosporins. in our study, rhinovirus/enterovirus, influenza, and adenovirus were the most commonly detected viruses in the etiology of ili. in a recent study by jain et al. [ ] , a population-based surveillance for community-acquired pneumonia among adults aged years and older was conducted. human rhinovirus, influenza a and b virus, and hmpv were the most commonly detected viruses in etiology. influenza virus and rhinovirus were reported to be the most commonly detected viruses in both adults and children in turkey [ ] . among inpatients older than years of age, % had lrti, and influenza a, rhinovirus, rsv, and hmpv were the most common agents. among children, % had lrti, and rhinovirus, rsv, and hmpv were the most common agents ( fig. ; fig. the most commonly detected viruses among all patients in whom at least one virus was detected. rsv: respiratory syncytial virus; hmpv: human metapneumovirus table ). any effort targeted to reduce the unnecessary use of antibiotics in viral pneumonia could be useful in this era of antibiotic resistance. because of the high rate of inappropriate antibiotic prescription despite the availability of mrt, we decided to improve training sessions about the diagnosis and management of respiratory system infections at the end of . then, we performed an observational comparison between the practice in and . there was a decrease in antibiotic use towards among all inpatients. however when analyzed separately, a significant reduction in children but not in adults was detected ( table ). the significant reduction of antibiotic use in children but not in adults could be explained by differences in physicians' experience in mrt. despite the fact that there was a reduction in antibiotic use in children after the detection of virus, antibiotic prescription rates were still high. in a recent study, the impact of mrt on antibiotic use was investigated and it was seen that antibiotics were still continued in about % of the patients, despite the detection of virus. this finding was explained by being a new test [ ] . in another study, afzal et al. [ ] reported that a positive result for mrt decreased antibiotic use duration and prescription rate but the decrease in antibiotic prescription was not statistically significant. timbrook et al. [ ] studied mrt in combination with pct and concluded that a lower level of pct and detection of virus by mrt were not associated with decreased use of antibiotics in rtis, but in another study, a lower level of pct in combination with detection of virus was found to be associated with shortened duration of antibiotic usage [ ] . in a randomized controlled study, the effect of both mrt and pct on antibiotic use was evaluated and the duration of antibiotic use was found to be decreased in cases of viral infection with lower levels of pct [ ] . one of the strongest parts of our study was having the opportunity of ordering mrt whenever needed in routine clinical practice, so we reached a large sample size. we had the opportunity of getting the results of c-reactive protein, pct, and mrt within a few hours, so we discriminated bacterial or viral etiology quickly. one of the limitations of this study was being conducted in a single center, but our center was unique for implementing this test in clinical practice. we are unique because mrt are still expensive to perform in routine clinical practice in other hospitals. future studies for rapid point-of-care testing for respiratory viruses might improve clinical care by reducing unnecessary antibiotic use [ ] . future cost-effective studies for the implementation of mrt will be useful. by using molecular rapid tests (mrt) in our hospital, inappropriate antibiotic use and also duration of inappropriate antibiotic use after the detection of virus was significantly decreased among inpatients. the treatment paradigm for respiratory tract infections (rtis) is changing, but molecular viral diagnostic tests are in their infancy. it is time to increase the awareness of the viral etiology in rtis and implement mrt in clinical practice. funding no funding of any kind has been received. the data were generated as part of routine work. conflict of interest none to declare. ethical approval koç university irb approved the study. informed consent not applicable. mean duration of inappropriate antibiotic use (days) . (sd . ) . (sd . ) < . . (sd . ) . (sd . ) . rates of hospitalizations for respiratory syncytial virus, human metapneumovirus, and influenza virus in older adults ecil- ): guidelines for diagnosis and treatment of human respiratory syncytial virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus community-acquired pneumonia requiring hospitalization among u.s. adults role of influenza and other respiratory viruses in admissions of adults to canadian hospitals antibiotic use for viral acute respiratory tract infections remains common ambulatory antibiotic prescribing for acute bronchitis and cough and hospital admissions for respiratory infections: time trends analysis antibiotic prescription rates for acute respiratory tract infections in us ambulatory settings prevalence of inappropriate antibiotic prescriptions among us ambulatory care visits implementing an antibiotic stewardship program: guidelines by the infectious diseases society of america and the society for healthcare epidemiology of america the strengthening the reporting of observational studies in epidemiology (strobe) statement: guidelines for reporting observational studies world health organization (who) ( ) who surveillance case definitions for ili and sari. case definitions for influenza surveillance prevalence and seasonal distribution of respiratory viruses during the - season in istanbul evaluating the impact of the multiplex respiratory virus panel polymerase chain reaction test on the clinical management of suspected respiratory viral infections in adult patients in a hospital setting clinical diagnosis, viral pcr, and antibiotic utilization in community-acquired pneumonia antibiotic discontinuation rates associated with positive respiratory viral panel and low procalcitonin results in proven or suspected respiratory infections the clinical impact of the detection of potential etiologic pathogens of community-acquired pneumonia serum procalcitonin measurement and viral testing to guide antibiotic use for respiratory infections in hospitalized adults: a randomized controlled trial routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (respoc): a pragmatic, open-label, randomised controlled trial key: cord- - uoberfu authors: tiwari, bhagyashree; sellamuthu, balasubramanian; drogui, patrick; tyagi, r.d. title: future impacts and trends in treatment of hospital wastewater date: - - journal: current developments in biotechnology and bioengineering doi: . /b - - - - . - sha: doc_id: cord_uid: uoberfu the world’s population growth and economic development result in the increased requirement of land, water, and energy. this increased demand leads to the deforestation, loss in biodiversity, imbalance in agriculture and food supply, climate change, and increase in food and travel trade, which result in emergence and reemergence of infectious diseases. this chapter discussed various emerging infectious diseases and their causative agents (buruli ulcer and bunyvirus). furthermore, this chapter further illustrates the emergence of superbugs and the associated threat due to the presence of pharmaceutical compounds in the environment. the prevalence of pharmaceuticals in the environment exerts ecotoxic effects on living organisms and causes thousands of death every year. the threats associated with the pharmaceutical presence in the environment were briefly discussed in this chapter. finally, this chapter provides the alternative methods to avoid the use of antibiotics and to develop novel treatment technologies (such as phage therapy) to degrade and remove the pharmaceutical compounds. infectious diseases are the second leading cause of death annually across the globe. the causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. since the s, an average of infectious diseases has been emerged and known to cause pandemics such as ebola, swine flu, chikungunya, and zika (table À ) [ ] . the emergence of infectious diseases has severe health and socioeconomic impacts; thus the following section discusses the various infectious disease that emerged within the last two decades and presenting few pandemic viral diseases as a suitable example [ , ] . factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (amr), and climate change. the factors responsible for the emergence of infectious diseases such as ( ) the evolution of new strain, ( ) the introduction of a host to enzootic, ( ) translocation of infected wildlife, ( ) farming practices, and ( ) others were provided. the viral evolution rate occurs through mutation and adaption, which are much faster than any other microscopic organisms that is why a large fraction of emerging and reemerging pathogens are viruses ( %). among these % of emerging viruses, rna viruses are prominent one because of their higher nucleotide substitution rate which enables them to invade and amplify in broad host range [ ] . the environment changes, social condition, and their interaction are the important factors which lead to the viral evolution and ultimately to disease emergence. the decrease in biological diversity due to deforestation, prevalence of micropollutant in natural environment, and climate change triggers the evolution of opportunistic pathogen [ ] . for instance, the outbreak of nipah virus diseases was occurred due anaplasma phagocytophilum [ ] buruli ulcers mycobacterium ulcerans [ ] to the extensive deforestation of a forest of southeast asia [ ] . the deforestation leads to migration of fruit bats for food quest to the agriculture land. these fruit bats are natural reservoir (host) of nipah virus and their migration to cultivable land lead to transmission of nipah virus disease in farm animals and subsequently in humans [ ] . the increase in temperature due to climate change affects the ecology, survival, and behavior of arthropod vectors, which subsequently changes population dynamic with increased disease transmission rate. for example, the rise in temperature from c to c decreases the proliferation time of plasmodium falciparum in anopheline mosquitoes vector from to days. usually, p. falciparum requires days to proliferate in the vector at c. however, the high temperature reduces its proliferation time by increasing egg production, by increasing metabolic rate, and by reducing the larval and pupal period duration [ ] . moreover, the proximity of natural host such as rodents and human is the ease and travel aids for the spread of emerging viruses. the viral infection begins from binding of virus to the receptor of host cell, and during the emergence of new disease, viruses develop either the ability to bind the new receptor or use homologue receptor in new host species. the spread of coronavirus (cov) which causes severe acute respiratory syndrome (sars) in human occurs due to cross-species transmission from raccoon dogs and chinese ferret badgers [ ] . the examination of wild species of cov did not have the sign of sarsÀcov infection but the cov viruses isolated from horseshoe bats have sarsÀcov infection. the cov binds to angiotensin-converting enzyme (ace ) receptor to infect humans. however, in bats, ace viral receptor is not use for infection by cov. later it was studied that the mutation in ace receptor aids the adaptation of cov in human cells. the spread of ebola, marburg, and measles viruses is some of the example of virus evolution and which contributes to the emergence of disease. the virus evolution and adaptation is difficult to predict and thus raises a question how the effect of emerging viral infection can be reduced. this requires a holistic approach to identify the drivers of emergence with effective surveillance. in an increased cases of severe fever with thrombocytopenia syndrome (sfts) were frequently reported in rural areas of china. the associated pathogens of thrombocytopenia and other similar diseases were not detected in majority of the pathogen samples which implies that the pathogen associated with sfts was newly evolved. the emergence of this unknown infection having average fatality rate of % due to organ failure leads to the implementation of enhanced surveillance to identify causative agent of sfts infection [ ] . the surveillance data revealed strain of viruses as causative of sfts infection and regarded as sfts viruses (sftsvs). sftsvs are rna virus with three single-stranded rna genomes. the complete sequencing of sftsv, rna genome reveals that they belong to genus phlebovirus, family bunyaviriade. the sftsv is transmitted in human through infected ticks and transmission of blood and other body fluid of infected person lead to human-to-human transmission of infection. the phlebovirus infection in human results in mild febrile illness. however, the major symptoms of sfts include thrombocytopenia, high fever, leukocytopenia, and lymphadenopathy. currently, it is believed that the vertical transmission of phlebovirus in arthropod vector (ticks such as haemaphysalis longicornis) helps in maintenance cycle of virus and amplification of virus occur in vertebrate host (human). the laboratory diagnosis of body fluid samples of sfts patient showed elevated level of serum and important enzymes and cofactor such as creatine kinase, alanine aminotransferase, lactate dehydrogenase, and aspartate aminotransferase. the sftsv replicates in the spleen of infected patient which increases the number of macrophages and platelets. the in vitro assay revealed that sftsv facilitates the phagocytosis of platelets by adhering on the surface of platelets and ultimately causing thrombocytopenia. the spread of sftsv in china and the detection of sftsv like viruses in other parts of world such as in the united states and europe emphasized on the urgent need of understanding of pathogenesis and transmission cycle of virus which help in the development of efficient vaccine. the changes in the hostÀenvironment lead to the evolution of opportunistic and novel pathogens due to which infectious diseases emerge. the forces which shape the emergence of disease in human are similar to the drivers found in wildlife and domestic animals. these drivers alter the interplay of hosts, environment, and pathogen thereby modulating disease ecology and developing or acclimatizing pathogen in hosts. the drivers alter interaction pattern of pathogenÀhost and environment which to either of three events ( ) altering the genetic trait of pathogen which causes severe disease in same host; ( ) emergence of pathogen in new hosts; and ( ) redistribution of pathogens that result in its establishment in new geographical area. frequent use of antimicrobial compounds and mass rearing of animals result in amr and eventually increase virulence pathogenicity of a pathogen. mass rearing of food animals to meet the demand of growing population results in intensification of genetically similar animals of same sex and age at confined place. this leads to transmission of pathogen with increases population turnover which supports emergence of novel trait. the transmission of highly pathogenic asian avian influenza a (h n hpai) is the well-known example of mass rearing [ ] . the drivers which are responsible for the disease emergence in new host include interspecies contact, wildlife migration, and increase contact between different hosts. the worldwide change in ecological landscape results in close contact between human and animals which eventually lead to transmission of microbial reservoir of animals (birds, rodents, and bats) to human. for instance, the emergence of nipah virus in human was due to transmission of virus from foraging fruit bat to pigs [ ] . the transport of food, live animals, plants with accompany insects for international trade, migration of birds, and wild animals results in geographical jump of pathogens. the bacterium ralstonia solanacearum hitchhikes to the united states via geranium plant which is imported from kenya [ ] . persisters are slow growing or nongrowing organisms which remain in stagnant during the presence of antimicrobial compound but have the capacity to resuscitate and grow under specific conditions. the persisters formation is mediated by variety of stress such as due to nutrient depletion, oxidative stress heat, acidic ph, and the presence of toxic compound (antibiotics). antibiotics such as tetracycline, rifampin, and ciprofloxacin were shown to enrich persisters formation by inhibiting protein synthesis, rna synthesis, or by antioxidative defense [ ] . persisters are the cause of biofilm infection, recurrent infection, and chronic infection and contribute toward prolongation of therapy time (e.g., tuberculosis, lyme disease). the repeated treatment of persistent infection may result in the development of drug-resistance microbes, often seen in the case of tuberculosis. persistent could be pre-or postantibiotic depending on its development in the host. the capacity of formation of persisters varies greatly among the bacterial species. for instance, persisters of mycobacterium tuberculosis are not removed from the host even after chemotherapy, while the single antibiotic treatment is sufficient for curing infection caused by streptococcus pneumoniae. the physical and psychological stress, host immune and hormonal factor, and coinfection also affect the persisters formation in the host. the mechanism behind the persisters formation is not well understood. however, it is believed that epigenetic changes, changes in dna modification, and posttranslational modification induce expression of persisters gene. the genes which involve in persisters formation are rela, sucb, hipa, ubif, and phou. the mutagenesis approach is used to study genes involved in persisters formation; however, the short antibiotic exposure, screening of partial mutant library, and aeration during antibiotic exposure are factors which result in failure of mutagenesis process for identifying persisters genes. zoonotic diseases are vector (mosquito, ticks, and bugs) aided or nonaided disease caused by bacteria, virus, parasites, prions and fungi, and transmitted from animals to human. various modes of transmission are direct contact between infected animal and human, via arthropod vector, consumption of contaminated animal food (meat and pork), and ingestion of aerosolized pathogens present in the environment. in last two decades, many vector borne pathogens spread in new geographical regions. the emergence and reemergence rate of zoonotic infection has increased inescapably due to urbanization, deforestation, climate change, international trade (frequent travel), population movement, and encroachment into animal habitats. the most emerging zoonotic vector borne diseases in the united states and canada include tick borne lyme disease, babesiosis, human granulocytic anaplasmosis and mosquito borne west nile virus (wnv), california serogroup viruses, and cache valley virus [ ] . the change in land use alters the abundance and interaction of vectors and hosts (wildlife and domestic animals) which results in emergence of vectors. for instance, deforestation in amazon and eastern africa enhances the breeding of anopheles' mosquito due to sunlight and standing water. similarly in north america, increased hunting changes the predator community and results in increased abundance of small animals such as mice, chipmunks, and shrew which are main host of spirochete borrelia burgdorferi, causative agent of lyme disease [ ] . socioeconomic changes and human activities are the another factor which governs spread and emergence of pathogen. the lyme disease was reported to occur more in high-income people in europe due to the more recreational activity and living in new homes in broad-leaf woodlands with cooccurrence of wildlife result in frequent exposure to vector. vector born zoonotic disease could be controlled by prompt identification of cause with subsequent action which requires integration of public health officials, researchers, and public [ ] . arbovirus is an acronym for arthropod-borne viruses. dengue virus, wnv, and chikungunya virus are recent examples of arboviruses which are transmitted from the arthropods (ticks, bugs, and mosquito) to vertebrate. arboviruses use arthropods as a vector (carrier) for transmission and do not causes any sickness in them. bunyaviridae, reoviridae, flaviviridae, and togaviridae are the most prevailing arboviruses families that cause diseases in human and animals [ ] . the emergence of arboviruses is governed by three factors, that is, high mutation frequency, varying anthropological behavior, and climate change. they easily adapt new host by altering receptor specificity, antigenicity, environmental conditions, and by efficient transmission. for instance, emergence of chikungunya virus in asia due to mutation in surface protein which increases its reproduction, transmission, and infection efficiency in aedes albopictus. they are able to maintain themselves for years in mosquito eggs or via attaining transstadial stages in ticks. domestic animals, livestock, and human are not important part of arbovirus life cycle because of nonviraemic transmission of arbovirus between ticks without infecting vertebrate host. this feature of arbovirus adds additional limitation for controlling disease emergence [ ] . mosquito eradication, development of live-attenuated vaccines, antiviral drugs, and molecule are few methods used to control and prevent arboviral infection. however, high mutational frequency will result in emergence of new pathogenic arboviruses. since it has been proven by genome sequencing of mosquitoes that they are the carrier of various known and unknown viruses, control of localized arthropod during endemic could be a possible solution for regulating the emergence of arbovirus [ ] . buruli ulcer (bu) is necrotizing skin disease caused by mycobacterium ulcerans recognized as one of most neglected tropical disease by world health organization (who). the bu lead to the formation of skin ulcers which results in osteomyelitis. it causes pandemic in humid tropical and subtopical region, often where humans are in proximity with slow moving or stagnant contaminated water. the transmission of m. ulcerans follows multihost transmission dynamics, that is, multiple hosts of aquatic environment such as scrapers, scavengers, and predators become contaminated with m. ulcerans and result in its passive dissemination via organism-to-organism contact. phylogenetic studies revealed that the m. ulcerans was emerged from species mycobacterium marinum which causes cutaneous disease in human and also shown to infect fish. m. ulcerans are widely distributed in africa; however, the bu cases reported in specific geographical villages. researchers postulates that a specific m. ulcerans strain might have pathogenicity or virulence to cause bu [ ] . the current knowledge lacks the understanding of spatiotemporal distribution of m. ulcerans and required detailed scenario of diversity of m. ulcerans strains existing in environment [ ] . superbug is a term coined for bacterial species which confers resistant toward majority of antibiotics. emergence of superbugs implies the frequent detection of novel bacterial pathogens which caused unrecognized life-threatening infections. the frequent emergence and spread of superbugs worldwide causes a concern that human life is heading back, toward the preantibiotic era, where the entire population of a society was wipe out due to the simple infection. united nation (un) general assembly of addresses the amr [ ] as a health emergency and acknowledge that amr has deleterious effect on human health and sustainable development. who identified a group of amr resistant "priority pathogens" that requires urgent strategic action (table À ) . who categorize these priority pathogens into three categories, that is, critical, high, and medium priority based on the need for new antibiotics. the criteria for prioritization of pathogens were developed using multicriteria decision analysis technique which includes amr pathogens which causes mortality, prevalence of resistance, transmissibility, treatability, healthcare and community burden, -year trend of resistance, preventability in hospital and community settings, and current pipeline [ ] . to fight against increasing prevalence of antibiotic-resistant superbugs and to limit the indiscriminate use of antibiotics, who prepared three groups of antibiotics namely access, watch, and reserve group to ensure appropriate prescription and use. access group comprises of antibiotics which are prescribe as in common infection as first and second choice. the first-choice antibiotics are narrow spectrum with low-resistant potential, whereas the second-choice antibiotics are broad spectrum having higher resistant potential. antibiotics such as β-lactam, chloramphenicol, and clindamycin come under this category. watch group identifies pharmacological antibiotic classes which prescribes as first or second choice but have a limited number of indication. the watch group has higher resistance potential compared with the access group. watch group comprises macrolides, quinolones and fluoroquinolones, and glycopeptides class of antibiotics [ ] . who created reserve group of antibiotics to reserve some antibiotics as the last resort in superbug infection. this group of antibiotics should be recommended as "last resort," in case of life-threatening infection when other alternatives are failed in treatment. reserve groups include eight antibiotic or antibiotic class which are aztreonam, fosfomycin, fourth-generation cephalosporins (cefepime), oxazolidinones (linezolid), fifth-generation cephalosporins (ceftaroline), tigecycline, polymyxins (polymyxin-b, colistin), and daptomycin [ ] . recently, among these eight antibiotic classes, resistant determinant against colistin was detected in people of rural vietnam. the prevalence of colistin resistant escherichia coli in intestine of resident of vietnam was extremely high, that is, approximately %. previously, mutation that causes colistin resistant was not transferable; thus it is not considered as pathogenic, as intestinal e. coli is nonpathogenic. finally, a transmissible colistin resistance gene (mcr) was detected in china, which has the potential to transfer colistin resistant to pathogenic microbes. the prevalence of mcr gene represents a serious concern regarding the emergence of superbugs that are resistant to last resort of antibiotic [ ] . currently, there are only fewer option (such as last resort antibiotics) to tackle antibiotic-resistant superbugs, and the finding of mcr gene indicates toward the needs of innovative research which results in better understanding of superbug emergence and also to research and development on quality, safe, efficacious, and affordable antimicrobial medicines, especially new antibiotics and alternative therapies, vaccines, and diagnostics. the various chapters of this book discussed about the occurrence and prevalence of human and veterinary pharmaceuticals (antibiotics, antidepressant, antidiabetic, radioactive agents, etc.) at different environmental sites. these pharmaceutical compounds are biologically active compounds that are known to have a specific mode of action (moa) in human and animals even at low concentration. due to genetic relatedness (presence of conserved gene) across species, these compounds interact with protein and cell lineage of nontarget organisms (conserved therapeutic drug targets) and elicit a response in their body (targets metabolic pathway, enzyme or mediators of cell signaling molecule). for instance, ibuprofen which is a cyclooxygenase inhibitor was found to interfere with arachidonic acid signaling pathway in marine clams ruditapes philippinarum [ ] . however, the effect of pharmaceuticals may vary from species to species due to difference in gene expression of the same gene across species or due to change in solubility or potency of drugs because of binding of pharmaceuticals with organic molecules present at environmental sites. therefore to understand the environmental risk posed by these contaminants, conceptual model of moa of pharmaceuticals was used. the moa [ ] approach involves the assessment of drug targets and its evolution between mammals and the model species. the conceptual model of moa approach in marine organisms reveals the presence of fluoxetine at environmental concentration was able to control the serotonin signaling pathway, and this alteration in physiological signaling pathway results in defects in reproduction, locomotion, and metabolism of aquatic organisms [ ] . many short-term toxicity studies reported that the drug molecules do not have an acute toxic effect on aquatic organisms because of their presence in low concentration (ng/l to low μg/l), but their constant release and exposure to aquatic biota have long-term chronic effects [ , ] . however, many laboratory studies at high concentration of pharmaceutical compounds report direct lethal effects. tetracycline concentration around À μg/l leads to low periphyton (nematode, bacteria, and algae) concentration in mesocosm stream [ ] . structure disruption in kidney and intestine of rainbow trout and brown trout due to diclofenac ( μg/l) was reported [ ] . prolonged exposure to pharmaceuticals in low concentration leads to the change in species trait and behavior of aquatic organisms. antidepressant and psychiatric drugs such as fluoxetine and oxazepam cause disruption in ecological interaction even in low concentration [ ] . indeed, even by considering that these drugs are diluted after their release, it is evident that they have a toxic effect on the aquatic ecosystem. the widespread occurrences of pharmaceuticals at various environmental sites such as in ocean, river, and groundwater raise a concern regarding the risk associated with human health. for instance, the birth control and growth stimulator agent like estrogen have the potential to cause prostate and breast cancer in humans (if the estrogen concentration is used above the threshold limit). the worldwide discharge of estrogen from livestock and human ranges approximately , and , kg/year, respectively. the us national toxicology program declared estrogen as carcinogen, the no adverse effect concentration of estrogen in human is . mg/day and frequent detection of estrogen in drinking water concentration ranging from . to . ng/l represent a health risk [ ] . estrogen was reported to cause abnormalities in animals such as permanent infertility (clover disease in sheep due to feeding on clover plant which has high phytoestrogen level) [ ] . however, human health risk assessment studies reported no appreciable risk to human due to exposure of pharmaceuticals mixture [ ] . due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. thus researchers focus on finding alternative methods to avoid use of antibiotics and developing novel treatment technologies to degrade and remove the pharmaceutical compounds. prediction of emerging signals by theoretical and bioinformatics tool will highly help to alarm the researchers, hospitals, and public about the nearby occurrence of resistant bug. such predictions are underway by monitoring microbial community dynamics in different environmental samples; however, these studies facing enormous challenges in the developmental face [ , À ] . several research studies have been conducted to observe a change in microbial metabolic pathways for a while. such study results could predict microbial interactions and route of evolution, and might apply to precisely pinpoint the emerging organism in the mixed microbial community. these studies are still under research stage, such studies are using genomic, metabolomic, and trancsriptomic tools to predict the bug emergence. recently, geoghegan and holmes [ ] attempted predicting the virus emergence with an interest of biomedicine and preventing unpredicted incidence [ ] . they have monitored the evolution of viruses in short-term period to highlight the cross-species transmission and emergence. they have concluded that predicting emergence requires a new mechanistic and integrated approach, which might permit or stop the emerging viral spread into new hosts [ ] . with the fact that microbial resistant to pharmaceuticals, the treatment options are reduced; however, alternative methods have been explored to protect human and animal from microbial illness. the microbial drug resistance leads to direct and indirect consequences as described by who report [ ] . the severe direct consequences are prolonged illness, impossible to protect the patients undergoing surgery and augmented treatment cost. whereas the indirect impacts of amr are depleting the global economy (due to the loss of productivity by sickness) and higher costs of treatment. thus who proposed a global action plan to assure preventing the transmission of infectious disease and providing complete treatment with the help of safe and effective medicines [ ] . to achieve the global action plan successfully, five objectives have been proposed by who: ( ) to improve awareness and understanding of amr; ( ) to strengthen knowledge through surveillance and research; ( ) to reduce the incidence of infection; ( ) to optimize the use of antimicrobial agents; and ( ) to ensure sustainable investment in countering amr. these objectives are likely to be met through political leaders, member states, the secretariat, and international and national partners across multiple sectors. notably, individual responsibilities like recycling unused medicines, intake of only prescribed medicines, and keeping the environment clean would highly help to achieve the who's global action plan for the betterment of human and animal health. increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. this has led to renewed interest in the potential of phage to treat bacterial pathogens. the term "phage therapy" usually refers to the treatment of bacterial infections with intact phage; however, there are other ways in which phage can be used as antibacterials. phage can be used as "lethal agent delivery systems" to introduce nonspecific or toxic antimicrobials [ , ] , or genes encoding antimicrobials [ ] into selected pathogenic bacteria. in another method (targeted gene transfer), filamentous phage can be modified to carry therapeutic genes and to target cell surface antigens or receptors on mammalian cells, transducing them by receptor-mediated endocytosis [ ] . although phages are not an antimicrobial tool in itself, this approach could be used to deliver antimicrobials to intracellular bacterial pathogens. phage secrets lysins enzymes which lyse the host bacteria. lysins are host specific and use cell wall components that are essential for viability as receptors; therefore bacterial resistance is rare [ ] . initial tests of lysins against clinically relevant gram-positive bacteria, such as methicillin-resistance staphylococcus aureus, look promising [ , ] . the use of multiple phage lysins with different cleavage sites could increase therapeutic effectiveness and further reduce the chance of bacteria developing resistance. lysins can also be used to make bacterial ghost vaccines. to produce better quality of treated sludge, wastewater treatment processes must achieve a minimum log reduction in e. coli loads and a final end product (sludge) with a maximum admissible concentration of e. coli cfu/g [dry solids (ds)] and zero salmonella in g (ds). similarly, united states environmental protection agency regulations are categorized into class a and class b sludges. class a pathogen reduction requirements are more stringent than those of class b sludges which are subject to application restrictions. class a sludges are required to reduce pathogens to below the detectable limit (, most probable number of salmonella, , plaque forming unit of enteric viruses, and , viable helminth ovum per g ds). treatment processes designed to achieve pathogen reduction to a required level can incur substantial capital and operating costs [ ] . development of phage treatment of sludge may provide long-term and cost-effective control of potentially pathogenic bacteria (e.g., e. coli and salmonella). successful phage treatment of wastewater bacterial pathogens would be dependent on the prevalence and diversity of pathogen species within wastewater. it would be virtually impossible to produce phage targeted at all pathogenic serotypes. for example, there is a high diversity of e. coli serotypes [ ] and around known salmonella serotypes [ ] . however, wastewater treatment conditions intrinsically reduce the numbers of some pathogenic bacteria. therefore there is potential for phage treatment to be used successfully in combination with biological sludge stabilization processes to reduce the abundance of specific pathogenic bacterial strains such as e. coli o . indeed, research on phage therapy for reduction of this pathogen in animal reservoirs is already underway [ ] . although phage-derived therapies have several advantages compared with antibiotics, the combined use of phage, or phage lysins, and antibiotics is an attractive treatment regime. indeed, such a product is available commercially in georgia: phagobioderm is a biodegradable polymer composite impregnated with a lytic phage cocktail and ciprofloxacin [ ] . using phage with antibiotics should increase the efficiency of treatment and reduce the emergence of resistant mutants because the surviving bacteria would need to acquire at least two separate resistance mechanisms. to kill the multidrug-resistant bacteria researchers from ibn (institute of bioengineering and nanotechnology), chin et al. [ ] developed a novel synthetic molecule and demonstrated selectively destroying five multidrug-resistant bacteria [ ] . recently polymer-based advanced drug designing to combat multidrug resistances is widely explored, which are described in detail [ , ] . due to climate change, a steady increase in temperature (about . c) was recorded in the past years, which was clearly observed on lands than the ocean in recent days [ ] . however, ice melting in north pole, increase in sea level, and alteration in raining patterns are clear and known effects of examples of global warming. climate change affects the water cycle in the following aspects: ( ) poor water quality, ( ) less availability (quantity for consumption and use), ( ) evaporation leads increases the microbial load (concentration) and toxic ions concentration, ( ) water depletion in animal-farming and agriculture (leads to food scarcity), and ( ) effects on freshwater biodiversity is still undetermined. ultimately, these changes will hugely affect wastewater microbiome (including beneficial and pathogenic microbes), the concentration of toxic pollutants and biological process performance, which was discussed in detail in chapter , treatment of wastewater containing pharmaceuticals: biological treatment. recently, who reported that climate change affects the infectious disease transmission pattern (fig. À ) . various infectious diseases and their agents (viruses, bacteria, protozoa, and multicellular parasites) have adapted (via evolution) humans as a primary host, which raises serious threat mankind to face in near future. due to the negligent, persistent and accidental activities of humans (industrial) raised the environmental pollution (chemicals including pharmaceuticals), which led to inseparable effect like climate change. furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health. thus researchers are continuously searching alternatives to these environmental problems. due to pharmaceuticals release in the environment and climate change, the survival of pathogens prolongs. high load of infectious bacterial strains dwelling in wastewater further favors the transfer of antibiotic-resistance gene. this could be a classical example for multidrug-resistant bacterial strains that are prevalence in tropical countries (like china and india). this draws immediate attention of public, health, and international sectors to fight against, pollution, climate change, and drug resistance. the advancement in medicinal research helps in control and elimination of various infectious diseases such as smallpox. however, emergence and reemergence of infectious diseases due to various factors, that is, natural evolution, climate change, amr, and many more, is a matter of concern. the knowledge about the evolution and life cycle of pathogens (bacteria, virus, or parasite) using omics study (proteome, metabolome, epigenome, and transcriptome) and via next-generation sequencing could help in the prevention and control of infectious diseases. the implantation of ecological approaches, network, and system biology approaches could provide a better understanding of the environmental factors of disease-emergence and drug-resistance mechanisms. the information gained from these approaches could help in assessing the immune mechanisms of pathogen and a developing treatment strategy. review on fate and mechanism of removal of pharmaceutical pollutants from wastewater using biological approach a highly pathogenic new bunyavirus emerged in china emerging infectious diseases of wildlife-threats to biodiversity and human health perspectives of public health laboratories in emerging infectious diseases persisters, persistent infections and the yin-yang model drivers, dynamics, and control of emerging vector-borne zoonotic diseases major emerging vector-borne zoonotic diseases of public health importance in canada global and local environmental changes as drivers of buruli ulcer emergence world health organization, global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics, world health organization carbapenem-resistant acinetobacter baumannii: epidemiology, surveillance and management complete genome sequence of pseudomonas aeruginosa pao , an opportunistic pathogen global spread of carbapenemase producing enterobacteriaceae multilevel population genetic analysis of vana and vanb enterococcus faecium causing nosocomial outbreaks in countries pathogenesis of methicillin-resistant staphylococcus aureus infection management of helicobacter pylori infection-the maastricht v/florence consensus report the disease burden associated with campylobacter spp incidence of invasive salmonella disease in sub-saharan africa: a multicentre population-based surveillance study molecular mechanisms of antibiotic resistance serotype distribution of streptococcus pneumoniae causing invasive disease in children in the post-pcv era: a systematic review and meta-analysis epidemiology of invasive haemophilus influenzae disease how do the virulence factors of shigella work together to cause disease? front host range and emerging and reemerging pathogens unhealthy landscapes: policy recommendations on land use change and infectious disease emergence anthropogenic deforestation, el niño and the emergence of nipah virus in malaysia climate change: effects on animal disease systems and implications for surveillance and control pathogen-host-environment interplay and disease emergence factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics the selection and use of essential medicines: report of the who expert committee, (including the th who model list of essential medicines and the th model list of essential medicines for children wide dissemination of colistin-resistant escherichia coli with the mobile resistance gene mcr in healthy residents in vietnam human pharmaceuticals in the marine environment: focus on exposure and biological effects in animal species health and ecological risk assessment of emerging contaminants (pharmaceuticals, personal care products, and artificial sweeteners) in surface and groundwater (drinking water) in the ganges river basin environmental impact of estrogens on human, animal and plant life: a critical review temporal dynamics of periphyton exposed to tetracycline in stream mesocosms water-borne diclofenac affects kidney and gill integrity and selected immune parameters in brown trout (salmo trutta f. fario) ocean viruses and their effects on microbial communities and biogeochemical cycles what is flux balance analysis? fast automated reconstruction of genome-scale metabolic models for microbial species and communities evolution of bidirectional costly mutualism from byproduct consumption a shared limiting resource leads to competitive exclusion in a cross-feeding system: role of environment for cross-feeder coexistence community structure follows simple assembly rules in microbial microcosms species interactions differ in their genetic robustness the spatial and metabolic basis of colony size variation predicting virus emergence amid evolutionary noise world health organization, global action plan on antimicrobial resistance targeting antibacterial agents by using drug-carrying filamentous bacteriophages use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections evolving phage vectors for cell targeted gene delivery bacteriophage lytic enzymes: novel anti-infectives phage lytic enzymes as therapy for antibiotic-resistant streptococcus pneumoniae infection in a murine sepsis model the recombinant phage lysin lysk has a broad spectrum of lytic activity against clinically relevant staphylococci, including methicillin-resistant staphylococcus aureus a novel sustained-release matrix based on biodegradable poly(ester amide)s and impregnated with bacteriophages and an antibiotic shows promise in management of infected venous stasis ulcers and other poorly healing wounds dictionary of microbiology and molecular biology antigenic formulas of the salmonella serovars bacteriophage-resistance systems in dairy starter strains: molecular analysis to application a macromolecular approach to eradicate multidrug resistant bacterial infections while mitigating drug resistance onset antibiotic-containing polymers for localized, sustained drug delivery recent advances in the treatment of pathogenic infections using antibiotics and nano-drug delivery vehicles, drug des van der valk, managing water resources under climate uncertainty key: cord- -vmsdhccp authors: mandell, lionel a.; wunderink, richard g.; anzueto, antonio; bartlett, john g.; campbell, g. douglas; dean, nathan c.; dowell, scott f.; file, thomas m.; musher, daniel m.; niederman, michael s.; torres, antonio; whitney, cynthia g. title: infectious diseases society of america/american thoracic society consensus guidelines on the management of community-acquired pneumonia in adults date: - - journal: clin infect dis doi: . / sha: doc_id: cord_uid: vmsdhccp nan improving the care of adult patients with communityacquired pneumonia (cap) has been the focus of many different organizations, and several have developed guidelines for management of cap. two of the most widely referenced are those of the infectious diseases society of america (idsa) and the american thoracic society (ats). in response to confusion regarding differences between their respective guidelines, the idsa and the ats convened a joint committee to develop a unified cap guideline document. the guidelines are intended primarily for use by emergency medicine physicians, hospitalists, and primary care practitioners; however, the extensive literature evaluation suggests that they are also an appro-reprints or correspondence: dr. lionel a. mandell priate starting point for consultation by specialists. substantial overlap exists among the patients whom these guidelines address and those discussed in the recently published guidelines for health care-associated pneumonia (hcap). pneumonia in nonambulatory residents of nursing homes and other long-term care facilities epidemiologically mirrors hospital-acquired pneumonia and should be treated according to the hcap guidelines. however, certain other patients whose conditions are included in the designation of hcap are better served by management in accordance with cap guidelines with concern for specific pathogens. . locally adapted guidelines should be implemented to improve process of care variables and relevant clinical outcomes. (strong recommendation; level i evidence.) it is important to realize that guidelines cannot always account for individual variation among patients. they are not intended to supplant physician judgment with respect to particular patients or special clinical situations. the idsa considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances. enthusiasm for developing these guidelines derives, in large part, from evidence that previous cap guidelines have led to improvement in clinically relevant outcomes. consistently beneficial effects in clinically relevant parameters (listed in table ) followed the introduction of a comprehensive protocol (including a combination of components from table ) that increased compliance with published guidelines. the first recommendation, therefore, is that cap management guidelines be locally adapted and implemented. documented benefits. . cap guidelines should address a comprehensive set of elements in the process of care rather than a single element in isolation. (strong recommendation; level iii evidence.) . development of local cap guidelines should be directed toward improvement in specific and clinically relevant outcomes. (moderate recommendation; level iii evidence.) almost all of the major decisions regarding management of cap, including diagnostic and treatment issues, revolve around the initial assessment of severity. site-of-care decisions (e.g., hospital vs. outpatient, intensive care unit [icu] vs. general ward) are important areas for improvement in cap management. hospital admission decision. . severity-of-illness scores, such as the curb- criteria (confusion, uremia, respiratory rate, low blood pressure, age years or greater), or prognostic models, such as the pneumonia severity index (psi), can be used to identify patients with cap who may be candidates for outpatient treatment. (strong recommendation; level i evidence.) . objective criteria or scores should always be supplemented with physician determination of subjective factors, including the ability to safely and reliably take oral medication and the availability of outpatient support resources. (strong recommendation; level ii evidence.) . for patients with curb- scores у , more-intensive treatment-that is, hospitalization or, where appropriate and available, intensive in-home health care services-is usually warranted. (moderate recommendation; level iii evidence.) physicians often admit patients to the hospital who could be well managed as outpatients and who would generally prefer to be treated as outpatients. objective scores, such as the curb- score or the psi, can assist in identifying patients who may be appropriate for outpatient care, but the use of such scores must be tempered by the physician's determination of additional critical factors, including the ability to safely and reliably take oral medication and the availability of outpatient support resources. icu admission decision. . direct admission to an icu is required for patients with septic shock requiring vasopressors or with acute respiratory failure requiring intubation and mechanical ventilation. (strong recommendation; level ii evidence.) . direct admission to an icu or high-level monitoring unit is recommended for patients with of the minor criteria for severe cap listed in table . (moderate recommendation; level ii evidence.) in some studies, a significant percentage of patients with cap are transferred to the icu in the first - h after hospitalization. mortality and morbidity among these patients appears to be greater than those among patients admitted directly to the icu. conversely, icu resources are often overstretched in many institutions, and the admission of patients with cap who would not directly benefit from icu care is also problematic. unfortunately, none of the published criteria for severe cap adequately distinguishes these patients from those for whom icu admission is necessary. in the present set of guidelines, a new set of criteria has been developed on the basis of data on individual risks, although the previous ats criteria format is retained. in addition to the major criteria (need for mechanical ventilation and septic shock), an expanded set of minor criteria (respiratory rate, breaths/min; arterial oxygen pressure/fraction of inspired oxygen (pao /fio ) ratio, ! ; multilobar infiltrates; confusion; blood urea nitrogen level, mg/dl; leukopenia resulting from infection; thrombocytopenia; hypothermia; or hypotension requiring aggressive fluid resuscitation) is proposed (table ). the presence of at least of these criteria suggests the need for icu care but will require prospective validation. . in addition to a constellation of suggestive clinical features, a demonstrable infiltrate by chest radiograph or other imaging technique, with or without supporting microbiological data, is required for the diagnosis of pneumonia. (moderate recommendation; level iii evidence.) recommended diagnostic tests for etiology. . patients with cap should be investigated for specific pathogens that would significantly alter standard (empirical) management decisions, when the presence of such pathogens is suspected on the basis of clinical and epidemiologic clues. (strong recommendation; level ii evidence.) recommendations for diagnostic testing remain controversial. the overall low yield and infrequent positive impact on clinical care argue against the routine use of common tests, such as blood and sputum cultures. conversely, these cultures may have a major impact on the care of an individual patient and are important for epidemiologic reasons, including the antibiotic susceptibility patterns used to develop treatment guidelines. a list of clinical indications for more extensive diagnostic testing (table ) was, therefore, developed, primarily on the basis of criteria: ( ) when the result is likely to change individual antibiotic management and ( ) when the test is likely to have the highest yield. . routine diagnostic tests to identify an etiologic diagnosis are optional for outpatients with cap. (moderate recommendation; level iii evidence.) . pretreatment blood samples for culture and an expectorated sputum sample for stain and culture (in patients with a productive cough) should be obtained from hospitalized patients with the clinical indications listed in table but are optional for patients without these conditions. (moderate recommendation; level i evidence.) . pretreatment gram stain and culture of expectorated sputum should be performed only if a good-quality specimen can be obtained and quality performance measures for collection, transport, and processing of samples can be met. (moderate recommendation; level ii evidence.) . patients with severe cap, as defined above, should at least have blood samples drawn for culture, urinary antigen tests for legionella pneumophila and streptococcus pneumoniae performed, and expectorated sputum samples collected for culture. for intubated patients, an endotracheal aspirate sample should be obtained. (moderate recommendation; level ii evidence.) the most clear-cut indication for extensive diagnostic testing is in the critically ill cap patient. such patients should at least have blood drawn for culture and an endotracheal aspirate obtained if they are intubated; consideration should be given to more extensive testing, including urinary antigen tests for l. pneumophila and s. pneumoniae and gram stain and culture of expectorated sputum in nonintubated patients. for inpatients without the clinical indications listed in table , diagnostic testing is optional (but should not be considered wrong). empirical antimicrobial therapy. empirical antibiotic recommendations (table ) have not changed significantly from those in previous guidelines. increasing evidence has strengthened the recommendation for combination empirical therapy for severe cap. only recently released antibiotic has been added to the recommendations: ertapenem, as an acceptable b-lactam alternative for hospitalized patients with risk factors for infection with gram-negative pathogens other than pseudomonas aeruginosa. at present, the committee is awaiting further evaluation of the safety of telithromycin by the us food and drug administration before making its final recommendation regarding this drug. recommendations are generally for a class of antibiotics rather than for a specific drug, unless outcome data clearly favor one drug. because overall efficacy remains good for many classes of agents, the more potent drugs are given preference because of their benefit in decreasing the risk of selection for antibiotic resistance. . a b-lactam plus a macrolide (strong recommendation; level i evidence) (preferred b-lactam agents include cefotaxime, ceftriaxone, and ampicillin; ertapenem for selected patients; with doxycycline [level iii evidence] as an alternative to the macrolide. a respiratory fluoroquinolone should be used for penicillin-allergic patients.) increasing resistance rates have suggested that empirical therapy with a macrolide alone can be used only for the treat-ment of carefully selected hospitalized patients with nonsevere disease and without risk factors for infection with drug-resistant pathogens. however, such monotherapy cannot be routinely recommended. inpatient, icu treatment . a b-lactam (cefotaxime, ceftriaxone, or ampicillin-sulbactam) plus either azithromycin (level ii evidence) or a fluoroquinolone (level i evidence) (strong recommendation) (for penicillin-allergic patients, a respiratory fluoroquinolone and aztreonam are recommended.) . for pseudomonas infection, use an antipneumococcal, antipseudomonal b-lactam (piperacillin-tazobactam, cefepime, imipenem, or meropenem) plus either ciprofloxacin or levofloxacin ( -mg dose) or the above b-lactam plus an aminoglycoside and azithromycin or the above b-lactam plus an aminoglycoside and an antipneumococcal fluoroquinolone (for penicillin-allergic patients, substitute aztreonam for the above b-lactam). (moderate recommendation; level iii evidence.) . for community-acquired methicillin-resistant staphylococcus aureus infection, add vancomycin or linezolid. (moderate recommendation; level iii evidence.) infections with the overwhelming majority of cap pathogens will be adequately treated by use of the recommended empirical regimens. the emergence of methicillin-resistant s. aureus as a cap pathogen and the small but significant incidence of cap due to p. aeruginosa are the exceptions. these pathogens occur in specific epidemiologic patterns and/or with certain clinical presentations, for which empirical antibiotic coverage may be warranted. however, diagnostic tests are likely to be of high yield for these pathogens, allowing early discontinuation of empirical treatment if results are negative. the risk factors are included in the table recommendations for indications for increased diagnostic testing. risk factors for other uncommon etiologies of cap are listed in table , and recommendations for treatment are included in table . pathogen-directed therapy. definitions and classification. . the use of a systematic classification of possible causes of failure to respond, based on time of onset and type of failure (table ) , is recommended. (moderate recommendation; level ii evidence.) as many as % of patients with cap may not respond appropriately to initial antibiotic therapy. a systematic approach to these patients (table ) will help to determine the cause. because determination of the cause of failure is more accurate if the original microbiological etiology is known, risk factors for nonresponse or deterioration (table ) figure prominently in the list of situations in which more aggressive and/ or extensive initial diagnostic testing is warranted ( [ ] . despite advances in antimicrobial therapy, rates of mortality due to pneumonia have not decreased significantly since penicillin became routinely available [ ] . groups interested in approaches to the management of cap include professional societies, such as the american thoracic society (ats) and the infectious diseases society of america (idsa); government agencies or their contract agents, such as the center for medicare and medicaid services and the department of veterans affairs; and voluntary accrediting agencies, such as the joint commission on accreditation of healthcare organizations. in addition, external review groups and consumer groups have chosen cap outcomes as major quality indicators. such interest has resulted in numerous guidelines for the management of cap [ ] . some of these guidelines represent truly different perspectives, including differences in health care systems, in the availability of diagnostic tools or therapeutic agents, or in either the etiology or the antibiotic susceptibility of common causative microorganisms. the most widely referenced guidelines in the united states have been those published by the ats [ , ] and the idsa [ ] [ ] [ ] . differences, both real and imagined, between the ats and idsa guidelines have led to confusion for individual physicians, as well as for other groups who use these published guidelines rather than promulgating their own. in response to this concern, the idsa and the ats convened a joint committee to develop a unified cap guideline document. this document represents a consensus of members of both societies, and both governing councils have approved the statement. purpose and scope. the purpose of this document is to update clinicians with regard to important advances and controversies in the management of patients with cap. the committee chose not to address cap occurring in immunocompromised patients, including solid organ, bone marrow, or stem cell transplant recipients; patients receiving cancer chemotherapy or long-term ( days) high-dose corticosteroid treatment; and patients with congenital or acquired immunodeficiency or those infected with hiv who have cd cell counts ! cells/mm , although many of these patients may be infected with the same microorganisms. pneumonia in children (р years of age) is also not addressed. substantial overlap exists among the patients these guidelines address and those discussed in the recently published guidelines for health care-associated pneumonia (hcap) [ ] . two issues are pertinent: ( ) an increased risk of infection with drugresistant isolates of usual cap pathogens, such as streptococcus pneumoniae, and ( ) an increased risk of infection with less common, usually hospital-associated pathogens, such as pseudomonas and acinetobacter species and methicillin-resistant staphylococcus aureus (mrsa). pneumonia in nonambulatory residents of nursing homes and other long-term care facilities epidemiologically mirrors hospital-acquired pneumonia and should be treated according to the hcap guidelines. however, certain other patients whose conditions are included under the designation of hcap are better served by management in ac-cordance with cap guidelines with concern for specific pathogens. for example, long-term dialysis alone is a risk for mrsa infection but does not necessarily predispose patients to infection with other hcap pathogens, such as pseudomonas aeruginosa or acinetobacter species. on the other hand, certain patients with chronic obstructive pulmonary disease (copd) are at greater risk for infection with pseudomonas species but not mrsa. these issues will be discussed in specific sections below. the committee started with the premise that mortality due to cap can be decreased. we, therefore, have placed the greatest emphasis on aspects of the guidelines that have been associated with decreases in mortality. for this reason, the document focuses mainly on management and minimizes discussions of such factors as pathophysiology, pathogenesis, mechanisms of antibiotic resistance, and virulence factors. the committee recognizes that the majority of patients with cap are cared for by primary care, hospitalist, and emergency medicine physicians [ ] , and these guidelines are, therefore, directed primarily at them. the committee consisted of infectious diseases, pulmonary, and critical care physicians with interest and expertise in pulmonary infections. the expertise of the committee and the extensive literature evaluation suggest that these guidelines are also an appropriate starting point for consultation by these types of physicians. although much of the literature cited originates in europe, these guidelines are oriented toward the united states and canada. although the guidelines are generally applicable to other parts of the world, local antibiotic resistance patterns, drug availability, and variations in health care systems suggest that modification of these guidelines is prudent for local use. methodology. the process of guideline development started with the selection of committee cochairs by the presidents of the idsa [ ] and ats [ ] , in consultation with other leaders in the respective societies. the committee cochairs were charged with selection of the rest of the committee. the idsa members were those involved in the development of previous idsa cap guidelines [ ] , whereas ats members were chosen in consultation with the leadership of the mycobacteria tuberculosis and pulmonary infection assembly, with input from the chairs of the clinical pulmonary and critical care assemblies. committee members were chosen to represent differing expertise and viewpoints on the various topics. one acknowledged weakness of this document is the lack of representation by primary care, hospitalist, and emergency medicine physicians. the cochairs generated a general outline of the topics to be covered that was then circulated to committee members for input. a conference phone call was used to review topics and to discuss evidence grading and the general aims and expectations of the document. the topics were divided, and committee members were assigned by the cochairs and charged with presentation of their topic at an initial face-to-face meeting, as well as with development of a preliminary document dealing with their topic. controversial topics were assigned to committee members, from each society. an initial face-to-face meeting of a majority of committee members involved presentations of the most controversial topics, including admission decisions, diagnostic strategies, and antibiotic therapy. prolonged discussions followed each presentation, with consensus regarding the major issues achieved before moving to the next topic. with input from the rest of the committee, each presenter and committee member assigned to the less controversial topics prepared an initial draft of their section, including grading of the evidence. iterative drafts of the statement were developed and distributed by e-mail for critique, followed by multiple revisions by the primary authors. a second face-to-face meeting was also held for discussion of the less controversial areas and further critique of the initial drafts. once general agreement on the separate topics was obtained, the cochairs incorporated the separate documents into a single statement, with substantial editing for style and consistency. the document was then redistributed to committee members to review and update with new information from the literature up to june . recommended changes were reviewed by all committee members by e-mail and/or conference phone call and were incorporated into the final document by the cochairs. this document was then submitted to the societies for approval. each society independently selected reviewers, and changes recommended by the reviewers were discussed by the committee and incorporated into the final document. the guideline was then submitted to the idsa governing council and the ats board of directors for final approval. grading of guideline recommendations. initially, the committee decided to grade only the strength of the evidence, using a -tier scale (table ) used in a recent guideline from both societies [ ] . in response to reviewers' comments and the maturation of the field of guideline development [ ] , a separate grading of the strength of the recommendations was added to the final draft. more extensive and validated criteria, such as grade [ ] , were impractical for use at this stage. the -tier scale similar to that used in other idsa guideline documents [ ] and familiar to many of the committee members was therefore chosen. the strength of each recommendation was graded as "strong," "moderate," or "weak." each committee member independently graded each recommendation on the basis of not only the evidence but also expert interpretation and clinical applicability. the final grading of each recommendation was a composite of the individual committee members' grades. for the final document, a strong recommendation required у (of ) of the members to consider it to be strong and the majority of the others to grade it as moderate. the implication of a strong recommendation is that most patients should receive that intervention. significant variability in the management of patients with cap is well documented. some who use guidelines suggest that this variability itself is undesirable. industrial models suggesting that variability per se is undesirable may not always be relevant to medicine [ ] . such models do not account for substantial variability among patients, nor do they account for variable end points, such as limitation of care in patients with end-stage underlying diseases who present with cap. for this reason, the committee members feel strongly that % compliance with guidelines is not the desired goal. however, the rationale for variation from a strongly recommended guideline should be apparent from the medical record. conversely, moderate or weak recommendations suggest that, even if a majority would follow the recommended management, many practitioners may not. deviation from guidelines may occur for a variety of reasons [ , ] . one document cannot cover all of the variable settings, unique hosts, or epidemiologic patterns that may dictate alternative management strategies, and physician judgment should always supersede guidelines. this is borne out by the finding that deviation from guidelines is greatest in the treatment of patients with cap admitted to the icu [ ] . in addition, few of the recommendations have level i evidence to support them, and most are, therefore, legitimate topics for future research. subsequent publication of studies documenting that care that deviates from guidelines results in better outcomes will stimulate revision of the guidelines. the committee anticipates that this will occur, and, for this reason, both the ats and idsa leaderships have committed to the revision of these guidelines on a regular basis. we recognize that these guidelines may be used as a measure of quality of care for hospitals and individual practitioners. although these guidelines are evidence based, the committee strongly urges that deviations from them not necessarily be considered substandard care, unless they are accompanied by evidence for worse outcomes in a studied population. . locally adapted guidelines should be implemented to improve process of care variables and relevant clinical outcomes. (strong recommendation; level i evidence.) enthusiasm for developing this set of cap guidelines derives, in large part, from evidence that previous cap guidelines have led to improvement in clinically relevant outcomes [ , [ ] [ ] [ ] . protocol design varies among studies, and the preferable randomized, parallel group design has been used in only a small minority. confirmatory studies that use randomized, parallel groups with precisely defined treatments are still needed, but a consistent pattern of benefit is found in the other types of level i studies. documented benefits. published protocols have varied in primary focus and comprehensiveness, and the corresponding benefits vary from one study to another. however, the most impressive aspect of this literature is the consistently beneficial effect seen in some clinically relevant parameter after the introduction of a protocol that increases compliance with published guidelines. a decrease in mortality with the introduction of guidelinebased protocols was found in several studies [ , ] . a -year study of , patients with pneumonia who were admitted during implementation of a pneumonia guideline demonstrated that the crude -day mortality rate was . % lower with the guideline (adjusted or, . ; % ci, . - . ) [ ] , compared with that among patients treated concurrently by nonaffiliated physicians. after implemention of a practice guideline at one spanish hospital [ ] , the survival rate at days was higher (or, . ; % ci, . - . ) than at baseline and in comparison with other hospitals without overt protocols. lower mortality was seen in other studies, although the differences were not statistically significant [ , ] . studies that documented lower mortality emphasized increasing the number of patients receiving guideline-recommended antibiotics, confirming results of the multivariate analysis of a retrospective review [ ] . when the focus of a guideline was hospitalization, the number of less ill patients admitted to the hospital was consistently found to be lower. using admission decision support, a prospective study of emergency department (ed) visits in hospitals randomized between pathway and "conventional" management found that admission rates among low-risk patients at pathway hospitals decreased (from % to % of patients in pneumonia severity index [psi] classes i-iii; p ! ) without differences in patient satisfaction scores or rate of . readmission [ ] . calculating the psi score and assigning the risk class, providing oral clarithromycin, and home nursing follow-up significantly ( ) decreased the number of low-p p . mortality-risk admissions [ ] . however, patient satisfaction among outpatients was lower after implementation of this guideline, despite survey data that suggested most patients would prefer outpatient treatment [ ] . of patients discharged from the ed, % required hospitalization within days, although another study showed lower readmission rates with the use of a protocol [ ] . admission decision support derived from the ats guideline [ ] recommendations, combined with outpatient antibiotic recommendations, reduced the cap hospitalization rate from . % to . % [ ] , and admission rates for other diagnoses were unchanged. not surprisingly, the resultant overall cost of care decreased by half ( ). p p . protocols using guidelines to decrease the duration of hospitalization have also been successful. guideline implementation in connecticut hospitals decreased the mean length of hospital stay (los) from to days ( ) [ ] . an ed-p ! . based protocol decreased the mean los from . to . days ( ), with the benefits of guideline implementation p ! . maintained years after the initial study [ ] . a -site trial, randomized by physician group, of guideline alone versus the same guideline with a multifaceted implementation strategy found that addition of an implementation strategy was associated with decreased duration of intravenous antibiotic therapy and los, although neither decrease was statistically significant [ ] . several other studies used guidelines to significantly shorten the los, by an average of . days [ , ] . markers of process of care can also change with the use of a protocol. the time to first antibiotic dose has been effectively decreased with cap protocols [ , , ] . a randomized, parallel group study introduced a pneumonia guideline in of small oklahoma hospitals [ ] , with the identical protocol implemented in the remaining hospitals in a second phase. serial measurement of key process measures showed significant improvement in time to first antibiotic dose and other variables, first in the initial hospitals and later in the remaining hospitals. implementing a guideline in the ed halved the time to initial antibiotic dose [ ] . . cap guidelines should address a comprehensive set of elements in the process of care rather than a single element in isolation. (strong recommendation; level iii evidence.) common to all of the studies documented above, a com- prehensive protocol was developed and implemented, rather than one addressing a single aspect of cap care. no study has documented that simply changing metric, such as time to first antibiotic dose, is associated with a decrease in mortality. elements important in cap guidelines are listed in table . of these, rapid and appropriate empirical antibiotic therapy is consistently associated with improved outcome. we have also included elements of good care for general medical inpatients, such as early mobilization [ ] and prophylaxis against thromboembolic disease [ ] . although local guidelines need not include all elements, a logical constellation of elements should be addressed. in instituting cap protocol guidelines, the outcomes most relevant to the individual center or medical system should be addressed first. unless a desire to change clinically relevant outcomes exists, adherence to guidelines will be low, and institutional resources committed to implement the guideline are likely to be insufficient. guidelines for the treatment of pneumonia must use approaches that differ from current practice and must be successfully implemented before process of care and outcomes can change. for example, rhew et al. [ ] designed a guideline to decrease los that was unlikely to change care, because the recommended median los was longer than the existing los for cap at the study hospitals. the difficulty in implementing guidelines and changing physician behavior has also been documented [ , ] . clinically relevant outcome parameters should be evaluated to measure the effect of the local guideline. outcome parameters that can be used to measure the effect of implementation of a cap guideline within an organization are listed in table . just as it is important not to focus on one aspect of care, studying more than one outcome is also important. improvements in one area may be offset by worsening in a related area; for example, decreasing admission of low-acuity patients might increase the number of return visits to the ed or hospital readmissions [ ] . almost all of the major decisions regarding management of cap, including diagnostic and treatment issues, revolve around the initial assessment of severity. we have, therefore, organized the guidelines to address this issue first. hospital admission decision. the initial management decision after diagnosis is to determine the site of care-outpatient, hospitalization in a medical ward, or admission to an icu. the decision to admit the patient is the most costly issue in the management of cap, because the cost of inpatient care for pneumonia is up to times greater than that of outpatient care [ ] and consumes the majority of the estimated $ . -$ billion spent yearly on treatment. other reasons for avoiding unnecessary admissions are that patients at low risk for death who are treated in the outpatient setting are able to resume normal activity sooner than those who are hospitalized, and % are reported to prefer outpatient therapy [ , ] . hospitalization also increases the risk of thromboembolic events and superinfection by more-virulent or resistant hospital bacteria [ ] . . severity-of-illness scores, such as the curb- criteria (confusion, uremia, respiratory rate, low blood pressure, age years or greater), or prognostic models, such as the psi, can be used to identify patients with cap who may be candidates for outpatient treatment. (strong recommendation; level i evidence.) significant variation in admission rates among hospitals and among individual physicians is well documented. physicians often overestimate severity and hospitalize a significant number of patients at low risk for death [ , , ] . because of these issues, interest in objective site-of-care criteria has led to attempts by a number of groups to develop such criteria [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . the relative merits and limitations of various proposed criteria have been carefully evaluated [ ] . the most interesting are the psi [ ] and the british thoracic society (bts) criteria [ , ] . the psi is based on derivation and validation cohorts of , and , hospitalized patients with cap, respectively, plus an additional combined inpatients and outpatients [ ] . the psi stratifies patients into mortality risk classes, and its ability to predict mortality has been confirmed in multiple subsequent studies. on the basis of associated mortality rates, it has been suggested that risk class i and ii patients should be treated as outpatients, risk class iii patients should be treated in an observation unit or with a short hospitalization, and risk class iv and v patients should be treated as inpatients [ ] . yealy et al. [ ] conducted a cluster-randomized trial of low-, moderate-, and high-intensity processes of guideline implementation in eds in the united states. their guideline used the psi for admission decision support and included recommendations for antibiotic therapy, timing of first antibiotic dose, measurement of oxygen saturation, and blood cultures for admitted patients. eds with moderate-to high-intensity guideline implementation demonstrated more outpatient treatment of low-risk patients and higher compliance with antibiotic recommendations. no differences were found in mortality rate, rate of hospitalization, median time to return to work or usual activities, or patient satisfaction. this study differs from those reporting a mortality rate difference [ , ] in that many hospitalized patients with pneumonia were not included. in addition, eds with low-intensity guideline implementation formed the comparison group, rather than eds practicing nonguideline, usual pneumonia care. the bts original criteria of have subsequently been modified [ , ] . in the initial study, risk of death was increased -fold if a patient, at the time of admission, had at least of the following conditions: tachypnea, diastolic hypotension, and an elevated blood urea nitrogen (bun) level. these criteria appear to function well except among patients with underlying renal insufficiency and among elderly patients [ , ] . the most recent modification of the bts criteria includes easily measurable factors [ ] . multivariate analysis of patients identified the following factors as indicators of increased mortality: confusion (based on a specific mental test or disorientation to person, place, or time), bun level mmol/l ( mg/dl), respiratory rate у breaths/min, low blood pressure (systolic, ! mm hg; or diastolic, р mm hg), and age у years; this gave rise to the acronym curb- . in the derivation and validation cohorts, the -day mortality among patients with , , or factors was . %, . %, and . %, respectively. mortality was higher when , , or factors were present and was reported as . %, %, and %, respectively. the authors suggested that patients with a curb- score of - be treated as outpatients, that those with a score of be admitted to the wards, and that patients with a score of у often required icu care. a simplified version (crb- ), which does not require testing for bun level, may be appropriate for decision making in a primary care practitioner's office [ ] . the use of objective admission criteria clearly can decrease the number of patients hospitalized with cap [ , , , ] . whether the psi or the curb- score is superior is unclear, because no randomized trials of alternative admission criteria exist. when compared in the same population, the psi classified a slightly larger percentage of patients with cap in the lowrisk categories, compared with the curb or curb- criteria, while remaining associated with a similar low mortality rate among patients categorized as low risk [ ] . several factors are important in this comparison. the psi includes different variables and, therefore, relies on the availability of scoring sheets, limiting its practicality in a busy ed [ ] . in contrast, the curb- criteria are easily remembered. however, curb- has not been as extensively studied as the psi, especially with prospective validation in other patient populations (e.g., the indigent inner-city population), and has not been specifically studied as a means of reducing hospital admission rates. in eds with sufficient decision support resources (either human or computerized), the benefit of greater experience with the psi score may favor its use for screening patients who may be candidates for outpatient management [ , [ ] [ ] [ ] . . objective criteria or scores should always be supplemented with physician determination of subjective factors, including the ability to safely and reliably take oral medication and the availability of outpatient support resources. (strong recommendation; level ii evidence.) studies show that certain patients with low psi or curb- scores [ , , ] require hospital admission, even to the icu [ , , ] . both scores depend on certain assumptions. one is that the main rationale for admission of a patient with cap is risk of death. this assumption is clearly not valid in all cases. another is that the laboratory and vital signs used for scoring are stable over time rather than indicative of transient abnormalities. this is also not true in all cases. therefore, dynamic assessment over several hours of observation may be more accurate than a score derived at a single point in time. although advantageous to making decisions regarding hospital admission, sole reliance on a score for the hospital admission decision is unsafe. reasons for the admission of low-mortality-risk patients fall into categories: ( ) complications of the pneumonia itself, ( ) exacerbation of underlying diseases(s), ( ) inability to reliably take oral medications or receive outpatient care, and/or ( ) multiple risk factors falling just above or below thresholds for the score [ ] . use of the psi score in clinical trials has demonstrated some of its limitations, which may be equally applicable to other scoring techniques. a modification of the original psi score was needed when it was applied to the admission decision. an arterial saturation of ! % or an arterial oxygen pressure (pao ) of ! mm hg as a complication of the pneumonia, was added as a sole indicator for admission for patients in risk classes i-iii as an added "margin of safety" in one trial [ ] . in addition to patients who required hospital admission because of hypoxemia, a subsequent study identified patients in low psi risk classes (i-iii) who needed hospital admission because of shock, decompensated coexisting illnesses, pleural effusion, inability to maintain oral intake, social problems (the patient was dependent or no caregiver was available), and lack of response to previous adequate empirical antibiotic therapy [ ] . of patients in low psi risk classes who were treated as inpatients, ( %) presented with at least of these factors. other medical or psychosocial needs requiring hospital care include intractable vomiting, injection drug abuse, severe psychiatric illness, homelessness, poor overall functional status [ ] , and cognitive dysfunction [ , ] . the psi score is based on a history of diseases that increase risk of death, whereas the curb- score does not directly address underlying disease. however, pneumonia may exacerbate an underlying disease, such as obstructive lung disease, congestive heart failure, or diabetes mellitus, which, by themselves, may require hospital admission [ , ] . atlas et al. [ ] were able to reduce hospital admissions among patients in psi risk classes i-iii from % in a retrospective control group to % in a psi-based intervention group. ten of patients in the latter group (compared with patients in the control population) were subsequently admitted, several for reasons unrelated to their pneumonia. also, the presence of rare illnesses, such as neuromuscular or sickle cell disease, may require hospitalization but not affect the psi score. the necessary reliance on dichotomous predictor variables (abnormal vs. normal) in most criteria and the heavy reliance on age as a surrogate in the psi score may oversimplify their use for admission decisions. for example, a previously healthy -year-old patient with severe hypotension and tachycardia and no additional pertinent prognostic factors would be placed in risk class ii, whereas a -year-old man with a history of localized prostate cancer diagnosed months earlier and no other problems would be placed in risk class iv [ ] . finally, patient satisfaction was lower among patients treated outside the hospital in one study with a psi-based intervention group [ ] , suggesting that the savings resulting from use of the psi may be overestimated and that physicians should consider additional factors not measured by the psi. . for patients with curb- scores у , more-intensive treatment-that is, hospitalization or, where appropriate and available, intensive in-home health care services-is usually warranted. (moderate recommendation; level iii evidence.) although the psi and curb- criteria are valuable aids in avoiding inappropriate admissions of low-mortality-risk patients, another important role of these criteria may be to help identify patients at high risk who would benefit from hospitalization. the committee preferred the curb- criteria because of ease of use and because they were designed to measure illness severity more than the likelihood of mortality. patients with a curb- score у are not only at increased risk of death but also are likely to have clinically important physiologic derangements requiring active intervention. these patients should usually be considered for hospitalization or for aggressive in-home care, where available. in a cohort of ∼ patients, the mortality with a curb- score of was only . %, whereas - points were associated with % mortality [ ] . because the psi score is not based as directly on severity of illness as are the curb- criteria, a threshold for patients who would require hospital admission or intensive outpatient treatment is harder to define. the higher the score, the greater the need for hospitalization. however, even a patient who meets criteria for risk class v on the basis of very old age and multiple stable chronic illnesses may be successfully managed as an outpatient [ ] . . direct admission to an icu is required for patients with septic shock requiring vasopressors or with acute respiratory failure requiring intubation and mechanical ventilation. (strong recommendation; level ii evidence.) the second-level admission decision is whether to place the patient in the icu or a high-level monitoring unit rather than on a general medical floor. approximately % of hospitalized patients with cap require icu admission [ ] [ ] [ ] , but the indications vary strikingly among patients, physicians, hospitals, and different health care systems. some of the variability among institutions results from the availability of high-level monitoring or intermediate care units appropriate for patients at increased risk of complications. because respiratory failure is the major reason for delayed transfer to the icu, simple cardiac monitoring units would not meet the criteria for a highlevel monitoring unit for patients with severe cap. one of the most important determinants of the need for icu care is the presence of chronic comorbid conditions [ ] [ ] [ ] [ ] [ ] . however, approximately one-third of patients with severe cap were previously healthy [ ] . the rationale for specifically defining severe cap is -fold: • appropriate placement of patients optimizes use of limited icu resources. • transfer to the icu for delayed respiratory failure or delayed onset of septic shock is associated with increased mortality [ ] . although low-acuity icu admissions do occur, the major concern is initial admission to the general medical unit, with subsequent transfer to the icu. as many as % of patients with cap who ultimately require icu admission were initially admitted to a non-icu setting [ ] . many delayed transfers to the icu represent rapidly progressive pneumonia that is not obvious on admission. however, some have subtle findings, including those included in the minor criteria in table , which might warrant direct admission to the icu. • the distribution of microbial etiologies differs from that of cap in general [ ] [ ] [ ] [ ] , with significant implications for diagnostic testing and empirical antibiotic choices. avoidance of inappropriate antibiotic therapy has also been associated with lower mortality [ , ] . • patients with cap appropriate for immunomodulatory treatment must be identified. the systemic inflammatory response/severe sepsis criteria typically used for generic sepsis trials may not be adequate when applied specifically to severe cap [ ] . for example, patients with unilateral lobar pneumonia may have hypoxemia severe enough to meet criteria for acute lung injury but not have a systemic response. several criteria have been proposed to define severe cap. most case series have defined it simply as cap that necessitates icu admission. objective criteria to identify patients for icu admission include the initial ats definition of severe cap [ ] and its subsequent modification [ , ] , the curb criteria [ , ] , and psi severity class v (or iv and v) [ ] . however, none of these criteria has been prospectively validated for the icu admission decision. recently, these criteria were retrospectively evaluated in a cohort of patients with cap admitted to the icu [ ] . all were found to be both overly sensitive and nonspecific in comparison with the original clinical decision to admit to the icu. revisions of the criteria or alternative criteria were, therefore, recommended. for the revised criteria, the structure of the modified ats criteria for severe cap was retained [ ] . the major criteriamechanical ventilation with endotracheal intubation and septic shock requiring vasopressors-are absolute indications for admission to an icu. in contrast, the need for icu admission is less straightforward for patients who do not meet the major criteria. on the basis of the published operating characteristics of the criteria, no single set of minor criteria is adequate to define severe cap. both the ats minor criteria [ ] and the curb criteria [ ] have validity when predicting which patients will be at increased risk of death. therefore, the ats minor criteria and the curb variables were included in the new proposed minor criteria (table ) . age, by itself, was not felt to be an appropriate factor for the icu admission decision, but the remainder of the curb- criteria [ ] were retained as minor criteria (with the exception of hypotension requiring vasopressors as a major criterion). rather than the complex criteria for confusion in the original curb studies, the definition of confusion should be new-onset disorientation to person, place, or time. three additional minor criteria were added. leukopenia (white blood cell count, ! cells/mm ) resulting from cap has consistently been associated with excess mortality, as well as with an increased risk of complications such as acute respiratory distress syndrome (ards) [ , , [ ] [ ] [ ] [ ] [ ] . in addition, leukopenia is seen not only in bacteremic pneumococcal disease but also in gram-negative cap [ , ] . when leukopenia occurs in patients with a history of alcohol abuse, the adverse manifestations of septic shock and ards may be delayed or masked. therefore, these patients were thought to benefit from icu monitoring. the coagulation system is often activated in cap, and development of thrombocytopenia (platelet count, ! , cells/mm ) is also associated with a worse prognosis [ , [ ] [ ] [ ] . nonexposure hypothermia (core temperature, ! Њc) also carries an ominous prognosis in cap [ , ] . the committee felt that there was sufficient justification for including these additional factors as minor criteria. other factors associated with increased mortality due to cap were also considered, including acute alcohol ingestion and delirium tremens [ , , ] , hypoglycemia and hyperglycemia, occult metabolic acidosis or elevated lactate levels [ ] , and hyponatremia [ ] . however, many of these criteria overlap with those selected. future studies validating the proposed criteria should record these factors as well, to determine whether addition or substitution improves the predictive value of our proposed criteria. with the addition of more minor criteria, the threshold for icu admission was felt to be the presence of at least minor criteria, based on the mortality association with the curb criteria. selecting criteria appears to be too nonspecific, as is demonstrated by the initial ats criteria [ ] . whether each of the criteria is of equal weight is also not clear. therefore, prospective validation of this set of criteria is clearly needed. . in addition to a constellation of suggestive clinical features, a demonstrable infiltrate by chest radiograph or other imaging technique, with or without supporting microbiological data, is required for the diagnosis of pneumonia. (moderate recommendation; level iii evidence.) the diagnosis of cap is based on the presence of select clinical features (e.g., cough, fever, sputum production, and pleuritic chest pain) and is supported by imaging of the lung, usually by chest radiography. physical examination to detect rales or bronchial breath sounds is an important component of the evaluation but is less sensitive and specific than chest radiographs [ ] . both clinical features and physical exam findings may be lacking or altered in elderly patients. all patients should be screened by pulse oximetry, which may suggest both the presence of pneumonia in patients without obvious signs of pneumonia and unsuspected hypoxemia in patients with diagnosed pneumonia [ , , ] . a chest radiograph is required for the routine evaluation of patients who are likely to have pneumonia, to establish the diagnosis and to aid in differentiating cap from other common causes of cough and fever, such as acute bronchitis. chest radiographs are sometimes useful for suggesting the etiologic agent, prognosis, alternative diagnoses, and associated conditions. rarely, the admission chest radiograph is clear, but the patient's toxic appearance suggests more than bronchitis. ct scans may be more sensitive, but the clinical significance of these findings when findings of radiography are negative is unclear [ ] . for patients who are hospitalized for suspected pneumonia but who have negative chest radiography findings, it may be reasonable to treat their condition presumptively with antibiotics and repeat the imaging in - h. microbiological studies may support the diagnosis of pneumonia due to an infectious agent, but routine tests are frequently falsely negative and are often nonspecific. a history of recent travel or endemic exposure, if routinely sought, may identify specific potential etiologies that would otherwise be unexpected as a cause of cap (see table ) [ ] . . patients with cap should be investigated for specific pathogens that would significantly alter standard (empirical) management decisions, when the presence of such pathogens is suspected on the basis of clinical and epidemiologic clues. (strong recommendation; level ii evidence.) the need for diagnostic testing to determine the etiology of cap can be justified from several perspectives. the primary reason for such testing is if results will change the antibiotic management for an individual patient. the spectrum of antibiotic therapy can be broadened, narrowed, or completely altered on the basis of diagnostic testing. the alteration in therapy that is potentially most beneficial to the individual is an escalation or switch of the usual empirical regimen because of unusual pathogens (e.g., endemic fungi or mycobacterium tuberculosis) or antibiotic resistance issues. broad empirical coverage, such as that recommended in these guidelines, would not provide the optimal treatment for certain infections, such as psittacosis or tularemia. increased mortality [ ] and increased risk of clinical failure [ , ] are more common with inappropriate antibiotic therapy. management of initial antibiotic failure is greatly facilitated by an etiologic diagnosis at admission. de-escalation or narrowing of antibiotic therapy on the basis of diagnostic testing is less likely to decrease an in- dividual's risk of death but may decrease cost, drug adverse effects, and antibiotic resistance pressure. some etiologic diagnoses have important epidemiologic implications, such as documentation of severe acute respiratory syndrome (sars), influenza, legionnaires disease, or agents of bioterrorism. diagnostic testing for these infections may affect not only the individual but also many other people. although pneumonia etiologies that should be reported to public health officials vary by state, in general, most states' health regulations require reporting of legionnaires disease, sars, psittacosis, avian influenza (h n ), and possible agents of bioterrorism (plague, tularemia, and anthrax). in addition, specific diagnostic testing and reporting are important for pneumonia cases of any etiology thought to be part of a cluster or caused by pathogens not endemic to the area. there are also societal reasons for encouraging diagnostic testing. the antibiotic recommendations in the present guidelines are based on culture results and sensitivity patterns from patients with positive etiologic diagnoses [ ] . without the accumulated information available from these culture results, trends in antibiotic resistance are more difficult to track, and empirical antibiotic recommendations are less likely to be accurate. the main downside of extensive diagnostic testing of all patients with cap is cost, which is driven by the poor quality of most sputum microbiological samples and the low yield of positive culture results in many groups of patients with cap. a clear need for improved diagnostic testing in cap, most likely using molecular methodology rather than culture, has been recognized by the national institutes of health [ ] . the cost-benefit ratio is even worse when antibiotic therapy is not streamlined when possible [ , ] or when inappropriate escalation occurs [ ] . in clinical practice, narrowing of antibiotic therapy is, unfortunately, unusual, but the committee strongly recommends this as best medical practice. the possibility of polymicrobial cap and the potential benefit of combination therapy for bacteremic pneumococcal pneumonia have complicated the decision to narrow antibiotic therapy. delays in starting antibiotic therapy that result from the need to obtain specimens, complications of invasive diagnostic procedures, and unneeded antibiotic changes and additional testing for false-positive tests are also important considerations. the general recommendation of the committee is to strongly encourage diagnostic testing whenever the result is likely to change individual antibiotic management. for other patients with cap, the recommendations for diagnostic testing focus on patients in whom the diagnostic yield is thought to be greatest. these priorities often overlap. recommendations for patients in whom routine diagnostic testing is indicated for the above reasons are listed in retrospective studies of outpatient cap management usually show that diagnostic tests to define an etiologic pathogen are infrequently performed, yet most patients do well with empir-ical antibiotic treatment [ , ] . exceptions to this general rule may apply to some pathogens important for epidemiologic reasons or management decisions. the availability of rapid point-of-care diagnostic tests, specific treatment and chemoprevention, and epidemiologic importance make influenza testing the most logical. influenza is often suspected on the basis of typical symptoms during the proper season in the presence of an epidemic. however, respiratory syncytial virus (rsv) can cause a similar syndrome and often occurs in the same clinical scenario [ ] . rapid diagnostic tests may be indicated when the diagnosis is uncertain and when distinguishing influenza a from influenza b is important for therapeutic decisions. other infections that are important to verify with diagnostic studies because of epidemiologic implications or because they require unique therapeutic intervention are sars and avian (h n ) influenza, disease caused by agents of bioterrorism, legionella infection, community-acquired mrsa (ca-mrsa) infection, m. tuberculosis infection, or endemic fungal infection. attempts to establish an etiologic diagnosis are also appropriate in selected cases associated with outbreaks, specific risk factors, or atypical presentations. . pretreatment blood samples for culture and an expectorated sputum sample for stain and culture (in patients with a productive cough) should be obtained from hospitalized patients with the clinical indications listed in the only randomized controlled trial of diagnostic strategy in cap has demonstrated no statistically significant differences in mortality rate or los between patients receiving pathogendirected therapy and patients receiving empirical therapy [ ] . however, pathogen-directed therapy was associated with lower mortality among the small number of patients admitted to the icu. the study was performed in a country with a low incidence of antibiotic resistance, which may limit its applicability to areas with higher levels of resistance. adverse effects were significantly more common in the empirical therapy group but may have been unique to the specific antibiotic choice (erythromycin). the lack of benefit overall in this trial should not be interpreted as a lack of benefit for an individual patient. therefore, performing diagnostic tests is never incorrect or a breach of the standard of care. however, information from cohort and observational studies may be used to define patient groups in which the diagnostic yield is increased. patient groups in which routine diagnostic testing is indicated and the recommended tests are listed in table . blood cultures. pretreatment blood cultures yielded positive results for a probable pathogen in %- % in large series of nonselected patients hospitalized with cap [ , , [ ] [ ] [ ] . the yield of blood cultures is, therefore, relatively low (although it is similar to yields in other serious infections), and, when management decisions are analyzed, the impact of positive blood cultures is minor [ , ] . the most common blood culture isolate in all cap studies is s. pneumoniae. because this bacterial organism is always considered to be the most likely pathogen, positive blood culture results have not clearly led to better outcomes or improvements in antibiotic selection [ , ] . false-positive blood culture results are associated with prolonged hospital stay, possibly related to changes in management based on preliminary results showing gram-positive cocci, which eventually prove to be coagulasenegative staphylococci [ , ] . in addition, false-positive blood culture results have led to significantly more vancomycin use [ ] . for these reasons, blood cultures are optional for all hospitalized patients with cap but should be performed selectively (table ). the yield for positive blood culture results is halved by prior antibiotic therapy [ ] . therefore, when performed, samples for blood culture should be obtained before antibiotic administration. however, when multiple risk factors for bacteremia are present, blood culture results after initiation of antibiotic therapy are still positive in up to % of cases [ ] and are, therefore, still warranted in these cases, despite the lower yield. the strongest indication for blood cultures is severe cap. patients with severe cap are more likely to be infected with pathogens other than s. pneumoniae, including s. aureus, p. aeruginosa, and other gram-negative bacilli [ - , , , ] . many of the factors predictive of positive blood culture results [ ] overlap with risk factors for severe cap (table ) . therefore, blood cultures are recommended for all patients with severe cap because of the higher yield, the greater possibility of the presence of pathogens not covered by the usual empirical antibiotic therapy, and the increased potential to affect antibiotic management. blood cultures are also indicated when patients have a host defect in the ability to clear bacteremia-for example, as a result of asplenia or complement deficiencies. patients with chronic liver disease also are more likely to have bacteremia with cap [ ] . leukopenia is also associated with a high incidence of bacteremia [ , ] . respiratory tract specimen gram stain and culture. the yield of sputum bacterial cultures is variable and strongly influenced by the quality of the entire process, including specimen collection, transport, rapid processing, satisfactory use of cytologic criteria, absence of prior antibiotic therapy, and skill in interpretation. the yield of s. pneumoniae, for example, is only %- % from sputum cultures from patients with bacteremic pneumococcal pneumonia in studies performed a few decades ago [ , ] . a more recent study of cases of bacteremic pneumococcal pneumonia found that sputum specimens were not submitted in % of cases and were judged as inadequate in another % of cases [ ] . when patients receiving antibiotics for h were excluded, gram stain showed pneumococci in % of sputum specimens, and culture results were positive in %. for patients who had received no antibiotics, the gram stain was read as being consistent with pneumococci in % of cases, and sputum culture results were positive in %. although there are favorable reports of the utility of gram stain [ ] , a meta-analysis showed a low yield, considering the number of patients with adequate specimens and definitive results [ ] . recent data show that an adequate specimen with a predominant morphotype on gram stain was found in only % of hospitalized patients with cap [ ] . higher psi scores did not predict higher yield. however, a positive gram stain was highly predictive of a subsequent positive culture result. the benefit of a sputum gram stain is, therefore, -fold. first, it broadens initial empirical coverage for less common etiologies, such as infection with s. aureus or gram-negative organisms. this indication is probably the most important, because it will lead to less inappropriate antibiotic therapy. second, it can validate the subsequent sputum culture results. forty percent or more of patients are unable to produce any sputum or to produce sputum in a timely manner [ , ] . the yield of cultures is substantially higher with endotracheal aspirates, bronchoscopic sampling, or transthoracic needle aspirates [ ] [ ] [ ] [ ] [ ] [ ] [ ] , although specimens obtained after initiation of antibiotic therapy are unreliable and must be interpreted carefully [ , , ] . interpretation is improved with quantitative cultures of respiratory secretions from any source (sputum, tracheal aspirations, and bronchoscopic aspirations) or by interpretation based on semiquantitative culture results [ , , ] . because of the significant influence on diagnostic yield and cost effectiveness, careful attention to the details of specimen handling and processing are critical if sputum cultures are obtained. because the best specimens are collected and processed before antibiotics are given, the time to consider obtaining expectorated sputum specimens from patients with factors listed in table is before initiation of antibiotic therapy. once again, the best indication for more extensive respiratory tract cultures is severe cap. gram stain and culture of endotracheal aspirates from intubated patients with cap produce different results than expectorated sputum from non-icu patients [ , ] . many of the pathogens in the broader microbiological spectrum of severe cap are unaffected by a single dose of antibiotics, unlike s. pneumoniae. in addition, an endotracheal aspirate does not require patient cooperation, is clearly a lower respiratory tract sample, and is less likely to be contaminated by oropharyngeal colonizers. nosocomial tracheal colonization is not an issue if the sample is obtained soon after intubation. therefore, culture and gram stain of endotracheal aspirates are recommended for patients intubated for severe cap. in addition to routine cultures, a specific request for culture of respiratory secretions on buffered charcoal yeast extract agar to isolate legionella species may be useful in this subset of patients with severe cap in areas where legionella is endemic, as well as in patients with a recent travel history [ ] . the fact that a respiratory tract culture result is negative does not mean that it has no value. failure to detect s. aureus or gram-negative bacilli in good-quality specimens is strong evidence against the presence of these pathogens. growth inhibition by antibiotics is lower with these pathogens than with s. pneumoniae, but specimens obtained after initiation of antibiotic therapy are harder to interpret, with the possibility of colonization. necrotizing or cavitary pneumonia is a risk for ca-mrsa infection, and sputum samples should be obtained in all cases. negative gram stain and culture results should be adequate to withhold or stop treatment for mrsa infection. severe copd and alcoholism are major risk factors for infection with p. aeruginosa and other gram-negative pathogens [ ] . once again, gram stain and culture of an adequate sputum specimen are usually adequate to exclude the need for empirical coverage of these pathogens. a sputum culture in patients with suspected legionnaires disease is important, because the identification of legionella species implies the possibility of an environmental source to which other susceptible individuals may be exposed. localized community outbreaks of legionnaires disease might be recognized by clinicians or local health departments because у patients might be admitted to the same hospital. however, outbreaks of legionnaires disease associated with hotels or cruise ships [ ] [ ] [ ] are rarely detected by individual clinicians, because travelers typically disperse from the source of infection before developing symptoms. therefore, a travel history should be actively sought from patients with cap, and legionella testing should be performed for those who have traveled in the weeks before the onset of symptoms. urinary antigen tests may be adequate to diagnose and treat an individual, but efforts to obtain a sputum specimen for culture are still indicated to facilitate epidemiologic tracking. the availability of a culture isolate of legionella dramatically improves the likelihood that an environmental source of legionella can be identified and remediated [ ] [ ] [ ] . the yield of sputum culture is increased to %- % when associated with a positive urinary antigen test result [ , ] . attempts to obtain a sample for sputum culture from a patient with a positive pneumococcal urinary antigen test result may be indicated for similar reasons. patients with a productive cough and positive urinary antigen test results have positive sputum culture results in as many as %- % of cases [ ] [ ] [ ] [ ] . in these cases, not only can sensitivity testing confirm the appropriate choice for the individual patient, but important data regarding local community antibiotic resistance rates can also be acquired. other cultures. patients with pleural effusions cm in height on a lateral upright chest radiograph [ ] should undergo thoracentesis to yield material for gram stain and culture for aerobic and anaerobic bacteria. the yield with pleural fluid cultures is low, but the impact on management decisions is substantial, in terms of both antibiotic choice and the need for drainage. nonbronchoscopic bronchoalveolar lavage (bal) in the ed has been studied in a small, randomized trial of intubated patients with cap [ ] . a high percentage ( %) of nonbronchoscopic bal culture results were positive, even in some patients who had already received their first dose of antibiotics. unfortunately, tracheal aspirates were obtained from only a third of patients in the control group, but they all were culture positive. therefore, it is unclear that endotracheal aspirates are inferior to nonbronchoscopic bal. the use of bronchoscopic bal, protected specimen brushing, or transthoracic lung aspiration has not been prospectively studied for initial management of patients with cap [ ] . the best indications are for immunocompromised patients with cap or for patients with cap in whom therapy failed [ , ] . antigen tests. urinary antigen tests are commercially available and have been cleared by the us food and drug administration (fda) for detection of s. pneumoniae and l. pneumophila serogroup [ , , [ ] [ ] [ ] [ ] . urinary antigen testing appears to have a higher diagnostic yield in patients with more severe illness [ , ] . for pneumococcal pneumonia, the principal advantages of antigen tests are rapidity (∼ min), simplicity, reasonable specificity in adults, and the ability to detect pneumococcal pneumonia after antibiotic therapy has been started. studies in adults show a sensitivity of %- % and a specificity of % [ , , ] . this is an attractive test for detecting pneumococcal pneumonia when samples for culture cannot be obtained in a timely fashion or when antibiotic therapy has already been initiated. serial specimens from patients with known bacteremia were still positive for pneumococcal urinary antigen in % of cases after days of therapy [ ] . comparisons with gram stain show that these rapidly available tests often do not overlap, with only % concordance ( of ) among patients when results of either test were positive [ ] . only ∼ % of binax pneumococcal urinary antigen-positive patients can be diagnosed by conventional methods [ , ] . disadvantages include cost (approximately $ per specimen), although this is offset by increased diagnosis-related group-based reimbursement for coding for pneumococcal pneumonia, and the lack of an organism for in vitro susceptibility tests. falsepositive results have been seen in children with chronic respiratory diseases who are colonized with s. pneumoniae [ ] and in patients with an episode of cap within the previous months [ ] , but they do not appear to be a significant problem in colonized patients with copd [ , ] . for legionella, several urinary antigen assays are available, but all detect only l. pneumophila serogroup . although this particular serogroup accounts for %- % of communityacquired cases of legionnaires disease [ , ] in many areas of north america, other species and serogroups predominate in specific locales [ , ] . prior studies of culture-proven legionnaires disease indicate a sensitivity of %- % and a specificity of nearly % for detection of l. pneumophila serogroup . the urine is positive for antigen on day of illness and continues to be positive for weeks [ , ] . the major issue with urinary bacterial antigen detection is whether the tests allow narrowing of empirical antibiotic therapy to a single specific agent. the recommended empirical antibiotic regimens will cover both of these microorganisms. results of a small observational study suggest that therapy with a macrolide alone is adequate for hospitalized patients with cap who test positive for l. pneumophila urinary antigen [ ] . further research is needed in this area. in contrast, rapid antigen detection tests for influenza, which can also provide an etiologic diagnosis within - min, can lead to consideration of antiviral therapy. test performance varies according to the test used, sample type, duration of illness, and patient age. most show a sensitivity of %- % in adults and a specificity approaching % [ ] [ ] [ ] . advantages include the high specificity, the ability of some assays to distinguish between influenza a and b, the rapidity with which the results can be obtained, the possibly reduced use of antibacterial agents, and the utility of establishing this diagnosis for epidemiologic purposes, especially in hospitalized patients who may require infection control precautions. disadvantages include cost (approximately $ per specimen), high rates of false-negative test results, false-positive assays with adenovirus infections, and the fact that the sensitivity is not superior to physician judgment among patients with typical symptoms during an influenza epidemic [ , , ] . direct fluorescent antibody tests are available for influenza and rsv and require ∼ h. for influenza virus, the sensitivity is better than with the point-of-care tests ( %- %). they will detect animal subtypes such as h n and, thus, may be preferred for hospitalized patients [ , ] . for rsv, direct fluorescent antibody tests are so insensitive (sensitivity, %- %) in adults that they are rarely of value [ ] . acute-phase serologic testing. the standard for diagnosis of infection with most atypical pathogens, including chlamydophila pneumoniae, mycoplasma pneumoniae, and legionella species other than l. pneumophila, relies on acute-and convalescent-phase serologic testing. most studies use a microimmunofluorescence serologic test, but this test shows poor reproducibility [ ] . management of patients on the basis of a single acute-phase titer is unreliable [ ] , and initial antibiotic therapy will be completed before the earliest time point to check a convalescent-phase specimen. a new pcr test (bd probetec et legionella pneumophila; becton dickinson) that will detect all serotypes of l. pneumophila in sputum is now cleared by the fda, but extensive published clinical experience is lacking. most pcr reagents for other respiratory pathogens (except mycobacterium species) are "home grown," with requirements for use based on compliance with nccls criteria for analytical validity [ ] . despite the increasing use of these tests for atypical pathogens [ , ] , a review by the centers for disease control and prevention (cdc) of diagnostic assays for detection of c. pneumoniae indicated that, of the pcr reagents, only satisfied the criteria for a validated test [ ] . the diagnostic criteria defined in this review are particularly important for use in prospective studies of cap, because most prior reports used liberal criteria, which resulted in exaggerated rates. for sars, several pcr assays have been developed, but these tests are inadequate because of high rates of false-negative assays in early stages of infection [ , ] . a major goal of therapy is eradication of the infecting organism, with resultant resolution of clinical disease. as such, antimicrobials are a mainstay of treatment. appropriate drug selection is dependent on the causative pathogen and its antibiotic susceptibility. acute pneumonia may be caused by a wide variety of pathogens (table ) . however, until more accurate and rapid diagnostic methods are available, the initial treatment for most patients will remain empirical. recommendations for therapy (table ) apply to most cases; however, physicians should consider specific risk factors for each patient (table ) . a syndromic approach to therapy (under the assumption that an etiology correlates with the presenting clinical manifestations) is not specific enough to reliably predict the etiology of cap [ ] [ ] [ ] . even if a microbial etiology is identified, debate continues with regard to pathogen-specific treatment, because recent studies suggest coinfection by atypical pathogens (such as c. pneumoniae, legionella species, and viruses) and more traditional bacteria [ , ] . however, the importance of treating multiple infecting organisms has not been firmly established. the majority of antibiotics released in the past several decades have an fda indication for cap, making the choice of antibiotics potentially overwhelming. selection of antimicrobial regimens for empirical therapy is based on prediction of the most likely pathogen(s) and knowledge of local susceptibility patterns. recommendations are generally for a class of antibiotics rather than a specific drug, unless outcome data clearly favor one drug. because overall efficacy remains good for many classes of agents, the more potent drugs are given preference because of their benefit in decreasing the risk of selection for antibiotic resistance. other factors for consideration of specific antimicrobials include pharmacokinetics/pharmacodynamics, compliance, safety, and cost. although cap may be caused by a myriad of pathogens, a limited number of agents are responsible for most cases. the emergence of newly recognized pathogens, such as the novel sars-associated coronavirus [ ] , continually increases the challenge for appropriate management. table lists the most common causes of cap, in decreasing order of frequency of occurrence and stratified for severity of illness as judged by site of care (ambulatory vs. hospitalized). s. pneumoniae is the most frequently isolated pathogen. other bacterial causes include nontypeable haemophilus influenzae and moraxella catarrhalis, generally in patients who have underlying bronchopulmonary disease, and s. aureus, especially during an influenza outbreak. risks for infection with enterobacteriaceae species and p. aeruginosa as etiologies for cap are chronic oral steroid administration or severe underlying bronchopulmonary disease, alcoholism, and frequent antibiotic therapy [ , ] , whereas recent hospitalization would define cases as hcap. less common causes of pneumonia include, but are by no means limited to, streptococcus pyogenes, neisseria meningitidis, pasteurella multocida, and h. influenzae type b. the "atypical" organisms, so called because they are not detectable on gram stain or cultivatable on standard bacteriologic media, include m. pneumoniae, c. pneumoniae, legionella species, and respiratory viruses. with the exception of legionella species, these microorganisms are common causes of pneumonia, especially among outpatients. however, these pathogens are not often identified in clinical practice because, with a few exceptions, such as l. pneumophila and influenza virus, no specific, rapid, or standardized tests for their detection exist. although influenza remains the predominant viral cause of cap in adults, other commonly recognized viruses include rsv [ ] , adenovirus, and parainfluenza virus, as well as less common viruses, including human metapneumovirus, herpes simplex virus, varicella-zoster virus, sars-associated coronavirus, and measles virus. in a recent study of immunocompetent adult patients admitted to the hospital with cap, % had evidence of a viral etiology, and, in %, a respiratory virus was the only pathogen identified [ ] . studies that include outpatients find viral pneumonia rates as high as % [ ] . the frequency of other etiologic agents-for example, m. tuberculosis, chlamydophila psittaci (psittacosis), coxiella burnetii (q fever), francisella tularensis (tularemia), bordetella pertussis (whooping cough), and endemic fungi (histoplasma capsulatum, coccidioides immitis, cryptococcus neoformans, and blastomyces hominis)-is largely determined by the epidemiologic setting (table ) but rarely exceeds %- % total [ , ] . the exception may be endemic fungi in the appropriate geographic distribution [ ] . the need for specific anaerobic coverage for cap is generally overestimated. anaerobic bacteria cannot be detected by diagnostic techniques in current use. anaerobic coverage is clearly indicated only in the classic aspiration pleuropulmonary syndrome in patients with a history of loss of consciousness as a result of alcohol/drug overdose or after seizures in patients with concomitant gingival disease or esophogeal motility disorders. antibiotic trials have not demonstrated a need to specifically treat these organisms in the majority of cap cases. smallvolume aspiration at the time of intubation should be adequately handled by standard empirical severe cap treatment [ ] and by the high oxygen tension provided by mechanical ventilation. resistance to commonly used antibiotics for cap presents another major consideration in choosing empirical therapy. resistance patterns clearly vary by geography. local antibiotic prescribing patterns are a likely explanation [ ] [ ] [ ] . however, clonal spread of resistant strains is well documented. therefore, antibiotic recommendations must be modified on the basis of local susceptibility patterns. the most reliable source is state/provincial or municipal health department regional data, if available. local hospital antibiograms are generally the most accessible source of data but may suffer from small numbers of isolates. drug-resistant s. pneumoniae (drsp). the emergence of drug-resistant pneumococcal isolates is well documented. the incidence of resistance appears to have stabilized somewhat in the past few years. resistance to penicillin and cephalosporins may even be decreasing, whereas macrolide resistance continues to increase [ , ] . however, the clinical relevance of drsp for pneumonia is uncertain, and few well-controlled studies have examined the impact of in vitro resistance on clinical outcomes of cap. published studies are limited by small sample sizes, biases inherent in observational design, and the relative infrequency of isolates exhibiting high-level resistance [ ] [ ] [ ] . current levels of b-lactam resistance do not generally result in cap treatment failures when appropriate agents (i.e., amoxicillin, ceftriaxone, or cefotaxime) and doses are used, even in the presence of bacteremia [ , ] . the available data suggest that the clinically relevant level of penicillin resistance is a mic of at least mg/l [ ] . one report suggested that, if cefuroxime is used to treat pneumococcal bacteremia when the organism is resistant in vitro, the outcome is worse than with other therapies [ ] . other discordant therapies, including penicillin, did not have an impact on mortality. data exist suggesting that resistance to macrolides [ ] [ ] [ ] and older fluoroquinolones (ciprofloxacin and levofloxacin) [ , , ] results in clinical failure. to date, no failures have been reported for the newer fluoroquinolones (moxifloxacin and gemifloxacin). risk factors for infection with b-lactam-resistant s. pneumoniae include age ! years or years, b-lactam therapy within the previous months, alcoholism, medical comorbidities, immunosuppressive illness or therapy, and exposure to a child in a day care center [ , [ ] [ ] [ ] . although the relative predictive value of these risk factors is unclear, recent treatment with antimicrobials is likely the most significant. recent therapy or repeated courses of therapy with b-lactams, macrolides, or fluoroquinolones are risk factors for pneumococcal resistance to the same class of antibiotic [ , , , ] . one study found that use of either a b-lactam or macrolide within the previous months predicted an increased likelihood that, if pneumococcal bacteremia is present, the organism would be penicillin resistant [ ] . other studies have shown that repeated use of fluoroquinolones predicts an increased risk of infection with fluoroquinolone-resistant pneumococci [ , ] . whether this risk applies equally to all fluoroquinolones or is more of a concern for less active antipneumococcal agents (levofloxacin and ciprofloxacin) than for more active agents (moxifloxacin and gemifloxacin) is uncertain [ , , ] . recommendations for the use of highly active agents in patients at risk for infection with drsp is, therefore, based only in part on efficacy considerations; it is also based on a desire to prevent more resistance from emerging by employing the most potent regimen possible. although increasing the doses of certain agents (penicillins, cephalosporins, levofloxacin) may lead to adequate outcomes in the majority of cases, switching to more potent agents may lead to stabilization or even an overall decrease in resistance rates [ , ] . ca-mrsa. recently, an increasing incidence of pneumonia due to ca-mrsa has been observed [ , ] . ca-mrsa appears in patterns: the typical hospital-acquired strain [ ] and, recently, strains that are epidemiologically, genotypically, and phenotypically distinct from hospital-acquired strains [ , ] . many of the former may represent hcap, because these earlier studies did not differentiate this group from typical cap. the latter are resistant to fewer antimicrobials than are hospitalacquired mrsa strains and often contain a novel type iv sccmec gene. in addition, most contain the gene for panton-valentine leukocidin [ , ] , a toxin associated with clinical features of necrotizing pneumonia, shock, and respiratory failure, as well as formation of abscesses and empyemas. the large majority of cases published to date have been skin infections in children. in a large study of ca-mrsa in communities, % of ca-mrsa infections were pneumonia [ ] . however, pneumonia in both adults [ ] and children has been reported, often associated with preceding influenza. this strain should also be suspected in patients who present with cavitary infiltrates without risk factors for anaerobic aspiration pneu-monia (gingivitis and a risk for loss of consciousness, such as seizures or alcohol abuse, or esophogeal motility disorders). diagnosis is usually straightforward, with high yields from sputum and blood cultures in this characteristic clinical scenario. ca-mrsa cap remains rare in most communities but is expected to be an emerging problem in cap treatment. outpatient treatment. the following regimens are recommended for outpatient treatment on the basis of the listed clinical risks. the most common pathogens identified from recent studies of mild (ambulatory) cap were s. pneumoniae, m. pneumoniae, c. pneumoniae, and h. influenzae [ , ] . mycoplasma infection was most common among patients ! years of age without significant comorbid conditions or abnormal vital signs, whereas s. pneumoniae was the most common pathogen among older patients and among those with significant underlying disease. hemophilus infection was found in %mostly in patients with comorbidities. the importance of ther-apy for mycoplasma infection and chlamydophila infection in mild cap has been the subject of debate, because many infections are self-limiting [ , ] . nevertheless, studies from the s of children indicate that treatment of mild m. pneumoniae cap reduces the morbidity of pneumonia and shortens the duration of symptoms [ ] . the evidence to support specific treatment of these microorganisms in adults is lacking. macrolides have long been commonly prescribed for treatment of outpatients with cap in the united states, because of their activity against s. pneumoniae and the atypical pathogens. this class includes the erythromycin-type agents (including dirithromycin), clarithromycin, and the azalide azithromycin. although the least expensive, erythromycin is not often used now, because of gastrointestinal intolerance and lack of activity against h. influenzae. because of h. influenzae, azithromycin is preferred for outpatients with comorbidities such as copd. numerous randomized clinical trials have documented the efficacy of clarithromycin and azithromycin as monotherapy for outpatient cap, although several studies have demonstrated that clinical failure can occur with a resistant isolate. when such patients were hospitalized and treated with a b-lactam and a macrolide, however, all survived and generally recovered without significant complications [ , ] . most of these patients had risk factors for which therapy with a macrolide alone is not recommended in the present guidelines. thus, for patients with a significant risk of drsp infection, monotherapy with a macrolide is not recommended. doxycycline is included as a cost-effective alternative on the basis of in vitro data indicating effectiveness equivalent to that of erythromycin for pneumococcal isolates. the use of fluoroquinolones to treat ambulatory patients with cap without comorbid conditions, risk factors for drsp, or recent antimicrobial use is discouraged because of concern that widespread use may lead to the development of fluoroquinolone resistance [ ] . however, the fraction of total fluoroquinolone use specifically for cap is extremely small and unlikely to lead to increased resistance by itself. more concerning is a recent study suggesting that many outpatients given a fluoroquinolone may not have even required an antibiotic, that the dose and duration of treatment were often incorrect, and that another agent often should have been used as firstline therapy. this usage pattern may promote the rapid development of resistance to fluoroquinolones [ ] . comorbidities or recent antimicrobial therapy increase the likelihood of infection with drsp and enteric gram-negative bacteria. for such patients, recommended empirical therapeutic options include ( ) a respiratory fluoroquinolone (moxifloxacin, gemifloxacin, or levofloxacin [ mg daily]) or ( ) combination therapy with a b-lactam effective against s. pneumoniae plus a macrolide (doxycycline as an alternative). on the basis of present pharmacodynamic principles, high-dose amox-icillin (amoxicillin [ g times daily] or amoxicillin-clavulanate [ g times daily]) should target % of s. pneumoniae and is the preferred b-lactam. ceftriaxone is an alternative to highdose amoxicillin when parenteral therapy is feasible. selected oral cephalosporins (cefpodoxime and cefuroxime) can be used as alternatives [ ] , but these are less active in vitro than highdose amoxicillin or ceftriaxone. agents in the same class as the patient had been receiving previously should not be used to treat patients with recent antibiotic exposure. telithromycin is the first of the ketolide antibiotics, derived from the macrolide family, and is active against s. pneumoniae that is resistant to other antimicrobials commonly used for cap (including penicillin, macrolides, and fluoroquinolones). several cap trials suggest that telithromycin is equivalent to comparators (including amoxicillin, clarithromycin, and trovafloxacin) [ ] [ ] [ ] [ ] . there have also been recent postmarketing reports of life-threatening hepatotoxicity [ ] . at present, the committee is awaiting further evaluation of the safety of this drug by the fda before making its final recommendation. inpatient, non-icu treatment. the following regimens are recommended for hospital ward treatment. level i evidence) . a b-lactam plus a macrolide (strong recommendation; level i evidence) (preferred b-lactam agents include cefotaxime, ceftriaxone, and ampicillin; ertapenem for selected patients; with doxycycline [level iii evidence] as an alternative to the macrolide. a respiratory fluoroquinolone should be used for penicillin-allergic patients.) the recommendations of combination treatment with a blactam plus a macrolide or monotherapy with a fluoroquinolone were based on retrospective studies demonstrating a significant reduction in mortality compared with that associated with administration of a cephalosporin alone [ ] [ ] [ ] [ ] . multiple prospective randomized trials have demonstrated that either regimen results in high cure rates. the major discriminating factor between the regimens is the patient's prior antibiotic exposure (within the past months). preferred b-lactams are those effective against s. pneumoniae and other common, nonatypical pathogens without being overly broad spectrum. in january , the clinical laboratory standards institute (formerly the nccls) increased the mic breakpoints for cefotaxime and ceftriaxone for nonmeningeal s. pneumoniae infections. these new breakpoints acknowledge that nonmeningeal infections caused by strains formerly considered to be intermediately susceptible, or even resistant, can be treated successfully with usual doses of these b-lactams [ , , ] . two randomized, double-blind studies showed ertapenem to be equivalent to ceftriaxone [ , ] . it also has excellent activity against anaerobic organisms, drsp, and most enterobacteriaceae species (including extended-spectrum b-lactamase producers, but not p. aeruginosa). ertapenem may be useful in treating patients with risks for infection with these pathogens and for patients who have recently received antibiotic therapy. however, clinical experience with this agent is limited. other "antipneumococcal, antipseudomonal" b-lactam agents are appropriate when resistant pathogens, such as pseudomonas, are likely to be present. doxycycline can be used as an alternative to a macrolide on the basis of scant data for treatment of legionella infections [ , , ] . two randomized, double-blind studies of adults hospitalized for cap have demonstrated that parenteral azithromycin alone was as effective, with improved tolerability, as intravenous cefuroxime, with or without intravenous erythromycin [ , ] . in another study, mortality and readmission rates were similar, but the mean los was shorter among patients receiving azithromycin alone than among those receiving other guideline-recommended therapy [ ] . none of the patients with erythromycin-resistant s. pneumoniae infections died or was transferred to the icu, including who received azithromycin alone. another study showed that those receiving a macrolide alone had the lowest -day mortality but were the least ill [ ] . such patients were younger and were more likely to be in lower-risk groups. these studies suggest that therapy with azithromycin alone can be considered for carefully selected patients with cap with nonsevere disease (patients admitted primarily for reasons other than cap) and no risk factors for infection with drsp or gramnegative pathogens. however, the emergence of high rates of macrolide resistance in many areas of the country suggests that this therapy cannot be routinely recommended. initial therapy should be given intravenously for most admitted patients, but some without risk factors for severe pneumonia could receive oral therapy, especially with highly bioavailable agents such as fluoroquinolones. when an intravenous b-lactam is combined with coverage for atypical pathogens, oral therapy with a macrolide or doxycycline is appropriate for selected patients without severe pneumonia risk factors [ ] . inpatient, icu treatment. the following regimen is the minimal recommended treatment for patients admitted to the icu. . a b-lactam (cefotaxime, ceftriaxone, or ampicillin-sulbactam) plus either azithromycin (level ii evidence) or a fluoroquinolone (level i evidence) (strong recommendation) (for penicillin-allergic patients, a respiratory fluoroquinolone and aztreonam are recommended.) a single randomized controlled trial of treatment for severe cap is available. patients with shock were excluded; however, among the patients with mechanical ventilation, treatment with a fluoroquinolone alone resulted in a trend toward inferior outcome [ ] . because septic shock and mechanical ventilation are the clearest reasons for icu admission, the majority of icu patients would still require combination therapy. icu patients are routinely excluded from other trials; therefore, recommendations are extrapolated from nonsevere cases, in conjunction with case series and retrospective analyses of cohorts with severe cap. for all patients admitted to the icu, coverage for s. pneumoniae and legionella species should be ensured [ , ] by using a potent antipneumococcal b-lactam and either a macrolide or a fluoroquinolone. therapy with a respiratory fluoroquinolone alone is not established for severe cap [ ] , and, if the patient has concomitant pneumococcal meningitis, the efficacy of fluoroquinolone monotherapy is uncertain. in addition, prospective observational studies [ , ] and retrospective analyses [ ] [ ] [ ] have found that combination therapy for bacteremic pneumococcal pneumonia is associated with lower mortality than monotherapy. the mechanism of this benefit is unclear but was principally found in the patients with the most severe illness and has not been demonstrated in nonbacteremic pneumococcal cap studies. therefore, combination empirical therapy is recommended for at least h or until results of diagnostic tests are known. in critically ill patients with cap, a large number of microorganisms other than s. pneumoniae and legionella species must be considered. a review of studies that included patients with cap who were admitted to the icu demonstrates that the most common pathogens in the icu population were (in descending order of frequency) s. pneumoniae, legionella species, h. influenzae, enterobacteriaceae species, s. aureus, and pseudomonas species [ ] . the atypical pathogens responsible for severe cap may vary over time but can account collectively for у % of severe pneumonia episodes. the dominant atypical pathogen in severe cap is legionella [ ] , but some diagnostic bias probably accounts for this finding [ ] . the recommended standard empirical regimen should routinely cover the most common pathogens that cause severe cap, all of the atypical pathogens, and most of the relevant enterobacteriaceae species. treatment of mrsa or p. aeruginosa infection is the main reason to modify the standard empirical regimen. the following are additions or modifications to the basic empirical regimen recommended above if these pathogens are suspected. pseudomonal cap requires combination treatment to prevent inappropriate initial therapy, just as pseudomonas nosocomial pneumonia does [ ] . once susceptibilities are known, treatment can be adjusted accordingly. alternative regimens are provided for patients who may have recently received an oral fluoroquinolone, in whom the aminoglycoside-containing regimen would be preferred. a consistent gram stain of tracheal aspirate, sputum, or blood is the best indication for pseudomonas coverage. other, easier-to-treat gram-negative microorganisms may ultimately be proven to be the causative pathogen, but empirical coverage of pseudomonas species until culture results are known is least likely to be associated with inappropriate therapy. other clinical risk factors for infection with pseudomonas species include structural lung diseases, such as bronchiectasis, or repeated exacerbations of severe copd leading to frequent steroid and/or antibiotic use, as well as prior antibiotic therapy [ ] . these patients do not necessarily require icu admission for cap [ ] , so pseudomonas infection remains a concern for them even if they are only hospitalized on a general ward. the major risk factor for infection with other serious gram-negative pathogens, such as klebsiella pneumoniae or acinetobacter species, is chronic alcoholism. (moderate recommendation; level iii evidence.) the best indicator of s. aureus infection is the presence of gram-positive cocci in clusters in a tracheal aspirate or in an adequate sputum sample. the same findings on preliminary results of blood cultures are not as reliable, because of the significant risk of contamination [ ] . clinical risk factors for s. aureus cap include end-stage renal disease, injection drug abuse, prior influenza, and prior antibiotic therapy (especially with fluoroquinolones [ ] ). for methicillin-sensitive s. aureus, the empirical combination therapy recommended above, which includes a b-lactam and sometimes a respiratory fluoroquinolone, should be adequate until susceptibility results are available and specific therapy with a penicillinase-resistant semisynthetic penicillin or first-generation cephalosporin can be initiated. both also offer additional coverage for drsp. neither linezolid [ ] nor vancomycin [ ] is an optimal drug for methicillin-sensitive s. aureus. although methicillin-resistant strains of s. aureus are still the minority, the excess mortality associated with inappropriate an-tibiotic therapy [ ] would suggest that empirical coverage should be considered when ca-mrsa is a concern. the most effective therapy has yet to be defined. the majority of ca-mrsa strains are more susceptible in vitro to non-b-lactam antimicrobials, including trimethoprim-sulfamethoxazole (tmp-smx) and fluoroquinolones, than are hospital-acquired strains. previous experience with tmp-smx in other types of severe infections (endocarditis and septic thrombophlebitis) suggests that tmp-smx is inferior to vancomycin [ ] . further experience and study of the adequacy of tmp-smx for ca-mrsa cap is clearly needed. vancomycin has never been specifically studied for cap, and linezolid has been found to be better than ceftriaxone for bacteremic s. pneumoniae in a nonblinded study [ ] and superior to vancomycin in retrospective analysis of studies involving nosocomial mrsa pneumonia [ ] . newer agents for mrsa have recently become available, and others are anticipated. of the presently available agents, daptomycin should not be used for cap, and no data on pneumonia are available for tigecycline. a concern with ca-mrsa is necrotizing pneumonia associated with production of panton-valentine leukocidin and other toxins. vancomycin clearly does not decrease toxin production, and the effect of tmp-smx and fluoroquinolones on toxin production is unclear. addition of clindamycin or use of linezolid, both of which have been shown to affect toxin production in a laboratory setting [ ] , may warrant their consideration for treatment of these necrotizing pneumonias [ ] . unfortunately, the emergence of resistance during therapy with clindamycin has been reported (especially in erythromycinresistant strains), and vancomycin would still be needed for bacterial killing. clinicians should be aware of epidemiologic conditions and/ or risk factors that may suggest that alternative or specific additional antibiotics should be considered. these conditions and specific pathogens, with preferred treatment, are listed in tables and . pathogen-directed therapy . once the etiology of cap has been identified on the basis of reliable microbiological methods, antimicrobial therapy should be directed at that pathogen. (moderate recommendation; level iii evidence.) treatment options may be simplified (table ) if the etiologic agent is established or strongly suspected. diagnostic procedures that identify a specific etiology within - h can still be useful for guiding continued therapy. this information is often available at the time of consideration for a switch from parenteral to oral therapy and may be used to direct specific oral antimicrobial choices. if, for example, an appropriate culture reveals penicillin-susceptible s. pneumoniae, a narrowspectrum agent (such as penicillin or amoxicillin) may be used. this will, hopefully, reduce the selective pressure for resistance. the major issue with pathogen-specific therapy is management of bacteremic s. pneumoniae cap. the implications of the observational finding that dual therapy was associated with reduced mortality in bacteremic pneumococcal pneumonia [ ] [ ] [ ] [ ] [ ] are uncertain. one explanation for the reduced mortality may be the presence of undiagnosed coinfection with an atypical pathogen; although reported to occur in %- % of cap cases in some studies [ , ] , much lower rates of undiagnosed coinfection are found in general [ ] and specifically in severe cases [ ] . an alternative explanation is the immunomodulatory effects of macrolides [ , ] . it is important to note that these studies evaluated the effects of initial empirical therapy before the results of blood cultures were known and did not examine effects of pathogen-specific therapy after the results of blood cultures were available. the benefit of combination therapy was also most pronounced in the more severely ill patients [ , ] . therefore, discontinuation of combination therapy after results of cultures are known is most likely safe in non-icu patients. oseltamivir or zanamivir is recommended for influenza a. (strong recommendation; level i evidence.) . use of oseltamivir and zanamivir is not recommended for patients with uncomplicated influenza with symptoms for h (level i evidence), but these drugs may be used to reduce viral shedding in hospitalized patients or for influenza pneumonia. (moderate recommendation; level iii evidence.) studies that demonstrate that treatment of influenza is effective only if instituted within h of the onset of symptoms have been performed only in uncomplicated cases [ ] [ ] [ ] [ ] . the impact of such treatment on patients who are hospitalized with influenza pneumonia or a bacterial pneumonia complicating influenza is unclear. in hospitalized adults with influenza, a minority of whom had radiographically documented pneumonia, no obvious benefit was found in one retrospective study of amantadine treatment [ ] . treatment of antigen-or culture-positive patients with influenza with antivirals in addition to antibiotics is warranted, even if the radiographic infiltrate is caused by a subsequent bacterial superinfection. because of the longer period of persistent positivity after infection, the appropriate treatment for patients diagnosed with only of the rapid diagnostic tests is unclear. because such patients often have recoverable virus (median duration of days) after hos-pitalization, antiviral treatment seems reasonable from an infection-control standpoint alone. because of its broad influenza spectrum, low risk of resistance emergence, and lack of bronchospasm risk, oseltamivir is an appropriate choice for hospitalized patients. the neuraminidase inhibitors are effective against both influenza a and b viruses, whereas the m inhibitors, amantadine, and rimantadine are active only against influenza a [ ] . in addition, viruses recently circulating in the united states and canada are often resistant to the m inhibitors on the basis of antiviral testing [ , ] . therefore, neither amantadine nor rimantadine should be used for treatment or chemoprophylaxis of influenza a in the united states until susceptibility to these antiviral medications has been reestablished among circulating influenza a viruses [ ] . early treatment of influenza in ambulatory adults with inhaled zanamivir or oral oseltamivir appears to reduce the likelihood of lower respiratory tract complications [ ] [ ] [ ] . the use of influenza antiviral medications appears to reduce the likelihood of respiratory tract complications, as reflected by reduced usage rates of antibacterial agents in ambulatory patients with influenza. although clearly important in outpatient pneumonia, this experience may also apply to patients hospitalized primarily for influenza. parenteral acyclovir is indicated for treatment of varicellazoster virus infection [ ] recent human infections caused by avian influenza a (h n ) in vietnam, thailand, cambodia, china, indonesia, egypt, and turkey raise the possibility of a pandemic in the near future. the severity of h n infection in humans distinguishes it from that caused by routine seasonal influenza. respiratory failure requiring hospitalization and intensive care has been seen in the majority of the recognized cases, and mortality is ∼ % [ , ] . if a pandemic occurs, deaths will result from primary influenza pneumonia with or without secondary bacterial pneumonia. this section highlights issues for consideration, recognizing that treatment recommendations will likely change as the pandemic progresses. more specific guidance can be found on the idsa, ats, cdc, and who web sites as the key features of the pandemic become clearer. additional guidance is available at http://www.pandemicflu.gov. the who has delineated phases of an influenza pandemic, defined by increasing levels of risk and public health response [ ] . during the current pandemic alert phase (phase : cases of novel influenza infection without sustained person-to-person transmission), testing should be focused on confirming all suspected cases in areas where h n infection has been documented in poultry and on detecting the arrival of the pandemic strain in unaffected countries. early clinical features of h n infection include persistent fever, cough, and respiratory difficulty progressing over - days, as well as lymphopenia on admission to the hospital [ , , ] . exposure to sick and dying poultry in an area with known or suspected h n activity has been reported by most patients, although the recognition of poultry outbreaks has sometimes followed the recognition of human cases [ ] . rapid bedside tests to detect influenza a have been used as screening tools for avian influenza in some settings. throat swabs tested by rt-pcr have been the most sensitive for confirming h n infection to date, but nasopharyngeal swabs, washes, and aspirates; bal fluid; lung and other tissues; and stool have yielded positive results by rt-pcr and viral culture with varying sensitivity. convalescent-phase serum can be tested by microneutralization for antibodies to h antigen in a small number of international reference laboratories. specimens from suspected cases of h n infection should be sent to public health laboratories with appropriate biocontainment facilities; the case should be discussed with health department officials to arrange the transfer of specimens and to initiate an epidemiologic evaluation. during later phases of an ongoing pandemic, testing may be necessary for many more patients, so that appropriate treatment and infection control decisions can be made, and to assist in defining the extent of the pandemic. recommendations for such testing will evolve on the basis of the features of the pandemic, and guidance should be sought from the cdc and who web sites (http://www.cdc.gov and http://www.who.int). patients with confirmed or suspected h n influenza should be treated with oseltamivir. most h n isolates since have been susceptible to the neuraminidase inhibitors oseltamivir and zanamivir and resistant to the adamantanes (amantidine and rimantidine) [ , ] . the current recommendation is for a -day course of treatment at the standard dosage of mg times daily. in addition, droplet precautions should be used for patients with suspected h n influenza, and they should be placed in respiratory isolation until that etiology is ruled out. health care personnel should wear n- (or higher) respirators during medical procedures that have a high likelihood of generating infectious respiratory aerosols. bacterial superinfections, particularly pneumonia, are important complications of influenza pneumonia. the bacterial etiologies of cap after influenza infection have included s. pneumoniae, s. aureus, h. influenzae, and group a streptococci. legionella, chlamydophila, and mycoplasma species are not important causes of secondary bacterial pneumonia after influenza. appropriate agents would therefore include cefotaxime, ceftriaxone, and respiratory fluoroquinolones. treatment with vancomycin, linezolid, or other agents directed against ca-mrsa should be limited to patients with confirmed infection or a compatible clinical presentation (shock and necrotizing pneumonia). because shortages of antibacterials and antivirals are anticipated during a pandemic, the appropriate use of diagnostic tests will be even more important to help target antibacterial therapy whenever possible, especially for patients admitted to the hospital. time to first antibiotic dose for cap has recently received significant attention from a quality-of-care perspective. this emphasis is based on retrospective studies of medicare beneficiaries that demonstrated statistically significantly lower mortality among patients who received early antibiotic therapy [ , ] . the initial study suggested a breakpoint of h [ ] , whereas the subsequent analysis found that h was associated with lower mortality [ ] . studies that document the time to first antibiotic dose do not consistently demonstrate this difference, although none had as large a patient population. most importantly, prospective trials of care by protocol have not demonstrated a survival benefit to increasing the percentage of patients with cap who receive antibiotics within the first - h [ , ] . early antibiotic administration does not appear to shorten the time to clinical stability, either [ ] , although time of first dose does appear to correlate with los [ , ] . a problem of internal consistency is also present, because, in both studies [ , ] , patients who received antibiotics in the first h after presentation actually did worse than those who re- temperature р . ؇c heart rate р beats/min respiratory rate р breaths/min systolic blood pressure у mm hg arterial oxygen saturation у % or po у mm hg on room air ability to maintain oral intake a normal mental status a note. criteria are from [ , , ] . po , oxygen partial pressure. a important for discharge or oral switch decision but not necessarily for determination of nonresponse. ceived antibiotics - h after presentation. for these and other reasons, the committee did not feel that a specific time window for delivery of the first antibiotic dose should be recommended. however, the committee does feel that therapy should be administered as soon as possible after the diagnosis is considered likely. conversely, a delay in antibiotic therapy has adverse consequences in many infections. for critically ill, hemodynamically unstable patients, early antibiotic therapy should be encouraged, although no prospective data support this recommendation. delay in beginning antibiotic treatment during the transition from the ed is not uncommon. especially with the frequent use of once-daily antibiotics for cap, timing and communication issues may result in patients not receiving antibiotics for h after hospital admission. the committee felt that the best and most practical resolution to this issue was that the initial dose be given in the ed [ ] . data from the medicare database indicated that antibiotic treatment before hospital admission was also associated with lower mortality [ ] . given that there are even more concerns regarding timing of the first dose of antibiotic when the patient is directly admitted to a busy inpatient unit, provision of the first dose in the physician's office may be best if the recommended oral or intramuscular antibiotics are available in the office. with the use of a potent, highly bioavailable antibiotic, the ability to eat and drink is the major consideration for switching from intravenous to oral antibiotic therapy for non-icu patients. initially, ramirez et al. [ ] defined a set of criteria for an early switch from intravenous to oral therapy (table ). in general, as many as two-thirds of all patients have clinical improvement and meet criteria for a therapy switch in the first days, and most non-icu patients meet these criteria by day . subsequent studies have suggested that even more liberal criteria are adequate for the switch to oral therapy. an alternative approach is to change from intravenous to oral therapy at a predetermined time, regardless of the clinical response [ ] . one study population with nonsevere illness was randomized to receive either oral therapy alone or intravenous therapy, with the switch occurring after h without fever. the study population with severe illness was randomized to receive either intravenous therapy with a switch to oral therapy after days or a full -day course of intravenous antibiotics. time to resolution of symptoms for the patients with nonsevere illness was similar with either regimen. among patients with more severe illness, the rapid switch to oral therapy had the same rate of treatment failure and the same time to resolution of symptoms as prolonged intravenous therapy. the rapid-switch group required fewer inpatient days ( vs. ) , although this was likely partially a result of the protocol, but the patients also had fewer adverse events. the need to keep patients in the hospital once clinical stability is achieved has been questioned, even though physicians commonly choose to observe patients receiving oral therapy for у day. even in the presence of pneumococcal bacteremia, a switch to oral therapy can be safely done once clinical stability is achieved and prolonged intravenous therapy is not needed [ ] . such patients generally take longer (approximately half a day) to become clinically stable than do nonbacteremic patients. the benefits of in-hospital observation after a switch to oral therapy are limited and add to the cost of care [ ] . discharge should be considered when the patient is a candidate for oral therapy and when there is no need to treat any comorbid illness, no need for further diagnostic testing, and no unmet social needs [ , , ] . although it is clear that clinically stable patients can be safely switched to oral therapy and discharged, the need to wait for all of the features of clinical stability to be present before a patient is discharged is uncertain. for example, not all investigators have found it necessary to have the white blood cell count improve. using the definition for clinical stability in table , halm et al. [ ] found that . % of patients were discharged from the hospital with у instability. death or readmission occurred in . % of patients with no instability on discharge, in . % of patients with instability, and in . % with у instabilities. in general, patients in higher psi classes take longer to reach clinical stability than do patients in lower risk classes [ ] . this finding may reflect the fact that elderly patients with multiple comorbidities often recover more slowly. arrangements for appropriate follow-up care, including rehabilitation, should therefore be initiated early for these patients. in general, when switching to oral antibiotics, either the same agent as the intravenous antibiotic or the same drug class should be used. switching to a different class of agents simply because of its high bioavailability (such as a fluoroquinolone) is probably not necessary for a responding patient. for patients who received intravenous b-lactam-macrolide combination therapy, a switch to a macrolide alone appears to be safe for those who do not have drsp or gram-negative enteric pathogens isolated [ ] . most patients with cap have been treated for - days or longer, but few well-controlled studies have evaluated the optimal duration of therapy for patients with cap, managed in or out of the hospital. available data on short-course treatment do not suggest any difference in outcome with appropriate therapy in either inpatients or outpatients [ ] . duration is also difficult to define in a uniform fashion, because some antibiotics (such as azithromycin) are administered for a short time yet have a long half-life at respiratory sites of infection. in trials of antibiotic therapy for cap, azithromycin has been used for - days as oral therapy for outpatients, with some reports of single-dose therapy for patients with atypical pathogen infections [ ] [ ] [ ] . results with azithromycin should not be extrapolated to other drugs with significantly shorter half-lives. the ketolide telithromycin has been used for - days to treat outpatients, including some with pneumococcal bacteremia or psi classes уiii [ ] . in a recent study, highdose ( mg) levofloxacin therapy for days was equally successful and resulted in more afebrile patients by day than did the -mg dose for - days ( . % vs. . %; p p ) [ ] . on the basis of these studies, days appears to be . the minimal overall duration of therapy documented to be effective in usual forms of cap. as is discussed above, most patients become clinically stable within - days, so longer durations of therapy are rarely necessary. patients with persistent clinical instability are often readmitted to the hospital and may not be candidates for shortduration therapy. short-duration therapy may be suboptimal for patients with bacteremic s. aureus pneumonia (because of the risk of associated endocarditis and deep-seated infection), for those with meningitis or endocarditis complicating pneumonia, and for those infected with other, less common pathogens (e.g., burkholderia pseudomallei or endemic fungi). an -day course of therapy for nosocomial p. aeruginosa pneumonia led to relapse more commonly than did a -day course of therapy [ ] . whether the same results would be applicable to cap cases is unclear, but the presence of cavities or other signs of tissue necrosis may warrant prolonged treatment. studies of duration of therapy have focused on patients receiving empirical treatment, and reliable data defining treatment duration after an initially ineffective regimen are lacking. drotrecogin alfa activated is the first immunomodulatory therapy approved for severe sepsis. in the united states, the fda recommended the use of drotrecogin alfa activated for patients at high risk of death. the high-risk criterion suggested by the fda was an acute physiologic and chronic health assessment (apache) ii score у , based on a subgroup analysis of the overall study. however, the survival advantage (absolute risk reduction, . %) of drotrecogin alfa activated treatment of patients in the cap subgroup was equivalent to that in the subgroup with apache ii scores у [ , , ] . the greatest reduction in the mortality rate was for s. pneumoniae infection (relative risk, . ; % ci, . - . ) [ ] . subsequent data have suggested that the benefit appears to be greatest when the treatment is given as early in the hospital admission as possible. in the subgroup with severe cap caused by a pathogen other than s. pneumoniae and treated with appropriate antibiotics, there was no evidence that drotrecogin alfa activated affected mortality. although the benefit of drotrecogin alfa activated is clearly greatest for patients with cap who have high apache ii scores, this criterion alone may not be adequate to select appropriate patients. an apache ii score у was selected by a subgroup analysis of the entire study cohort and may not be similarly calibrated in a cap-only cohort. two-organ failure, the criterion suggested for drotrecogin alfa activated use by the european regulatory agency, did not influence the mortality benefit for patients with cap [ ] . therefore, in addition to patients with septic shock, other patients with severe cap could be considered for treatment with drotrecogin alfa activated. those with sepsis-induced leukopenia are at extremely high risk of death and ards and are, therefore, potential candidates. conversely, the benefit of drotrecogin alfa activated is not as clear when respiratory failure is caused more by exacerbation of underlying lung disease rather than by the pneumonia itself. other minor criteria for severe cap proposed above are similar to organ failure criteria used in many sepsis trials. consideration of treatment with drotrecogin alfa activated is appropriate, but the strength of the recommendation is only level ii. . hypotensive, fluid-resuscitated patients with severe cap should be screened for occult adrenal insufficiency. (moderate recommendation; level ii evidence.) a large, multicenter trial has suggested that stress-dose ( - mg of hydrocortisone per day or equivalent) steroid treatment improves outcomes of vasopressor-dependent patients with septic shock who do not have an appropriate cortisol response to stimulation [ ] . once again, patients with cap made up a significant fraction of patients entered into the trial. in addition, small pilot studies have suggested that there is a benefit to corticosteroid therapy even for patients with severe cap who are not in shock [ ] [ ] [ ] . the small sample size and baseline differences between groups compromise the conclusions. although the criteria for steroid replacement therapy remain controversial, the frequency of intermittent steroid treatment in patients at risk for severe cap, such as those with severe copd, suggests that screening of patients with severe cap is appropriate with replacement if inadequate cortisol levels are documented. if corticosteroids are used, close attention to tight glucose control is required [ ] . patients who do not require immediate intubation but who have either hypoxemia or respiratory distress should receive a trial of niv [ , , ] . patients with underlying copd are most likely to benefit. patients with cap who were ran-domized to receive niv had a % absolute risk reduction for the need for intubation [ ] . the use of niv may also improve intermediate-term mortality. inability to expectorate may limit the use of niv [ ] , but intermittent application of niv may allow for its use in patients with productive cough unless sputum production is excessive. prompt recognition of a failed niv trial is critically important, because most studies demonstrate worse outcomes for patients who require intubation after a prolonged niv trial [ , ] . within the first - h of niv, failure to improve respiratory rate and oxygenation [ , , ] or failure to decrease carbon dioxide partial pressure (pco ) in patients with initial hypercarbia [ ] predicts niv failure and warrants prompt intubation. niv provides no benefit for patients with ards [ ] , which may be nearly indistinguishable from cap among patients with bilateral alveolar infiltrates. patients with cap who have severe hypoxemia (pao /fio ratio, ! ) are also poor candidates for niv [ ] . . low-tidal-volume ventilation ( cm /kg of ideal body weight) should be used for patients undergoing ventilation who have diffuse bilateral pneumonia or ards. (strong recommendation; level i evidence.) distinguishing between diffuse bilateral pneumonia and ards is difficult, but it may not be an important distinction. results of the ardsnet trial suggest that the use of low-tidalvolume ventilation provides a survival advantage [ ] . pneumonia, principally cap, was the most common cause of ards in that trial, and the benefit of the low-tidal-volume ventilatory strategy appeared to be equivalent in the population with pneumonia compared with the entire cohort. the absolute risk reduction for mortality in the pneumonia cohort was %, indicating that, in order to avoid death, patients must be treated [ ] . other aspects of the management of severe sepsis and septic shock in patients with cap do not appear to be significantly different from those for patients with other sources of infection. recommendations for these aspects of care are reviewed elsewhere [ ] . because of the limitations of diagnostic testing, the majority of cap is still treated empirically. critical to empirical therapy is an understanding of the management of patients who do not follow the normal response pattern. although difficult to define, nonresponse is not uncommon. overall, %- % of hospitalized patients with cap do not respond to the initial antibiotic treatment [ , , , ] . the incidence of treatment failure among patients with cap who are not hospitalized is not well known, because population-based studies are required. almirall et al. [ ] described an overall hospitalization rate of % in a population-based study, but the rate of failure among the % of patients who initially presented to their primary care physician was not provided. the frequency of prior antibiotic therapy among medicare patients admitted to the hospital with cap is %- % [ , ] , but the percentage who received prior antibiotic therapy for the acute episode of pneumonia itself versus other indications is unclear. for patients initially admitted to the icu, the risk of failure to respond is already high; as many as % will experience deterioration even after initial stabilization in the icu [ ] . mortality among nonresponding patients is increased several-fold in comparison with that among responding patients [ ] . overall mortality rates as high as % have been reported for an entire population of nonresponding hospitalized patients with cap [ , , ] , and the mortality rate reported in one study of early failure was % [ ] . apache ii score was not the only factor independently associated with mortality in the nonresponding group, suggesting that the excess mortality may be due to factors other than severity of illness at presentation [ ] . . the use of a systematic classification of possible causes of failure to respond, based on time of onset and type of failure (table ) , is recommended. (moderate recommendation; level ii evidence.) the term "nonresponding pneumonia" is used to define a situation in which an inadequate clinical response is present despite antibiotic treatment. lack of a clear-cut and validated definition in the literature makes nonresponse difficult to study. lack of response also varies according to the site of treatment. lack of response in outpatients is very different from that in patients admitted to the icu. the time of evaluation is also important. persistent fever after the first day of treatment differs significantly from fever persisting (or recurring) at day of treatment. table provides a construct for evaluating nonresponse to antibiotic treatment of cap, based on several studies addressing this issue [ , , , ] . two patterns of unacceptable response are seen in hospitalized patients [ ] . the first is progressive pneumonia or actual clinical deterioration, with acute respiratory failure requiring ventilatory support and/or septic shock, usually occurring within the first h of hospital admission. as is noted above, as many as % of patients with cap who ultimately require icu admission are initially admitted to a non-icu setting and are transferred because of deterioration [ ] . deterioration and development of respira-tory failure or hypotension h after initial treatment is often related to intercurrent complications, deterioration in underlying disease, or development of nosocomial superinfection. the second pattern is that of persistent or nonresponding pneumonia. nonresponse can be defined as absence of or delay in achieving clinical stability, using the criteria in table [ , ] . when these criteria were used, the median time to achieve clinical stability was days for all patients, but a quarter of patients took у days to meet all of these criteria for stability [ ] . stricter definitions for each of the criteria and higher psi scores were associated with longer times to achieve clinical stability. conversely, subsequent transfer to the icu after achieving this degree of clinical stability occurred in ! % of [ ] . given these results, concern regarding nonresponse should be tempered before h of therapy. antibiotic changes during this period should be considered only for patients with deterioration or in whom new culture data or epidemiologic clues suggest alternative etiologies. finally, nonresolving or slow-resolving pneumonia has been used to refer to the conditions of patients who present with persistence of pulmonary infiltrates days after initial pneumonia-like syndrome [ ] . as many as % of these patients will be found to have diseases other than cap when carefully evaluated [ ] . two studies have evaluated the risk factors for a lack of response in multivariate analyses [ , ] , including those amenable to medical intervention. use of fluoroquinolones was independently associated with a better response in one study [ ] , whereas discordant antimicrobial therapy was associated with early failure [ ] . in table , the different risk and protective factors and their respective odds ratios are summarized. specific causes that may be responsible for a lack of response in cap have been classified by arancibia et al. [ ] (table ) . this classification may be useful for clinicians as a systematic approach to diagnose the potential causes of nonresponse in cap. although in the original study only ( %) of cases could not be classified [ ] , a subsequent prospective multicenter trial found that the cause of failure could not be determined in % [ ] . management of nonresponding cap. nonresponse to antibiotics in cap will generally result in у of clinical responses: ( ) transfer of the patient to a higher level of care, ( ) further diagnostic testing, and ( ) escalation or change in treatment. issues regarding hospital admission and icu transfer are discussed above. an inadequate host response, rather than inappropriate antibiotic therapy or unexpected microorganisms, is the most common cause of apparent antibiotic failure when guidelinerecommended therapy is used. decisions regarding further diagnostic testing and antibiotic change/escalation are intimately intertwined and need to be discussed in tandem. information regarding the utility of extensive microbiological testing in cases of nonresponding cap is mainly retrospective and therefore affected by selection bias. a systematic diagnostic approach, which included invasive, noninvasive, and imaging procedures, in a series of nonresponding patients with cap obtained a specific diagnosis in % [ ] . in a different study, mortality among patients with microbiologically guided versus empirical antibiotic changes was not improved (mortality rate, % vs. %, respectively) [ ] . however, no antibiotic changes were based solely on sputum smears, suggesting that invasive cultures or nonculture methods may be needed. mismatch between the susceptibility of a common causative organism, infection with a pathogen not covered by the usual empirical regimen, and nosocomial superinfection pneumonia are major causes of apparent antibiotic failure. therefore, the first response to nonresponse or deterioration is to reevaluate the initial microbiological results. culture or sensitivity data not available at admission may now make the cause of clinical failure obvious. in addition, a further history of any risk factors for infection with unusual microorganisms (table ) should be taken if not done previously. viruses are relatively neglected as a cause of infection in adults but may account for %- % of cases [ ] . other family members or coworkers may have developed viral symptoms in the interval since the patient was admitted, increasing suspicion of this cause. the evaluation of nonresponse is severely hampered if a microbiological diagnosis was not made on initial presentation. if cultures were not obtained, clinical decisions are much more difficult than if the adequate cultures were obtained but negative. risk factors for nonresponse or deterioration (table ) , therefore, figure prominently in the list of situations in which more aggressive initial diagnostic testing is warranted (table ) . blood cultures should be repeated for deterioration or progressive pneumonia. deteriorating patients have many of the risk factors for bacteremia, and blood cultures are still high yield even in the face of prior antibiotic therapy [ ] . positive blood culture results in the face of what should be adequate antibiotic therapy should increase the suspicion of either antibiotic-resistant isolates or metastatic sites, such as endocarditis or arthritis. despite the high frequency of infectious pulmonary causes of nonresponse, the diagnostic utility of respiratory tract cultures is less clear. caution in the interpretation of sputum or tracheal aspirate cultures, especially of gram-negative bacilli, is warranted because early colonization, rather than superinfection with resistant bacteria, is not uncommon in specimens obtained after initiation of antibiotic treatment. once again, the absence of multidrug-resistant pathogens, such as mrsa or pseudomonas, is strong evidence that they are not the cause of nonresponse. an etiology was determined by bronchoscopy in % of patients with cap, mainly in those not responding to therapy [ ] . despite the potential benefit suggested by these results, and in contrast to ventilator-associated pneumonia [ , ] , no randomized study has compared the utility of invasive versus noninvasive strategies in the cap population with nonresponse. rapid urinary antigen tests for s. pneumoniae and l. pneumophila remain positive for days after initiation of antibiotic therapy [ , ] and, therefore, may be high-yield tests in this group. a urinary antigen test result that is positive for l. pneumophila has several clinical implications, including that coverage for legionella should be added if not started empirically [ ] . this finding may be a partial explanation for the finding that fluoroquinolones are associated with a lower incidence of nonresponse [ ] . if a patient has persistent fever, the faster response to fluoroquinolones in legionella cap warrants consideration of switching coverage from a macrolide [ ] . stopping the b-lactam component of combination therapy to exclude drug fever is probably also safe [ ] . because one of the major explanations for nonresponse is poor host immunity rather than incorrect antibiotics, a positive pneumococcal antigen test result would at least clarify the probable original pathogen and turn attention to other causes of failure. in addition, a positive pneumococcal antigen test result would also help with interpretation of subsequent sputum/tracheal aspirate cultures, which may indicate early superinfection. nonresponse may also be mimicked by concomitant or subsequent extrapulmonary infection, such as intravascular catheter, urinary, abdominal, and skin infections, particularly in icu patients. appropriate cultures of these sites should be considered for patients with nonresponse to cap therapy. in addition to microbiological diagnostic procedures, several other tests appear to be valuable for selected patients with nonresponse: • chest ct. in addition to ruling out pulmonary emboli, a ct scan can disclose other reasons for antibiotic failure, including pleural effusions, lung abscess, or central airway obstruction. the pattern of opacities may also suggest alternative noninfectious disease, such as bronchiolitis obliterans organizing pneumonia. • thoracentesis. empyema and parapneumonic effusions are important causes of nonresponse [ , ] , and thoracentesis should be performed whenever significant pleural fluid is present. • bronchoscopy with bal and transbronchial biopsies. if the differential of nonresponse includes noninfectious pneumonia mimics, bronchoscopy will provide more diagnostic information than routine microbiological cultures. bal may reveal noninfectious entities, such as pulmonary hemorrhage or acute eosinophilic pneumonia, or hints of infectious diseases, such as lymphocytic rather than neutrophilic alveolitis pointing toward virus or chlamydophila infection. transbronchial biopsies can also yield a specific diagnosis. antibiotic management of nonresponse in cap has not been studied. the overwhelming majority of cases of apparent nonresponse are due to the severity of illness at presentation or a delay in treatment response related to host factors. other than the use of combination therapy for severe bacteremic pneumococcal pneumonia [ , , , ] , there is no documentation that additional antibiotics for early deterioration lead to a better outcome. the presence of risk factors for potentially untreated microorganisms may warrant temporary empirical broadening of the antibiotic regimen until results of diagnostic tests are available. vaccines targeting pneumococcal disease and influenza remain the mainstay for preventing cap. pneumococcal polysaccharide vaccine and inactivated influenza vaccine are recommended for all older adults and for younger persons with medical conditions that place them at high risk for pneumonia morbidity and mortality (table ) [ , ] . the new live attenuated influenza vaccine is recommended for healthy persons - years of age, including health care workers [ ] . postlicensure epidemiologic studies have documented the effectiveness of pneumococcal polysaccharide vaccines for prevention of invasive infection (bacteremia and meningitis) among elderly individuals and younger adults with certain chronic medical conditions [ ] [ ] [ ] [ ] . the overall effectiveness against invasive pneumococcal disease among persons у years of age is %- % [ , , ] , although efficacy may decrease with advancing age [ ] . the effectiveness of the vaccine against pneumococcal disease in immunocompromised persons is less clear, and results of studies evaluating its effectiveness against pneumonia without bacteremia have been mixed. the vaccine has been shown to be cost effective for general populations of adults - years of age and у years of age [ , ] . a second dose of pneumococcal polysaccharide vaccine after a у -year interval has been shown to be safe, with only slightly more local reactions than are seen after the first dose [ ] . because the safety of a third dose has not been demonstrated, current guidelines do not suggest repeated revaccination. the pneumococcal conjugate vaccine is under investigation for use in adults but is currently only licensed for use in young children [ , ] . however, its use in children ! years of age has dramatically reduced invasive pneumococcal bacteremia among adults as well [ , ] . the effectiveness of influenza vaccines depends on host factors and on how closely the antigens in the vaccine are matched with the circulating strain of influenza. a systematic review demonstrates that influenza vaccine effectively prevents pneumonia, hospitalization, and death [ , ] . a recent large observational study of adults у years of age found that vaccination against influenza was associated with a reduction in the risk of hospitalization for cardiac disease ( % reduction), cerebrovascular disease ( %- % reduction), and pneumonia or influenza ( %- % reduction) and a reduction in the risk of death from all causes ( %- % reduction) [ ] . in longterm-care facilities, vaccination of health care workers with influenza vaccine is an important preventive health measure [ , , ] . because the main virulence factors of influenza virus, a neuraminidase and hemagglutinin, adapt quickly to selective pressures, new vaccine formulations are created each year on the basis of the strains expected to be circulating, and annual revaccination is needed for optimal protection. many people who should receive either influenza or pneumococcal polysaccharide vaccine have not received them. according to a survey, only % of adults у years of age had received influenza vaccine in the past year, and only % had ever received pneumococcal polysaccharide vaccine [ ] . coverage levels are lower for younger persons with vaccine indications. among adults - years of age with diabetes, % had received influenza vaccine, and % had ever received pneumococcal vaccine [ ] . studies of vaccine delivery methods indicate that the use of standing orders is the best way to improve vaccination coverage in office, hospital, or long-term care settings [ ] . hospitalization of at-risk patients represents an underutilized opportunity to assess vaccination status and to either provide or recommend immunization. ideally, patients should be vaccinated before developing pneumonia; therefore, admissions for illnesses other than respiratory tract infections would be an appropriate focus. however, admission for pneumonia is an important trigger for assessing the need for immunization. the actual immunization may be better provided at the time of outpatient follow-up, especially with the emphasis on early discharge of patients with cap. patients with an acute fever should not be vaccinated until their fever has resolved. confusion of a febrile reaction to immunization with recurrent/superinfection pneumonia is a risk. however, immunization at discharge for pneumonia is warranted for patients for whom outpatient follow-up is unreliable, and such vaccinations have been safely given to many patients. the best time for influenza vaccination in north america is october and november, although vaccination in december and later is recommended for those who were not vaccinated earlier. influenza and pneumococcal vaccines can be given at the same time in different arms. chemoprophylaxis can be used as an adjunct to vaccination for prevention and control of influenza. oseltamivir and zanamivir are both approved for prophylaxis; amantadine and rimantadine have fda indications for chemoprophylaxis against influenza a infection, but these agents are currently not recommended because of the frequency of resistance among strains circulating in the united states and canada [ , ] . developing an adequate immune response to the inactivated influenza vaccine takes ∼ weeks in adults; chemoprophylaxis may be useful during this period for those with household exposure to influenza, those who live or work in institutions with an influenza outbreak, or those who are at high risk for influenza complications in the setting of a community outbreak [ , ] . chemoprophylaxis also may be useful for persons with contraindications to influenza vaccine or as an adjunct to vaccination for those who may not respond well to influenza vaccine (e.g., persons with hiv infection) [ , ] . the use of influenza antiviral medications for treatment or chemoprophylaxis should not affect the response to the inactivated vaccine. because it is unknown whether administering influenza antiviral medications affects the performance of the new live attenuated intranasal vaccine, this vaccine should not be used in conjunction with antiviral agents. other types of vaccination can be considered. pertussis is a rare cause of pneumonia itself. however, pneumonia is one of the major complications of pertussis. concern over waning immunity has led the acip to emphasize adult immunization for pertussis [ ] . one-time vaccination with the new tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine-adsorbed (tdap) product, adacel (sanofi pasteur)is recommended for adults - years of age. for most adults, the vaccine should be given in place of their next routine tetanus-diphtheria booster; adults with close contact with infants ! months of age and health care workers should receive the vaccine as soon as possible, with an interval as short as years after their most recent tetanus/diphtheria booster. smoking is associated with a substantial risk of pneumococcal bacteremia; one report showed that smoking was the strongest of multiple risks for invasive pneumococcal disease in immunocompetent nonelderly adults [ ] . smoking has also been identified as a risk for legionella infection [ ] . smoking cessation should be attempted when smokers are hospitalized; this is particularly important and relevant when these patients are hospitalized for pneumonia. materials for clinicians and patients to assist with smoking cessation are available online from the us surgeon general (http://www.surgeongeneral.gov/tobacco), the centers for disease control and prevention (http://www.cdc.gov/ tobacco), and the american cancer society (http://www .cancer.org). the most successful approaches to quitting include some combination of nicotine replacement and/or bupropion, a method to change habits, and emotional support. given the increased risk of pneumonia, the committee felt that persons unwilling to stop smoking should be given the pneumococcal polysaccharide vaccine, although this is not currently an aciprecommended indication. . cases of pneumonia that are of public health concern should be reported immediately to the state or local health department. (strong recommendation; level iii evidence.) public health interventions are important for preventing some forms of pneumonia. notifying the state or local health department about a condition of interest is the first step to getting public health professionals involved. rules and regulations regarding which diseases are reportable differ between states. for pneumonia, most states require reporting for legionnaires disease, sars, and psittacosis, so that an investigation can determine whether others may be at risk and whether control measures are necessary. for legionnaires disease, reporting of cases has helped to identify common-source outbreaks caused by environmental contamination [ ] . for sars, close observation and, in some cases, quarantine of close contacts have been critical for controlling transmission [ ] . in addition, any time avian influenza (h n ) or a possible terrorism agent (e.g., plague, tularemia, or anthrax) is being considered as the etiology of pneumonia, the case should be reported immediately, even before a definitive diagnosis is obtained. in addition, pneumonia cases that are caused by pathogens not thought to be endemic to the area should be reported, even if those conditions are not typically on the list of reportable conditions, because control strategies might be possible. for other respiratory diseases, episodes that are suspected of being part of an outbreak or cluster should be reported. for pneumococcal disease and influenza, outbreaks can occur in crowded settings of susceptible hosts, such as homeless shelters, nursing homes, and jails. in these settings, prophylaxis, vaccination, and infection control methods are used to control further transmission [ ] . for mycoplasma, antibiotic prophylaxis has been used in schools and institutions to control outbreaks [ ] . . respiratory hygiene measures, including the use of hand hygiene and masks or tissues for patients with cough, should be used in outpatient settings and eds as a means to reduce the spread of respiratory infections. (strong recommendation; level iii evidence.) in part because of the emergence of sars, improved respiratory hygiene measures ("respiratory hygiene" or "cough etiquette") have been promoted as a means for reducing transmission of respiratory infections in outpatient clinics and eds [ ] . key components of respiratory hygiene include encouraging patients to alert providers when they present for a visit and have symptoms of a respiratory infection; the use of hand hygiene measures, such as alcohol-based hand gels; and the use of masks or tissues to cover the mouth for patients with respiratory illnesses. in a survey of the us population, the use of masks in outpatient settings was viewed as an acceptable means for reducing the spread of respiratory infections [ ] . for hospitalized patients, infection control recommendations typically are pathogen specific. for more details on the use of personal protective equipment and other measures to prevent transmission within health care settings, refer to the healthcare infection control practices advisory committee [ ] . performance indicators are tools to help guideline users measure both the extent and the effects of implementation of guidelines. such tools or measures can be indicators of the process itself, outcomes, or both. deviations from the recommendations are expected in a proportion of cases, and compliance in %- % of cases is generally appropriate, depending on the indicator. four specific performance indicators have been selected for the cap guidelines, of which focus on treatment issues and of which deals with prevention: • initial empirical treatment of cap should be consistent with guideline recommendations. data exist that support the role of cap guidelines and that have demonstrated reductions in cost, los, and mortality when the guidelines are followed. reasons for deviation from the guidelines should be clearly documented in the medical record. • the first treatment dose for patients who are to be admitted to the hospital should be given in the ed. unlike in prior guidelines, a specific time frame is not being recommended. initiation of treatment would be expected within - h of presentation whenever the admission diagnosis is likely cap. a rush to treatment without a diagnosis of cap can, however, result in the inappropriate use of antibiotics with a concomitant increase in costs, adverse drug events, increased antibiotic selection pressure, and, possibly, increased antibiotic resistance. consideration should be given to monitoring the number of patients who receive empirical antibiotics in the ed but are admitted to the hospital without an infectious diagnosis. • mortality data for all patients with cap admitted to wards, icus, or high-level monitoring units should be collected. although tools to predict mortality and severity of illness exist-such as the psi and curb- criteria, respectivelynone is foolproof. overall mortality rates for all patients with cap admitted to the hospital, including general medical wards, should be monitored and compared with severity-adjusted norms. in addition, careful attention should be paid to the percentage of patients with severe cap, as defined in this document, who are admitted initially to a non-icu or a high-level monitoring unit and to their mortality rate. • it is important to determine what percentage of at-risk patients in one's practice actually receive immunization for influenza or pneumococcal infection. prevention of infection is clearly more desirable than having to treat established infection, but it is clear that target groups are undervaccin-ated. trying to increase the number of protected individuals is a desirable end point and, therefore, a goal worth pursuing. this is particularly true for influenza, because the vaccine data are more compelling, but it is important to try to protect against pneumococcal infection as well. coverage of % of adults у years of age should be the target. the burden of 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pertussis vaccine among adolescents and adults cigarette smoking and invasive pneumococcal disease. active bacterial core surveillance team surveillance for legionnaires' disease: risk factors for morbidity and mortality sars in healthcare facilities an outbreak of multidrugresistant pneumococcal pneumonia and bacteremia among unvaccinated nursing home residents azithromycin prophylaxis during a hospital outbreak of mycoplasma pneumoniae pneumonia respiratory hygiene/cough etiquette in health-care settings experiences with influenza-like illness and attitudes regarding influenza prevention-united states, - influenza season guideline for isolation precautions in hospitals. the hospital infection control practices advisory committee the committee wishes to express its gratitude to robert balk, christian brun-buisson, ali el-sohl, alan fein, donald e. low, constantine manthous, thomas j. marrie, joseph f. plouffe, and david a. talan, for their thoughtful review of an earlier version of the guidelines. supplement sponsorship. this article was published as part of a supplement entitled "infectious diseases society of america/american thoracic society consensus guidelines on the management of community-acquired pneumonia in adults," sponsored by the infectious diseases society of america. key: cord- - fhhuzg authors: hoffman, paul s. title: antibacterial discovery: st century challenges date: - - journal: antibiotics (basel) doi: . /antibiotics sha: doc_id: cord_uid: fhhuzg it has been nearly years since the golden age of antibiotic discovery ( – ) ended; yet, we still struggle to identify novel drug targets and to deliver new chemical classes of antibiotics to replace those rendered obsolete by drug resistance. despite herculean efforts utilizing a wide range of antibiotic discovery platform strategies, including genomics, bioinformatics, systems biology and postgenomic approaches, success has been at best incremental. obviously, finding new classes of antibiotics is really hard, so repeating the old strategies, while expecting different outcomes, seems to boarder on insanity. the key questions dealt with in this review include: ( ) if mutation based drug resistance is the major challenge to any new antibiotic, is it possible to find drug targets and new chemical entities that can escape this outcome; ( ) is the number of novel chemical classes of antibacterials limited by the number of broad spectrum drug targets; and ( ) if true, then should we focus efforts on subgroups of pathogens like gram negative or positive bacteria only, anaerobic bacteria or other group where the range of common essential genes is likely greater?. this review also provides some examples of existing drug targets that appear to escape the specter of mutation based drug resistance, and provides examples of some intermediate spectrum strategies as well as modern molecular and genomic approaches likely to improve the odds of delivering st century medicines to combat multidrug resistant pathogens. infectious diseases are a leading cause of death worldwide, yet the miracle antibiotics developed to combat them are being lost to the rapid emergence of drug resistance. modern medicine is heavily dependent on antibiotics that enable many procedures including abdominal surgeries, bone marrow and organ transplants, managing immune compromised patients and cancer patients and for routine hip and knee replacements [ , ] . while one might presume that new antibiotics would be discovered at a sufficient pace to replace those rendered obsolete by resistance, this has not happened. worse, the few antibiotics that recently entered the clinic are derivatives of older drugs and are susceptible to the same existing drug resistance mechanisms. it is hard to imagine that the last new chemical class of antibiotic for treating infections caused by gram negative (superbug) bacteria (gnb) was the quinolones, discovered over years ago. and, it is not much better for the gram positives (gp) with linezolid and daptomycin discovered nearly years ago. while fleming and waksman are well known discoverers of antibiotics (penicillin and streptomycin, respectively), it is unlikely that anyone today knows someone that delivered a new class of antibiotic from bench to clinic. thus, unlike most disciplines of science and technology, there are no experts to advise us. worse, there seems to be no cumulative knowledge gained from the many failures upon which to build a winning strategy [ ] . while it has been argued that the discovery of antibiotics is one of the greatest achievements in medicine in the th century; our failure to build a sustainable antibiotic discovery platform has left us with one of the greatest liabilities, and now in the st century, one of the greatest challenges. some blame the lack of funding or of effort, but in retrospect the effort was substantial, particularly by the pharmaceutical industry in the 's, and most agree that massive investments would have made little difference. while much has been written recently to explain these failures [ ] [ ] [ ] [ ] ; few have provided tactical approaches that might fare any better [ ] . emergence of drug resistance remains the greatest concern and biggest challenge to future discovery efforts. many believe it is impossible to create an antibiotic to which bacteria cannot evolve resistance and based on some recent experience, the therapeutic window for any new one is projected to be less than five years-a major disincentive. if indeed antibiotic resistance (mutation-based drug resistance) is the major challenge; then, why have we not focused on identifying drug targets less prone to mutation-based resistance? with scarce resources and many suggestions for how to find next generation antibiotics, where do you place your bets [ ] ? this review examines current discovery approaches and their intrinsic liabilities; challenges some myths associated with antibiotic resistance; and concludes by exploring promising st century discovery strategies along with some examples of antibacterials that might escape the specter of drug resistance. there are many headwinds and challenges to antibacterial discovery and delivery of new medicines to the clinic that are not discussed herein (societal, regulatory and marketing) that readers are directed elsewhere for more comprehensive coverage [ ] [ ] [ ] [ ] . most of the antibiotics used in the clinic today were derived from natural products (np) identified in screens of environmental material using variations of the waksman platform strategy [ ] . synthetic antibacterials trace back to paul ehrlich who identified chemical compounds like salvarsan that was active in the treatment of syphilis. later, domagk discovered the dye prontosil and its active metabolite sulfanilamide that inhibited folic acid biosynthesis. this work led to development of the sulfa drugs [ ] . medicinal chemistry and the advent of high throughput screens of compound libraries (target based) replaced np searches in the mid 's and reintroduced the idea of synthetic chemistry as a strategy for creating next generation antibacterials. advances in computational biology (bioinformatics, systems biology, and metagenomics) and structural biological technologies (crystal structures of protein targets, ligand screens via docking software, the so called designer drug strategy) have led to a third discovery strategy-synthetic biology. while all these technologies engender some optimism, the main reason for the antibiotic discovery void in the first place is that creating new chemical classes is really hard. is repeating history a viable strategy?-probably not. one definition of insanity is repeating the same task over and over again while expecting a different outcome. this is especially applicable to antibiotic discovery research where much emphasis has been placed on finding new natural product (np) antibiotics [ ] . after all, the vast majority of antibiotics used in the clinic are derivatives of nps. the insanity with continuing on this path is that for all of these np antibiotics, resistance mechanisms predated their therapeutic use and this is unlikely to change [ , , ] . moreover, we know from past discovery efforts that nps tend to be redundant-with the same targets and mechanisms of action appearing over and over again [ ] . casting a wider net will not change this reality, because the number of broad spectrum drug targets is quite small [ ] . hypothesis. the number of antibiotic classes is limited by the number of broad spectrum drug targets. it follows that the number of resistance mechanisms will generally parallel the number of antibiotic classes. hence, modifying the genes associated with secondary metabolism, while potentially improving an existing scaffold, is unlikely to produce new chemical classes of antibacterials. another issue with nps is that since they have evolved in natural environments and not in the human milieu, most nps are structurally complex and as such are by default poor pharmacophores (pk/pd), requiring much medicinal chemistry to improve bioavailability, to reduce drug metabolism or to reduce intrinsic toxicities. the pharmaceutical industry abandoned np divisions long ago in favor of high throughput screens of compound libraries against novel drug targets (another failure, see below); or, more productively to create next generation derivatives of existing antibiotics, a strategy that has worked well and continues today as judged by the number of analogues in the current pipeline. despite the continuum of second, third and fourth generation β-lactams (penicillin, cephalosporin and carbapenem derivatives) [ ] , by far the largest group of antibiotics used in the clinic today, has not solved the resistance problem originally pointed out by alexander fleming in the late 's. while logic dictates that we should abandon further development of this class, advances in pairing them with β-lactamase inhibitors (clavulinate, avibactam, and vaborbactam to mention a few) has restored their effectiveness and extended their clinical lifetimes [ ] . since β-lactamases and β-lactam targets (penicillin binding proteins, pbp) share conserved structural attributes that can be altered via mutation, resistance will eventually defeat them, but for now this strategy is both viable and profitable. the current antibacterial pipeline is populated with new derivatives based on the scaffolds for quinolones, tetracyclines, macrolides and aminoglycosides [ ] . new chemistries around existing scaffolds has the potential to overcome current resistance mechanisms by improving binding complexity with the drug target, and or improve pharmacological properties. in this regard, the ketolides were supposed to overcome resistance to macrolides, but the tradeoff is increased toxicities. however, given our experiences with np antibiotics in general, it is unlikely that continued searches for new ones, regardless of where one looks, will be any more successful than past efforts. in the mid 's, the pharmaceutical industry turned to molecular biology and genomics to sort through microbial genomes for novel drug targets that could be cloned and their products configured into assays amenable to robotic high throughput screens of massive compound libraries (target-based platform). after all, new medicines were found in library screens in other therapeutic areas, including antivirals [ ] . the fatal assumption in antibacterial screens was the belief that antibiotic-like material was present in these chemical libraries [ ] [ ] [ ] [ ] . in reality, they contained little that resembled antibiotics, because antibiotics are often of high molecular weight and far more complex than can be synthesized by chemists. worse, most of these compounds were poor pharmacophores (hydrophobic with poor pk/pd properties) and failed both lipinski's rule of five and hergenrother's rules for penetration of gn bacteria [ ] [ ] [ ] . unfortunately, efforts to assemble libraries composed of more "antibiotic like material" have yet to deliver an antibacterial to the clinic. what does "antibiotic like" really mean anyway? the experiences of glaxosmithkline, astrazeneca and others are well documented and today there seems to be little enthusiasm for revisiting this approach [ , , ] . however, the lists of potential therapeutic drug targets identified in these bioinformatics initiatives and others remain to be exploited. one of the targets in the gsk screen, fabi, an enoyl-acp reductase and rate-limiting step in fatty acid biosynthesis is the target of a novel therapeutic (afabicin, formerly debio- ) that is active against staphylococcus [ ] . importantly, the failure of hts to deliver new therapeutics to the clinic should not be confused with whether or not synthetic antibacterials can be developed de novo as part of a rational or designer drug strategy (see later section). every healthcare worker can tell you why antibiotic resistance is bad for patients and why antimicrobial stewardship (judicious use) is so important, but few have any deep understanding of the diversity of underlying molecular and genetic mechanisms. this has created a "chicken little" effect; where strong opinions based on shallow thinking, perpetuation of myths and intolerance of new ideas have unnecessarily complicated the discovery process. much of antibiotic theory has evolved over nearly years of history and mostly from experiences with nps. antibiotics and their respective resistance mechanisms have co-evolved over millions or even billions of years of internecine microbial warfare that is ongoing in the environment. these resistance mechanisms are encoded in dna and can be disseminated throughout the microbial world via mobile genetic elements and horizontal transfer [ ] . it is not surprising that soil and aquatic microbes transfer these resistance determinants to human and animal pathogens, often in clinical settings where antibiotics are in heavy use. there is no good outcome to the continued use of nps and as discussed previously it is unlikely that new ones will fare any better. this is best exemplified by the emergence of resistance (mcr- family) to colistin, a polymyxin class antibiotic that has been around for decades, but little used, until the emergence of carbapenem resistance in klebsiella (kpc) and other carbapenem resistant enteric superbugs (cre) made it the drug of last resort [ ] . the rapid and global emergence of mcr- just underscores the point. the resistance problem is further exacerbated by globalization, increasing population density and international travel that has brought us mcr- as well as the ndm- β-lactamase resistance determinant [ ] . the covid- pandemic, unfortunately, is another example of the accelerated global spread of biological agents. it follows from the previous paragraph on nps, that synthetic antibacterials that inhibit targets "mother nature" has yet to find would require millions of years of evolution for resistance determinants to emerge. note that this hypothesis also holds true for new chemistries against established drug targets, provided that they are also not susceptible to existing resistance mechanisms. a good example is linezolid, a synthetic antibacterial discovered nearly years ago and more recent derivatives (tedizolid), that inhibit protein synthesis in gp bacteria [ ] . one might think that synthetic antibacterials would enjoy a long clinical life. unfortunately, synthetic classes of antibacterials, including linezolid, are often defeated by mutation-based drug resistance. mutations occur naturally (probability of~ in ) in dna and since microbial infections involve hundreds of billions of bacteria, microbes tend to win the probability game. survival is the prime directive for any lifeform and in particular, the stress of antibiotics on bacteria, especially at sub-inhibitory levels, provides strong selection for these resistant variants to emerge and flourish. it should be pointed out that mutation-based drug resistance also underlies resistance for nearly all nps. this reality led eric lander and john p. holdren to conclude in a summary of their report by the committee on antimicrobial resistance to the president's council on science and technology that: "in the fight against microbes, no permanent victory is possible: as new treatments are developed, organisms will evolve new ways to become resistant" [ ] . this grim prediction is certainly supported by a recent clinical trial of promising synthetic boron containing heterocycle leucyl trna synthetase inhibitor which was halted due to rapid emergence of drug resistance [ ] . this novel drug inhibited a non-essential proof-reading region of the essential enzyme in which mutations could accumulate and thereby defeat the inhibitor without total loss of function [ ] . the lessons learned here include: ( ) focus on the essential catalytic center of a prospective drug target, ( ) ensure amino acid conservation within this region (resists mutation), and ( ) confirm by co-crystallization that leads indeed are binding within the catalytic pocket of the target. it is also helpful early on to explore possible off target activities against human drug targets related to a particular enzyme class. attention to these details might lead to medicines that slow the inevitable pace to drug resistance. it raises another critical question "can we find drug targets that by catalytic mechanism are capable of escaping mutation-based drug resistance? targets that might defeat mutation based drug resistance do exist. one example is the lipid ii and lipid iii targets associated with cell wall biosynthesis [ ] . these targets are composed of lipid and not amino acids and are the target of a new np antibiotic teixobactin that is in early clinical development for treatment of infections caused by gp bacteria [ ] . another type of target that had not been previously considered is pyruvate: ferredoxin oxidoreductase (pfor) whose catalytic center is highly conserved through evolution and for which there are no np inhibitors [ ] . the pfor catalytic mechanism involves a uniquely positioned and contorted vitamin cofactor (vitamin b or thiamine pyrophosphate, tpp) [ , ] . redox cycling via iron/sulfur centers activates the vitamin to enable binding of substrate pyruvate. the nitrothiazolide class of synthetic antibiotics (fda approved nitazoxanide and analogue amixicile in clinical development) deactivates the vitamin via a proton abstraction mechanism that is dependent on a functional enzyme [ , ] . two key points here are that mutations to the enzyme (loss of function) or that alter the vitamin, a small molecule, are lethal ( ). tpp is also a cofactor in many enzymes (pyruvate dehydrogenase [pdh] and pyruvate carboxylase), but these are not inhibited by nitazoxanide or amixicile [ , ] . importantly for nitazoxanide, there are no toxicities in humans or mitochondria which lack the drug target. importantly, in over years of clinical use, there are no reports of drug resistance with nitazoxanide. a hint at possible resistance to nitazoxanide comes from studies of lab generated resistant mutants of human parasite giardia, where whole genome sequencing found no single correlating mutation among resistant strains [ ] . from this study and others, it is possible to suggest that second site compensatory mutations may lead to metabolic shifts that produce a "tolerance like phenotype", much like over expression of efflux systems incrementally raise mic for quinolones. is this evolution at work? it could be, as efflux buys time for mutations in gyrase and topoisomerase genes to manifest. alternatively, as noted with nitazoxanide tolerance in helicobacter pylori, it may be an example of the microbe "faking it", i.e., tinkering with limited metabolic regulatory choices to enable survival [ ] . in this case, tolerance can be overcome by increasing the therapeutic dose, i.e., one that the microbe cannot overcome by tinkering. the jury is still out though, as only time will tell if such tolerance mechanisms can be inherited. there are several caveats from the pfor example that might be useful in identifying new targets: ( ) pfor is an ancient enzyme highly conserved through evolution; ( ) the vitamin cofactor is uniquely positioned and tightly bound within the enzyme; ( ) the critical amino acids required for cofactor function are absolutely conserved based on analysis of available sequences of pfor enzymes (> ) despite whether pfor is a dimer of high molecular weight monomers or like in helicobacter pylori, a dimer comprised of multiple subunits [ ] ; and ( ) all of these traits are found in the entire broad family of the alpha-keto-acid oxidoreductases (multiple essential targets). perhaps most important in this example is that nitazoxanide and amixicile work by a "theft" mechanism that requires a functional enzyme and cofactor. the phenotype to the affected pathogen is one of slow starvation (pyruvate) with no definable selective mechanism or means to overcome inevitable death by starvation. in retrospect, few searches for new drug targets considered mutation frequency as a criterion for prioritization. finding catalytic centers that are highly conserved and potentially druggable can be relatively straightforward, but like pfor, would likely yield targets of limited spectrum. "highly conserved" generally means that mutations in these regions lead to loss of function or lethality. these potential targets can be catalogued by comparative genomics (blastp approach) by comparing genomes (gene products) from a target group of pathogens. by setting the probably of the match (identity) bar to be more stringent (e − or e − ) creates a shorter list of protein matches whose amino acid sequences are highly conserved [ , ] . further analysis would include amino acid conservation within the catalytic center along with other evaluative criteria that includes chemical space, catalytic mechanism, participation of cofactors and uniqueness from orthologues found in humans or mitochondria. crystal structure of the enzyme is crucial in this process and in silico screening of chemical libraries becomes an early first step in finding developable leads. a number of recent examples can be used to guide this process [ , , ] . the power of computational biology and chem-informatics has yet to be fully exploited, so this area has room to grow. an advantage of this approach is that objective criteria replace age old empiric rationale (guesswork) in choosing drug targets. however, the reality of finding new broad spectrum drug targets is close to nil. this is because microbial genomes are small and the major targets for broad spectrum antibiotics are already known (protein synthesis, dna and rna synthesis, cell wall biosynthesis and a few central metabolic pathways) [ ] [ ] [ ] [ ] [ ] . as discussed below, we need to consider targets of more limited spectrum. the number of broad spectrum drug targets among microbes that meet the criteria of essential and non-redundant is predicted to be quite small, perhaps fewer than several hundred [ , ] . most targets are already known and come with the baggage of preexisting antibiotic resistance mechanisms and the reality that they will cause collateral damage to normal flora when deployed. the problem with narrow spectrum antibiotics is that clinicians do not use them when the pathogen responsible for an infection is not known or is potentially polymicrobial. broad spectrum antibiotics are a hedge and provide liability coverage in the event of an adverse outcome. this reluctance also plagues new antibacterials that enter the clinic, another headwind to drug development. ironically, getting a new broad spectrum antimicrobial through the food and drug administration (fda) today is nearly impossible because for each indication a separate clinical trial is generally required and the additive costs are prohibitive. antibacterials currently in clinical development (gepotidacin) and those that have recently entered the clinic like oritavancin, dalbavancin and tedizolid are examples where the potential use is purposefully limited [ ] . in the distant past, the spectrum for an antimicrobial was often established by the process of "off label" use (trial and error), but today, hospital practice/malpractice and liabilities have essentially ended this strategy. we can expect in the future that the number of indications for antibacterials will continue to be limited by development costs [ ] . perhaps a more productive antibacterial strategy is to focus on groups of microbes sharing common essential drug targets as exampled by pfor. in this example, nitazoxanide exhibits the same spectrum as metronidazole, providing broad anaerobic coverage (gp and gn), treatment of infections caused by anaerobic human parasites and potentially treatment of infections caused by members of the epsilon proteobacteria (helicobacter and campylobacter). along these lines, developing antimicrobials that target either gp or gn bacteria would exploit new drug targets unique to each, such as teixobactin for gpb. similarly, drugs that are selective against mycobacterium tuberculosis are highly desirable since resistance is a major problem [ ] . recent new chemical classes of anti-tubercular therapeutics include the nitroimadazole delamanid that targets the f deazaflavin nitroreductase [ ] . similarly, pathogen selective therapeutics such as ridinilazole, a novel synthetic drug in clinical development for treatment of colitis caused by clostridioides difficile, are developed in response to an urgent clinical need [ ] . in this case, ridinilazole targets cell division by an unknown mechanism that is likely to uncover a novel drug target and mechanism. microbiome studies support limited collateral damage with ridinilazole and the frequency of drug resistance appears to be low [ ] . since there is an urgent need to develop gn-selective therapeutics, focusing on targets unique to them and vetted by objective criteria (including resistance to mutation) should be encouraged. indeed, ongoing drug discovery efforts are targeting lps biosynthesis (lpxc, lepb, msba) [ ] , essential enzymes associated with beta-barrel assembly machine (bam), lipoprotein assembly (lol), and even the periplasmic disulfide bond isomerase (dsba, dsbc, dsbd) enzymes [ ] [ ] [ ] [ ] [ ] . unfortunately, lead compounds targeting lps biosynthetic systems have proven toxic and reminds us that finding new chemistries of low toxicity remains a significant challenge. focus on anti-virulence strategies, particularly for gn superbugs, is now gaining momentum as inhibitors are emerging against secretion systems, pili, motility, quorum sensing and toxins [ , ] . conceptually, if virulence systems contribute to antibiotic resistance or tolerance, inhibition of these systems might result in regulatory changes that restore or enhance susceptibility to mainline antibiotics. as better rapid diagnostics come onboard, narrow or limited spectrum antibacterials will see increased usage, and when treating polymicrobic infections, therapeutic strategies would likely mix and match the appropriate therapeutics. even better, we might consider creating bi-functional or hybrid antibacterials that provide dual function that likely will extend both coverage and timelines to resistance. repurposing of drugs, especially fda approved medicines, for use as antibacterials has gained in interest since they skip the early preclinical and clinical development stages [ ] . it is also believed that such drugs would also come with novel modes of action and perhaps escape preexisting drug resistance mechanisms. perhaps the most studied of these compounds is auranofin, a drug developed to treat rheumatoid arthritis and cancer, that is a potent inhibitor of thioredoxin reductase found in many human pathogens including clostridioides difficile [ ] . for repurposed drugs in general the primary indication is still a secondary target of the new application. in order to gain therapeutic efficacy (serum levels greater than mic), repurposed drugs would likely be administered at concentrations exceeding levels required for efficacy of the original use. in reality, drugs that actively target human enzymes, often come with undesirable side effects or toxicities. still, for treatment of infections such as tuberculosis, gonorrhea or by c. difficile and h. pylori, repurposed drugs in combination with other therapeutics might aid overcoming drug resistance. the goal of this review was to point out basic science challenges to the discovery of new classes of antibacterials and to provide some suggestions on how to move forward in a more productive manner. we know that the "waksman platform" for discovery of new nps and the "hts-target based platform" for screening chemical libraries have both failed to deliver new antibacterials. does repeating these strategies boarder on insanity? from a business perspective, investment in antibacterial discovery is mitigated by concerns over rapid emergence of drug resistance and loss of investment. if indeed mutation-based drug resistance is the greatest impediment to the discovery effort, then why not work backwards from the problem as a discovery strategy? this review provides a few examples of such drug targets (pfor and lipid ii) and respective inhibitors that shows that this approach has merit. structure based drug design has yielded therapeutics in other areas including hiv/aids (protease inhibitors), antivirals (zanamivir for influenza), and even inhibitors of cyclooxygenase, so why not for antibacterials? bioinformatics can be used to collate essential targets and provide a probability score for evaluating risk for mutation based drug resistance. structure based drug design tools have been steadily evolving and their use in evaluating three dimensional structure and chemical space for ligand binding can be integrated with in silico screens of synthetic chemical libraries to produce early leads. lead optimization and structure activity relationships (sar) can be modeled and synthetic chemistry and chem-informatics can be used to optimize candidates in areas of pk/pd, drug metabolism and toxicology, essential to building safe medicines. it should be obvious that antibacterial development in the future will require a wide range of biological, chemical, computational and pharmacological disciplines working towards a common goal to progress st century medicines. while the pharmaceutical industry used to contain this expertise, we need to find a way to fund such initiatives that also removes the shareholders and corporate return on investment metrics from the equation. while carb-x and other related initiatives are critical in the clinical development of antibacterials via cost sharing with startup companies, the real bottleneck occurs much earlier in the early discovery process. if years of effort has not yielded a novel class of gn therapeutic, one might imagine the failure rate for any new initiative might be close to %, not a viable strategy for "bean" counters. we have to ask "how much are we willing to invest in order to get one new antibiotic to the clinic?" we already know many ways not to make an antibiotic, perhaps now we can find 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lipopolysaccharide transporter msba the small molecule nitazoxanide selectively disrupts bam-mediated folding of the outer membrane usher protein thinking outside the bug: molecular targets and strategies to overcome antibiotic resistance defeating antibiotic-resistant bacteria: exploring alternative therapies for a post-antibiotic era drug repurposing for the treatment of bacterial and fungal infections repurposing auranofin as a clostridioides difficile therapeutic key: cord- -ll j i authors: phuong, nguyen t. k.; hoang, tran t.; van, pham h.; tu, lolyta; graham, stephen m.; marais, ben j. title: encouraging rational antibiotic use in childhood pneumonia: a focus on vietnam and the western pacific region date: - - journal: pneumonia (nathan) doi: . /s - - - sha: doc_id: cord_uid: ll j i globally, pneumonia is considered to be the biggest killer of infants and young children (aged < years) outside the neonatal period, with the greatest disease burden in low- and middle-income countries. optimal management of childhood pneumonia is challenging in settings where clinicians have limited information regarding the local pathogen and drug resistance profiles. this frequently results in unnecessary and poorly targeted antibiotic use. restricting antibiotic use is a global priority, particularly in asia and the western pacific region where excessive use is driving high rates of antimicrobial resistance. the authors conducted a comprehensive literature review to explore the antibiotic resistance profile of bacteria associated with pneumonia in the western pacific region, with a focus on vietnam. current management practices were also considered, along with the diagnostic dilemmas faced by doctors and other factors that increase unnecessary antibiotic use. this review offers some suggestions on how these issues may be addressed. childhood pneumonia is a major contributor to under- mortality, especially in developing countries [ , ] . in the western pacific region, the highest burden of childhood pneumonia and pneumonia-related deaths occur in six countries: cambodia, china, laos, papua new guinea, the philippines and vietnam [ ] . these countries report at least . pneumonia episodes per child year-more than times the rates reported in developed countries from the same region such as australia, new zealand and japan [ ] . the management of childhood pneumonia is problematic in settings where a microbiological diagnosis is rarely pursued and the drug resistance profiles of common bacteria which cause respiratory disease are not readily available [ ] . in many asian countries this encourages excessive use of broad-spectrum antibiotics, irrespective of the child's disease severity. in the authors' experience, children are frequently hospitalized with pneumonia to administer intravenous antibiotics, despite relatively mild disease. unnecessary hospitalization for intravenous antibiotics increases healthcare cost, as well as treatment-related complications and the likelihood of nosocomial disease transmission. in order to encourage more rational use of intravenous antibiotics in children with communityacquired pneumonia, the authors performed a comprehensive review of common bacterial pathogens and their reported drug resistance profiles in the western pacific region-vietnam in particular. factors that increase unnecessary antibiotic use (and measures that might reduce use) were also considered. pubmed, google scholar and embase databases were searched using the following terms: antibacterial agents or antibiotics or drug therapy and community acquired pneumonia or acute respiratory tract infection and child or children or childhood. manuscript titles and abstracts were reviewed to identify original research papers that included children less than years of age with pneumonia, with a geographic focus on vietnam and the western pacific region. in addition, the references of selected publications were reviewed, and co-authors suggested additional relevant papers. the term 'acute respiratory tract infection (arti)' describes all acute infections that involve the lungs or airways (upper and lower). the world health organization (who) defines 'pneumonia' as a child with tachypnoea, with or without signs of respiratory distress. given the huge overlap in how these terms are applied in clinical practice, the authors considered 'pneumonia' and acute lower respiratory tract infection (lrti) to be synonymous for the purpose of this review. bacteria classically described to cause communityacquired pneumonia in children include streptococcus pneumoniae, haemophilus influenzae type b (hib) and staphylococcus aureus [ ] . table presents an overview of pathogens commonly associated with acute lrtis in children less than years of age. with enhanced diagnostic tools, respiratory viruses and atypical bacteria such as mycoplasma pneumonia are commonly detected in children with community-acquired pneumonia, particularly in studies from the western pacific region [ ] [ ] [ ] . this review focused on bacterial pathogens because they are the major cause of pneumonia-related mortality and the primary indication for antibiotic use. however, it is important to appreciate that accurate differentiation between viral and/or bacterial infection is a major challenge to clinicians and complicates management [ ] . this review provides a brief overview of the most common bacterial pathogens and their reported drug resistance profiles from surveys conducted in the western pacific region. the development of resistance mutations against multiple antibiotics is well documented in s. pneumoniae, as well as the expansion of resistant clones under antibiotic pressure. resistance has been recorded against penicillin, tetracycline, cotrimoxazole, chloramphenicol, fluoroquinolones and macrolides [ , , ] . although the correlation between in vitro and in vivo resistance remains contentious, it is generally assumed that penicillin (at adequate dosages) should still be effective against pneumococcal pneumonia (not meningitis) caused by strains with low or intermediate levels of resistance in vitro [ ] . this is difficult to verify, as many factors that influence the outcome of pneumonia treatment-such as underlying comorbid conditions, disease severity and supportive treatment-are poorly described in historical datasets and adequately powered head-to-head comparisons are rare [ ] [ ] [ ] . another important factor to take into consideration is the roll-out of pneumococcal conjugate vaccines. routine administration of pneumococcal conjugate vaccine (pcv) in infancy has led to major reductions in pneumonia hospitalization and invasive pneumococcal disease in young children [ ] . given that the most common drug resistant strains were included in -and -valent pneumococcal conjugate vaccines, drug resistant pneumococcal disease has been greatly reduced in areas with high vaccine uptake [ ] , while reductions in strain carriage also reduced secondary pneumonia cases among older adults [ ] . however, recent studies from canada and the united kingdom demonstrated substantial increases in multidrug resistant non-vaccine serotypes in both colonizing and invasive strains since introducing pcv , with similar findings for colonizing strains after introducing pcv in korean children [ ] [ ] [ ] . high penicillin and macrolide resistance rates have been reported in published surveys, but many of these surveys included select patient populations and used minimal inhibitory concentration (mic) breakpoints with variable stringency, and were also done prior to routine pcv delivery [ , , ] . the use of variable mic breakpoints in different studies is a major source of confusion and complicates study comparison. mic breakpoints defined by the clinical and laboratory standards institute (clsi) are widely used in the united states, while europe has adopted the european committee on antimicrobial susceptibility testing (eucast) standards. they use broadly similar in vitro methods and specify mic breakpoints by considering the pharmacokinetic-pharmacodynamic (pk-pd) properties of the drug, the clinical site of disease and the specific mechanism of drug resistance [ ] . studies have shown reasonable comparability between antibiotic susceptibility profiles using revised clsi and eucast breakpoints [ , ] , but some significant differences remain. against s. pneumoniae and h. influenzae, cefuroxime and cefaclor breakpoints still produce divergent results [ ] . global surveillance efforts would be greatly enhanced if uniform surveillance criteria can be agreed upon and mic breakpoint definitions harmonized. a study conducted in asian countries reported a low ( . %; / ) prevalence of penicillin resistance in s. pneumoniae from non-meningeal isolates, [ ] but it used an mic breakpoint of ≥ μg/ml as recommended by clsi, which is much higher than the > . μg/ml breakpoint proposed by eucast. a small case series of children with s. pneumoniae septicemia in china reported high drug resistance rates ( %; / ) [ ] , but mic breakpoints were not specified. in malaysia, % ( / ) of s. pneumoniae isolated from blood in children with community-acquired pneumonia was resistant to penicillin (using revised clsi breakpoints) [ ] . since nasopharyngeal carriage may create a reservoir of resistant s. pneumoniae clones, it is important to monitor resistance in carriage specimens as well [ ] . nasopharyngeal s. pneumoniae carriage has been reported in % ( / ) of healthy chinese children; % were resistant to macrolides by the e-test method [ ] . in rural vietnam, s. pneumoniae carriage has been detected in % of children, with higher rates in those less than years of age ( - months). the resistance rate to amoxicillin and benzylpenicillin was low ( %; / ), based on revised clsi breakpoints, but % were resistant to at least one antibiotic (cotrimoxazole %, erythromycin %, ciprofloxacin %) [ ] . a more recent vietnamese survey confirmed excellent penicillin susceptibility in s. pneumoniae isolates from respiratory specimens (penicillin % using revised clsi breakpoints), although cephalosporin and macrolide susceptibility was poor (cefuroxime %, cefaclor %; azithromycin %) [ ] . this supports the vietnam national guidance to use high dose ( mg/kg/day) amoxicillin as first-line treatment of community-acquired pneumonia in children [ ] . although the prevalence of h. influenzae type b (hib) has declined dramatically with widespread roll-out of conjugated hib vaccine [ , ] , it remains prevalent in settings with poor vaccine uptake. b-lactamase production is commonly associated with hib infection. in vietnam, % of respiratory hib isolates produced βlactamase and % were β-lactamase non-producing ampicillin-resistant [ ] . however, it is impossible to differentiate clinical infection from asymptomatic colonization using respiratory specimens from nonsterile sites. in china, hib carriage decreased from % in to % in , but β-lactamase-producing isolates increased from to % over the same time period. amoxicillin/clavulanic acid and nd or rd generation cephalosporins remained universally effective [ ] . despite the national hib vaccine roll-out in vietnam, hib remains a common invasive pathogen [ ] , but this is expected to decrease as vaccine uptake improves. with increased vaccination uptake, the role of other encapsulated h. influenzae strains have increased [ ] . a study in china found that % of h. influenzae strains identified in the sputum of children with pneumonia were non-typable; % ( / ) were β-lactamasepositive and % were β-lactamase non-producing ampicillin-resistant or intermediately resistant [ ] . s. aureus remains a common cause of communityacquired pneumonia. pioneering lung puncture studies performed in chile and papua new guinea identified s. aureus as a common pathogen in children with community-acquired pneumonia [ ] . more recent studies found the pathogen predominantly in children at the severe end of the pneumonia disease spectrum, with increased frequency in severely malnourished children [ , ] . s. aureus also poses particular problems following influenza or measles infection, and as a secondary infection in hospitalized children [ , , ] . a major challenge has been the emergence of methicillin-resistant s. aureus (mrsa) and more recently, a decrease in vancomycin susceptibility [ , ] . among positive s. aureus blood cultures in australian and new zealand children, mrsa has been reported in % ( / , ) with three times the average rate (incidence rate ratio, [ %, ci: - ]), found among aboriginal and pacific islander populations [ , ] . a recent malaysian survey reported mrsa in % ( / ) of children with communityacquired s. aureus bacteremia; % had skin or soft tissues infections and % had community-acquired pneumonia [ ] . a study assessing the prevalence of heterogeneous vancomycin-intermediately-resistant s. aureus (hvisa) in asian countries (including south korea, taiwan, hong kong, thailand, the philippines, vietnam, india and sri lanka) reported that among mrsa isolates, . % were hvisa, with the highest prevalence in south korea and vietnam ( . %) [ ] . a more extensive report on antibiotic resistance in hospitals throughout vietnam found mrsa in % of children and adults with s. aureus bacteremia; vancomycin resistance rates were very low [ ] . mycoplasma pneumoniae is highly prevalent in children diagnosed with pneumonia in the western pacific region [ ] . m. pneumoniae is inherently resistant to all βlactams antibiotics and vancomycin, because it does not have a cell wall. with excessive macrolide use in recent years, reported macrolide resistance is near universal ( - %) in parts of asia [ ] . most countries report high rates of macrolide resistance (japan % [ , ] , china - % [ , , ] , south korea % [ ] , hong kong % [ ] , taiwan % [ ] ), although the methods for m. pneumoniae susceptibility testing are poorly standardized. m. pneumoniae remains susceptible to macrolides in australia where it is less frequently used [ ] . resistance to tetracyclines and fluoroquinolones have not been reported in clinical isolates and may provide a treatment alternative in some children, although reduced in vitro susceptibility has been reported [ ] . however, most m. pneumoniae cases recover either without antibiotic treatment or despite documented drug resistance, thus the clinical value of antibiotic treatment remains uncertain [ ] . treatment of artis is a major driver of antibiotic use in children. it is important for clinicians to be familiar with the most common bacterial causes, their local drug resistance profiles and the likely impact of antibiotic therapy (both positive and negative) in order to develop a rational treatment approach. because a timely and definitive bacteriological diagnosis is currently impossible, empiric antibiotic treatment is justified in any acutely ill child. however, there is a need to critically consider factors that promote unnecessary and irrational antibiotic use, especially in children who are not acutely ill. antibiotic use generates selective pressure that increases the prevalence of drug resistant strains; hence, strategies to improve rational antibiotic use are important to protect antibiotics as a precious resource. a study of antibiotic use in vietnamese hospitals showed that a large proportion of in-patients received inappropriate antibiotic therapy [ ] . the main factors that promote unnecessary antibiotic use in the western pacific region, using vietnam as an exemplar, are listed below. given unrestricted access to over-the-counter antibiotics, treatment of any respiratory infection with antibiotics is a common practice in vietnam, malaysia, and south korea [ ] . in vietnam, the pharmaceutical law passed in requires an antibiotic prescription, but % of caregivers still access antibiotics without any formal medical assessment [ ] ; even injectable antibiotics can be acquired at local shops without prescription [ ] . in the western pacific region, antibiotic use before presentation to a doctor is common; more than % in mongolia [ ] and more than % of children admitted with artis in the philippines [ ] . a study in nine international sites-colombia, ghana, india, mexico, pakistan, south africa ( sites), vietnam and zambia-found that the use of antibiotics in the h prior to hospital admission was associated with treatment failure (or: . ; % ci: . - . ) [ ] . in addition, agricultural use of antibiotics remains essentially unregulated in most asian countries, with high rates of colistin and cephalosporin use in the pig and poultry industries, resulting in increased rates of drug-resistant infections in human populations [ , ] . limited awareness among the general public (including politicians) is a challenge in all settings; the who recently launched a program to increase awareness about antimicrobial resistance and the need for more prudent antibiotic use [ ] . in response, country-specific strategies to limit antimicrobial resistance have been launched in the united kingdom, the united states and australia [ ] [ ] [ ] , but few asian countries have followed suit. unrealistic public expectation is a major factor driving excessive antibiotic use [ , ] . a study in rural vietnam showed that just % of caregivers had correct knowledge about acute respiratory infections and % of caregivers self-managed common colds by buying antibiotics without prescription at the local pharmacy [ ] . in malaysia, % of people believed antibiotics to be effective against viral infections, with % using antibiotics during a common cold [ ] . moreover, antibiotic use is strongly influenced by cultural preferences and beliefs. patients in vietnam and china believe injectable antibiotics are more potent than oral options, and readily access injectable antibiotics without prescription [ ] . a lack of adequate knowledge is also a problem among healthcare providers. a study in vietnam demonstrated poor awareness about the risks and consequences of drug resistance among rural health-care providers when treating artis; only % complied with recommended guidelines and % used antibiotics for common colds [ ] . table provides an overview of physician-related factors that explains some of the excessive antibiotic use seen in vietnam and parts of the western pacific region. the difficulty in accurately differentiating viral from bacterial pneumonia is a major challenge in all settings. a study in finland showed that of the routine blood tests, only the c-reactive protein (crp) level differed significantly between bacterial and viral pneumonia patients [ ] . most children with dense lobar infiltrates on chest radiograph had laboratory evidence of a bacterial infection, but interstitial infiltrates were seen in both viral and bacterial pneumonia [ ] . a recent randomizedcontrolled trial in vietnam showed that point-of-care crp testing reduced inappropriate antibiotic use for non-severe artis [ ] . a previous randomizedcontrolled trial in china investigated whether serum pro-calcitonin (pct) could reduce unnecessary antibiotic use [ ] , but although the mean duration of antibiotic treatment was shorter in the pct group, the antibiotic prescription rate was higher. it is hoped that rapid point-of-care testing for common respiratory viruses and biomarkers of severe bacterial infection will offer better bedside guidance in the near future, assisting more appropriate antibiotic use. because most child pneumonia deaths are caused by bacterial pathogens, current who guidelines recommend antibiotic use in all pneumonia cases, as defined by the presence of fast breathing. this approach may encourage the overuse of antibiotics, especially in children without danger signs who present with wheezing as a sign of reactive airway disease, which usually indicates a viral infection. audible wheezing has been noted in % of vietnamese children admitted with 'pneumonia' [ ] , which may identify a subgroup that does not require antibiotics [ ] . who guidelines previously advised intravenous antibiotics in all children diagnosed with severe pneumonia (signs of respiratory distress), but oral amoxicillin was found to be effective in % ( / , ) of children with a clinical diagnosis of severe pneumonia in pakistan [ ] . subsequent trials demonstrated that home-based treatment can be applied to a wide variety of settings [ ] . a multi-center study conducted in bangladesh, egypt, ghana and vietnam reported % ( % ci: - %) treatment failure with days of high dose oral amoxicillin ( - mg/kg/day), varying from % ( % ci: - %) in ghana to % ( % ci: - %) in vietnam [ ] . a sizeable (but unknown) proportion of cases enrolled in these "clinical pneumonia" studies would have had viral infections. therefore, it is not clear how much "treatment failure" actually resulted from inadequate antibiotic treatment for bacterial pneumonia; most children found to be "unresponsive to antibiotics" probably had viral pneumonia [ , ] . despite the available evidence, most doctors in vietnam routinely hospitalize children with "clinical pneumonia" to administer intravenous antibiotics; unnecessary hospitalization increases both healthcare cost and the risk of nosocomial infection. actions and recommendations to improve rational antibiotic use in both the community and hospital environment are summarized in table . unrestricted antibiotic access and self-medication are firmly entrenched in vietnam and most other asian countries [ ] . given the multiple vested interests that protect the status quo, strong regulation and effective law enforcement will be required to limit excessive antibiotic use. in addition to public education programs, better training of healthcare providers to critically review the need for antibiotic use is essential [ ] . only % of countries in the western pacific region report high awareness of antimicrobial resistance among their healthcare providers [ ] . an educational program in indonesia, including face-to-face clinician visits and group discussions, significantly professional hierarchy • junior physicians adopt the prescription habits of senior physicians without rigorous discussion or review of the evidence [ ] . • in vietnam, inappropriate antibiotic use is a particular problem in obstetrics, gynecology and surgery wards where professional hierarchy is most pronounced [ ] no consideration of "societal risk" • doctors and patients often prefer newer and more expensive antibiotics, which are considered more "powerful" [ ] • physicians provide antibiotics to help individual patients; potential societal risks are not considered [ ] ; • in the absence of functional microbiology services, physicians have limited information on local drug-resistance profiles and the impact of excessive antibiotic use; perceived patient/ parent expectation • doctors strive for patient satisfaction and if patients request antibiotics it is usually prescribed [ , ] ; in korea, % of doctors prescribe antibiotics for a common cold if requested by parents [ ] ; in malaysia, % of patients believe that antibiotics help for viral infections [ ] • doctors have no time or motivation to explain the rationale for not using antibiotics fear of poor patient outcome or litigation • fear of poor patient outcomes is often listed as a key motivation for the use of broad-spectrum antibiotics by doctors [ , , ] • fear of litigation is not yet a major driver in the western pacific, but is likely to become a more prominent factor with increased development [ ] inadequate microbiology services • near universal use of empiric broad spectrum antibiotics is common in places with poor microbiology services [ , ] . • in vietnam, antibiotic use was reduced in hospitals with functional microbiology laboratories [ ] financial incentives to use antibiotics • doctors' prescribing habits is influenced by personal income generated and incentives provided by pharmaceutical companies [ , , ] . in china, as in many other western pacific countries, drug prescriptions supplement a doctor's income [ ] . • in south-korea drug dispensing by health care workers was banned in , resulting in major reductions in antibiotic use [ ] reduced the use of injectable drugs [ ] , but has not been replicated elsewhere. in , the who facilitated a meeting of western pacific region countries in manila to identify feasible antimicrobial resistance (amr) strategies [ ] , but this has not yet translated into revised childhood pneumonia guidance or management practices. in vietnam, the vietnam resistance (vinares) project aims to strengthen laboratory surveillance and reduce irrational antibiotic use. the project covers participating hospitals [ ] , but outside of the participating hospitals amr surveillance remains weak. laboratory capacity to assist microbiological diagnosis and guide clinical management is insufficient throughout the region [ ] . functional antibiotic stewardship programs have been established in some countries, but this should become standard practice and be adapted to the local context [ ] . an antibiotic stewardship program in chinese hospitals set targets for antibiotic prescriptions and penalized doctors who prescribed antibiotics inappropriately [ ] . after years, antibiotic prescriptions decreased by - % in inpatients and - % in outpatients [ ] . an antimicrobial stewardship program is currently being implemented in vietnam (through vinares), but the scope of the program is limited and there is a need for similar programs, including regular audits of antibiotic use, in every hospital [ ] . optimal child pneumonia management presents an opportunity to reduce excessive antibiotic use in the western pacific region. however, encouraging the rational use of antibiotics requires education of healthcare professionals, facilitation of cultural change, improved clinical guidance and the establishment of functional microbiology laboratories to monitor disease etiology and drug resistance patterns, together with the removal of inappropriate incentives and effective enforcement of national regulations to restrict antibiotic use in healthcare and agriculture. in addition, a detailed assessment of pneumonia case management should be conducted to understand clinical decision-making and provide more pragmatic guidance to clinicians in the field. exemplars of comprehensive national strategies to address antimicrobial resistance and limit excessive antibiotic use include the united kingdom, the united states and australia [ ] [ ] [ ] global burden of childhood pneumonia and diarrhoea monitoring health for the sdgs integrated management of childhood illness (imci) implementation in the western pacific region: information package. world health organ wpg child pneumonia in the western pacific region surveillance of resistance in bacteria causing community-acquired respiratory tract infections community-acquired pneumonia in children first report on prevalence and risk factors of severe atypical pneumonia in vietnamese children aged - years detection of viruses and atypical bacteria associated with acute respiratory infection of children in hubei population based cohort study for pediatric infectious diseases research in vietnam differentiation of bacterial and viral pneumonia in children a review of streptococcus pneumoniae infection treatment failures associated with fluoroquinolone resistance changing trend of antimicrobial resistance and serotypes in streptococcus pneumoniae in asian countries: an ansorp study penicillins for treatment of pneumococcal pneumonia: does in vitro resistance really matter? update on community-acquired pneumonia: impact of antibiotic resistance on clinical outcomes controversies in the treatment of pneumococcal community-acquired pneumonia outcomes in lower respiratory tract infections and the impact of antimicrobial drug resistance vaccines to prevent pneumonia in children-a developing country perspective (epub ahead of print) antibiotic resistance and the potential impact of pneumococcal conjugate vaccines population structure and drug resistance patterns of emerging non streptococcus pneumoniae serotypes f, a, and isolated from adults in ontario rise of multidrug-resistant non-vaccine serotype a streptococcus pneumoniae in the united kingdom prevalent multidrug-resistant nonvaccine serotypes in pneumococcal carriage of healthy korean children associated with the low coverage of the seven-valent pneumococcal conjugate vaccine optimizing antibacterial therapy for community-acquired respiratory tract infections in children in an era of bacterial resistance clinical characteristics of children with streptococcus pneumoniae septicemia and drug sensitivity of streptococcus 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pre-submission inquiries • our selector tool helps you to find the most relevant journal submit your next manuscript to biomed central and we will help you at every step: key: cord- - cql hu authors: baquero, fernando; levin, bruce r. title: proximate and ultimate causes of the bactericidal action of antibiotics date: - - journal: nat rev microbiol doi: . /s - - - sha: doc_id: cord_uid: cql hu during the past years of antibiotic use, we have learned a great deal about how these ‘miracle’ drugs work. we know the molecular structures and interactions of these drugs and their targets and the effects on the structure, physiology and replication of bacteria. collectively, we know a great deal about these proximate mechanisms of action for virtually all antibiotics in current use. what we do not know is the ultimate mechanism of action; that is, how these drugs irreversibly terminate the ‘individuality’ of bacterial cells by removing barriers to the external world (cell envelopes) or by destroying their genetic identity (dna). antibiotics have many different ‘mechanisms of action’ that converge to irreversible lethal effects. in this perspective, we consider what our knowledge of the proximate mechanisms of action of antibiotics and the pharmacodynamics of their interaction with bacteria tell us about the ultimate mechanisms by which these antibiotics kill bacteria. antibiotics have been used to treat bacterial infections for nearly years, or more than a century if paul ehrlich's arsenate, also called 'compound ' or 'salvarsan' , is included . during this time, we have learned a great deal about these drugs. we know their molecular structure and that of their targets in the bacteria, how they bind to those targets and the immediate consequences of that binding on the physiology and structure of the exposed bacteria. curiously, for the vast majority of antibiotics, what is not known, and is subject of some controversy, is how these drugs actually kill bacteria and/or prevent their replication . for example, why do some ribosome-targeting drugs, such as most but not all aminoglycosides, rapidly kill bacteria, whereas others, such as the macrolides, prevent replication and kill at low rates if at all? why is inhibition of protein synthesis lethal in some cases and only static in others? it is useful to put this question into the context of what ernst mayr described as cause and effect in evolutionary biology [ ] [ ] [ ] . mayr used 'proximate causation' to refer to immediate factors (for example, physiology or mutation) of processes and 'ultimate causation' to refer to the 'final reasons' for the outcome (for example, by convention. in an essay written many years ago, peter medawar defined death as the non-reversible loss of individuality, a state that requires physical destruction of the biological "structure of the self " (ref. ), dissipation of the internal content of the cell by irreversible membrane damage or irreversible breaks and disorganization of its individual genetic content produces death. other changes in the structural and physiological status quo may not result in death, but from the limited perspective of bench scientists conveniently working with bacteria whose viable cell densities can be estimated from data on colony-forming units, if a bacterium cannot form a colony, it is officially dead. deadly events are those for which the antimicrobial agents or procedures immediately destroy the integrity of the cell (similar to a crash or explosion), whereas deadly processes resemble a mortal illness (acute or chronic), finally leading to the collapse of physical or genetic individuality. probably, most of the deadly processes result from the antimicrobial-induced starvation or destruction of a key cellular components needed to maintain the cellular envelope or genetic integrity. in this way, an antimicrobial, including chemical disinfectants, could produce virtually immediate death of a bacterium at higher concentrations and at lower concentrations could produce morbidity and a slow approach to death. chlorine and its effects on the membranes of bacteria is an excellent example of this , . one antibiotic, many actions traditionally, in vitro studies of bacteria and antibiotics ignore the inconvenient reality of the physical and temporal heterogeneity of bacterial populations and their interactions with these drugs. however, it is clear that for a comprehensive understanding of how antibiotics do their bactericidal and bacteriostatic actions, this complexity must be considered, but rarely is. for convenience and the parametric reductionism manifest in so much of biology, the study of antibiotic action is treated as a static process´, and the use of minimum inhibitory concentrations as the unique pharmacodynamic parameter is reflection of this approach . the interaction natural selection or evolution). we use these terms similarly to respectively refer to the primary biochemical mechanisms by which antibiotics exert their action (the traditional 'mechanisms of action') and the final result of the process (bactericidal action).we know a great deal about the proximate causes of antibiotic action, how antibiotics interact with the cell, but we know vastly less about the ultimate causes, why, when confronted with antibiotics, bacteria die, and why they do so at different rates. in this perspective, we consider what the knowledge of the proximate causes of antibiotic action tells us about these ultimate causes, and what we know and need to know to truly understand how antibiotics kill bacterial cells. we discuss these processes in general and for antibiotics of specific classes. when is a bacterium dead? central to understanding how antibiotics kill or prevent the replication of their target bacteria is knowing when a bacterium is dead and when it is no longer capable of dividing. whereas the former is irreversible, the latter is expected to be transient, but if cell division is prevented for a long time, the bacterium is effectively dead between antibiotics and their target bacteria is a dynamic process. bacteria are in a continuous state of flux: their populations are heterogeneous and composed of cells of a diversity of ages (corresponding to the time since they were produced by cell division) and physiological states. antibiotics act at variable concentrations, and their effects on bacteria might differ with the number of molecules effectively interacting with each cell. the concept of 'hormesis' applies here. the term 'hormesis' was coined by southam and ehrlich in to describe biphasic dose responses of the same compound acting on a biological substrate . this term was resurrected by julian davies in reference to different types of action at different antibiotic concentrations, ranging from promoting death to serving as signals in interbacterial communication , . hormesis is considered a fundamental concept in medicine and biology , . hormesis and, more generally, multiphasic processes are certainly a reality for the antibiotic treatment of bacterial infections. in treated patients, the concentrations of antibiotics vary in time and space (intracellular, tissues or organic fluids); pharmacokinetics is a highly dynamic process. the individual cells of the target bacteria are confronted with variable concentrations of the treating drug, which has different but overlapping effects on their physiology. antibiotic susceptibility tests based on agar diffusion or the response of bacteria to antibiotics in continuous culture offer a more realistic view of the antibiotic action than the gold standard of estimating the minimum concentration of antibiotics necessary to prevent replication (the minimum inhibitory concentration) by exposing well-mixed bacterial populations at relatively low densities growing exponentially to fixed antibiotic concentrations. we have considered hormesis for individual cells, as it should be. however, the consequences of the 'one antibiotic, many actions' paradigm are particularly relevant in assays to determine killing curves, which are normally performed on relatively dense bacterial populations (on the order of cells per millilitre). such high numbers ensure substantial heterogeneity in the physiological conditions of each bacterial cell, so different antibiotic actions are expected to apply in a population of cells with different ages and physiological states. what does the relationship between the concentration of antibiotics and the rate of growth and death of bacteria (that is, pharmacodynamics) tell us about how antibiotics do their bacteriostatic and bactericidal actions? as can be seen in fig. , antibiotics differ considerably in the rates at which they kill bacteria. although the drug dose, relative to the minimum inhibitory concentration, to which these growing populations of staphylococcus aureus are exposed ( times the minimum inhibitory concentration) is the same for the nine drugs, the rates at which the viable cell densities decline (that is, the raters at which the bacteria are killed) differ considerably among these drugs. antibiotics that are deemed bacteriostatic kill at low rates, whereas those deemed bactericidal kill at higher but very different rates. the rates at which oxacillin and vancomycin kill during the hours of the experiment are not much greater than those of the bacteriostatic antibiotics. the rates of decline in the density of s. aureus exposed to gentamicin, daptomycin, ciprofloxacin and rifampin are not monotonic. in the case of rifampin, resistant mutants emerged. for the other three drugs, there is a levelling off in the kill rate, which can be attributed to persistence , . the bacteria recovered from these time-kill experiments were as susceptible to these three drugs as their ancestors used to start the experiment. there are a number of possible, but not mutually exclusive, explanations for these differences in killing rates, which we illustrate in fig. . we believe the following explanations to be particularly relevant: ( ) only free drug is active against the target bacteria, and protein binding of the drug decreases the rate of killing ; ( ) there are structures (such as porins) and mechanisms facilitating drug uptake, but also barriers that prevent the drug from entering the cells ; ( ) the drug can be pumped out, so the concentration needed for killing takes longer to achieve , ; ( ) the antibiotics with weak target-binding affinity will take longer to achieve the doses necessary for killing than those with greater affinity ; ( ) the targeted function might increase in the presence of the drug, thereby compensating for the inhibition by the drug ; ( ) the target function corresponds to the build-up of a cellular structure with slow turnover, which increases the amount of time for the antibiotic to kill , ; ( ) the cells repair the damage produced by the antibiotics at rates that differ between drugs ; ( ) the damaged bacteria have inducible antibiotic-deactivating mechanisms ; ( ) the bacteria use alternative metabolic pathways that, to some extent, bypass those inhibited by the antibiotic , ; ( ) antibiotics differ in the extent to which they induce reactive oxygen species (ros; deleterious) or sos (potentially protective) responses and thereby the rate at which they kill the exposed bacteria [ ] [ ] [ ] [ ] ; ( ) members of the antibiotic-exposed populations are either www.nature.com/nrmicro not replicating or are replicating slowly, and as such are killed at lower rates than the more active members of the population or their death is delayed; ( ) the antibiotics produce a kind of 'stationary phase' by activating the general rpos-mediated stringent response . notably, under very effective 'death-delaying conditions' , before the point of no return is reached, it would be difficult to determine whether a cell is in the process of dying. however, when this point of no return is surpassed, the last resources are invested in programmed cell death, and the bacterium induces its own lysis and dna degradation (apoptosis) . although it is convenient for investigators to separately consider the pharmacodynamics of the interaction of antibiotics and bacteria and the changes in antibiotic concentration with different therapeutic schedules (that is, the pharmacokinetics of the drug), bacteria do not have that luxury -the pharmacodynamics of antibiotic action is highly dependent on pharmacokinetics. on first consideration, it would seem the higher the concentration of the drug to which the bacteria are exposed, the higher the rate at which they are killed. this is the case for many antibiotics, but not for all. commonly, but not universally, the rate at which bacteria are killed by antibiotics is proportional to the maximum rates of growth of their populations . one interpretation of this association is that death occurs when the demand for resources is great, and the amount of resources is severely limited by drug action. if only a fraction of the population of bacteria is in a 'susceptible mode' (replicating) at any time, the full bactericidal activity will be achieved only after prolonged periods of exposure (time-dependent killing, as is the case of β-lactams) . on the pharmacodynamics side, it may well be that the rate at which bacteria are killed depends on the multiplicity of targets simultaneously affected by antibiotic action, which provokes a chaotic and difficult-to-compensate chemical destructuring of the cell. this sort of mechanism has been invoked to explain the rapid killing (minutes) by most biocides, such as disinfectants or antiseptics , . this rapid death by 'multiple targets' is also consistent with the frequent increase in the bactericidal effect measured in time-kill curves of synergistic antibiotic combinations or in phage-antibiotic combinations , . considering the plethora of factors contributing to the rates at which antibiotics kill bacteria, we can appreciate the difficulty of maintaining the tradition of classifying antibiotics as bactericidal and bacteriostatic. as noted in fig. , at the concentration used, as measured by decline in colony-forming unit estimates of densities, all nine antibiotics examined killed s. aureus, although those deemed bacteriostatic killed at a lower rate than those considered bactericidal. moreover, the rate at which a bacteriostatic antibiotic kills one species of bacteria, for example, escherichia coli, can be markedly less than the rate at which it kills another species, for example, campylobacter jejuni . a possibility for dealing with this conceptual challenge is to attribute a bactericidal coefficient to each pair of antibiotic and bacterial species, considering the amount of killing at a given antibiotic concentration and time in established standardized conditions. this view originated in the field of disinfectants (phenol coefficient, a measure of the bactericidal activity of a chemical compound in relation to phenol), and the calculation of 'specific bactericidal activities' (sba method) is supported by the national committee for clinical laboratory standards - but we are urging for the updating of such an approach . death by exogenous disruption of cell envelopes. cell envelopes are the hallmark of cellular individuality, the limit between the 'self ' and 'non-self ' . many antimicrobial agents kill cells by direct disruption of cell envelopes . of course, mechanical disruption of these envelopes by grinding, abrasion, high-pressure carbon dioxide or passing them through a narrow valve under high pressure (similar to a french press), ultrasonication and cavitation produces only free drug is active ( ) and protein binding, for example to albumin or other plasma proteins, can reduce the level of available and thus active drug, as commonly observed for β-lactams. uptake systems (such as porins) and barriers can prevent the drug from entering cells ( ) or the drug is pumped out ( ). greater or weaker target-binding affinity also influences activity ( ). the targeted function can also increase in the presence of the drug, thereby compensating for inhibition ( ; for example, upregulation of rpob by rifampin in mycobacteria). the target function involves the build-up of a cellular structure with slow turnover (for example, peptidoglycan), which increases the amount of time for the antibiotic to kill ( ) . the cells repair the damage produced by the drug ( ), involving the sos system. the bacteria have inducible antibiotic-deactivating mechanisms ( ; for example, β-lactamases). the bacteria use alternative functions, bypassing those that are inhibited ( ) . antibiotics differ in the extent to which they induce reactive oxygen species (ros; deleterious) or sos (potentially protective) responses ( ) . low replication rates (involving the sos system) reduce the killing activity ( ) . activation of the rpos-mediated stringent response produces a kind of 'stationary phase', reducing bactericidal potency ( ) . the two ultimate causes (bottom right) of a bactericidal effect are loss of spatial individuality by rupture of the limits with the environment (broken green line indicating disruption of the cell envelope) and loss of genetic individuality (broken blue line indicating disruption of the genome). rapid bacterial death . other physical destructuring methods include use of dry ice with ethanol, boiling, osmotic or hydrostatic pressure and extreme ph values. chemical disruptors of cell envelopes include detergents, biocides, halogens and toxic gases . more similar to therapeutic antimicrobials are cell wall-destroying enzymes, bacteriocins and antimicrobial peptides, including host defence peptides of insects, reptiles or higher animals (for example, cecropins, magainins and defensins). these agents rapidly kill bacteria by producing holes in their envelopes (particularly the cellular membrane). a number of antibiotics that are used clinically, such as the cyclic peptides (polymyxin b and colistin) and lipopeptides (telavancin and daptomycin), kill by disrupting cell membranes. similarly to that of detergents, the killing action of these agents may be better described as 'physical' rather than biological. at low concentrations of these agents, bacteria can compensate or repair the resulting damage and they can replicate at a rate that exceeds the killing rate. bacteria can commit suicide by disrupting their cell envelopes, leading to stiffness, strength loss and osmotic lysis. autolysins, first studied in streptococcus pneumoniae, are enzymes that degrade the peptidoglycan (cell wall) substrate and include glycosidases (muramidases, as lyta, lysozymes, glucosaminidases and transglycosylases), amidases and endopeptidases , . the cidabc and lrgab operons of s. aureus have been shown to influence bacterial death by posttranslational regulation of peptidoglycan hydrolase activity . in all these cases, as well as in e. coli, β-lactams trigger autolysin release by disturbing the balance between peptidoglycan synthesis and hydrolysis, which is necessary for growth of the cell wall . bacterial growth requires constant synthesis and turnover of the cell wall to insert new molecules, and the latter process relies on peptidoglycan cleavage enzymes, including glycosidases, amidases and endopeptidases . the same enzymes can produce lethal damage -the physiology of growth can be converted into the physiology of death. the effect of autolytic enzymes seems to depend on teichoic acids in grampositive bacteria (at least in s. pneumoniae) and on lipopolysaccharides (lps) in gram-negative bacteria. the mechanism of antibiotic induction of autolysins, as shown in s. pneumoniae, is based on the sequestration of the major autolysin lyta by membrane-bound lipoteichoic acids. in mutant bacillus subtilis strains, in which teichoic acid-autolysin binding is altered by reduction of positively charged d-alanine esters in teichoic acids, autolysis is increased under β-lactam exposure . in s. pneumoniae, the availability of precursors and products of teichoic acids regulates the protease ftsh, influencing the balance between lipid membrane-associated teichoic acids and cell wall (peptidoglycan)-associated teichoic acids. teichoic acid polymers can account for more than % of the mass of the gram-positive cell wall . under penicillin (a β-lactam) exposure (or prolonged stationary phase), ftsh degrades the lipid membrane-associated teichoic acid synthase tacl, leading to a short circuit in the normal teichoic acid balancing mechanism, favouring synthesis of cell wall-associated teichoic acids, which stimulates cell wall-destructive lyta activity, ending in cell lysis . in gram-negative bacteria, lps in the outer membrane is the functional equivalent of the lipid membrane-associated teichoic acids in gram-positive bacteria. in this case, the protease ftsh alter the turnover of lpxc, an essential enzyme for virtually all gram-negative bacteria, which is involved in the first step of lps biosynthesis, formation of lipid a . similarly to ftsh in s. pneumoniae, ftsh in gram-negative bacteria is regulated by the availability of precursors and products of the lps synthetic pathway, including acyl-acyl carrier protein (acyl-acp) precursors. acyl-acp accumulation probably correlates with a decrease in fatty acid synthesis in s. aureus and also in e. coli, as in vivo data are consistent with acyl-acp targeting the same two proteins in both species , . in e. coli, the outer membrane lps and the cell membrane phospholipid synthesis pathways compete for fatty acids , leading to a destabilization of the outer membrane (less lps). it should be remembered that the maintenance of the outer membrane integrity in gram-negative bacteria is probably as important as the maintenance of the integrity of the cell wall, and its failure produces blebbing and killing . in summary, the viability of the cell depends on a balanced synthesis of membrane phospholipids, fatty acids and cell wall constituents , and this coordination is altered by β-lactam exposure. however, autolysis can also occur without specific induction of autolysins but rather as a consequence of disbalance (uncoupling) between cell wall synthesis and degradation, owing to lack of control of peptidoglycan hydrolase turnover, typically involving low molecular weight penicillin-binding proteins that function as peptidoglycan-binding peptidases in e. coli [ ] [ ] [ ] . how endogenous mechanisms can degrade the cytoplasmic membrane is less clear. aminoglycosides interact with ribosomes, leading to production of mistranslated proteins. these proteins are misassembled in the membrane and are rapidly degraded, which contributes to bacterial killing , . degradation of misassembled membrane proteins is the result of a proteolytic 'quality control' system, which includes the membrane-integrated protease ftsh . other atp-dependent aaa+ proteases, including clpp and the lon proteases, which are present in many bacterial species, are also involved in the proteolysis of defective and misfolded proteins. as in the case for the cell wall, a disbalance in physiological proteolytic processes of the cell might result in membrane alteration and cell death , . as described in the following section, antibiotics might promote the formation of superoxides, leading to the oxydation of cysteine and methionine, resulting in protein damage. in other words, we can consider the replacement of senescent or damaged proteins as a requirement for maintaining life , . an intriguing possibility that we believe is worthy of further exploration is a lethal threshold, a minimum rate of protein synthesis that bacteria require to repair or compensate structural damage. in the absence of structural repair, bacteria are killed . similarly to the disruption of cellular membranes, the disruption of dna integrity is a marker of the loss of individuality. endogenous cellular mechanisms damage dna integrity, which can be the result of a stress response that induces the production of ros (see earlier), reactive nitrogen species, reactive carbonyl species, lipid peroxidation products and endonucleases. of course, external conditions can also damage cellular dna, including uv light, ionizing radiation and genotoxic chemicals. a number of antibiotics directly cause dna breaks, such as bleomycin. also, exposure to fluoroquinolones results in dna breaks . extensive dna damage can induce a special mode of cell death. single-stranded dna resulting from damage triggers the protein reca, which is involved www.nature.com/nrmicro in the inactivation of lexa. lexa is a repressor of sos response genes, and its inactivation leads to a cascade of events resulting in an alteration of the cellular membrane and dna fragmentation. lexa is one of the most over-represented transcriptional regulators following fluoroquinolones treatment . dna double-strand breaks can also be produced by antibiotic exposure and are potentially more lethal than single-strand breaks. a major inducer of the sos response are ros, producing dna double-breaks. their (not necessarily entirely successful) repair involves the recbcd system, comprising a helicase that unwinds dna strands and a nuclease that makes single-stranded nicks . probably the main driver leading to double-strand breaks is -oxo- ′deoxyguanosine, which is produced by oxidation of precursor deoxyguanosine triphosphate and causes breaks in conjugation with muty and mutm, proteins involved in dna mismatch repair . as previously stated, it has been proposed that some bactericidal antibiotics ultimately kill bacteria by generating dna double-strand breaks; chemicals producing breaks are synergistic with these antibiotics , and thus it can be expected that a shortage of protein synthesis might reduce repair functions, contributing to cell death . however, this effect is not always apparent in studies using combinations of protein-inhibiting drugs with dna-damaging antimicrobials or chemical mutagens , . perhaps sequential rather than simultaneous exposure of dna breaking and protein synthesis-inhibiting drugs would be a more effective way to use combinations of these antibiotics with these different modes of action. it may well be that antibiotics that drive bacteria into an unspecific stress status mimic other conditions as oligothropy or starvation reduce the viability of bacteria by reducing the availability of nutrients required for essential energy-consuming functions, including dna repair . certainly, e. coli has excess capacity for dna repair, which compensates dna damage from nutritional stress . perhaps exposure to dna-breaking antibiotics can surpass this repair capacity. a paradox that is observed across all fields of biology (including human infections, such as sepsis) is that the very same mechanisms responsible for physiological adaptation, defence and damage repair on crossing a threshold promote death . in this interpretation, some antibiotics kill by generating an irreversible cascade of events; for example, chromosomal lesions trigger the production of ros, which damages dna, which in turn triggers the release of sos response products intending to rescue the cell from death, but (not fully demonstrated) under high cytotoxicity could lead to destabilization of homeostasis, including iron-sulfur clusters, eventually increasing ros levels further, resulting in more chromosomal breaks. is there a unique mechanism by which antibiotics prevent the replication of bacteria? a few years ago, along with other colleagues, we presented a hypothesis for how ribosome-targeting antibiotics that are deemed bacteriostatic not only prevent the replication of bacteria but might also be lethal . in accord with our hypothesis, these drugs tie up enough ribosomes for cells not to be able to synthesize enough essential enzymes and other proteins required for replication or to ensure the healthy turnover of envelope components, including the most frequently transcribed proteins in the cell, ribosome proteins and membrane lipoproteins . as predicted by the model on which this 'numbers game' hypothesis was based, as the number of ribosomes is reduced, ribosome-targeting antibiotics will become increasingly bactericidal. two lines of evidence were presented in support of this hypothesis, both of which were based on the number of ribosomal rna (rrn) operons. e. coli strains with deletions of five or six of the seven rrn operons were killed at a higher rate by azithromycin, chloramphenicol and tetracycline than the ancestral mg strain or strains with more than two rrn operons. in c. jejuni, which has three rrn operons rather than seven as in e. coli, chloramphenicol and azithromycin are bactericidal rather than bacteriostatic as they are for e. coli . these results suggest that a low number of functional ribosomes might lead to a kind of lethal protein synthesis threshold. but we restrained ourselves from asserting that crossing this threshold is the ultimate mechanism by which these ribosome-targeting 'bacteriostatic' antibiotics kill bacteria. as mentioned already, shortage in key proteins involved in the cellular envelope structure might result in killing, but the association with the quantity of these proteins, or the number of active ribosomes, remains to be demonstrated. in , a then graduate student, michael kohanski, working with james collins, presented a general hypothesis for how different bactericidal antibiotics kill both gram-positive and gram-negative bacteria and evidence in support of that hypothesis. in accord with that hypothesis, these drugs stimulate the production of highly deleterious hydroxyl radicals, which kill bacteria by oxidative damage, inhibit the tricarboxylic acid cycle, transiently deplete nadh, destabilize iron-sulfur clusters and stimulate the fenton reaction, resulting in lethal dna breaks . in , a series of articles were published pointing out the limitations of the experiments on which kohanski and colleagues based their hypothesis that bactericidal antibiotics work through a common cell death mechanism involving ros [ ] [ ] [ ] . these authors did not present alternative mechanisms for the bactericidal activity of antibiotics. this is not a forum to rant on about the details of the experiments performed in these studies and the inferences drawn. it is, however, useful to consider what came out of the ros 'debate' in respect to our understanding of the ultimate mechanism responsible for how antibiotics kill bacteria. to wit, the debate is a compelling argument that there is not a unique mechanism by which antibiotics kill bacteria. in the years since the publication of the article by kohanski and colleagues , there have been a number of studies confirming that ros have an important role in antibiotic-mediated killing of bacteria. these studies present evidence that ros are frequently synergistic in the killing process with the damage directly caused by the antibiotic in the primary target, and dependent on the background state of cells already stressed by the antibiotic , as suggested by yang and colleagues , this killing is not simply a matter of how the drugs act on their targets but is rather the result of an array of downstream consequences of the effects of the drug on that target. as indicated in a recent study by hong and colleagues , ros do indeed have a role in those downstream processes. in the following sections, we separately consider antibiotics of six classes, what is known, what has been postulated and what should be known about the ultimate mechanisms by which they kill bacteria. see fig. for a graphic summary of what follows. aminoglycosides. the confidence of clinicians in aminoglycoside therapy is commonly based on the known strong bactericidal effect of these drugs. although a great deal is known about the proximal mechanism of action of aminoglycosides , , no widely accepted or supported hypothesis exists so far for the ultimate mechanism by which these drugs kill bacteria. three not mutually exclusive hypotheses stand out. a fourth hypothesis, death by superoxides, applies to all bactericidal antibiotics and will be considered separately. the most commonly offered explanation for the bactericidal action of this class of drugs is that the ribosome-aminoglycoside interactions, mediated by the number and basicity of amino groups in the drug, give rise to toxic mistranslated proteins, which kill by increasing the permeability of the cell membrane . however, to our knowledge, these toxic proteins have not been isolated, and how they actually kill remains undemonstrated. it is also unclear why these postulated products of mistranslation are not destroyed by the proteases that usually remove mistranslated and misfolded proteins. on the other hand, in opposition of the toxic mistranslated protein hypothesis as the unique mechanism of killing by these drugs is the observation that killing occurs in the absence of aminoglycoside-ribosome binding, as happens with gentamicin in ribosomal a>g mutants that have a single rrn operon (b.r.l. and f.b., unpublished observations) and in the presence of the antibiotic resistance gene arma, encoding a s ribosomal rna guanine -n -methyltransferase . there is also a pharmacodynamic observation consistent with the toxic mistranslated protein hypothesis. in accord with this hypothesis, the rate of ribosome binding, and thereby the abundance of toxic proteins generated by mistranslation, should be proportional to the growth rate of the target population and the number of ribosomes, which indeed has been observed . however, some observations question the uniqueness of the toxic mistranslated protein mechanism explaining the bactericidal effect of aminoglycosides. most importantly, gentamicin can kill e. coli and s. aureus in the stationary phase, when the number of ribosomes is minimal , and is more bactericidal in e. coli variants with a reduced number of rrn operons . collectively, these observations suggest a ribosome-independent (but not alternative) mechanism by which aminoglycosides kill bacteria. ribosome-independent killing by aminoglycosides involves direct killing by 'surface action' . the polycationic aminoglycoside molecules replace mg + cations and thus destabilize key lipid structures of the outer membrane , - . after aminoglycoside exposure, potassium and intracellular molecules such as nucleotides leak from the bacterial cell immediately, certainly no later than protein synthesis inhibitory effects , , . besides, aminoglycoside exposure increases alarmone levels, resulting in increased membrane damage as stated before, a direct effect of aminoglycosides on the bacterial cell membrane is not incompatible with the need for ribosomal interaction. binding to the ribosome triggers a massive secondary, energy-dependent uptake of aminoglycosides . this uptake will produce a 'cationic disturbance' of the membrane integrity and thereby kill without further involvement of ribosomes. the quinolones. fluoroquinolones bind to dna gyrase and topoisomerase iv, leading to the formation of stable drug-enzyme-dna complexes that block dna replication and result in dna double-strand breaks . recombination and excision repair is involved in the repair of quinolone-damaged dna, but continuous induction of these systems in response to exposure to the drug triggers the sos response , . initially, the quinolone-gyrase-dna complexes are unstable, and bacteria can recover in the absence of quinolone exposure. which results in structural damage and/or quantitative or qualitative deficiencies of essential cell components. these changes, in turn, lead to envelope stress, dna damage and/or the production of an excess of reactive oxygen species, which further contribute to the destructuring of cell membranes and nucleic acids. the net effect of these different processes (green) is the ultimate mechanism responsible for the loss of the cell's individuality, its death (red). however, if exposure is maintained, the complexes become stable, the sos response continues and when a threshold is crossed, the death process becomes irreversible, even in the absence of the drug , . the activity of ciprofloxacin decreases when bacteria reduce their growth rates . this effect might contribute to explaining the biphasic dose response of most quinolones, producing a single concentration of maximum kill. the optimal bactericidal concentration probably depends on the sos response, the formation of superoxides and dna breaks. concentrations higher than the optimal bactericidal concentration provoke an immediate sos-independent inhibition of respiration and growth, with decreased ros production and less death . conversely, at the optimal bactericidal concentration, sos-derived apoptosis-like death occurs. this pathway depends on reca and lexa, resulting in cell death associated with membrane depolarization and ros-induced dna fragmentation . in summary, ultimate death by quinolones occurs by the disintegration of dna mediated by ros . rifamycins. the target of rifampin (and, in general, rifamycins) is the product of the rpob gene, the dna-dependent rna polymerase. the drug strongly binds to the β-subunit of the core enzyme, thereby inhibiting initiation of transcription; that is, preventing effective protein synthesis . on first consideration, it may seem that inhibition of protein synthesis is not sufficient to provide rapid killing. however, in practice, rifamycins are considered to have an early bactericidal effect, not only in s. aureus ( fig. ) and e. coli, but even in slowly growing bacteria such as mycobacterium tuberculosis. in addition, the killing effect of rifampin is concentration dependent , . high rifampin concentrations can even kill bacteria with some types of resistance mutations in the rpob gene . by targeting rna polymerases, rifamycins affect both translation and transcription, which together ensure the coordination of transcriptional activity to the translational needs under various growth rates , . an interesting question is whether the inhibition of transcription might produce lethal effects independently from blocking protein synthesis. a classic transcription inhibitor is the toxin mazf, a component of the stress-induced mazf-maze toxinantitoxin machinery. in the absence of the antitoxin maze, mazf inhibits protein synthesis by cleaving mrna, resulting in later death . what are the causes of death? it has been suggested that there are a group of mrnas that are resistant to cleavage by mazf, encoding 'death proteins' , some of which damage cell envelopes . a similar mechanism of death can be suggested for rifampin, which also selectively affects the transcription of different genes . it is possible that rifampin, similarly to ribosome-binding antibiotics, reshapes the cellular proteome rather than just blocking global protein synthesis , , but both effects might be synergistic for killing, particularly in species with a low number of rrn operons . rifamycins do not stimulate the production of hydroxyl radical production, which could contribute to cell death . β-lactam antibiotics. β-lactams target penicillin-binding proteins involved in the biogenesis of peptidoglycan . there is a clear correlation between bacterial growth rate, needs of peptidoglycan biogenesis and cell lysis induced by β-lactams . lysis requires functional assembly of the divisome, the cell division machinery , suggesting that lysis specifically occurs when the cell is ready for division . why is the loss of cell wall integrity and lysis the result of reduced peptidoglycan biogenesis? the traditional answer is induction of peptidoglycan autolysins or simply that these lysins continue their activity without compensation by biogenesis (see earlier). more recently, it has been proposed that inhibition of penicillin-binding proteins by β-lactams produces a deleterious 'futile cycle' of metabolic pathways involved in peptidoglycan synthesis and degradation running simultaneously in opposite directions and promoting deintegration and lysis . besides, disruption of cell envelope integrity, leading to bubbling and 'explosion' of the cell, particularly in gram-negative bacteria, is probably triggered by lacking coordination of the multicomponent machinery that links the growth of the different envelope layers, and involves sensing of unassembled outer membrane proteins and lps in the periplasm . the possibility of biophysical shearing of different layers, owing to disbalance between cell wall and membrane growth [ ] [ ] [ ] and resulting in cell lysis, cannot be discarded and is worth further and deeper consideration. finally, there is evidence that β-lactam antibiotics are bactericidal through dna damage by ros , . vancomycin. vancomycin is a lipophilic cationic antibiotic that inhibits synthesis of the bacterial cell wall by binding to the dipeptide terminus d-ala-d-ala of peptidoglycan pentapeptide precursors, preventing subsequent transpeptidation and transglycosylation and thus peptidoglycan crosslinking . deficient crosslinking of the long sugar backbone chains of n-acetylglucosamine/ n-acetylmuramic chains results weakens the cell to osmotic damage, leading to cell disintegration. similarly, this effect explains why vancomycin-exposed cells are much more sensitive to ultrasound . in s. aureus, the bactericidal effect of vancomycin is generally weaker than that of most β-lactams . this difference can be explained by the huge size of vancomycin ( , da) compared with oxacillin ( da), which impedes diffusion through the cell wall, which is also supported by the finding that thicker peptidoglycan reduces the effect of vancomycin . consistently, time-kill curves show that varying the concentration of vancomycin has no effect on the rate or extent of bacterial killing , probably owing to vancomycin clogging in the cell wall. independently from the membrane-cell wall shearing effect (see the section "β-lactam antibiotics"), direct membrane damage can probably be excluded, as vancomycin does not act on protoplasts or mycoplasma spp., both of which have no cell wall. superoxide anions might also be involved in the bactericidal activity of vancomycin in enterococcus spp. and staphylococcus spp. . sulfonamides and trimethoprim are bacteriostatic, but the combination is synergistic, and has a strongly bactericidal effect . the two drugs inhibit two sequential steps in tetrahydrofolate synthesis (required for nucleotide synthesis), but this cannot explain the bactericidal synergism. the synergy is more likely due to the disruption of a previously unrecognized metabolic feedback loop by trimethoprim, which results in cyclic mutual potentiation of the effects of the two drugs, leading to amplified depletion of tetrahydrofolate, an essential cofactor in the biosynthesis of thymine , . however, the ultimate mechanism of killing by thymine deficiency (the classic 'thymineless killing') remains elusive; the deprivation of nutritional requirements normally has a biostatic, but not lethal, effect , . most probably, thymine starvation promotes cell killing by ros-mediated dna damage . surely, we would all love to have a unique, broadly supported hypothesis for how antibiotics kill bacteria; this is particularly so if we were the investigators responsible for providing that hypothesis. this is not the case; there is no a priori reason to expect that the same antibiotics targeting different species of susceptible bacteria would reach these ultimate (killing) effects by the same processes under different growth conditions. on the other, more positive, side, this perspective suggests that antibiotics with markedly different structures, targets and effects on the structure and physiology of bacteria have proximate mechanisms of action that converge through different processes in the death of bacteria by physical or genetic destructuring, the ultimate effects ( fig. ). moreover, we believe that the links between proximate and ultimate mechanisms of the bactericidal and bacteriostatic actions can be elucidated for specific antibiotics and different species of bacteria under different growth conditions. a multifactorial perspective of bacterial killing will be needed to fully understand how the effects of the primary antibiotic action on targets can be modulated, and eventually amplified, in the context of complex interactions and changes of cell metabolism, and general cellular responses, including ros production, sos induction and rpos regulatory effects. certainly many of these responses are sensitive to the environment, and therefore the bactericidal effect is expected to differ in various circumstances, bacterial species and lifestyles. a wide field of research is being opened. but is it worth the effort? we know that bacteria are killed and/or prevented from replicating when exposed to antibiotics, and we know a great deal about the conditions under which these drugs have these bactericidal and bacteriostatic effects. is this information, which is critical to the clinical applications of these drugs, not entirely sufficient? we suggest it is not. elucidating how and when different antibiotics prevent the replication of bacteria and kill them is not just an academic exercise. this information will be useful for developing much-needed new antibiotics. it will also be helpful for designing protocols for the administration of existing antibiotics and combinations of antibiotics that are effective clinically, and at the same time minimize the likelihood of emergence and rise of resistance to these drugs in target bacteria and commensals and disturbance of the microbiota. address in 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resistance to fosfomycin sos response induction by betalactams and bacterial defense against antibiotic lethality ampc beta-lactamases novel mechanism of beta-lactam resistance due to bypass of dd-transpeptidation in enterococcus faecium massive overproduction of dihydrofolate reductase in bacteria as a response to the use of trimethoprim bactericidal activities of five quinolones for escherichia coli strains with mutations in genes encoding the sos response or cell division a common mechanism of cellular death induced by bactericidal antibiotics sos response induces persistence to fluoroquinolones in escherichia coli post-stress bacterial cell death mediated by reactive oxygen species antibiotic killing of diversely generated populations of nonreplicating bacteria for the greater good: programmed cell death in bacterial communities the rate of killing of escherichia coli by beta-lactam antibiotics is strictly proportional to the rate of bacterial growth kinetics of antimicrobial activity mechanisms of antimicrobial action of antiseptics and disinfectants: an increasingly important area of investigation bacterial target sites for biocide action antibiotic combinations: should they be tested? synergy and order effects of antibiotics and phages in killing pseudomonas aeruginosa biofilms adjunct phage treatment enhances the effectiveness of low antibiotic concentration against staphylococcus aureus biofilms in vitro bactericidal index: a new way to assess quinolone bactericidal activity in vitro superior bactericidal activity of n-bromine compounds compared to their n-chlorine analogues can be reversed under protein load methods for determining bactericidal activity of antimicrobial agents, approved guideline (clsi antibiotic efficacy-context matters molecular mechanisms of membrane targeting antibiotics bacterial cell disruption: a key unit operation in the recovery of intracellular products inhibition and destruction of the microbial cell choline-containing teichoic acid as a structural component of pneumococcal cell www.nature.com/nrmicro wall and its role in sensitivity to lysis by an autolytic enzyme the molecular characterization of the first autolytic lysozyme of streptococcus pneumoniae reveals evolutionary mobile domains triggering of autolytic cell wall degradation in escherichia coli by beta-lactam antibiotics structural basis of peptidoglycan endopeptidase regulation d-alanine deprivation of bacillus subtilis teichoic acids is without effect on cell growth and morphology but affects the autolytic activity the bacterial cell envelope a switch in surface polymer biogenesis triggers growth-phase-dependent and antibiotic-induced bacteriolysis when, how and why? regulated proteolysis by the essential ftsh protease in escherichia coli phosphatidylglycerol homeostasis in glycerol-phosphate auxotrophs of staphylococcus aureus the escherichia coli phospholipase plda regulates outer membrane homeostasis via lipid signaling distinct single-cell morphological dynamics under beta-lactam antibiotics intricate crosstalk between lipopolysaccharide, phospholipid and fatty acid metabolism in escherichia coli modulates proteolysis of lpxc analysis of the sodium dodecyl sulfate-stable peptidoglycan autolysins of select gram-negative pathogens by using renaturing polyacrylamide gel electrophoresis peptidoglycan hydrolases of bacterial peptidoglycan (murein) hydrolases the bactericidal action of streptomycin: membrane permeabilization caused by the insertion of mistranslated proteins into the cytoplasmic membrane of escherichia coli and subsequent caging of the antibiotic inside the cells due to degradation of these proteins mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death quality control of cytoplasmic membrane proteins in escherichia coli clpp protease, a promising antimicrobial target dysregulation of bacterial proteolytic machinery by a new class of antibiotics not quite dead enough: on bacterial life, culturability, senescence, and death oxidative stress, protein damage and repair in bacteria requirement for protein synthesis in rec-dependent repair of deoxyribonucleic acid in escherichia coli after ultraviolet or x irradiation quinolone-mediated bacterial death gyrase inhibitors induce an oxidative damage cellular death pathway in escherichia coli crystal structure of recbcd enzyme reveals a machine for processing dna breaks oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics exploring synergy between classic mutagens and antibiotics to examine mechanisms of synergy and antibiotic action antagonism between bacteriostatic and bactericidal antibiotics is prevalent chromosomal fragmentation in dutpase-deficient mutants of escherichia coli and its recombinational repair nutritional conditions and oxygen concentration affect spontaneous occurrence of homologous recombination events but not spontaneous mutagenesis in escherichia coli bacterial programmed cell death: making sense of a paradox quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources markerless escherichia coli rrn deletion strains for genetic determination of ribosomal binding sites a. damage by hydrogen peroxide through the fenton reaction in vivo and in vitro fe-s cluster biosynthesis controls uptake of aminoglycosides in a ros-less death pathway cell death from antibiotics without the involvement of reactive oxygen species killing by bactericidal antibiotics does not depend on reactive oxygen species antibiotics induce redox-related physiological alterations as part of their lethality unraveling the physiological complexities of antibiotic lethality mechanism of bactericidal action of aminoglycosides kinetics of bactericidal activity of aminoglycosides during dynamic dilution mistranslation and genetic variability: the effect of streptomycin roles of 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escherichia coli growth rate and bacterial susceptibility to ciprofloxacin effects of rifampicin on synthesis and functional activity of dna-dependent rna polymerase in escherichia coli concentration-dependent mycobacterium tuberculosis killing and prevention of resistance by rifampin could high-concentration rifampicin kill rifampicin-resistant m. tuberculosis? rifampicin mic test in rifampicin-resistant isolates from patients with osteoarticular tuberculosis a nuse:nusg complex links transcription and translation cooperation between translating ribosomes and rna polymerase in transcription elongation mazfmediated cell death in escherichia coli: a point of no return escherichia coli mazf leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins rifamycin action on rna polymerase in antibiotic-tolerant mycobacterium tuberculosis results in differentially detectable populations selective protein synthesis by ribosomes with a drugobstructed exit tunnel inhibition of rna polymerase by rifampicin and rifamycin-like molecules mechanism of action of penicillins: a proposal based on their structural similarity to acyl-d-alanyl-d-alanine rapid beta-lactam-induced lysis requires successful assembly of the cell division machinery robust, linear correlations between growth rates and beta-lactam-mediated lysis rates the mechanism of the irreversible antimicrobial effects of penicillins: how the betalactam antibiotics kill and lyse bacteria beta-lactam antibiotics induce a lethal malfunctioning of the bacterial cell wall synthesis machinery excess membrane synthesis drives a primitive mode of cell proliferation evolution of cell division: from shear mechanics to complex molecular machineries structural basis for the coordination of cell division with the synthesis of the bacterial cell envelope mutual potentiation drives synergy between trimethoprim and sulfamethoxazole glycopeptide antibiotics: from conventional molecules to new derivatives lack of bactericidal antagonism or synergism in vitro between oxacillin and vancomycin against methicillinsusceptible strains of staphylococcus aureus novel mechanism of antibiotic resistance originating in vancomycin-intermediate staphylococcus aureus the concentration-independent effect of monoexponential and biexponential decay in vancomycin concentrations on the killing of staphylococcus aureus under aerobic and anaerobic conditions analysis of the tolerance of pathogenic enterococci and staphylococcus aureus to cell wall active antibiotics bactericidal activity of trimethoprim alone and in combination with sulfamethoxazole on susceptible and resistant escherichia coli k- nature of the bacterial action of sulfonamides and trimethoprim, alone and in combination thymine metabolism and thymineless death in prokaryotes and eukaryotes thymineless death in escherichia coli is unaffected by chromosomal replication complexity the authors are grateful to their awesome wives, ros and adriana, for putting up with them during this period of covid- quarantine and supporting their playing fun games such as reviewing the literature and writing this perspective.they thank i. mccall for a careful reading of this manuscript, and j. rodríguez-beltrán for discussion about some critical concepts. this research was funded by grants from the u.s. national institutes of general medical science (gm - and r gm - ) to b.r.l and from the regional government of madrid (ingemics-b /bmd- ) and the ramón areces foundation to the f.b. laboratory. the authors dedicate this perspective to the memory of j. acar , with whom they would have loved to have discussed the question of how antibiotics kill; from those conversations with jacques, the authors know they would have had much more to tell you about the answer. the authors contributed equally to all aspects of the article. the authors declare no competing interests. nature reviews microbiology thanks the anonymous reviewer(s) for their contribution to the peer review of this work. springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. key: cord- -t z ynt authors: nan title: speaker presentations date: - - journal: international journal of antimicrobial agents doi: . /s - ( ) - sha: doc_id: cord_uid: t z ynt nan increased mortality rates in patients infected with major resistant pathogens are as follows; • mrsa: mrsa can cause almost -fold higher mortality (or . ) compared with mssa strains according to a meta-analysis (cosgrove et al. ) . mrsa kills more american people every year (∼ , ) than emphysema, hiv/aids, parkinson's disease and homicide combined (klevens et al. ). • esbl-producing gram-negative bacilli: a meta-analysis showed that crude rrs were significantly higher mortality in esbl-associated bacteremia ( pooled rr . ) (schwaber et al. ). • carbapenem-resistant k.pneumoniae: in patients with carbapenem-resistant k.pneumoniae bacteremia, the crude mortality rate was . %, while it was . % in control subjects (borer et al. ). a mortality risk ratio was . for patients with carbapenem-resistant k. pneumoniae bacteremia. increased mortality and morbidity in resistant infections is due to treatment failure of antibiotic therapy which is associated with bacterial fitness, greater severity of underlying illness, delays in initiating effective therapy and lack of effective therapy (friedman et al. ) . due to mismatch between choice of empirical antibiotics and in vitro susceptibility test results, administration of effective antibiotics was delayed by -times in the case of antibiotic-resistant e.coli and k.pneumoniae infections compared with susceptible strains ( hours vs hours) (lautenbach et al. ) . also, patients infected with resistant strains are more frequently associated with more severe underlying illness requiring longer hospitalization. for example, patients with cre infections are more likely to be a transplant recipient, require mechanical ventilation, a prolonged hospitalization, icu stays, or use of central venous catheters (borer et al. ). patients infected with resistant strains are more likely to develop complications and long-term sequelae. for example, mrsa infection caused higher incidence of complications by % compared with mssa infection. the most frequent complications are a progression of the local infection (rr . ) and pneumonia (rr . ) (cecchini et al. ) . once amr emerges in the hospital, resistant pathogens can cause additional cases of bacterial infections that affect more patients. emergence of amr in major human pathogens also affects safety and efficacy of surgical procedures, cancer chemotherapy, organ transplantation, and intensive care. therefore, amr is not just an infectious disease issue, but rather an issue in surgery, cancer care, organ transplantation and whole health system. amr can also negatively affect the daily hospital activities such as total closure of an affected ward or unit or cancellation of elective surgery. economic impact of amr is difficult to quantify, which consists of direct costs associated with use of more expensive antibiotics, special equipments, longer hospital stay, and isolation procedures etc., and indirect costs mainly due to loss of productivity of the patients. according to the world bank report to estimate the amr impact on global gdp in - (world bank, , in the optimistic "low-amr" scenario, global economic output is projected to be % lower by ($ trillion) and . % lower by than in the base case. in the pessimistic "high-amr impact" scenario, global economic output would be . % lower in ($ . trillion) and . % lower by than in the base case. it means that in the "high-amr" scenario, economic damage will be greater than that in - global financial crisis which caused . % drop in the global gdp. economic impact of amr differs by countries with different economic level. low-income and lower middle-income countries would have greater impact of economic loss ( . % loss of gdp) due to amr compared with high-income countries ( . % loss of gdp), particularly in the "high-amr" scenario. global economy is negatively affected by amr in various aspects such as international trade, livestock production, and healthcare expenditures. by , the volume of global real exports may decrease by . % in the "low-amr" scenario and by . % in the "high-amr" scenario. in the "high-amr" scenario, healthcare expenditures in would be as % higher than the baseline values for low-income countries, % higher for middle-income countries, and % higher for high-income countries. the additional expenditures in would be $ . trillion annually in the "high-amr" scenario. in the us, cdc estimated the cost of amr as a total of $ billion per year : $ billion in excess for direct healthcare costs and $ billion for indirect societal costs due to loss of productivity (cdc, ) . in europe, the overall economic burden of amr was estimated to be at least . billion euros; % for direct costs and % for indirect costs (ecdc/emea, ). data on the economic impact of amr in major pathogens showed that healthcare costs significantly increase in the treatment of infections caused by antibiotic-resistant strains (maragakis et al. ) ; mrsa bacteremia (us$ , ), mrsa surgical site infection (us$ , ) , vre infection (us$ , ) , and esbl or kpc-producing e.coli or klebsiella infection ( . fold increase). amr is obviously one the most serious and urgent issues with devastating impact on clinical medicine, economic growth and societal system and function. g leaders' declaration which was announced in july also underlined the importance of combating amr through international collaboration. for more effective and robust implementation of global action plan to combat amr, appropriate evaluation of impact of amr should be performed, particularly in developing world which would have greater damage due to amr. school of public health, the university of hong kong, china the development, large-scale production and widespread use of antimicrobial drugs in the twentieth century was a turning point in human history, resulting in dramatic improvements in medical care and reduction of deaths. over time, however, rising levels of antimicrobial resistance (amr) among a wide range of pathogens has placed such gains at risk of being lost. reducing amr is now a top-level global public health priority. in principle, the major high-level goals consist of optimizing the use of such drugs in health and agriculture and minimizing environmental contamination; sustaining the development of new classes of antimicrobials drugs and other medicines and making them affordable and accessible to all who need them; and much more effective application of infection control and prevention principles. for decades, technical solutions have been the primary approach used for addressing amr. more recently, fao, oie and who in combination with like-mined champions have embarked upon a more political and broader "one health" approach to increase awareness and engagement beyond scientific and medical groups. this change is the basis for the global action for amr, the high level meeting on amr held at the un general assembly and attention to amr by groups such as the g . while such results have been instrumental in broadening the awareness and attention paid to amr, it is now critical to adopt concrete and focused activities to consolidate and build upon these gains. the fundamental building blocks will be proposed and discussed. murdoch university, australia methicillin-resistant staphylococcus aureus (mrsa) was initially a healthcare associated pathogen limited to distinct lineages often associated with multi-drug resistance. however, in the late s mrsa began to emerge in the community. in the beginning, this was mostly confined to closed communities, i.e. australian aboriginals, but around the late s community-associated mrsa (ca-mrsa) emerged worldwide in the general population. the ca-mrsa clones evolved independently of the ha-mrsa clones, and typically, possessed type iv or v sccmec elements, were non multi-drug resistant, and were positive for the panton valentine leucocidin (pvl) toxin. whilst regionally many unique ca-mrsa clones have emerged, only a few clones predominate within a region, and even fewer clones have a global distribution. the reasons for the variation in the prevalence and dominance of ca-mrsa clones between different geographical niches remains unclear. although the epidemiology of ca-mrsa varies considerably, four major global ca-mrsa clones have been described: st -mrsa-iv (usa ) and st -mrsa-iv (south west pacific clone) which and are considered pandemic; st -mrsa-iv (european clone) which predominates in europe, africa and the middle east; and st -mrsa-iv/v t (taiwan/asia pacific clone) in asia. however, using whole genome sequencing analysis, at least two of the clones have different clades that have evolved independently of each other. in clonal complex nine phylogenetic clades with at least eight independent events of methicillin-resistance acquisition have been identified. subsequently, it has been hypothesised usa did not evolve from the healthcare-associated st -iv usa clone, the historic ca-mrsa from western australia, or the pvl-positive mssa clone from trinidad and tobago or western africa, but most likely from pvl-positive mssa circulating within the usa. the ancestor of the usa clade emerged in central europe in the mid- th century and exported to north america in the early th century. once in north america the clone progressively acquired the usa characteristic genetic specifications, diversified and spread globally including africa. within the usa clade two closely related st -iv clones are recognised: usa , primarily isolated in north america (st -mrsa-iva, spa t luks-pv/lukf-pv, acme positive, msra-mediated macrolide resistance genes) and the usa latin american variant, primarily isolated in south america (st -mrsa-ivc, spa t , luks-pv/lukf-pv, acme negative, tetk, copper and mercury resistance genes). similarly, st mrsa is also not a single clone but consists of two major clades, one originating in the usa and the other in east asia. furthermore, two distinct subclades within the east asia clade have been identified: pvlnegative st -mrsa-iv (asia pacific clone) and the multi-resistant pvl positive st -mrsa-v t (taiwan clone) which possesses two distinct ccrc genes. recently three newly described pvl-positive ca-mrsa clones have been reported in multiple countries: st -mrsa-iv (queensland ca-mrsa) from australia, and st -mrsa-v t (bengal bay) and st -mrsa-iv from the indian subcontinent. st -mrsa-iv, first reported in india in , is genetically distinct from the healthcare associated st -mrsa-iv (emrsa- ) having acquired different sccmec types and sub types. of concern, st -mrsa-v t and st -mrsa-iv are multi-resistant hyper-virulent ca-mrsa that have recently been associated with nosocomial transmission. the co-emergence of multiple ca-mrsa lineages that have risen independently in most parts of the world has been striking. to date no single genetic or epidemiological factor has been identified that accounts for the extraordinary success of some genetically distinct ca-mrsa clones. over time, some ca-mrsa clones will replace ha-mrsa clones, which will have significant clinical and public health implications. along the way they will become increasing antibiotic resistant making the distinctions between ha-mrsa and ca-mrsa blurred and antimicrobial treatment difficult. methicillin-resistant staphylococcus aureus (mrsa) has been a major cause of healthcare-associated infections with significant morbidity and mortality, and it has become one of the most important nosocomial pathogens in many countries worldwide since s. in particular, several mrsa clones have been successful in spreading and causing infections in the hospitalized patients. the prevalence rates of mrsa in s. aureus isolates from the hospitalized patients have become high enough to spread into the community. interestingly, during the past two decades, the emergence of community-associated (ca-) mrsa clones has greatly affected the global epidemiology of s. aureus infection. circulating ca-mrsa clone varies according to the region, and it includes st (usa ), st , st , st , st , st and st which mostly belong to sccmec type iv or v. as a result, the proportion of mrsa in community-acquired s. aureus infections has been significantly increasing in many countries. furthermore, many reports have shown that ca-mrsa clones have replaced traditional hospital-endemic mrsa clones. such an influx of dominant ca-mrsa clones into the hospitals has been making the 'search and destroy' policy which have contributed to maintain low mrsa rates in some countries difficult to maintain. in addition, there has been concern that healthcareassociated infections such as surgical site infection caused by ca-mrsa may increase. in this talk, an update on ca-mrsa epidemiology in healthcare-associated infection and concerns on infection prevention and control will be discussed. the newly emerging middle east respiratory syndrome coronavirus (mers-cov) causes a severe respiratory infection with a high mortality rate (∼ %), and has been a global threat due to continuous outbreaks in the arabian peninsula and international spread by infected travelers since . from may to july , a large outbreak initiated by an infected traveler from the arabian peninsula swept south korea, and resulted in confirmed cases with deaths (case-fatality rate: . %). here, we show the rapid emergence and spreading of a mutant mers-cov with reduced affinity to the human receptor, cd , during the korean outbreak. we isolated thirteen new viral genomes from fourteen infected patients treated at a hospital and found that twelve of them possess a point mutation in the receptor-binding domain (rbd) of viral spike (s) protein. we also analyzed clinical data and specimens from fourteen mers patients treated in a hospital who collectively represent a wide spectrum of disease severity, ranging from mild febrile illness to fatal pneumonia. comparative and kinetic analyses revealed that high viral loads, weak antibody responses, and lymphopenia accompanying thrombocytopenia were associated with disease mortality, whereas persistent and gradual increases in lymphocyte responses might be required for effective immunity against mers-cov infection. the correlation of the virological and immunological responses with disease severity and mortality, as well as their responses to current antiviral therapy, may have prognostic significance during the early phase of mers. severe fever with thrombocytopenia syndrome (sfts) was discovered as an infectious disease caused by a novel bunyavirus in china in (n engl j med, . the causative agent for sfts is named sfts virus (sftsv), which is a tick-borne virus and belongs to the family buniyaviridae, genus phlebovirus. the virus infection causes generalized infections with a high case fatality rate. in late , it was discovered that sfts was also endemic to japan (takahashi t, et al., jid, ) . sfts is endemic to china, south korea, and japan. since the discovery of sfts endemic to japan in january , approximately patients with sfts have been reported to the national institute of infectious diseases. the case fatality is about %. most of the patients were aged over 's. the pathophysiology of sfts has been studied through the pathological examination of sfts patients, who died. through the pathological studies on sfts, sftsv is present in the lymph node tissues. there are two pathological types, sftsv-positive lymph node-localized type and sftsv-positive lymph node-generalized types. all the patients, in whom bone marrow aspiration test was performed, showed hemophagocytic syndrome, indicating that cytokine storm plays an important role in pathogenesis of sfts. most fatal sfts patients showed symptoms of hemorrhage and deterioration in consciousness. one of the patients showed a symptom of bloody vomit. real time imaging of the stomach by endoscopic examination revealed the presence of ulcerative lesions with whoozing hemorrhage (kaneyuki s, et al., jjid, ) . the pathophysiological features behind the high case fatality rate in sfts are hemophagocytosis, hemorrhagic tendencies due to thrombocytopenia, disseminated intravascular coagulation, and ulcerative lesions appeared in the gastrointestinal tracts, and multi-organ failure. the efficacy of antiviral agent, favipiravir, which was developed by dr. furuta y and his colleagues (toyama chemical co., ltd, japan), in the treatment of sfts was evaluated using mice lacking the type i interferon alpha receptor (ifnar −/− ) (tani h, et al., msphere, ) . favipiravir inhibited replication of sftsv in vero cells by log units, with a % inhibitory concentration (ic ) and ic of . and µm, respectively. intraperitoneal or oral administration of favipiravir for days to ifnar−/− mice infected with lethal sftsv significantly improved survival rates ( % survival) without causing body weight loss and reduced the viral load in the serum. although ribavirin also inhibited sftsv replication, it was quite less effective than favipiravir both in vitro and in vivo. a time-of-drug-addition study revealed that therapeutic favipiravir treatment of sftsv infection in ifnar−/− mice was effective. these results suggest that favipiravir might be a promising candidate as antiviral drug against sfts. the study suggested that favipiravir is a candidate drug for the treatment of sfts. in the presentation, i will present the overview of the epidemiology and pathophysiology evaluated through pathological autopsy, and the development strategy of antiviral drug therapy for sfts. this disease, sfts, continues to be endemic to china, korea, and japan for the future. we can not escape from the risk being infected with sftsv. on the other hand, there is a potential that favipiravir has a therapeutic effect in the treatment of sfts. safe and efficacious vaccine against sfts should be developed. furthermore, i will discuss the issues to be addressed to reduce the sfts disease burden. the challenges posed by infectious diseases in the st century are forever growing more complex and numerous. there are no magic bullets or simple solutions that we can employ in our battle against the array of pathogens that every day attack humans, animals and plants. but there is much that we can do to mitigate the changing landscape of infectious diseases threats. this presentation will expand upon dr. osterholm's previous plenary session lecture. it will go into detail describing the major steps we can and must take to tip the balance between the growing threat of infectious diseases and our ability to anticipate these threats and prevent and control them before they can result in increased morbidity and mortality. the polymyxins, colistin ( polymyxin e) and polymyxin b, are effective antibiotics against most multidrug-resistant (mdr) gram-negatives and are currently considered as the last-line drugs for treating severe bacterial infections. polymyxin resistance among gram-negatives has increased gradually for the last few years, and knowledge of its multifaceted resistance mechanisms is expanding. typically, colistin resistance is due to chromosomally mediated modulation of two-component regulatory systems leading to modification of lipid a that resulted in reduced affinity to polymyxins. clones of polymyxin-resistant gram-negatives have spread in some hospitals, but have not significantly affected the use of polymyxins. these resistance genes are generally not transmissible between bacteria and so have not disseminated widely. however, a newly discovered plasmid-mediated polymyxin resistance gene mcr- has been detected in many countries in different geographical regions of the world since its first report in . therefore, it seems inevitable that plasmid-mediated transfer of polymyxin resistance will seriously reduce the lifespan of the polymyxins as the backbone of regimens against infections due to mdr gram-negatives. this review provides an update on epidemiology and mechanisms of polymyxin resistance among different commonly encountered mdr gram-negative bacilli. some unresolved questions with respect to polymyxin resistance are also discussed. one of the few remaining options for the infectious disease caused by multiple-drug resistant gram-negative bacilli is colistin. accordingly, emerging mobile colistin resistance mcr- for phosphoethanolamine transferase became a death threat to public health. various enterobacteriaceae carrying mcr- -plasmids from human beings, animals, and environments were reported in asia, europe, africa, and north and south america. in south korea, by the retrospective screening for the animal-oriented escherichia coli strains, the mcr- positive isolates have been identified. to evaluate mcr- -positive clinical strains, a total of enterobacteriaceae isolates collected between and were screened and, finally, three strains, two escherichia coli belonging to either st or st and one enterobacter aerogenes, harboring the gene were identified. all possessed inci mcr- -plasmids and colistin mics were g/ml in e. coli strains and g/ml in e. aerogenes. the bla ctx-m- gene for extended-spectrum beta-lactamase was co-carried in the mcr- -plasmid of e. aerogenes and extra plasmids carrying bla ctx-m- , bla ctx-m- , and bla ndm- were co-harbored by e. coli strains. one of the e. coli strains produced complete conjugal machinery presenting the best efficiency of plasmid transfer while e. aerogenes having a truncated prepilin peptidase pilu resulting in complete loss of conjugal activity. the plasmid in e. coli transferred efficiently to e. coli recipients compared to k. pneumoniae and to enterobacter cloacae probably due to the species-specificity allowed by rearranged shufflon. previously identified mcr- -positive e. coli strains of animal-origin from south korea also possessed inci mcr- -plasmid and the non-self-transferable mcr- -plasmid in e. aerogenes was closely associated to those, while the self-transferable mcr- -plasmid in e. coli strains were alike to each other. the plasmid carrying the gene, or the bacterial host harboring the plasmid, has come from animals as the previous reports illustrated. better stewardship for the proper usage of antimicrobials as well as a collaborating surveillance study as a concept of one-health is needed. what to use in the clinical practice? yohei doi md, phd university of pittsburgh, usa while colistin resistance in enterobacteriaceae due to the plasmid-mediated mcr genes has drawn much attention, the threat of colistin resistance that impacts patient care most currently exists in extensively drug-resistant (xdr) bacteria which have acquired colistin resistance through chromosomal mutations in species such as klebsiella pneumoniae, pseudomonas aeruginosa and acinetobacter baumannii. unlike the mcr mechanisms that readily spread horizontally via plasmids, colistin resistance in these xdr species usually arises through selective pressure in patients upon treatment with colistin, though outbreaks have also been reported on occasions. development of colistin resistance in these strains means few or even no remaining active agents. however, patients who are affected by these bacteria are medically complex, heterogenous, and difficult to enroll into clinical trials for many reasons. consequently, clinical data associating colistin resistance, antimicrobial therapy given and patient outcome are scarce and retrospective in nature for the most part. for k. pneumoniae, limited data suggest that mortality of infection from colistin-resistant strains may be lower when treated with gentamicin-containing regimens than those without gentamicin, but this approach is only applicable when the infecting strain is susceptible to this agent. fortunately, the approval of ceftazidime-avibactam has ameliorated concerns over colistin resistance in k. pneumoniae at least for the time being, as therapy with ceftazidime-avibactam appears to improve clinical outcome of infected patients over those treated with colistin-based regimens. interestingly, gastrointestinal decolonization with gentamicin may reduce infections and mortality in those known to be colonized with colistin-resistant k. pneumoniae, but the recent spread of mcr genes in humans brings into question the long-term viability of this approach. there are even less clinical data regarding the treatment of infections caused by colistin-resistant p. aeruginosa and a. baumannii. in vitro data variably support colistin-based combinations with partner agents including carbapenems, rifampicin, fosfomycin, and even gram-positive agents like vancomycin in the case of a. baumannii, but without accompanying robust clinical data. there are several novel agents with activity against colistin-resistant strains in late-stage clinical development. they include novel beta-lactam-beta-lactamase inhibitor combinations, a siderophore cephalosporin, an aminoglycoside and tetracyclines. most of them target carbapenem-resistant enterobacteriaceae, while some are also active against p. aeruginosa and a. baumannii. these new agents are bound to change the paradigm for the treatment of infections caused by colistin-resistant gram-negatives, but uncertainties are still likely to remain, including which agent to use, how to optimize dosing in to maximize efficacy and minimize toxicity as well as potential for development of resistance, and whether use of more than one agent would still be needed. analyte health, usa in the united states, telehealth represents a rapid, convenient, and cost-effective solution for non-life threatening conditions, including acute respiratory infections, urinary tract infection (uti), and sexually transmitted infections (stis). over . billion outpatient "bricks and mortar" visits occur annually in the us, and it is estimated that one third of these visits ( million) can be handled through telehealth. furthermore, one third of this subgroup of consults ( million) are related to infectious disease causes. until recently, the provision of diagnostic testing, in conjunction with telemedicine physician consults, was difficult due to diverse geo-locations of patients, physicians and testing laboratories. for example, in the virtual world of telehealth, a patient can be located in california, with the physician licensed to practice in california located three time zones away in new york. linkage of the physician and patient is now easily accomplished by electronic means (e.g., video conferencing, phone calls, text messaging). however, obtaining specimens from the patient and then transporting the specimen to the appropriate testing laboratory has been a challenge, such that most telemedicine consults are performed without diagnostic testing and empiric treatment is provided. this approach, especially with acute respiratory infection, could result in overuse or underuse of antibiotics. this lecture will describe new approaches to diagnostic testing for infectious diseases in the telehealth ecosystem. included is a description of the infrastructure requirements required and/or recently developed to accommodate specimen acquisition and testing through aggregation ("uber"-ization), of both physicians and laboratory patient service centers, provision of "round the clock" mobile collection (in-home collection) services and self-collection and self-testing. also, the cost-savings of these approaches, in contrast to traditional bricks and mortar approaches will be discussed. rapid molecular, point of care testing instruments are now available for the accurate and complete (no confirmation testing required) testing for group a streptococcus for throat swab specimens, and influenza and rsv for nasopharyngeal swab specimens; future testing capabilities include sexually transmitted diseases like neisseria gonorrhoeae, chlamydia trachomatis and human papilloma virus (hpv). these new devices will accommodate the next inflection point in virtual medicine: point of patient testing, including testing the patients in their homes. the world bank estimates that epidemics will cost $ trillion dollars in the st centuryroughly $ billion per year. the $ billion cost of the ebola epidemic was its economic impact (in countries that can least afford it); however the impact of ebola on families, social customs, and health infrastructure will have long term consequences. in addition, funding for epidemic diseases waxes and wanes with the passage of the epidemic, and as a consequence longer term preventive solutions, such as vaccines, have little means for progressing. in several nations and charitable foundations launched a new enterprise known as cepi, the coalition for epidemic preparedness innovations. cepi will fund the development of vaccine candidates for diseases of epidemic potential, the initial candidates are mers, nipah and lassa fever. we will review product development activities in these diseases and also detail attempts by international organizations to try to develop a framework around responses to public health emergencies of international concern. carbapenemases, from kpc to ndm to oxa- : diverse enzymes in diverse clones david m. livermore norwich medical school, university of east anglia, norwich nr tj, uk carbapenemase-producing enterobacteriaceae present a growing problem. the predominant enzymes are members of the kpc, ndm, imp, vim and oxa- families. rarer types include imi, sme and fri enzymes, also some members of the ges family. kpc, imi, sme, fri and ges enzymes belong to class a; ndm, imp and vim are class b metallo carbapenemases, whilst oxa- and its relatives, e.g. oxa- , belong to class d. this diversity of enzymes is reflected in a diversity of properties. kpc carbapenemases hydrolyse all widely available β-lactams and are inhibited by avibactam and vaborbactam. by contrast the metallo types evade avibactam and vaborbactam and attack all β-lactams except monobactams, which are often compromised by co-produced esbl and ampc enzymes. oxa- , which is inhibited by avibactam but not vaborbactam, has little activity against oxyimino-cephalosporins but, again, is often accompanied by cephalosporin-hydrolysing esbls. the origins of most clinically-important carbapenemases are obscure; the exception is oxa- , which is a chromosomal escape from shewenella spp. it is assumed that other carbapenemase genes similarly escaped from unknown environmental organisms. escape often entails gene mobilisation by insertion sequences, followed by capture by transposons and plasmids, which then facilitate dissemination. bla kpc , regardless of geographic origin, is generally carried by tn , often within pkpqil plasmids, whilst bla oxa- is often encoded by tn -related elements, carried on a small range of plasmids. bla oxa- differs only slightly from bla oxa- but appears to be a separate escape from shewenella, being associated with an isecp element on tn , a quite different transposon; moreover bla oxa- is epidemiologically linked to india, whereas classical bla oxa- links to turkey and the middle east. bla imp and bla vim metallo-carbapenemases occur as cassettes within class i integrons. bla ndm is generally linked to isaba , carried by a wide diversity of different plasmids and may have arisen as a chimera between apha , encoding its first six amino acids but otherwise deleted, and a pre-existing metallocarbapenemase gene of unknown origin. the plasmids encoding oxa- -like enzymes and all the major metallo types (i.e. imp, ndm and vim) spread among strains and species. these enzymes all have a predilection for klebsiella pneumoniae, but frequently occur also in escherichia coli, enterobacter and other enterobacteriaceae species. individual producer strains cause local outbreaks but no single strain has become nationally or globally widespread. rather, when producers became prevalent, the common pattern is one of small clusters within a wider epidemiology of plasmid transfer among strains. by contrast, kpc carbapenemases (carried by tn transposons within pkpqil plasmids) are strongly associated with k. pneumoniae st . this lineage, along with its variants (e.g. st ), has become internationally widespread and is responsible for the major expansion of 'carbapenemase-producing enterobacteriaceae' in e.g. greece, italy, brazil and israel. only in the last of these countries has it been brought under control, achieved by a determined and centrally mandated infection control effort. not all kpc problems are linked to st . in manchester, england, the problem is more akin to that with other carbapenemase types, entailing plasmid transfer among strains and species. the plasmids responsible are pkpqil variants with large substitutions resulting in the replacement of the partitioning and replication functions, potentially explaining their spread. the diversity of carbapenemase types and hosts exacerbates the problem of resistance. self-evidently, it harder to devise new pharmaceuticals that inhibit or evade multiple carbapenemase families than to develop those that inhibit or evade single or closely related enzyme types. what is more, experience suggests that it is harder to mobilise infection control staff and efforts against 'plasmid epidemics,' as with most carbapenemases, than against single strains epidemics. carbapenem-resistant enterobacteriaceae (cre) has been increasingly reported worldwide in the past years, which represents a serious threat to public health. invasive cre infections are associated with high mortality, and cre has the potential to spread widely. carbapenem resistance in enterobacteriaceae can mainly result from two different mechanisms. some cre, which possess either ampc or extended-spectrum β-lactamase (esbl) with concomitant porin mutations, can render the organism non-susceptible to carbapenems. more importantly, some cre may result from production of carbapenemases that break down carbapenems. carbapenemases belong to heterogenous group of β-lactamases: molecular class a ( penicillinases), class b (metalloenzymes), and class d (oxacillinases). in , clsi and eucast updated the carbapenem clinical breakpoints for enterobacteriaceae, in order to better predict treatment outcomes and to provide therapeutic alternatives for carbapenem-resistant bacteria. these breakpoints were based on patient response, pharmacokinetic/pharmacodynamic information, and in vitro minimal inhibitory concentration data. with the new lower breakpoints, routine testing for carbapenemase in clinical laboratory became not required for patient care. however, by these updated breakpoints, not all carbapenemase producing cre were non-susceptible to carbapenems. using the updated breakpoints, a study identified that occasional isolates of klebsiella pneumoniae with kpc or vim carbapenemases were susceptible to one or more carbapenem. as of now, few clinical data are available to support that mic is more important than presence of carbapenemase when predicting carbapenem treatment outcome. the different breakpoints for imipenem and meropenem in clsi and eucast may need evaluation for optimal patient care as well as epidemiologic study. carbapenemase detection and characterization are recommended for public health and infection control. currently, there are a variety of the phenotypic assays such as modified hodge test, the carba np test, modified carbapenemase inactivation method, and molecular assays. none of the currently described phenotypic test can detect all carbapenemases. molecular tests are often used as the golden standard, but they have inherent limitations such as missing novel variants and/or previously undescribed enzymes. cre continue to present challenges related to both treatment decisions by physicians and detection methods applied at laboratories. continued efforts to improve detection methods, by making them rapid, sensitive, and unbiased for specific carbapenemase, will hopefully allow for better patient care and prevention of further cre dissemination. ami neuberger, m.d. infections caused by carbapenem-resistant enterobacteriacea (cre) are more difficult to treat both because our current arsenal of antibiotics is limited and because some of the available antibiotics are less efficacious or have not been rigorously studied. the presentation will provide a brief overview of the future of treatment of cre infections. there are a number of controversies regarding the modes of administration of antibotics for cre infections: high versus lower dose, continuous or prolonged versus intermittent administration, duration of antibiotic treatment, and mono versus dual therapy. current evidence supports prolonged or continuous administration of β-lactam antibiotics. new randomized controlled trials of mono versus dual antimicrobial therapy, and short versus long duration of treatment for gram-negative bacteremia are ongoing, with results expected to be available in . older antibiotics, such as colistin, aminoglycosides, fosfomycin, and tigecycline are increasingly used together with newly approved drugs such as ceftazidime-avibactam. some new antibiotics in advanced stages of development ( phase or trials) will be reviewed. these drugs will include combinations of carbapenems or aztreonam with β-lactamses inhibitors, new combinations of cephalosporins with β-lactamses inhibitors, cefiderecola novel cephalosporin, plazomicinan aminoglycoside, and eravacyclinea new fluorocycline. the advantages and disadvantages of these drugs will be discussed. novel approaches to antibiotic development include the use of antibacterials produced from previously "non-culturable" bacteria, and development of new entry mechanisms of antibiotics into gram-negative bacilli. treatment of cre infections is likely to undergo rapid changes in the upcoming years, but any such change will have to be accompanied by comprehensive infection-control programs, antibiotic stewardship programs in hospitals and in the community, and judicious use of new antibiotics. one health approaches, 'one hdealth, one medicine', have been globally recognized to control zoonotic diseases. world organization of animal health (oie) has reported % of human pathogens are animal origin and more than % of emerging animal diseases are zoonoses. this means collaboration and cooperation between animal and human medicine together can only solve the problem. recent huge outbreaks of highly pathogenic avian influenza (hpai) and middle east respiratory syndrome (mers) in korea have been more pay attention to implement one health approaches in practice. we experienced several hpai epidemics past ten years and the mers in and had to bear huge damages. one health becomes a key approach to control zoonotic diseases systemically and effectively. a 'one health' approach to minimize the antimicrobial resistance in humans and animals need collaboration among the responsibility of all three parts; human health, animal health and environmental health-communities. surveillance of antimicrobial usage and resistance provides important data for the identification of resistance problems and contributing factors for the development and spread of resistance at a national and local level. through the painful korean experience of these zoonotic diseases and global challenge to amr brings us to establish the effective preventive method and early diagnosis as critical control strategies. prevention and control of infections is essential in fighting antimicrobial resistance. thus, to minimize infections in animal and human and to decrease the volume of antimicrobials used, collaborative efforts should be implemented to improve animal and human health. one health activities on nipah in bangladesh: a high risk country for zoonotic disease spillover to man epidemiological investigations in bangladesh implicated consumption of date palm sap as the major route of transmission of the virus from bats to humans. in bangladesh date palm sap is collected from date palm trees for consumption either as fresh or as fermented beverage. the sap is collected in clay pots attached to the top portion of the tree, where the tree has been denuded of bar, so that the sap can ooze overnight into the collection pots. outbreaks of disease typically occur in the winter months, the interval in which date palm sap is collected. as well, case-control studies have identified consumption of date palm sap beverage as a risk factor at the individual level. videos using infrared cameras have documented that fruit bats visit date palm trees at night and contaminate the collection pots by licking the oozing sap and by urinating in the collection pots. ethnographic studies of affected populations has enabled development of a behavior change intervention to reduce consumption of date palm sap. in addition, bamboo skirts placed around the denuded bark area of the date palm trees and collection pots have been developed to obstruct contamination of collected date palm sap by bat saliva and urine. of great concern, epidemiological studies in bangladesh have also identified person-to-person transmission of the virus between patients and persons who are in close contact with patient secretions, often in hospital settings. a study of nipah outbreaks between and attributed % of all cases to person-to-person transmission, though only % of patients were assessed as having transmitted their infection onward via this route. importantly, handwashing seemed to be effective in reducing person-to-person transmission. in aggregate, these studies illustrate the power of multidisciplinary collaborations under the rubric of one health, and, in view of the documented person-to-person transmission in bangladesh and the potential for emergence of new genetic variants of nipah that are capable of sustained human-to-human transmission, underscore the need for continued surveillance and control efforts, including development of effective vaccines. mycoplasma pneumoniae (mp) is one of the most common causes of community-acquired pneumonia in children and young adults. emerging resistance to macrolides among mp is of great concern since a macrolide-resistant mp strain was first reported in , most notably in japan, china, and korea. although macrolides are recommended for the first-line treatment for mp pneumonia, the efficacy of macrolides in the treatment of m. pneumoniae infection remains unclear. in addition, with the increase in macrolide resistance, concerns about the efficacy of macrolides for the treatment of mp pneumonia in children have been raised. given the versatile features of mp pneumonia, which are determined by the patient's age, the immunologic response of the host, and extrapulmonary manifestations, a more comprehensive approach must be established to analyze the clinical outcome of mp pneumonia according to the presence of macrolide resistance. initially, treatment of mp pneumonia with antimicrobials was supported by a randomized trial of marine recruits that showed a shortening of fever duration, alleviation of cough, and improvement of chest x-rays. a recent systematic review that evaluated the effect of treating mp pneumonia demonstrated that there was no significant clinical benefit of antimicrobial therapy in children with mp pneumonia. although much is not known about clinical impact of macrolide resistance on the severity of mp pneumonia, macrolide resistance alone does not seem to explain the severity of mp pneumonia. some studies have reported that patients infected with macrolide-resistant strains had more febrile days and a longer duration of persistent cough than those infected with macrolide-susceptible strains, suggesting poorer response to macrolide treatment in macrolide-resistant strains. the results highlight the need for well-designed prospective studies to assess a therapeutic benefit from macrolides and an adjunctive therapeutic strategy in the treatment of children with macrolide-resistant mp pneumonia. mayo clinic, usa mycoplasma pneumoniae (mp) can cause upper and lower respiratory tract infections in children and adolescents, with communityacquired pneumonia (cap) comprising the major burden of the disease. mp infections are generally mild and self-limiting. some patients, of any age, may develop severe and fulminant infection with pulmonary complications and/or extrapulmonary manifestations that may affect almost every organ. this presentation will focus on pulmonary infections due to mp. it is estimated that - % of children with mp respiratory infection develop cap and less than % are severe enough to require hospitalization, although this may change with increasing prevalence of mrmp. children with mp cap present with a longer duration of fever compared with children with cap due to other organisms. complicating the diagnosis of mp has been the insensitivity of testing as the organism does not grow well in culture, the inability to perform reliable and sequential serologic testing or pcr testing; the co-existence of mp with other pathogens; and asymptomatic carriage of mp in - % of patients. pathogenic effects on the respiratory tract may be direct by active infection, indirect by infection-induced immune mechanisms, or both. the immunopathology is poorly understood, in particular the role of cell-mediated immunity (cmi). studies have demonstrated increased concentrations in il- and il- in acute phase serum and pleural fluid samples and inf gamma, il- and ip- in patients with mrmp and that severity of cap correlated positively with the size of cutaneous induration following intradermal injection of mp antigens. it's been postulated that cytoadherence of mp to the respiratory epithelium initiates an immune response with progression to an excessive inflammatory response and a vigorous cmi response leading to pulmonary injury and severe clinical illness. macrolides have been and remain the drugs of choice for treatment of mp infections in children. alternative drugs such as tetracyclines and fluoroquinolones are not first line due to age-related adverse effects. macrolide resistant m. pneumoniae (mrmp) have been reported as early as the s in japan with rates now greater than % in areas of japan and china. korea reported mrmp in . mrmp in north america was reported in with a prevalence now of approximately %. europe has reported rates of - % and israel as high as %. many countries have unreported rates likely due to the lack of susceptibility testing. the mechanism of resistance is genetic with point mutations in a few positions of the domain v of the peptides transferase loop of the s rrna where macrolides bind the s rrna subunit. mp pneumonia was more prevalent throughout korea in and caused more severe clinical features than at any other time, which led to an unpublished observation that it may be associated with mrmp. despite the increasing prevalence of resistance, macrolides remain the drugs of choice for treatment of mp infections in children, but require antimicrobial stewardship. with increasing clinical severity of mp pneumonia and growing evidence for the role of an overreactive host defense, the role of corticosteroids has been investigated. in a study of healthy patients followed retrospectively all had either severe pneumonia (high fever, respiratory distress or initial lobar pneumonic consolidation with or without pleural effusion) or refractory pneumonia ( prolonged fever of > days or persistent consolidation of more than one lobe of the lung despite appropriate antimicrobial therapy), were diagnosed serologically, had no viral co-infection, received appropriate antimicrobials (macrolide or beta-lactam) and methylprednisolone at mg/kg/day × days. all improved. although mrmp may cause severe refractory mp, susceptibility testing was not performed in the above study. most often, mp causes a benign respiratory illness that may involve both upper and lower respiratory tracts. but mp has the potential to cause severe disease. the emergence of mrmp has led to severe mp pneumonia. but macrolide resistance is only one potential cause of severe disease. an exuberant host inflammatory response with release of cytokines and, perhaps mediated largely by cmi, appears to play a role in some children and adolescents. in the latter situation, corticosteroids may prove beneficial but more research needs to be done. over the last three decades, many studies have investigated the best approaches to promote hand hygiene practices and improve hand hygiene indicators, in particular healthcare workers' (hcws) compliance. early studies on hand hygiene improvement in healthcare were focused on single interventions promoting the importance of handwashing and introducing the use of antimicrobial soaps. in , our group in geneva conducted the first large-scale epidemiological research on hand hygiene, identifying major risk factors for noncompliance and demonstrating the critical role of alcohol-based handrubs (abhrs) as major system change to replace handwashing with soap and water, while included in a multimodal strategy to change hcw behavior. the strategy combines easy access to abhr ( proven to bypass the time constraint on hcws), hcw education, performance monitoring and feedback, reminders in the workplace and institutional safety climate. the strategy (referenced as the "geneva model of hand hygiene promotion) was proven successful, and hand hygiene improvement was associated with significant reduction in healthcare-associated infections (hais) and spread of multi-resistant organisms. between and , the "geneva model of hand hygiene promotion" was replicated in single, as well as multiple healthcare institutions, at local, regional and national level, with success. since , the world health organization (who) mandated our group to lead the first global patient safety challenge (clean care is safer care) with the main objectives to raise awareness about hai worldwide, mobilize nations toward ipc activities and promote best ipc practices, in particular hand hygiene. the recent meta-analysis by luangasanatip et al. demonstrates the critical role of the who multimodal approach in successful hand hygiene promotion. nevertheless, several knowledge gaps in hand hygiene monitoring and efficacy remain. in my lecture i will focus on the following topic areas related to key questions in the hand hygiene research agenda: • studies on direct and indirect monitoring of hand hygiene compliance, including new devices for observation and feedback; • studies of the influence of i) handrubbing duration; ii) volume of abhr used, and iii) the optimal sequence of the handrubbing steps within the "how to handrub" -step technique, in the reduction of bacterial counts on hcws hands; • studies on the burden of disease and implementation of infection prevention and control strategies worldwide; • studies of the possible role of patient participation and empowerment in hand hygiene promotion. hepatitis c virus (hcv) infection is one of the most common chronic liver disease. globally, it was estimated that in , more than million people had hcv antibodies ( prevalence of . %). most patients infected with hcv acquired the disease through intravenous drug use or blood transfusion, the latter of which has become rare since routine testing of the blood supply for hcv began in . nosocomial transmission of hcv has been documented in several health care settings. where there are stringent infection control protocols to prevent transmission, particularly through unsafe medication injection practices, nosocomial transmission has still been reported, generally because of breaches in protocol. rare sources of transmission of hcv include contaminated equipment used during the performance of procedures and other breakdowns of infection control procedures or aseptic techniques leading to person-to-person transmission. screening for hepatitis c virus (hcv) infection is an important component of successful control of hcv for the infected individual and for public health purposes. diagnostic tests for hepatitis c virus (hcv) are serologic assays that detect antibodies to hepatitis c, and molecular assays that detect or quantify hcv rna, other investigations such as genotype testing, serum fibrosis panels and liver biopsy may help to predict the response to treatment and prognosis. most cases of acute hcv infection are anicteric and asymptomatic, with fewer than % being clinically apparent. fulminant hepatitis c is rare. of those who go on to have chronic infection, a substantial proportion will develop cirrhosis, and a subset of those develop hepatocellular carcinoma. active surveillance based on mdr gram-negative pathogens? anucha apisarnthanarak md active surveillance is one of the common strategies employed to control mdr-gram negative pathogens. although listed in the guideline, the true value of active surveillance for mdr gram-negative pathogens has never been demonstrated. several considerations should be made when infection preventionists implement active surveillance as part of control measures. these include the specific reservoir of each specific mdr gram-negative pathogens, resource availability for isolation precaution, the turn-around time of active surveillance culture, whether institution is able to implement other infection prevention strategies together with active surveillance culture. in this session, i will address the pro-and con-for active surveillance culture for mdr gram-negative pathogens. application of active surveillance culture in resource-limited settings will also be discussed. also, rates of catheter associated urinary tract infection (cauti) and c-line associated blood stream infection (clbsi) significantly decreased from . to . ( per catheter-days, f = . , p < . ) and from . to . ( per , catheter-days, f = . , p < . ). in subgroup analysis, rates of vap, cauti and clbsi were significantly decreased regardless of organizational and institutional characteristics of icus. in summary, all of the da-hais have shown a significant reduction in the last years, however v-ur has year-wise significantly increased trend for past -years, also uc-ur and cl-ur have not decreased trend significantly. we need effort to make reduction of device utilization ratios and associated infections. invasive fungal infections (ifi) are primary causes of mortality, and rapid and accurate diagnostic laboratory tests are required to improve patient outcomes. although histopathologic examinations of tissues can detect ifis, tissue morphology alone is insufficient to distinguish between aspergillus and other fungi, including fusarium, scedosporium, or mucorales. therefore, species identification using culture and non-culture methods is necessary. recently, assays targeting ribosomal dna have been used to identify infectious fungi in tissues. notably, analyses using frozen tissues were superior to those using formalin-fixed paraffin-embedded tissues. because pan-fungal primers hybridized dna from other eukaryotes, the pan-fungal approach was limited in tissues that primarily contained human dna and little fungal dna. diagnostic tests that rely on fungal cultures are common for ifis. recently, however, dna sequencing and matrix-assisted laser desorption/ ionization time-of-fight mass spectrometry (maldi-tof ms) have been used to rapidly and accurately identify fungal pathogens recovered from cultures. sequence-based identifications have been particularly useful for identifying cryptic species that were misidentified by microscopic analyses or were identified only to the complex level. some cryptic species are resistant to azole antifungal agents, and molecular methods have been developed to detect azole-and echinocandin-resistant candida species as well as azole-resistant aspergillus species. blood cultures are the gold standard for diagnosing candidemia; however, cultures require - days of growth followed by an additional - days for identification and antifungal susceptibility testing. such timeframes lead to delays in treatment initiation. additionally, up to onethird of patients with invasive candidiasis fail to test positive in blood cultures. pcr and the , -β-d-glucan (bdg) assay are more sensitive than blood cultures for patients with deep-seated candidiasis. bdg is a cell wall component in candida and other fungal species, except mucorales and cryptococcus, and is included in the eortic/msg revised diagnostic criteria for invasive fungal diseases. however, bdg assays are expensive and labor-intensive, making them unavailable in most developing countries. the bdg assay is highly sensitive but lacks specificity; thus, it is typically suitable only for ruling out the causes of candidiasis. serum galactomannan (gm) is a cell wall component of aspergillus, and can be detected in serum using a commercial test (platelia™ aspergillus eia; biorad, usa). the serum gm test is considered aspergillus-specific, and multiple studies demonstrated high sensitivities (∼ %) in sera from patients with hematological malignancies or allogeneic hematopoietic stem cell transplantations. however, gm sensitivity is low in non-neutropenic patients and recipients of solid organ transplants. additionally, the gm test is associated with poor predictive values in patients receiving mold-active antifungal prophylaxis. however, the detection of gm in bal fluid is high (> %) even among patients receiving mold-active antifungal therapies. multiple studies have shown that pcr was more sensitive than culture methods at detecting aspergillus in blood and respiratory fluids. multiple pcr assays are commercially available for the detection of aspergillus spp.; however, none is fda-approved. moreover, aspergillusspecific pcr is not recommended for clinical use as only few assays are standardized and validated. the t candida assay (t biosystems, usa) was recently introduced for the detection of five common candida species from whole-blood samples. the t candida assay is the only fda-approved diagnostic test that offers rapid diagnosis ( - hours) and specific organism identification with detection limits of cfu/ml. the development of additional diagnostic tests will facilitate the early diagnosis and management of ifis in high-risk patients. the newest treatment strategies for candidemia thomas f. patterson professor of medicine, ut health san antonio, san antonio, texas usa candidemia is an important cause of morbidity and mortality especially in hospitalized and immunocompromised patients. despite advances in antifungal therapy, the number antifungal drugs and drug classes for treating these serious infectious remains limited. management is further complicated by the fact that it remains difficult to establish an accurate diagnosis which is compounded by the need for early therapy. fluconazole remains a useful antifungal agent especially for follow-on therapy after stabilization of infection but resistance is high for some species including c. glabrata. thus, the echinocandins have become recommended as primary therapy in most patients. however, development of echinocandin drug resistant strains has been reported worldwide. the development of drug resistance has often been tied to antifungal drug use, particularly for some species like candida glabrata. while multidrug resistance is uncommon, increasing reports of multidrug resistance to the azoles, echinocandins and polyenes have occurred in several candida species, most notably candida glabrata and more recently candida auris. new agents are under development for candidemia, including echinocandins improved pharmacokinetic profiles and those available for oral use. in addition, other agents with new targets of action are also undergoing preclinical development. diagnosis of infection and detection of antifungal resistance is critical to the successful management of patients with these infections. new therapies are aimed at improving outcomes in candidemia. epidemiology and management of mucormycosis and invasive aspergillosis: are there lessons to be learned? centre for infectious diseases and microbiology laboratory services, icpmr, westmead hospital, university of sydney, new south wales, australia the epidemiology of aspergillus and mucorales infections may be changing. although invasive aspergillosis (ia) remains a substantive cause of morbidity in patients with neutropenia, hematologic malignancy and organ transplants, there is an expansion in the spectrum of at risk patients. patients in the intensive care unit (icu), with chronic lung disease, hiv/aids and those on immunomodulating drugs are amongst relatively understudied populations. diagnostic difficulties including the interpretation of aspergillus cultures contribute to this limitation. other than the expansion in host risk groups, is the shift in etiology of ia, with cryptic or uncommon species emergent. in addition, azoleresistant a. fumigatus infections pose an increasing dilemma in regions of europe and asia (< - % resistance rates). in general, voriconazole is recommended for the primary treatment of ia regardless of site of infection. other azoles, the echinocandins or amphotericin b compounds may be used as second line or salvage therapy. primary combination therapy is not routinely advised. surgical derbridement or resection is an important adjunct where feasible. in the presence of azole resistance, either liposomal amphotericin b (l-amb) or a voriconazole-echinocandin combination is preferred. in vitro susceptibility testing is recommended for all ia cases. isavuconazole has good activity against aspergillus and new antifungal drugs with anti-aspergillus activity are in development. many cases of mucormycosis affect hosts with malignancy and stem cell transplantation, but organ transplantation, diabetes mellitus and iron overload are also important underlying conditions although the use of certain calcineurin inhibitors may be associated with lower risk. emerging risks include underlying rheumatological/autoimmune conditions. trauma-related cases may also be increasing and outbreaks of infection following natural disasters and iatrogenic exposure described. pathogen epidemiology varies with region with emergence of uncommon genera such as apophysomyces. despite best practice management and reversal of risks, mortality is up to %. treatment is based on case series and expert opinion. surgical debridement/resection combined with antifungals improves outcomes. initial treatment with l-amb is preferred agent although optimal dosage is uncertain. isavuconazole appears to be as efficacious as l-amb. combination polyene-echinocandin can be considered for extensive disease or salvage therapy, with posaconazole typically employed as step-down therapy. treatment algorithms may change with wider availability of iv posaconazole; other new drugs are in the pipeline. endemic fungal infection in the asia-pacific region (in the context of altered immunity) national university health system, singapore less is known about the incidence and characterization of deep mycoses in the asia pacific region. geoclimatic conditions, population demographics and health resource accessibility vary within the respective asian countries and also differ from west. invasive fungal diseases (ifd) encountered in the region will be discussed with specific highlights on the unique challenges faced pertaining to host immune susceptibility and in the management of these diseases. candidemia and candidiasis constitute the highest proportion of the ifds. in particular, the contribution by candida tropicalis in tropical asia pacific is not to be overlooked. candida tropicalis infection, linked to more severe disease, is seen in patients with weakened immunity such as hematological malignancies and in neonates. the host immune factors recently identified as predisposing to oro-esophageal candidiasis will also be discussed. chronic (cavitatory) pulmonary aspergillosis (cpa) in asia is often a sequelae to old tuberculosis as well as aspergillosis in the critically ill is under-recognized. the immune interplay between the ubiquitous mold and the host defense during severe illness will be explored. cryptococcosis and penicilliosis have traditionally been seen in patients infected with the human immunodeficiency virus (hiv). while cryptococcus infections have been recognized to occur beyond the context of hiv and even in apparently immunocompetent subjects, it is only recently that the immune susceptibility of such patients to cryptococcus are being dissected. similarly the notable predilection of talaormyces marneffei (and other rare fungi) in the asia pacific region is being linked to other non-hiv-attributed host immune defects including a novel disease trait seemingly distinct to asians. pre-exposure prophylaxis: from science to implementation rossana a. ditangco md prep for hiv refers to the preventive strategy of taking a medical agent prior to hiv exposure. this method specifically involves the oral intake of an antiretroviral drug (arv) by hiv-negative individuals who are at high risk of acquiring the virus in order to prevent hiv infection. recent studies have demonstrated safety and efficacy of dual antiretroviral (arv) oral pre-exposure prophylaxis (prep) in preventing sexual and parenteral transmission of hiv infection. the iprex study, a randomized controlled efficacy trial in men who have sex with men (msm) and a small contingent of male-to-female transgender women (tgw) is particularly relevant to asia and the pacific. in this study, emticitrabine/tenofovir disoproxil fumarate (ftc/tdf or truvada ® ) safely achieved a % per-protocol reduction in new hiv infections. however, risk reduction was % in ftc/tdf recipients having detectable study-drug blood levels, indicative of much greater efficacy associated with increased adherence. subsequent pharmacologic modeling and follow-up studies demonstrated daily use of these agents not being required for achieving optimal protection, declining on a gradual scale associated with decreased frequency of use . this research showed a reduction of hiv infection risk of % for doses, % for doses and % for doses of ftc/tdf per week. the protective efficacy of non-daily dosing ( % risk reduction) was subsequently confirmed in a placebo-controlled trial of intermittent (on-demand) ftc/tdf prep among msm in france and canada. mathematical modeling using iprex findings demonstrated substantial reductions in new hiv infection associated with modest prep program coverage in msm, while increased prep adherence was shown to have the largest population level preventive impact with greatest cost-effectiveness . prep implementation has been shown feasible in open-label extensions and project sites with research and program capacity. despite its excellent safety and efficacy profile, the proof of implementation of prep in resource-limited settings outside of these situations still needs to be delivered. applications of prep in resource limited situations must be grounded in the reality of existing health systems and the interface between community-level primary care clinic-and hospital-based services. a number of unknowns remain with respect to the delivery of hiv prep for msm/tgw in these environments. among others, access, uptake and adherence, effectiveness and behavioral and social impact effects are not described. taking part in a prep project or using arv drugs may disclose same-sex behavior and hiv risk. these in turn may provoke negative reactions or undue pressures in the social, professional and family environment. participants may see certain services or privileges being revoked or denied. in a worst case scenario, disclosure may lead to denial or termination of health or life-insurance, rental agreements, employment or promotion. these negative repercussions constitute violations of individual rights and may adversely impact project participation and prep access, uptake and adherence. of particular concern are poor adherence and increases in sexual risk behavior, the latter potentially accelerating sexually transmitted infections (sti) followed by increased hiv acquisition and transmission in the non-prep serviced portion of at risk population. at present countries are at varying stages of introducing daily oral prep using tdf/ftc, which is now recommended by who as an option for people at substantial risk of hiv. some countries have national programs; others have smaller-scale programs; others aren't offering prep at all. the benefit of prep as a prevention strategy goes beyond its clinical efficacy. prep programs could increase hiv testing uptake and contact with health care provider for hiv counseling and education services and early diagnosis and treatment of sexually transmitted infection. scientific evidence of efficacy and safety of prep, mathematical models for cost effectiveness and potential elimination of new hiv infection and projected benefit beyond clinical effectiveness provide rationale for making prep available as additional layer of hiv prevention strategy. center for aids research, kumamoto university, kumamoto, japan despite the significant reduction in morbidity and mortality following combination antiretroviral therapy (art) there is emerging evidence that people with successfully treated hiv infection by art age prematurely, leading to progressive multi-organ disease referred as comorbidities. one of the major factors involved in this pathogenic process is residual viral replication by persistently infected cells surviving in vivo and subsequent chronic inflammation. in contrast to the current art that only targets viral replication neutralizing or nonneutralizing antibodies against the envelope proteins of hiv- have been reported to have an adcc (antibody-mediated cellular cytotoxicity) activity that eliminate hiv- infected cells in vitro. the discovery of potent and broadly neutralizing antibodies (bnabs) against hiv has made passive immunization a potential strategy for the prevention and treatment of hiv infection. the bnabs bnc and vrc targeting the hiv cd -binding site has been tested in treatment naïve patients and on treatment patients for the delay in plasma viral rebound after the discontinuation of art. monoclonal antibody - targets the v glycan supersite was used at the highest dose of mg/kg and showed a rapid decline in viremia. however, virologic analyses revealed the emergence of multiple independent neutralization resistant mutants in every case. we conducted a phase b clinical trial of passive transfer of neutralizing monoclonal antibody kd- , which is reactive against the tip of the v region. eligible subjects were randomized to receive one of the doses of kd- and the treatment was found safe and well tolerated. we observed significant decrease in hiv-rna in the mg/kg cohort of kd- with two in six cases who achieved > log reduction of hiv-rna. long-term suppression of viral load was observed for one patient despite significant decrease in plasma concentration of kd- , suggesting effects of antibody other than neutralization. we previously reported that the neutralization escape mutants to kd- became sensitive to chemokine cc receptor (ccr) inhibitors such as maraviroc or cenicriviroc. conversely, resistance mutants to ccr inhibitors became sensitive to several neutralizing antibodies including kd- . furthermore, a series of in vitro experiments suggested synergistic effects of the combination of kd- and ccr antagonists including maraviroc (figure) . these results taken together, suggest that the combination of neutralizing antibodies with ccr -inhibitors would be a promising candidate of intensification therapy added onto the current suppressive art aiming toward functional cure of the disease. programmable nucleasesincluding zinc-finger nucleases (zfns), transcription activator-like effector nucleases (talens) and rna-guided engineered nucleases (rgens) derived from the bacterial clustered regularly interspaced short palindromic repeat (crispr)-cas (crisprassociated) systemenable targeted genetic modifications in cultured cells, as well as in whole animals and plants. the value of these enzymes in research, medicine and biotechnology arises from their ability to induce site-specific dna cleavage in the genome, the repair (through endogenous mechanisms) of which allows high-precision genome editing. however, these nucleases differ in several respects, including their composition, targetable sites, specificities and mutation signatures, among other characteristics. knowledge of nucleasespecific features, as well as of their pros and cons, is essential for researchers to choose the most appropriate tool for a range of applications. group cpf is a recently reported effector endonuclease protein of the class crispr-cas system. cpf has several differences from cas : cleavage with ' overhangs, shorter guide rna, and a longer distance between the seed sequence and cleavage site, which could provide potential advantages for some cases of genome editing such as nonhomologous end joining-based gene insertion and efficient genome editing using homology-directed repair. however, limited information is available about cpf activity profiles in mammalian cells, precluding its wide use for genome editing. furthermore, both selection of highly efficient guide rnas and collection of big data for determination of parameters of rna-programmable nucleases are currently laborious and costly due to lack of a reliable high-throughput approach to determine rnaprogrammable nuclease activity in mammalian cells. here, we performed en masse evaluation of guide rna and cpf activity using synthetic target sequences and deep sequencing. using this in vivo high-throughput approach, we determined on-and off-target activity profiles and protospacer adjacent motif (pam) sequences of cpf . we found that sequence features of high activity ascpf guide rnas are distinct from those of spcas and that the pam of as and lbcpf in mammalian cells is tttv, rather than tttn, which was previously determined using an in vitro system. evaluation of off-target activity showed that cpf target sequences can be divided into three regions: a base pair (bp) seed, a bp trunk, and a bp promiscuous region. these results should serve as a useful guide to select cpf as a genome editing tool. more importantly, our in vivo high-throughput evaluation system will greatly facilitate both the selection of efficient and precise guide rnas and the generation of big data for the development of advanced prediction programs for on-and off-target activities. tasp works if an infected person knows his/her hiv status. a diagnosis should have been made as early as possible, and treatment offered promptly, so that the time gap between infection and viral suppression can be narrowed. around the world, late diagnosis is still common. early diagnosis often hinges not just on easy access to voluntary testing, freedom from stigma, but also the availability of screening. selftesting and the submission of specimens (urine, saliva, dried blood spots) for laboratory testing are some solutions, albeit the existence of technical problems, and the need for establishing linkage to care. periodic testing campaigns could impact hiv epidemiology, as illustrated in our modelling study parametrized by hong kong's surveillance data. for patients enrolled in treatment programs, optimization of regimen is crucial to ensure lifelong maintenance of haart without adverse reactions. in the developed world, integrase inhibitor is now used in first-line regimens, which has the capacity of reducing viral load to undetectable range within weeks. their access and that of single tablet regimens, are however limited in places where most hiv patients are. for some antiretrovirals, for example abacavir and efavirenz, knowledge of the host genotype (hla-b and cyp b - gt respectively) could minimize the occurrence of adverse reactions which might otherwise compromise adherence. notably adherence is the key to lifelong maintenance of virus suppression, and there is no simple solution to guarantee adherence over years, or tens of years. whereas all efforts could be made to promote testing and improve treatment coverage, the underdiagnosed interval is often where the achilles heel is. except for a small number of cases presenting as acute infection, the seroconversion time is often unknown. using modified back calculation methods to estimate the seroconversion year of over , patients in hong kong, we found that the interquartile range of their underdiagnosed intervals was - years with a range between and years. the lengths of undiagnosed intervals were associated with age and the routes of hiv transmission. obviously people with low perceived risk of hiv infection had longer undiagnosed interval and were more likely to be late for diagnosis. from mathematical modelling, increase of undiagnosed intervals would offset infections averted by tasp even if good coverage and high adherence were assumed. apparently, tasp is a necessary yet insufficient intervention to achieve hiv elimination. tasp targets people infected with hiv, whereas interventions for non-infected individuals would contribute to the reduction of the size of populations requiring tasp. one good example of the latter is pre-exposure prophylaxis, but it's only accessible to handfuls of people at risk around the world. effective protocols are needed, and risk compensation is a new concern. let's not forget promotion of protected sex, provision of methadone maintenance (and other harm reduction measures) for injection drug users, and community-level behavioral interventions. they continue to be powerful components of the armamentarium of measures to combat hiv, complementing tasp to achieve hiv elimination. stephan harbarth health care-associated infection (hcai) is a major global issue in patient safety. it affects hundreds of millions of people worldwide, complicates the delivery of patient care, contributes to patient deaths and disability, promotes resistance to antibiotics, and generates additional expenditure to that already incurred by the patients' underlying disease. indeed, hcai is a growing international problem. patients are becoming more susceptible to infections because of more serious underlying illnesses. poor compliance with hand hygiene by health care staff, increased recourse to invasive medical devices, and care of the critically ill as well as lack of access to safe water and unclean instruments and environmental surfaces all play a role. the environment of patient care is also important. factors such as understaffing, high bed occupancy, and increased patient transfers all create new risks of infection. the first global patient safety challenge created a worldwide focus on reducing hcai as a vital element of the safety of patient care. the last two years provided important and clinically relevant research data for prevention of hcai in different patient populations. my presentation will summarise the results of clinical trials and systematic reviews for the reduction of various types of hcai, and will discuss them in the context of the current relevant scientific and clinical background. in particular, i will discuss recent data on the epidemiology and prevention of nosocomial infections in intensive care units, present new approaches to prevention of surgical site infections as well as catheter-related bloodstream infections, describe recent advances in hand hygiene research and attempt to briefly summarise specific challenges related to the management of infections caused by multidrugresistant microorganisms. overall, hcais remain one of the key challenges of hospital care and significantly contributes to morbidity and mortality. papers published in the last years remind us that further reductions of hcai rates are possibleoften with the help of simple and rather inexpensive interventions. rapid and accurate diagnosis is critical for the effective treatment of life threatening infections, such as bloodstream, respiratory tract and complicated urinary tract infections (utis). these clinical syndromes are difficult to diagnose due to complex aetiology and challenging clinical sample types (e.g. blood, sputum). current culture based diagnosis often has sub-optimal specificity and sensitivity and is too slow to impact on patient management. shotgun metagenomics sequencing has the potential to change the way we diagnose infection, combining rapidity with comprehensiveness beyond that of current methods. real-time nanopore sequencing technology provides the rapid turnaround necessary for infectious diseases diagnostics applications at point-of-care. there are challenges in applying sequencing to infection diagnosis, however, including high human:pathogen nucleic acid ratios, low pathogen numbers and low quality nucleic acid, depending on the disease and the clinical sample type. it is, therefore, vital to carefully design, develop, and optimise diagnostics pipelines before attempting to apply them to clinical samples. i will describe how we develop our minion based infectious diseases diagnostics pipelines with examples from our ongoing research on pneumonia, sepsis and utis. protein synthesis enzymes as primary defense system against infection aminoacyl-trna synthetases (arss) are essential protein synthesis enzymes, making a covalent linkage of their cognate amino acids to trnas. since the catalytic activities of arss are always required for the viability of organisms, they are constitutively expressed and ubiquitously present. due to these features, arss are the first to be exposed to broad spectrum of stresses and challenges. in fact, they have shown diverse roles as rapid responding signal mediators beyond protein synthesis. here we show our recent findings on arss as primary defense system against bacterial and viral infections. for instance, tryptophanyl-trna synthetase (wrs), is rapidly secreted out from monocytes upon bacterial infection and primes innate immune responses. the secretion was far more rapid than the induction of innate immune system. in another case, glutamyl-prolyl-trna synthetase (eprs) plays a unique role in viral clearance. eprs blocks pcbp mediated ubiquitination of mavs (mitochondrial antiviral signaling protein), leading to the inhibition of viral replication. based on these findings, other arss are expected to play unique roles against infection, thereby collectively serve as a primary shielding system. victor lim international medical university, kuala lumpur, malaysia the world is facing a crisis in antimicrobial resistance (amr). it has been projected that if nothing is done million people will die from antimicrobial-resistant infections annually by and the economic cost will also be correspondingly high at one hundred trillion us dollars. the overuse of antimicrobial agents is a major driver for the emergence of resistance. improving antibiotic stewardship is therefore crucial in meeting the challenges posed by amr. to do so would require recognition of the problem by all stakeholders at all levels and the political will to solve. adequate planning and provision of resources (including legislation) are essential. most importantly however, it would require a behaviour change among all stakeholders. there is increasing recognition that providing evidence from health research while necessary is insufficient for the delivery of optimal health care. there is a need to translate knowledge into action. the field of knowledge translation (kt) is the scientific study of methods for closing the knowledge-to-practice gap, and of the barriers and facilitators inherent in this process and such methods must be employed if we are to enjoy any success in antibiotic stewardship. the esrc working group on amr report stated that although amr involves biological processes, the context which determines the operation of these biological mechanisms is shaped by social, cultural, political, and economic processes. behavioural science is a multidisciplinary study of human (and animal) behavior and encompasses the disciplines of psychology, anthropology, sociology and economics. the contribution of behavioural science in improving antibiotic stewardship is crucial but has only been recognized lately. antibiotic prescribing is a complex behaviour, carried out by an informed individual often making a subjectively rational choice. a recent report by the department of health and public health england summarised the evidence on behavioural change and antibiotic prescribing in healthcare settings. it pointed out the lack of underpinning psychological theory and behavioural science in most of the studies which have been done so far. as a result interventions may not be effective in changing behavior. to change behavior we need to understand the drivers of behavior. drivers of prescriber behavior may be intrinsic or extrinsic. intrinsic factors include an altruistic motivation to do one's best for the patient, ignorance, duration of practice, the tendency to yield to patient demands, fear (both of progression of disease and losing the patient), and a lack of understanding of the resistance problem. extrinsic factors would include patient demands, the influence of the pharmaceutical industry, diagnostic uncertainty, patient comorbidities and social class, workload and time pressures, role modelling by senior colleagues and financial incentives. interventions to improve antibiotic stewardship had included prescriber education and training, the issuance of antibiotic guidelines, the use of electronic decision support systems, audit and feedback, rapid and near patient testing to reduce diagnostic uncertainty, restriction strategies (pharmacy and laboratory) as well as financial strategies. to increase awareness of the problem of amr among the public social marketing strategies have been employed including the use of the mass media. although a variety of interventions have been employed over the last decades; their overall effectiveness is subject to question. results have been variable. what works in one setting may not work in another as behavior change is a complex process and influenced by social, economic, ethnic and cultural beliefs. many studies are cross-sectional in nature and the sustainability of the intervention is not measured. to design any strategy or intervention there is a need to understand both prescriber and patient/public behavior and the factors that drive it using methodologies that are established in the behavioural sciences. any intervention has to be specific to the local context and the target population. a combination of strategies may be necessary to modify behavior for desired outcomes. department of infectious diseases, institute of infectious diseases and epidemiology, tan tock seng hospital, singapore antimicrobial resistance in hospitals is characterized by widespread dissemination of multidrug-resistant and extensively drug resistant bacteria, including methicillin-resistant staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase and carbapenemase producing enterobacteriaceae, and pandrug-resistant acinetobacter baumannii. a combination of enhanced infection control and antimicrobial stewardship is often recommended to combat antimicrobial resistance in hospitals. multiple strategies are recommended by professional societies for antimicrobial stewardship, with differing levels of evidence and effectiveness. several recent well conducted systematic reviews and meta-analyses have shown that antimicrobial stewardship is effective in reducing broadspectrum antibiotic use and antimicrobial resistance without increasing adverse clinical outcomes. restrictive strategies produce more immediate effects but persuasive strategies are associated with more sustained impact. in addition to commonly adopted strategies of pre-authorization and prospective review and feedback, a greater variety of antimicrobial stewardship interventions are now recommended. in particular, evidence-based clinical care paths for common infections are associated with improved mortality. however antimicrobial use in hospitals is part of the greater context of antimicrobial use and resistance within the one health continuum. increasingly national and regional antimicrobial stewardship efforts must move outside of hospitals. damps: neutrophil dysfunction in experimental sepsis and post-septic complications related to immunosuppression jaroslaw zmijewski university of alabama at birmingham, usa damps: neutrophil dysfunction in experimental sepsis and post-septic complications related to immunosuppression bone using a murine model of polymicrobial septic peritonitis, we demonstrated that treatment with anti-hmgb ab significantly diminished sepsis-induced dysfunction of neutrophil nadph oxidase activity. importantly, confirmatory experiments revealed that blocking hmgb prevents neutrophils dysfunction. in summary, these results suggest that hmgb accumulation in the late phase of sepsis plays a specific role in the development of immunosuppression and specifically affects neutrophil-dependent antibacterial function in sepsis survivors. epidemiology of extensively-resistant gram-negative in mainland china hui wang peking university people's hospital, pr china multidrug resistance in gram-negative bacteria, especially carbapenem-resistant enterobacteriaceae (cre), is a critical public health threat in china advances in next-generation sequencing (ngs) platforms and microbial bioinformatics have positioned ngs to play an increasing role in clinical microbiology laboratories. next-generation sequencing is being applied to microbial isolates as well as directly to clinical specimens benchtop sequencers suitable for use in clinical microbiology laboratories are now available. sequences may be generated with various approaches (e.g., paired-end, mate-pair) and either aligned against a reference strain or assembled de novo with subsequent analytic strategies including single nucleotide polymorphism (snp) analysis and core genome multilocus sequence typing (cgmlst), among others. these approaches impact turnaround time, cost, technical difficulty, and accuracy. how results compare to those of historical methods not only does it allow for pathogen identification, but gene content information can also be used for resistance prediction, typing, and assessment for other relevant genes, such as those encoding virulence factors. our experience applying this approach to the diagnosis of prosthetic joint infection will be presented we found that loss of parkin, ubiquitin ligase implicated in autophagy and mitophagy occurs several hours after pro-inflammatory engagement in macrophages and lungs of mice subjected to intratracheal instillation of endotoxin. parkin dissipation was also accompanied with diminished activity in ampactivated protein kinase (ampk), a major sensor and metabolic regulator of immune homeostasis. we hypothesize that ampk activation will overcome loss in parkin-mediated autophagy and thus, diminish severity of ali. we found that ampk activators metformin or aicar did not recover the amounts of parkin. however, ampk activation promoted autophagy and improved bacterial clearance. in summary, our results show that parkin deficiency increased macrophage pro-inflammatory activation and the severity of ali mayo clinic, usa infectious diseases diagnostic testing is currently in a revolution vis-à-vis delivering new technologies. a myriad of new technologies are in use or under development, including matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (maldi-tof ms), rapid multiplex (i.e., panel) nucleic acid amplification tests (naats), point-of-care microbiology naats, and rapid phenotypic bacterial susceptibility testing, to name a few. these technologies provide new tools to combat antimicrobial resistance, which is especially important in an era of rising resistance. today, there is increased use of unneeded broad spectrum therapy because of the need to address the possibility of resistance until such a time as results of conventional diagnostic tests are available. this situation can potentially be ameliorated by more rapid diagnostics. in addition, over-prescription of antibacterial agents in general can potentially be addressed by rapid tests which exclude the need to prescribe antibacterial agents in the first place. an overview of new rapid diagnostics for infectious diseases that can potentially help combat antimicrobial resistance will be presented.ideal new diagnostics are more rapid, less expensive, and more accurate than existing diagnostics. unfortunately, not all new diagnostics meet all these criteria, with cost often being high. to address this situation, outcomes studies evaluating new diagnostics have assumed an important role. outcomes that should be addressed include antibiotic and further test avoidance, patient outcomes (e.g., length of stay, morbidity, mortality), patient and provider satisfaction, and infection transmission. results of outcomes studies then need to be used to inform the development of practice guidelines for use of these tests (which may vary from practice-to-practice) and also to inform ideal reconfiguration/development of tests by diagnostics companies. our experience with a recent randomized controlled clinical trial evaluating a rapid multiplex naat for testing positive blood culture bottles will be presented.it is an exciting time for diagnostics, with new technologies and opportunities for studies to determine how best to use these technologies in patient care. div. infectious diseases, dept. internal medicine, the catholic university of korea, koreasepsis is a significant syndrome in medicine and one of a major contributing cause of death world-widely.prompt recognition and aggressive management is the key element of improving survival from this brutal disease. unfortunately, sepsis is very complex immunologic event according to etiology and individuals' characteristics. as a result, a degree of organ dysfunction result from sepsis, an effect of protocolized treatment, and outcome could not be same.resuscitation with fluid and vasopressors is an initial and essential treatment of severe sepsis and septic shock. surviving sepsis campaign (ssc) continues to revise the treatment guideline and the initial steps for treatment are converged to use crystalloid fluid and use norepinephrine to whom do not respond to fluid therapy. in , rivers et al suggested protocolized quantitative resuscitation method, otherwise known as early goal-directed therapy (egdt). this method was attractive in hospital settings because of clear notification of parameters, target, and drugs. the uncertainty of the effect of the individual component of bundle approach in treating severe sepsis/septic shock has been debated and egdt has been challenged following the failure to show a mortality reduction in subsequent large multicenter randomized controlled trials. effective fluid resuscitation means an effective restoration of tissue perfusion. although mean arterial pressure (map) can be a representative marker of tissue perfusion, central venous pressure (cvp) and serum lactic acid do not. as you already know, we do not have precise parameters of individual patient's hemodynamic status and also evaluating an effect of therapy we do. what is the proper volume of resuscitating fluid and how to monitor are also important issues we should have interest? although the crystalloid fluid is recommended as an initial therapy of resuscitation, the benefit, and harm of colloidal fluid, and alternative fluid is still evaluating.vasopressor therapy is needed to who do not respond fluid resuscitation. but there are many unresolved questions such as target map, optimal timing, and duration. norepinephrine has been recommended since the first ssc guideline, because more potent and effective at reversing hypotension, and less adverse events compared to dopamine. epinephrine and vasopressin are regarded as next-line or partner drug with norepinephrine. the effect of other vasopressors such as angiotensin ii and endothelin- are evaluating.medical experience clearly says that fluid resuscitation and vasopressor are very essential and initial element to improve the survival of the sepsis and septic shock patients. but we do not exactly know how to do accurately and properly. i will briefly present the current consensus and controversies about fluid resuscitation, monitoring of patient's hemodynamics, and use of vasopressors in septic patients in this lecture. the antimicrobial stewardship program (asp) is recognized as the most important tool for proper use of antibiotics. however, in order to properly implement asp, systematic training and tools are needed for medical staff prescribing antibiotics.basic education consists of face-to-face training for medical staffs. however, face-to-face education alone is difficult to maximize its effectiveness. when medical staffs prescribe, a variety of tools are being used to prescribe antibiotics properly.the most basic program is the antibiotic prescription restriction program. this program is a system that antibiotics which can only be used for certain resistant strains in hospitals are used with the permission of an antibiotic manager (usually an infectious diseases specialist).most hospitals in korea with infectious diseases specialists have this system. the infectious disease division of hallym universuty kangnam sacred heart hospital have a list of restricted antibiotics that contain vancomycin, linezolid, carbapenem, piperacillin/tazobactam, tigecycline, liposomal amphotericin b, echinocandin, voriconazole as restricted antibiotics.since the s, antibiotic prescription programs have been introduced in korea and used in various hospitals. the purpose of this program is to recommend appropriate antibiotics according to the impression at the time of admission to the patient. when the causative bacteria are cultured, they help to prescribe appropriate antimicrobial agents according to the cultures. advanced programs automatically adjust the antibiotic dose according to the renal function. the number of antibiotic doses is also automatically recommended. when antibiotics need to be mixed with other solutions, it is automatically recommended that the solutions be mixed.currently, these antibiotic prescription programs have begun to apply the learning function of artificial intelligence and recommend antibiotics that frequently used depending on the name of diagnosis. if you are using antibiotics which could be expected to be drug interactions, you can also show alarms via pop-ups.in , the korean society for chemotherapy developed a mobile app to help prescribe antibiotics. from to , the korean society of chemotherapy and korea cdc (center for disease control and prevention) are conducting this project together. the antibiotic program is a collaborative project with hospital and clinic antibiotic prescription programs.this lecture will discuss antibiotic prescription programs used in korea and discuss the developmental direction of this program. key: cord- -tx hirm authors: whiteside, james l; whiteside, john w title: acute bronchitis: a review of diagnosis and evidence-based management date: - - journal: primary care update for ob/gyns doi: . /s - x( ) - sha: doc_id: cord_uid: tx hirm abstract obstetricians and gynecologists are increasingly involved in primary care. acute bronchitis is among the most common ambulatory complaints. although the cause of acute bronchitis is predominantly viral, – % of patients presenting with this condition are treated with antibiotics. because of the increasing bacterial resistance to antibiotics, the cost of prescription drugs, and the potential adverse reactions to them, the present management of acute bronchitis has important shortcomings. also, inhaled bronchodilators are underused for symptomatic management. improved awareness among physicians about the recommended management of acute bronchitis has been targeted as an important means of decreasing unnecessary antibiotic use. patient satisfaction motivates physicians to prescribe antibiotics in managing acute bronchitis. however, patient satisfaction does not necessarily correlate with prescribing of antibiotics but rather with patient education. we present a review of the diagnosis and differential diagnosis of acute bronchitis and its management. the practice of obstetrics and gynecology in the united states is in transition. a key feature of this transition is enhanced emphasis on primary care. acute bronchitis is a common problem for primary care physicians, representing roughly the ninth most common health problem encountered in an ambulatory setting. , in a recent survey, more than % of those obstetricians and gynecologists surveyed independently manage acute upper respiratory tract infections (uris), and nearly % manage acute lower respiratory tract infections without aid of consultation. more common and apparently insignificant disorders such as acute bronchitis are often overlooked in physician training; yet management of acute bronchitis has been shown to often be inappropriate, even among internists and family practitioners. acute bronchitis accounts for an estimated to million physician visits per year in the united states. , , in , upper respiratory tract illness and acute bronchitis precipitated . million emergency department visits, making them the leading infection-related cause for emergency department visits in the united states. although acute bronchitis is caused by a virus in nearly % of patients, % of patients with symptoms of acute bronchitis are given prescriptions for antibiotics. , thus, acute bronchitis is among the most important targets for decreasing inappropriate antibiotic use in ambulatory practice. from $ to $ mil-lion annually is spent needlessly in the united states to treat acute bronchitis, regardless of the risks incurred from increased microbial resistance and potential antibiotic side effects. also, effective treatments for cough associated with acute bronchitis are underused, further contributing to its societal costs. obstetricians and gynecologists should be adept at diagnosing and managing acute bronchitis to practice effective primary care medicine and limit public costs. we review the cause, diagnosis, and evidencebased management of acute bronchitis. in addition, we consider the barriers to evidence-based management of acute bronchitis. acute bronchitis was described originally in as inflammation of the mucous membranes of the bronchi. today, it is still thought of as inflammation of the airways in response to infection. specifically, mucous membranes of the tracheobronchial tree become hyperemic and edematous, with increased bronchial secretion and impaired mucociliary function. , in addition, airway reactivity and resistance are heightened, not unlike in asthma, manifesting as a cough or signs of bronchial obstruction such as wheezing or dyspnea on exertion that can persist up to weeks. , unlike the case in asthma, the in-flammatory changes of the tracheobronchial tree found in acute bronchitis are transient and resolve with clearance of the infection. infectious agents, in most cases, are the same respiratory viruses associated with the common cold, such as rhinovirus and coronavirus, but include more invasive viruses such as adenovirus and influenza virus. other less common viral causes of acute bronchitis include measles virus, respiratory syncytial virus, parainfluenza virus, and herpes simplex virus. nonviral causes of acute bronchitis represent less than % of cases and include bacteria and inhaled lung irritants. mycoplasma pneumoniae, bordetella pertussis, and chlamydia pneumoniae (taiwan acute respiratory strain) are the accepted bacterial causes of acute bronchitis. , the role of streptococcus pneumoniae or the haemophilus species in acute bronchitis is unclear because these organisms may represent transient indigenous flora of the upper respiratory tract. results of spirometric studies done in patients with acute bronchitis mirror the results of studies in patients with mild asthma. in one study, % of patients had spirometric studies, such as forced expiratory volume in second (fev ), peak flow value, and mean forced expiratory flow between % and % of forced vital capacity (fef %- % ), in which the values were less than % of the predicted values. patients in whom acute bronchitis is diagnosed are more likely than normal subjects to have the diagnosis of asthma in the future, despite the aforementioned spirometric abnormalities having been shown to be reversed after weeks. , this suggests that many patients with acute bronchitis may actually have an irritable airway that reacts to common triggers such as uris. despite being a common ambulatory complaint, acute bronchitis lacks precise diagnostic criteria. acute bronchitis is a clinical diagnosis, and physicians would have better agreement on treatment if the consensus on diagnosis were better. even among family physicians, the diagnostic criteria used to identify acute bronchitis vary considerably. current textbooks and studies of acute bronchitis have varied in their descriptions; yet most physicians think that acute bronchitis is distinguished by the presence of cough with accompanying clinical features of a uri such as rhinorrhea and sore throat. clinically, a better definition might be acute onset of cough without a history of chronic pulmonary disease or evidence of pneumonia or sinusitis. this definition highlights the first two steps for treatment: ) identify patients who have chronic pulmonary disease or other coexisting medical illnesses such as congestive heart failure or immunosuppression and ) appropriately rule out other causes of acute cough, such as pneumonia and sinusitis. after this has been done, the bulk of outpatient presentations of acute cough will be from "uncomplicated acute bronchitis," which has a nonbacterial cause in more than % of cases. on the basis of pathophysiologic findings in acute bronchitis, symptoms of airway obstruction would be expected. cough, either dry or productive with a clear to yellowgreen sputum; chest tightness; or burning with or without wheezing are all commonly associated with acute bronchitis. as expected for a viral syndrome, characteristic symptoms also include headache, low-grade fever, rhinorrhea, sore throat, malaise, and myalgia. the cough, which often is worse in the morning and disrupts sleep, typi-cally lasts between and days. however, it can persist for more than a month in up to % of patients. physical examination may show signs of airway constriction such as wheezing or prolongation of the expiratory phase, but this sign is inconsistent. to elicit wheezing, auscultation of patients during forced expiration in a prone position has been recommended. patients with acute bronchitis would not be expected to have focal changes on auscultation, such as crackles, fremitus, or egophony. diagnostic studies cannot be recommended routinely because no available test can lead to definitive diagnosis of acute bronchitis. studies are used mainly to rule out other diseases included in the differential diagnosis. for example, chest radiographs may be useful for patients with suspected pneumonia. a productive cough, either purulent or otherwise, is not predictive of bacterial infection, and microscopic examination or culture of sputum is nearly always unrevealing. spirometric studies, although potentially abnormal during an episode of acute bronchitis, should be performed only when asthma or chronic obstructive lung disease is suspected and then only after resolution of the acute illness. the loose definition of "acute bronchitis" as cough in the presence of other respiratory symptoms leaves room for its inappropriate use by clinicians. during the examination, other potential causes of cough must be considered. an important cause of acute and chronic cough is postnasal drip. this is not associated with airway inflammation and can result from viral uris, acute sinusitis, or allergic rhinitis. patients with pneumonia can also present with cough associated with fever, wheezing, and malaise. how-ever, these patients usually have focal changes on lung auscultation and radiographs. clearly, patients with asthma and many of those with chronic obstructive lung disease are predisposed to the development of obstructive airway symptoms in response to common triggers such as uris. patients with lung neoplasms and congestive heart failure exacerbations can present with a new cough and dyspnea. inhalation of toxic or irritating substances such as air pollution, ammonia, chlorine, sulfur dioxide, nitrogen dioxide, or ozone can also lead to airway irritation and cough. other more chronic causes of cough include cystic fibrosis, gastroesophageal reflux, and medications such as angiotensin-converting enzyme inhibitors. clearly, the differential diagnosis for acute cough includes many diseases that are not selflimited and some that may be lifethreatening. these alternative diagnoses must be considered in all patients and an appropriate evalua t i o n m u s t b e p e r f o r m e dparticularly in those older than years of age with marked lung impairment or those who have a poor performance status with other coexisting medical conditions. for the patient who presents with acute onset of cough and no history of chronic pulmonary disease or evidence of other more serious illnesses, studies have consistently shown either no benefit or, at best, modest benefit from the use of antibiotics. this benefit, where evident, has shortened the duration of cough or sputum production by approximately day. for an illness that spontaneously resolves in to days, this cannot be regarded as a substantial benefit. the value of this benefit is further challenged by the cost of antibiotics, the risk of adverse effects, and the negative consequences on antibiotic resistance patterns among bacteria colonizing the individual patient and existing at large. some studies have identified subgroups in which antibiotics might have a justifiable benefit. data are weak, but authors of recent metaanalyses have suggested that patients older than years of age and those without coryza and sore throat may benefit from antibiotic therapy. least likely to benefit are those whose symptoms have been present for less than week and whose cough is accompanied by uri symptoms. on the basis of microbiologic findings of acute bronchitis, it is not unexpected that antibiotics would have little benefit. however, antiviral agents are available for treating influenza, and this pathogen is frequently associated with acute bronchitis. these antiviral agents include neuraminidase inhibitors such as oseltamivir and zanamivir, as well as amantadine and rimantadine. the major advantage of neuraminidase inhibitors is their activity against influenza b. however, although patterns change yearly, % of reported influenza cases in the - season were from influenza a. although it would seem that these agents would hold great promise for the treatment of a primarily viral illness, their usefulness in the treatment of acute bronchitis is hindered severely by their weak efficacy against influenza in general. also, these drugs are relatively expensive and, historically, physicians have been poor at accurately predicting the presence of influenza, even at the height of a seasonal epidemic. these agents have been shown to decrease the duration of influenza symptoms by about day, but only if the treatment is initiated within the first hours of the symptomatic period. , however, because of problems with cost, poor efficacy, and difficulties with accurate diagnosis of influenza, these agents cannot be recommended for routine treatment of acute bronchitis. patients with acute bronchitis desire treatment of their symptoms and, in particular, relief from coughing. albuterol has been studied as a treatment for acute bronchitis and has inconsistently demonstrated benefit in decreasing the duration and severity of cough. a meta-analysis of the studies by the cochrane collaboration is currently ongoing. preparations containing dextromethorphan and codeine and humidification of the airways may slightly improve the cough of acute bronchitis, but there is little supporting evidence for this. decongestants may also help a cough precipitated by postnasal drip. patients often perceive antibiotics as a panacea and seek an antibiotic prescription at any sign of potential infection. physicians are generally aware of this and feel obliged to comply with this perceived demand. failure to comply leads to patient dissatisfaction, and ultimately it may lead a patient to seek care from another provider. furthermore, to the individual physician, the negative effect of antibiotic overuse is difficult to appreciate. clinicians do prescribe antibiotics in response to patient expectations. the assumption, however, that patients are more satisfied with an antibiotic prescription is false. hamm et al. found no association between patient satisfaction and prescriptions for antibiotics among patients seeking care for respiratory infections. instead, educating patients about the cause of their ailment and spending time with them correlated with patient satisfaction. gonzales et al. reinforced this finding by comparing antibiotic prescription rates for acute bronchi-tis with a baseline period and a study period at four primary care practices. they found that antibiotic use decreased in practices that provided education and clinical contact to patients. an examination of factors associated with an antibiotic prescription for acute bronchitis showed that physicians respond to clinical factors such as cough, sputum production, pharyngeal erythema, and cervical lymphadenopathy. because these signs and symptoms are equally common in patients with and those without pneumonia, physicians appear to prescribe antibiotics based on the diagnosis of acute bronchitis alone. , this pattern is remarkable given the abundant information urging physicians to refrain in most instances from prescribing antibiotics for this condition. even more disappointing is that physicians nationally are more likely to prescribe antibiotics for cough to patients who are white, non-hispanic, and younger than years, a population arguably least likely to benefit from such an intervention. the risk to the individual and to the community from the rise in antibiotic resistance is also important. the cause for this rise is multifactorial; however, selective pressure of frequent antibiotic use encourages resistant strains to multiply and spread. for example, it has been demonstrated in daycare centers that previous antibiotic use is the most consistent factor for carriage of penicillin-resistant pneumococcus. before the mid- s, virtually all strains of streptococcus pneumoniae were sensitive to penicillin. today, in some areas of the country, more than % of s. pneumoniae isolates demonstrate an intermediate to high level of resistance to penicillin. usually, these strains are also resistant to other antibiotics such as macrolides, trimethoprim-sulfamethoxazole, and cephalosporins. the risk of adverse effects is at least as important as the benefit associated with the use of antibiotics. recent meta-analyses have shown that with antibiotic use, the "number needed to harm" ranges from to , whereas the "number needed to treat" ranges from to . , this means that the use of antibiotics for treating acute bronchitis is almost as likely to result in adverse effects as it is to result in reducing cough. in fact, all three recent meta-analyses on the topic concluded that routine antibiotic treatment for acute bronchitis in adults is not justified. , , acute bronchitis is an important medical problem that is commonly seen in an ambulatory care practice. despite a predominantly viral cause and numerous randomzied controlled studies documenting no meaningful benefit from antibiotics, more than % of patients presenting with acute bronchitis are given antibiotic prescriptions. consequently, penicillin resistance of s. pneumoniae and other bacteria has increased, prompting requests to reduce unnecessary antibiotic use. diagnosis and management of this problem are flawed, even among providers most involved in ambulatory medicine. obstetricians and gynecologists are increasingly involved in providing primary care and should be knowledgeable about the evidence regarding the cause and management of acute bronchitis. antibiotics for acute bronchitis (cochrane review) current management of acute bronchitis in ambulatory care: the use of antibiotics and bronchodilators primary care by obstetricians and gynecologists: attitudes of the members of the south atlantic association of obstetricians and gynecologists antibiotic prescribing for adults with colds, upper respiratory tract infections and bronchitis by ambulatory care physicians how do we achieve cost-effective options in lower respiratory tract infection therapy? airway infection antibiotic prescribing for patients with colds, upper respiratory tract infections, and bronchitis: a national study of hospital-based emergency departments acute bronchitis diagnosis of acute bronchitis in adults: a national survey of family physicians pulmonary function test in acute bronchitis: evidence for reversible airway obstruction an association between acute bronchitis and asthma principles of appropriate antibiotic use for treatment of uncomplicated acute bronchitis: background factors associated with antibiotic use for acute bronchitis antibiotics in acute bronchitis: a meta-analysis efficacy and safety of the oral neuraminindase inhibitor oseltamivir in treating acute influenza: a randomized controlled trial neuraminidase inhibitors for preventing and treating influenza in healthy adults (cochrane review) treatment of acute bronchitis in adults without underlying lung disease antibiotics and respiratory infections. are patients more satisfied when expectations are met? decreasing antibiotic use in ambulatory practice: impact of a multidimensional intervention on the treatment of uncomplicated acute bronchitis in adults clinical prediction rule for pulmonary infiltrates national trends in the use of antibiotics by primary care physicians for adult patients with cough drug resistant streptococcus pneumoniae: kentucky and tennessee are antibiotics effective treatment for acute bronchitis? a meta-analysis antibiotics for acute bronchitis (cochrane review) quantitative systematic review of randomised controlled trials comparing antibiotic with placebo for acute cough in adults key: cord- -gryp khc authors: edwards, m. r.; walton, r. p.; jackson, d. j.; feleszko, w.; skevaki, c.; jartti, t.; makrinoti, h.; nikonova, a.; shilovskiy, i. p.; schwarze, j.; johnston, s. l.; khaitov, m. r. title: the potential of anti‐infectives and immunomodulators as therapies for asthma and asthma exacerbations date: - - journal: allergy doi: . /all. sha: doc_id: cord_uid: gryp khc asthma is responsible for approximately , deaths annually in europe despite available medicines that maintain asthma control and reduce asthma exacerbations. better treatments are urgently needed for the control of chronic asthma and reduction in asthma exacerbations, the major cause of asthma mortality. much research spanning > years shows a strong association between microorganisms including pathogens in asthma onset, severity and exacerbation, yet with the exception of antibiotics, few treatments are available that specifically target the offending pathogens. recent insights into the microbiome suggest that modulating commensal organisms within the gut or lung may also be a possible way to treat/prevent asthma. the european academy of allergy & clinical immunology task force on anti‐infectives in asthma was initiated to investigate the potential of anti‐infectives and immunomodulators in asthma. this review provides a concise summary of the current literature and aimed to identify and address key questions that concern the use of anti‐infectives and both microbe‐ and host‐based immunomodulators and their feasibility for use in asthma. research in asthma over the last years or more repeatedly shows an overwhelming link between the actions of microorganisms and asthma. , from acting as direct pathogens, to educating the immune system and preventing opportunistic pathogen colonization through occupying specific niches, it is now well accepted that viruses, bacteria and fungi are positively associated with asthma onset, , asthma severity, , asthma exacerbation (ae) , and asthma management and even secondary prevention strategies of asthma (summarized in table ). despite these important associations, the use of antiinfectives (antibiotics, antivirals, antifungals, vaccines) that specifically target known pathogens, or drugs that are based on or exploit microbe-host receptor interactions (toll-like receptor agonists, bacterial lysates) or are immunomodulators (vitamin d), and/or may work in part by altering our associated microbiology (probiotics) are, with the exception of severe asthma, seldom considered in asthma treatment, prevention and guidelines. these treatment options are summarized in figure . task force on anti-infectives in asthma was initiated in to ask open questions about the potential use of anti-infectives and immunomodulators as treatments for asthma and ae. we thus provide a thorough review of the field ( table for search methods and terms), and specifically, have considered several important points in relation to the use and implementation of anti-infectives in asthma, thus identifying important challenges for the field. in our investigation, we chose to include any such studies of treatment that is based on microorganisms or host molecules, or exploits microbe-host interactions and thus alters the host response or microbiome. in this review, we offer our findings on the above points and consider the role of anti-infectives, immunomodulators and alteration of host microbiology in both asthma development and ae. we include findings from recent clinical trials and discuss the relative merits of these approaches in the light of the many challenges facing asthma research and the state of the art of the field. this review thus provides important insights aimed at young researchers and clinicians and also experienced researchers in the field to inform and stimulate scientific discussion of this important topic. overall, antibiotic use is associated with asthma risk rather than protection at most stages of human development, including pregnancy, , early life and childhood, although why this is so is a subject widely debated. in denmark, antibiotic use in pregnancy use was shown to increase risk of ae in five-year-old children by twofold if used in the third trimester. antibiotic exposure in foetal life was associated with an increased risk of asthma in cohort analyses, and this association more than tripled if antibiotics were used to treat respiratory tract infections rather than antibiotics used for either urinary tract or skin infections. these associations decreased, however, when sibling analysis was included (when nonaffected siblings are used as controls). early antibiotic use is also believed to increase asthma risk by two-to threefold in seven-to eight-year-olds. t a b l e common respiratory tract pathogens linked with asthma and ae. this aspect of the field has been thoroughly reviewed elsewhere can produce aerosolized allergen common in asthma epidemics associated with thunder storms, involved in severe asthma with fungal sensitization (safs) the potential negative impact of antibiotics was explored in a birth-cohort study at age from manchester, united kingdom. there was a significantly higher risk of physician-confirmed wheezing after antibiotic prescription and a twofold increase in severe wheeze or ae after antibiotic prescription. in children who wheezed, the risk of ae and admissions to hospital were also significantly increased in the years after the first antibiotic prescription. children who received antibiotics in infancy had significantly lower induction of cytokines from pbmcs (taken at age ) stimulated ex vivo with viruses, but surprisingly, not bacteria. the authors concluded that an increased susceptibility to viral infections is associ- the microbiome describes the bacteria, fungi and other microorganisms that are present in the environment and co-exist within our bodies. the respiratory microbiome can now be studied by s rrna sequencing, and certain microbial phyla or genera are thought to be harmful or protective. , antibiotics may negatively affect bacterial ecology in early life and this in turn affects asthma development. in retrospective studies, the association between antibiotic use and increased risk of asthma or wheezing in children is further confused due to the potential of reverse causation. , in experimental animals, the negative impact of antibiotics has already been shown, and long-term oral antibiotic treatment affects the gut microbiome, which in turn affects lung immunity to influenza virus. indeed, how diet and the gut microbiome affect mucosal immunity including respiratory immunology is now a subject of wide interest; , hence antibiotics through regulating the gut microbiota thus directly affect f i g u r e summary of anti-infectives, immunomodulators and microbiome modulators and their methods of action. anti-infectives (such as antibiotics, antifungals and antivirals) directly act on the pathogen or its receptor limiting infection or replication. vaccines work by boosting both innate and importantly, adaptive immune responses (provided by dendritic cells, t and b lymphocytes) to the pathogen providing longlasting protection. immunomodulators including tlr agonists, bl, vitamin d act on the immune system, boosting innate immune responses providing short-term protection. vitamin d may act on underlying immune responses, such as inflammatory responses or allergic inflammation, reducing pathogen-driven inflammation or pathogen-driven enhanced allergic inflammation. microbiome modulators such as probiotics may alter the microbiome of the gut. this may have important downstream effects on the immune system, such as those that affect respiratory immunology and asthma the development of the immune system. the potential of antibiotic-induced changes in the developing microbiome to be directly responsible for asthma or ae risk is yet to be formally proven, however. macrolide antibiotics are a class of antibiotic commonly prescribed for respiratory tract infections or inflammatory respiratory disorders. macrolides may have additional properties to their bacteriostatic function, such as anti-inflammatory and even antiviral activity. , despite their ability to inhibit both bacteria and virus infections, only a few studies have tested macrolides as therapies for asthma or ae. guidelines state very little on macrolide use in asthma, and studies have shown positive effects on severe and neutrophilic asthma, yet the evidence supporting this is conflicting. these studies in both stable asthma and ae have been recently reviewed, and the data suggest macrolide-responsive subgroups (eg neutrophilic asthma) may exist. , additionally, recent studies also report a reduction in severe lrti rates and asthma-like symptoms antibiotics are associated with asthma risk and their use should be discouraged for asthma or wheeze-like illnesses. a possible explanation for this association is that antibiotics affect the microbiome in a negative way and thus increase susceptibility to disease. with the realization that the microbiome is key in controlling host immunity early in life, and the design of supportive animal studies that have modelled this association and identified protective genera, this idea has merit but the overall hypothesis remains to be thoroughly tested in human clinical models. antibiotics may also be associated with asthma via other, as yet to be identified mechanisms, and likely involve reverse causation. the narrower antibacterial spectrum of some macrolide antibiotics, combined with their other advantageous properties, suggests that these may have use in ae but their use remains controversial. the prophylaxis with intramuscular/intravenous antibody palivizumab has been shown to effectively decrease respiratory syncytial virus (rsv)-induced bronchiolitis-related hospitalization, need for mechanical ventilation and recurrent wheezing. interestingly, it has also decreased recurrent wheezing induced by other viruses postbronchiolitis. the second-generation monoclonal antibody motavizumab has also markedly reduced hospitalization with rsv. but the development programme has been discontinued. only a few patients benefit from the m ion channel inhibitors, amantadine and rimantadine, drug resistance is high, and they have significant adverse events. neutralizing antibodies against rsv, coronaviruses and influenza viruses are being developed. inhibiting virus replication through interfering with viral enzymes active within cells poses additional problems in drug discovery; however, several useful inhibitors for respiratory tract viruses have found their way into phase i/ii clinical trials. few, however, have been specifically tested in asthma. favipiravir is a novel antiviral compound that selectively and potently inhibits the rna-dependent rna polymerase of many rna viruses including influenza virus, enteroviruses and paramyxoviruses. a phase iii clinical trial of favipiravir for influenza therapy has been just completed in japan and the united states. rupintrivir is a potent, irreversible inhibitor of rv c protease. it has a broad antipicornaviral spectrum, but the development programme has been discontinued. the nucleoside inhibitor ribavirin is a synthetic purine nucleoside analogue exhibiting antiviral activity against a broad range of both dna and rna viruses in vitro. it is the only antiviral agent currently available against rsv infection, but its use has many concerns. als- is an oral rsv replication inhibitor (a cytidine nucleoside analogue). in randomized, double-blind, clinical trial in healthy adults inoculated with rsv, more rapid rsv clearance and a greater reduction in viral load were observed in the groups of patients treated with als- than in the placebo group. small interfering rna (sirna) infected with wild-type rsv. it was well tolerated, effective as well as decreased the incidence and progression of bronchiolitis obliterans syndrome in lung transplant recipients with naturally occurring rsv infection. the development of cidofovir and its derivative, brincidofovir, broad-spectrum antivirals active against five families of dsdna viruses (including adenoviruses), are currently in phase iii clinical trials. the neuraminidase inhibitors prevent influenza virus release from infected cells and infection of adjacent cells. oral oseltamivir and inhaled zanamivir are recommended for the treatment and chemoprophylaxis of influenza in children and adults. inhaled laninamivir has shown good safety and efficacy profiles in the treatment for influenza in patients with chronic respiratory tract diseases and has been approved in japan. single dose of intravenous peramivir has been shown to be noninferior to oseltamivir and to have good safety profile also in patients with chronic respiratory tract diseases. biologically, interferons (ifns) are induced within hours of infection and consequently induce the expression of hundreds of antiviral effecter molecules blocking virus replication. the effectiveness of itraconazole in the treatment for abpa has been confirmed in two randomized, placebo-controlled trials , leading to the recommendation for azole use in asthma-abpa by the cochrane collaboration. pooled data from these studies suggest itraconazole is effective in around % of asthma-abpa patients. newer triazoles including voriconazole and posaconazole have also been studied in abpa with promising results. however, the greater incidence of drug toxicity with voriconazole, and substantial financial costs of both voriconazole and posaconazole limit their current widespread use. more recently, the use of azoles has also been studied in safs. in the first such study by denning et al, subjects with over half having to discontinue treatment due to bronchospasm. consequently, the prospect of amphotericin b use in asthma remains unlikely. the majority of reports to date have investigated the use of antifungal agents in adult asthmatics; however, the potential for their use in children has also been highlighted in a recent paediatric study describing sensitization to fungal allergens in % of severe asthmatic children. unfortunately, reports of azole use in asthmatic children are limited to a few subjects only leading to the current joint ers/ats guideline recommending the consideration of treatment only after detailed evaluation in a specialist severe asthma centre. in summary, to date, there have only been a handful of placebo-con- heterogeneity of asthma continues to develop, it is possible that subgroups within abpa/safs will emerge in whom treatment with antifungal therapy will be predictably beneficial. however, we still remain some distance away from this goal at present. influenza infections can precipitate acute aes and may be more severe among asthma patients more studies are needed to validate these findings. a comparison of laiv with tiv also failed to show significant differences in ae numbers in adults or children (> years). thus, the potential role of influenza vaccines in ae prevention requires further in-depth study, in virologically confirmed influenza and with improved definition and characterization of asthmatic subgroups. aes. three large cross-over trials show no evidence of increases in aes in the two weeks following tiv in adults or children. concerns that laiv could increase aes, wheezing episodes and hospitalizations in children were allayed the absence of an association of laiv with ae in high-risk children. f i g u r e challenges and unknowns facing new treatments for asthma exacerbations that target respiratory pathogens. challenges facing the design and implementation of therapies that directly target pathogens or their biology (in blue) include site of infection and site of drug delivery, route of delivery, specific mechanism of action, the drug's pharmacodynamics (pd) and pharmacokinetics (pk) and also the patient demographic (pt), subset or specific endophenotype of asthma concerned. these challenges can at least in part be addressed by preclinical studies and are often taken into account during drug design. unknowns are also identified (in red) and can be model or pathogen specific. these include, but are not limited to, the window of therapeutic opportunity (dt) for therapeutic treatments, which defines the time between infection and onset of clinical disease (lrti symptoms for asthma), and importantly, this variable thus describes the window in which suppressing replication in theory will suppress symptoms and/or clinical disease. how pathogen load affects clinical disease is also controlled by a second variable (dl), which defines the quantity of pathogen that has to be affected to observe a quantitative change in clinical disease or symptoms. the unknown c defines a comparison, between a new drug (eg antiviral) versus the standard treatment (eg gc). this unknown is important as regulatory authorities will not approve a new drug if does not show improvements or a better safety profile compared with the standard treatment already available. the unknown d represents duration of treatment; this takes into account other variables that are often difficult to predict and include the possible effects of secondary infections (eg bacterial co-infection), drug resistance (eg as seen with macrolides), plasticity of endophenotype treated and other complexities that can impact on clinical disease after pathogen load is decreased as defined by dl. theoretical relationships between pathogen and load and clinical disease are based on human challenge studies with rv, in asthmatic individuals , the presence of streptococcus pneumoniae (pneumococcus) has been linked to ae, and in children, early-life pneumococcal colonization is associated with an increased risk of wheezing and asthma later in childhood. furthermore, asthma is a risk factor for invasive pneumococcal disease (ipd), warranting pneumococcal vaccination, which is recommended for all people with asthma over years of age if they did not receive routine childhood pneumococcal immunization. the there has been concern over potential pro-allergic and pro-asthmatic effects of childhood immunizations, in particular regarding measles, mumps and rubella vaccine (mmr). however, the suspected association between mmr and asthma (since been discredited) was based on a small study comparing anthroposophic to nonanthroposophic children and was not confirmed in a subsequent multinational study in these populations. a wealth of studies has also failed to show evidence of pro-asthmatic effects of vaccination against poliovirus, pertussis, tetanus, hepatitis b or haemophilus influenzae. in contrast, significant evidence suggests antiasthmatic effects of childhood vaccinations. inverse associations between childhood asthma prevalence and high cumulative vaccine doses, pertussis vaccination and mmr have been found and reduced asthma hospitalization rates and medication use in mmr-vaccinated children. the immunogenic potential of different vaccine formulations in asthma has been questioned, but normal antibody responses to pertussis, varicella, hepatitis b, measles and rubella vaccination have been reported. mumps antibody titres after mmr were lower and measles antibodies waned more quickly from years of age in asthmatics. treatment with inhaled glucocorticoids (gcs) did not affect the antibody response to hepatitis b or varicella immunization, but these were impaired by oral gc therapy. the vaccinations discussed are safe and effective in asthma, may help prevent asthma development, and pneumococcal and annual influenza vaccination in particular should be offered to asthmatics. future vaccines against rv and rsv, which are the main triggers for aes and have been linked to asthma inception, should help reduce asthma morbidity and mortality. host responses bacterial lysates (bl) have been extensively used in europe to effectively reduce the number of seasonal acute respiratory illnesses (ari). bl are microbial products that when given orally, may exhibit certain immunostimulatory and immunomodulatory effects. their effectiveness was confirmed in numerous interventional trials (reviewed in ref. ) . bl have been successfully tested in preventing wheezing attacks provoked by aris in preschool children demonstrating a % reduction in symptomatic wheezing and a decrease in the number of urti. there is only one interventional clinical study to date, demonstrating a promising antiallergic potential of an orally applied bl. therefore, one may speculate that bacteria-derived preparations may become an interesting class of immune modulators for the future. recognition of invading microbes is controlled by a range of innate pattern recognition receptors including tlrs which are directed at highly conserved molecular motifs expressed on the invading pathogen. this ancient surveillance network provides a form of first line of defence in the airway. signalling through tlrs produces a broad range of pro-inflammatory cytokines, chemokines and importantly, antimicrobial proteins. therefore, precise targeting of individual tlr pathways could provide a mechanism of promoting specific immunity, allowing for tailored immunomodulation, an approach that is highly attractive in chronic diseases such as asthma where numerous immunological disparities are evident. withdrawal of inhaled gcs whilst asthma conditions remain stable or even improved. the proposed mechanism is the restoration of the th /th balance. however, supporting evidence is yet to be provided. a follow-up, double-blind, placebo-controlled study carried out in poorly controlled, moderate-to-severe asthmatics where cyt a was administered as an add-on to current gcs and b agonist therapy showed no significant advantage over placebo in relation to the primary outcome of change from baseline in asthma control questionnaire (acq) or in secondary outcomes of change from baseline in prebronchodilator forced expiratory volume (fev ). these data suggest that whilst cyt a may have a use in initial control of disease in gc-sensitive patients, it has no efficacy as an add-on therapy for more severe patients. in addition, more prolonged administration of the tlr agonist, assessing its ability to readdress the supposed th skewing, was not conducted. additional concerns stem from recent reports of potential impairment of tlr function in pbmcs in severe asthmatic patients. evidence is accumulating on the potential of vitamin d in immunoregulation, particularly in lymphocyte function and cytokine production, suggesting its potential in modifying asthma incidence and severity. the association between low levels of vitamin d and asthma has been supported by many observational and epidemiologic studies. a recent meta-analysis of epidemiological studies demonstrated a positive association of vitamin d deficiency and asthma (rr . % ci . - . ). parallel-conducted, prospective, observational studies on vitamin d supplementation in infancy, however, showed rather conflicting data and do not support these implications. other studies in pregnant woman, including two large clinical trials, did not find protective effects on offspring wheeze. , interpretations of existing evidence argue an advantage of vitamin d supplementation. however, interventional trials in infants receiving both pre-and probiotics in allergy and/or asthma prevention provided equivocal results. whilst moderate positive effects in infant eczema were found, a lack of evidence that probiotics prevent any other allergy including asthma in three other similar meta-analyses remains a matter of concern. [ ] [ ] [ ] in view of two well-conducted meta-analyses, an opportunity of asthma/wheezing prevention with probiotics seemed to not be plausible. , one may speculate, however, that the studies to date may not have used the right probiotic, the right dose, the right timing or duration and/or population. therefore, more studies are still needed. evidence to date suggested that modulation of the gut microbiome may represent an interesting therapeutic or preventative opportunity for the prevention of allergic asthma and ae, whilst clinical trials do not confirm initial enthusiastic expectations. in view of the recent systematic reviews, probiotics cannot be recommended as adjunctive therapy for asthma or asthma prevention. though, recent technological developments that permit identification of the most promising microbial strains and their products that may exhibit more profound positive effects will keep this area active and interesting to follow. with the exception of antibiotics and antifungals, current guidelines do not take into account the potential of specific or broader-spectrum anti-infectives or immunomodulatory agents in asthma or ae. despite wide interest and active research in this area, the basis for this is likely due to a lack of clinical studies that allow robust or clear conclusions to be made regarding efficacy. for the clinical studies that have been performed with available anti-infectives or immunomodulatory agents, conclusions are often contradictory or show a lack of robust evidence supporting an effect. reasons for these outcomes include a small number of studies, differences in study design making direct comparisons difficult or studies that are underpowered for primary or secondary endpoints, or subgroup analysis. as shown in table there is also a substantial body of literature investigating preclinical development of anti-infectives and immunomodulatory drugs and preparations in animal models, with many studies endeavouring to better understand the scientific principles behind their mechanism (s) of action. this is an absolute necessity in the anti-infective drug discovery pipeline; however, there is some confusion regarding how best to progress these anti-infectives in these studies in clinical trials, or alternatively, how interpretations of preclinical work can best inform on future clinical trials is a subject of wide debate. much consideration still needs to be given to how future drug targets related to anti-infectives are progressed, and how drug discovery programmes are best implemented to exploit these. this manuscript is the result of a task microbes and mucosal immune responses in asthma the microbiology of asthma short-and long-term efficacy of prednisolone for first acute rhinovirus-induced wheezing episode childhood asthma after bacterial colonization of the airway in neonates disordered microbial communities in asthmatic airways airway microbiota and bronchial hyperresponsiveness in patients with 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elderly persons with chronic lung disease asthma in the elderly: a study of the role of vitamin d eaaci anti-infectives in asthma and asthma exacerbations task force. the potential of anti-infectives and immunomodulators as therapies for asthma and asthma exacerbations interests in respect to this publication. all authors participated in the discussion and approved the final version of this position paper. key: cord- -aktfbriw authors: cots, josep m.; alós, juan-ignacio; bárcena, mario; boleda, xavier; cañada, josé l.; gómez, niceto; mendoza, ana; vilaseca, isabel; llor, carles title: recommendations for management of acute pharyngitis in adults date: - - journal: acta otorrinolaringologica (english edition) doi: . /j.otoeng. . . sha: doc_id: cord_uid: aktfbriw abstract acute pharyngitis in adults is one of the most common infectious diseases seen in general practitioners’ consultations. viral aetiology is the most common. among bacterial causes, the main agent is streptococcus pyogenes or group a β-haemolytic streptococcus (gabhs), which causes %– % of the episodes. in the diagnostic process, clinical assessment scales can help clinicians to better predict suspected bacterial aetiology by selecting patients who should undergo a rapid antigen detection test. if these techniques are not performed, an overdiagnosis of streptococcal pharyngitis often occurs, resulting in unnecessary prescriptions of antibiotics, most of which are broad spectrum. consequently, management algorithms that include the use of predictive clinical rules and rapid tests have been set up. the aim of the treatment is speeding up symptom resolution, reducing the contagious time span and preventing local suppurative and non-suppurative complications. penicillin and amoxicillin are the antibiotics of choice for the treatment of pharyngitis. the association of amoxicillin and clavulanate is not indicated as the initial treatment of acute infection. neither are macrolides indicated as first-line therapy; they should be reserved for patients allergic to penicillin. the appropriate diagnosis of bacterial pharyngitis and proper use of antibiotics based on the scientific evidence available are crucial. using management algorithms can be helpful in identifying and screening the cases that do not require antibiotic therapy. pharyngitis; adult; diagnosis; treatment; streptococcus pyogenes; antibiotics abstract acute pharyngitis in adults is one of the most common infectious diseases seen in general practitioners' consultations. viral aetiology is the most common. among bacterial causes, the main agent is streptococcus pyogenes or group a ␤-haemolytic streptococcus (gabhs), which causes %--- % of the episodes. in the diagnostic process, clinical assessment scales can help clinicians to better predict suspected bacterial aetiology by selecting patients who should undergo a rapid antigen detection test. if these techniques are not performed, an overdiagnosis of streptococcal pharyngitis often occurs, resulting in unnecessary prescriptions of antibiotics, most of which are broad spectrum. consequently, management algorithms that include the use of predictive clinical rules and rapid tests have been set up. the aim of the treatment is speeding up symptom resolution, reducing the contagious time span and preventing local suppurative introduction acute pharyngitis (ap) in adults is one of the most common respiratory infections in our environment. ap results in a significant amount of sickness absence from work, each episode resulting in up to an average of . days' sick leave. , it is also one of the most common reasons for prescribing antibiotics in our country, with an approximate prescription rate of %. however, the most frequent bacterial agent, streptococcus pyogenes or group a beta-haemolytic streptococcus (gabhs), is responsible for %--- % of all cases of pharyngitis in children and %--- % in adults. , establishing a suspected differential aetiological diagnosis on which to base the most appropriate treatment is one of the main problems which ap poses for primary care physicians. antibiotics are in general overprescribed for ap, as most of its causes are viral. the excessive use of antibiotics results in possible side effects for the patient, resistance selection and the consequent increase in health expenditure. --- in normal practice, a diagnosis is made based on clinical criteria (fever, tonsillar exudate, anterior cervical lymphadenopathy and no cough), which are of low sensitivity in predicting gabhs ( %--- %), and therefore the indication for the prescription of antibiotics increases as there are a great many false positives. the benchmark test for a diagnosis of ap is tonsillar exudate culture, which has very high sensitivity and specificity ( %--- % and > %, respectively). the time period necessary for reading the culture is its main limitation for regular diagnostic use. for this reason, rapid, easy-to-use, low-cost immunological techniques have been developed which can detect the streptococcal antigen in a few minutes. most of these tests currently have high specificity (> %), but their sensitivity is approximately %, with a range between % and %, although it varies according to the commercial brand and the patients' signs and symptoms. in terms of treatment, gabhs continues to be % sensitive to penicillin and should remain the treatment of choice. aetiology several viruses and bacteria can cause ap in immunocompetent patients. adenoviruses are the most common. other viruses involved are rhinovirus, enterovirus, influenza viruses a and b, parainfluenza virus, respiratory syncytial virus, coronavirus, human metapneumovirus, epstein---barr virus, herpes simplex virus, cytomegalovirus and human immunodeficiency virus type (hiv- ). the most common bacterial cause is gabhs, responsible for up to % of cases in children, but less frequent in adults. asymptomatic carriers are common, chiefly amongst children. other bacteria involved in ap in our environment are streptococcus dysgalactiae subsp. equisimilis (␤-haemolytic group c and g streptococci). more rarely, ap can be caused by fusobacterium necrophorum, borrelia vincentii, arcanobacterium haemolyticum, neisseria gonorrhoeae (in adolescents and adults who practice oral-genital sex), mycoplasma pneumoniae (which also causes acute bronchitis or upper respiratory infection) and chlamydophila pneumoniae. , to date, the streptococci which cause ap remain sensitive to penicillin and other ␤-lactam antibiotics, despite their massive use. no strain which is resistant to penicillin has been described, and penicillin g minimum inhibitory concentrations have not varied significantly for the past years. macrolides and lincosamides (clindamycin) are considered the treatment of choice in patients who are allergic, or suspected to be allergic, to ␤-lactam antibiotics. in recent years, resistance to these groups has increased in different parts of the world, including spain. however, this problem does not affect everybody in the same way; while -atom macrolides (erythromycin, clarithromycin) and atom macrolides (azithromycin) present resistance rates of %--- %, those of atoms (midecamycin, josamycin) and lincosamides remain below % resistance. the prevalence of resistance to macrolides and lincosamides should be known and updated in each area so that alternatives to penicillin can be made available. acute infections of the oropharyngeal mucosa and tissue are one of the main causes of primary care consultations ( % of consultations for upper respiratory infection) even in emergency departments, in hospital and out-of-hospital settings. many are self-limiting and the use of antibiotics in these cases would not be indicated. in daily medical practice, infections caused by gabhs are of particular concern. , these are rare in children under years of age, peak with the highest incidence between the ages of and which then lowers to between % and % in young adults, and are very rare in people over . in terms of presentation, the highest incidence of all infections is usually in winter and spring. there are some exceptions, such as those caused by rhinoviruses or other viruses which cause upper respiratory tract infections, common at the end of spring or even at the beginning of summer, such as those caused by the adenovirus group. the transmission mechanism is usually the respiratory route, via droplets of saliva expelled through coughing, sneezing or even when an infected person talks to a susceptible host. outbreaks have also been described from contaminated food or water, and spread is also possible via the hands. it is possible to contract streptococcal pharyngitis a family history, families living in overcrowded conditions and environmental pollution, which includes chronic smoking, are highlighted as risk factors. all population groups are equally exposed, regardless of their socioeconomic level or profession. in the case of adult patients, the presentation incidence is considerably lower, but it can also be a frequent reason for primary healthcare consultations, especially in the case of viral infections. if the cause is gabhs, it generally results in absence from work, which can involve sick leave of up to days per episode. most ap cases are viral in origin and occur in the context of a common cold. they usually present in the form of epidemic outbreaks and are accompanied by viral symptoms such as nasal congestion, low-grade fever, cough, dysphonia, headache and myalgia. the course of bacterial ap is the acute onset of high fever with chills, severe odynophagia and dysphagia, but no general viral symptoms. table shows the main clinical differences between viral and bacterial aetiologies. table shows the main signs and symptoms suggestive of a specific aetiology in ap. ap which is viral in origin is traditionally classified as red ap and bacterial ap as white, based on the presence or otherwise of exudate. however, clinical findings very often overlap. thus, up to % of viral ap have pharyngeal exudate and % of bacterial ap can have no exudate. these occur due to the involvement of structures contiguous to the infection, or by the infections spreading to drainage areas. they include peritonsillar abscess and phlegmon, retropharyngeal abscess, acute otitis media, sinusitis, mastoiditis and suppurative cervical adenitis. thrombophlebitis immunosupressed patients, with multiple antibiotic treatments, inhaled cortico-steroids or chemoradiotherapy. whitish exudate in pharynx and oral cavity. surface involvement, with no fever or adenitis. of the internal jugular vein (lemierre's syndrome), necrotising fascitis, meningitis or metastatic abscess through haematogenous spread are more exceptional. suppurative complications can appear in %--- % of bacterial ap which are untreated or treated with an inappropriate, insufficiently completed antibiotic. several studies published over the last years highlight that germs other than gabhs can cause these complications much more frequently than gabhs, such as s. anginosus, for example. the possible role played by fusobacterium in these complications is also currently under discussion. some publications have suggested that the decreased prescription of antibiotics for upper respiratory infections could be associated with an increase in complications. however, these studies have not managed to determine whether this increase was more frequent in the untreated group than in the treated group. --- petersen et al. described that with the use of antibiotics the risk of suppurative complications during the first month after diagnosis decreased significantly, the number needed to treat to prevent one serious complication being over . little et al. prospectively analysed the predictive factors of suppurative complications after ap. complications included tonsillitis, peritonsillar abscess, otitis media, sinusitis, impetigo, and the need for a further consultation as a result of unresolved symptoms during the month following diagnosis. suppurative complications were present in . % of patients, irrespective of whether they had been treated with antibiotics immediately, by delayed prescription, or not treated at all. however, two thirds of the complications presented more frequently in patients with --- centor criteria. . % required a further consultation. severe tonsillar inflammation and severe earache were independent complication risk factors. from a clinical perspective, we should suspect the possibility of a complication when the clinical evolution does not follow a satisfactory course. the onset of intense unilateral pain, with dysphagia and trismus of variable intensity, should make us consider cellulitis or peritonsillar abscess. in these cases, examination reveals bulging of the soft pallate and displacement of the tonsil towards the midline. the infection in these cases is usually polymicrobial, and in most patients will require surgical drainage. exceptionally, the abscess can spread to the deep cervical spaces, and more rarely cause necrotising fascitis or thrombophlebitis of the internal jugular vein. acute rheumatic fever and post-streptococcal glomerulonephritis are worthy of mention; they occur after a latency period of a few weeks. rheumatic fever is very rare in developed countries; with an annual incidence of one case per inhabitants, but it remains the main cause of acquired cardiac disease in children in developing countries. given the evidence which is currently available, the primary care physician should first identify gabhs infection, as these cases need to be treated with antibiotics. diagnosis is usually clinical in our country. the clinical findings which usually accompany ap caused by gabhs are: sore throat, often of sudden onset, fever, headache, nausea, vomiting and abdominal pain, inflammation and/or the presence of tonsillar exudates and painful cervical lymph adenopathies, with no cough. however, none of these signs and symptoms is specific to ap caused by gabhs, so that the clinical criteria are of little use in distinguishing streptococcal cause from other causes. various studies have assessed clinical prediction scales which increase the probability of infection caused by gabhs. the most well-known is that of centor, which uses criteria: fever, pharyngotonsillar exudates, tender anterior cervical lymphadenopathy and lack of cough, where a point is added for each of the criteria present and the overall score is between and . other prognostic scales have been created, such as those of mcisaac, and latterly feverpain, created by british researchers. however the centor scale is the simplest and most used, and this score should be recommended. patients with none or only one of these criteria present a very low risk of gabhs infection, and therefore do not require any approach, either diagnostic or therapeutic. this is what is recommended by the most influential clinical practice guidelines, such as those of the infectious diseases society of america and the national institute for health and clinical excellence (nice). , most experts believe that these clinical score scales cannot be used without an additional evaluation for ap caused by gabhs because, as doctors, we are used to overestimating the probability of infections from this cause. this is supported by studies which show that patients with criteria present between a % and % probability of presenting a gabhs-positive pharyngeal swab ( table ). the highest percentages are found in studies performed on children aged between and , and the lowest in people over the age of . therefore, the use of these scales is not sufficient to establish precisely whether or not the patient presents an ap caused by gabhs. in fact, sensitivity of clinical judgement varies between % and %, and specificity between % and %. furthermore, we as primary care physicians, assess the different centor criteria differently; thus, in spain, doctors attach much more importance to pharyngotonsillar exudate in an ap, since we prescribe antibiotics times more if this sign is present, than to the other criteria (fewer than times more if these criteria are present). pharyngeal culture is the benchmark test to discover the aetiology of the infection. its main disadvantage is the time it takes to obtain results. however, it is very probable that aetiology due to anaerobic infections has been underestimated to date, since strict anaerobic culture conditions are required to identify them, which few microbiology laboratories possess. rapid antigen detection tests for gabhs (strep a) were developed in the eighties in samples taken with swabs. these techniques presented the advantage that the result was available during the consultation. they are based on extracting the carbohydrate antigen from the gabhs from the microorganisms obtained from pharyngeal exudates. they are easy to apply in the surgery; the sample should be taken using a tongue depressor, keeping the tongue immobilised, taking the sample from the tonsil and posterior pharynx area, and from any inflamed or ulcerated area. it is essential to avoid the swab being rubbed by the uvula, oral mucosa, lips or tongue, before and after taking the sample. the swab samples are deposited in cuvettes to which a reagent is added which contains anti-streptococcal antibodies. validity depends on the sample collection technique (false-negative results can be given when little material has been obtained), on the area from which it is collected (there is a better yield when collected from the tonsils and/or the wall posterior to the pharynx), on the culture procedure and conditions, on the probability of streptococcal infection (some authors have found a spectrum bias, so that the sensitivity of strep a increases the higher the centor criteria number presented by a patient), the presence of other germs in the pharynx (false-positive results can be given if the pharynx presents major growth of staphylococcus aureus), on the use of tests which are past their expiry date, and on commercial brand. another aspect to be considered is that strep a positivity does not distinguish acute carrier state infection, neither does the culture. the percentage of asymptomatic carriers can be up to %, but its prevalence in adults does not reach %. it has been observed that doctors who use rapid antigen detection tests prescribe fewer antibiotics for ap than those who do not use them. however, although the negative predictive value is very high, a recent clinical study showed that spanish doctors prescribed antibiotics for little more than % of cases with negative strep a. this could be due to the custom of systematically prescribing antibiotics for patients presenting with at least centor criteria. the rapid antigen detection tests used for the aetiological diagnosis of ap are specific for gabhs and do not rule out other aetiologies, such as those caused by s. dysgalactiae and s. anginosus, which have similar clinical manifestations. these tests offer the advantage of diagnosing streptococcal ap in a few minutes, with an associated specificity greater than % when used in patients with or more centor criteria. nevertheless, not only are these tests of no use in ruling out causes other than gabhs, but it was observed in a recent study that they do not prevent the onset of complications when their results are false-negative. for these reasons, it is necessary to continue to research new, more reliable, rapid diagnostic tests in order to help the primary care physician in making a clearer decision as to whether or not to treat an ap with antibiotics. strep a is the rapid diagnosis test to be used in primary care at present; its use is only recommended in cases where a streptococcal infection is suspected. in patients with one or no centor criterion, expert recommendations and clinical practice guidelines agree that no test or antibiotic is necessary. in patients with centro criteria, the situation has not been specified, and at present the nice guideline suggests delayed prescription of antibiotics for this group. in a study published recently, little et al. observed that patients given delayed prescription of antibiotics consumed fewer than half the antibiotics and reconsulted % less than patients treated immediately with antibiotics. are any of the following criteria present? -has there been an outbreak of gabhs in the community (eg. scarlet fever) -immunosupression -history of rheumatic fever -serious symptoms (pgc, earache, severe inflammation) figure recommended approach for acute pharyngitis in adults. gabhs: group a beta-haemolytic streptococcus; pgc: poor general conditions. the most cost-effective strategy is to perform rapid antigen tests on patients with a greater probability of gabhs infection and, based on the result, treat the positive cases. from this perspective, the best recommendation for patients with or more centor criteria would be to undertake rapid antigen detection techniques (strep a) (fig. ) . this recommendation coincides with the latest proposal of the sociedad española de medicina familiar y comunitaria (spanish society for family and community medicine). the following are the objectives of antibiotic treatment of pharyngitis caused by gabhs: • to shorten the course of the disease. antibiotic treatment has proved effective in reducing, although very marginally, the duration of symptoms of pharyngitis caused by gabhs, in h, to be specific. this difference is greater in adolescents and young adults, as antimicrobial treatment can reduce symptoms in these groups in days. • to eradicate the germ. in primary care it is important to identify the ap caused by gabhs, since the patients presenting with it benefit from antimicrobial treatment. • to prevent contagion. antibiotic treatment renders the culture negative in the first h in % of cases, reducing the risk of contagion to other people. • to prevent complications. in some studies antibiotic treatment of ap caused by gabhs has reduced the incidence of acute suppurative and non-suppurative complications, such as rheumatic fever, although this effect has not been observed in all publications. • to improve symptoms. in patients with ap we should use drugs to reduce the main symptom, sore throat, using the correct prescription of anti-inflammatories and/or analgesics. articles have been published in recent years on the possible benefits of treating other causes of ap with antibiotics. there is debate as to the need to treat infection caused by other ␤-haemolytic streptococci, principally groups c and g. antibiotic treatment of group c streptococcus ap might be associated with a slightly shorter duration of symptoms, but only in adults (one day). it has also been proved that group c streptococcus can cause glomerulonephritis and can also cause cases of acute rheumatic fever. there are more questions regarding the benefit of antibiotic treatment in ap caused by group c streptococcus. another cause which has merited a lot of attention in recent years, is infection by f. necrophorum. however there is no certainty as to whether therapy with antibiotics can reduce the duration of the symptoms of ap caused by this anaerobic bacterium. as we mentioned earlier, the need to treat the aetiology from streptococci of the anginosus group is not clear either. antibacterial treatment should be administered for at least days, although preferably for days, since most studies have been undertaken with this duration. in the case of strep a positivity, the use of phenoxymethyl penicillin or penicillin v is recommended ( i.u./ h orally), as gabhs has been and remains sensitive to this antibiotic globally. in the event of intolerance to the treatment of choice, amoxicillin mg/ h can be given. a first-generation cephalosporin can also be administered, such as cefadroxil mg/ h. if there is confirmed allergy to penicillin, it is advised that clindamycin mg/ h is used for days or a -atom macrolide such as josamycin g/ h for days, since gabhs resistance, although it has decreased in recent years, remains greater to and -atom macrolides than to -atom macrolides. in the case of repeated streptococcal ap, the association of amoxicillin and clavulanic acid / mg/ h for days can be used (table ). rest is recommended while there is a fever; ensure an adequate intake of fluids, avoid irritants and gargle with warm water and salt. the recent european guideline on the management of ap recommends the use of analgesics and anti-inflammatories as non-antibiotic drug treatment. ibuprofen and diclofenac are slightly more effective than paracetamol in relieving sore throats. flurbiprofen, a local action anti-inflammatory, has been demonstrated to be more effective than a placebo in the relief of sore throat. , in this regard, the use of local action anti-inflammatories could be an alternative in the treatment of sore throat symptoms without a high fever. the evidence for the benefit of phytotherapy and acupuncture in ap is inconsistent. there are further doubts about the benefit of oral corticosteroids. in a review of placebocontrolled clinical trials, which included patients, it was observed that a short course of oral or intramuscular corticosteroids was more beneficial than the placebo in relieving pain in ap. this benefit was greater for adult patients, those with greater symptomatology and those with streptococcal ap. however, the quality of the studies was poor and the majority took place in emergency departments. a variety of topical agents, administered in the form of tablets, mouthwashes or aerosols, have been used to relieve symptoms of ap. ambroxol mg has been shown to produce a slight reduction in symptoms in a recently published metaanalysis, but the quality of the studies included was poor. in a cochrane library review, zinc gluconate was found to have a slight effect in relieving sore throat compared to the placebo, but it presented more side effects, and therefore is not recommended for ap. some preparations contain topical anaesthetics, such as lidocaine and benzocaine, which produce rapid early relief of pain, although studies demonstrate little methodological quality and heterogeneous doses were used. , there is no evidence on the use of sweets or honey. most ap are diagnosed and treated first-line. on occasion we are presented with situations where hospital referral is necessary, and therefore the cases need to be defined where the primary care physician should opt for referral, so that they can solve the patient's problems, rationalise available resources and be more efficient. we need to differentiate between emergency and delayed referral. in cases where a hospital admission or immediate instrument-assisted manipulation is necessary, or when the process might compromise a good outcome for the patient , : • cases of over weeks' duration, with poor outcome. • cases with a high inflammatory component which, despite treatment, impedes normal swallowing. • suspicion of lingual pharyngitis with obstruction of the aerodigestive tract. • pharyngitis with suspicion of lymphomatous infiltration or any other neoplastic process. • adenitis which evolves into an adenophlegmon. • phlegmons and peritonsillar abscesses. • infections of the parapharyngeal space. • infections of the retropharyngeal spaces, with high risk of evolving into mediastinitis. • pronounced torticollis, which could be atlanto-axoid subluxation (grisel syndrome). lemierre's syndrome: thrombophlebitis of the internal jugular vein (worsening with chills, fever, pain and ipsilateral cervical swelling at the angle of the jaw and along the sternocleidomastoid muscle and stiff neck). when management in hospital is required and usually with reference to a tonsillectomy. the indications for tonsillectomy are as follows : repeated or recurring tonsillitis: clinical situations with the following characteristics: • seven or more episodes of acute tonsillitis each year, in the past year, or • five episodes each year over the past years, or • three episodes each year over the past years, or • persistent symptoms for at least a year. furthermore, each episode should meet at least one of the following clinical criteria: • purulent tonsillar exudate. • fever ≥ • c. • tender anterior cervical lymphadenopathy. • gabhs ---positive pharyngeal culture. these criteria are termed minimally acceptable. nonetheless, each case should be assessed individually weighing up factors such as how debilitating the symptoms are, and the repercussions on the patient and their family. surgery will be indicated after consecutive cases of ipsilateral peritonsillar abscess. defined as: • acute inflammation of multiple cervical adenopathies. • fever ≥ • c and general malaise. • more than days' duration. • no lower respiratory infection. • coexistence of upper respiratory infection or acute tonsillitis. the frequency criteria and the considerations when assessing these cases are the same as those described for recurrent tonsillitis. sore throat is a common reason for seeking healthcare advice, often in community pharmacies. community pharmacies are accessible healthcare centres; therefore, this disease should be approached in a protocolised manner in order to decide whether to act from the community pharmacy or whether referral to a doctor is necessary. pharmacist prescription is the professional service which is offered when a patient or service-user goes to the pharmacy without knowing the medicine they require and asks the pharmacist for the most appropriate remedy for a specific health problem. if the service requires a medicine to • if the bacterial aetiology criteria are fulfilled, the pharmacist will offer to perform a strep a test, if the technique has been validated and the pharmacist has been correctly trained to perform the test. • performing this diagnostic test in the community pharmacy is helpful in : ---dissuading the patient from asking for antibiotic treatment without a medical prescription ---screening for bacterial ap ---providing the doctor with a diagnosis of the disease • if the test result is negative the appropriate pharmaceutical action will be taken • in the event of a positive result, in addition to being given symptomatic treatment, the patient will be advised to consult their physician to confirm the diagnosis and start the appropriate treatment be dispensed, this must be done in line with pharmaceutical care criteria ensuring, after an individual assessment, that the patient receives and uses the medication in way which is appropriate to their clinical needs, in precise doses according to the patient's individual requirements, for an appropriate amount of time, providing the information to use the medication in the correct way, and in accordance with prevailing legislation. within the procedure to be followed on consultation for a sore throat, the pharmacist should consider the points below ( fig. ) : ---the person making the consultation. check whether the person consulting is the person who has the health problem. ---the reason for the consultation: sore throat. ---the pharmacist should ask about the symptoms: only selflimiting health problems are treated in the community pharmacist. ---check: • signs and symptoms. if bacterial aetiology criteria are met, refer to the doctor or offer a strep a test if the technique has been validated and the pharmacist has been correctly trained to perform it (table ). • whether there has been previous treatment with no improvement. • the use of other medication for other reasons. • concomitant illnesses or recent hospitalisation. • allergies or intolerances. • any special physiological circumstance (pregnancy. . .). ---assess: • criteria for referral to the doctor (table ). • contraindications. • possible interactions of the patient's base medication with the treatment which is going to be recommended. ---act. using one or more options from the following: • advise without dispensing. dietary and hygiene advice: ---increase intake of fluids. ---light diet. ---use disposable paper tissues. ---wash hands frequently. ---do not smoke. ---keep a humidified, well-ventilated atmosphere. ---do not strain your voice. presence of a swollen palate or nasal speech if the patient has taken an antibiotic less than a week ago without improvement ---avoid sudden changes of temperature. • dispense drug treatment which does not require a medical prescription ---non-steroid local action analgesic/antiinflammatory: flurbiprofen. ---non-steroid systemic analgesic/anti-inflammatory: ibuprofen. ---analgesic: paracetamol. • recommend drug free treatment ---saline solution. • refer to the doctor if necessary. • monitor medication to maximise the effectiveness and safety of the treatments, minimising risks, and to contribute towards the rational use of medicines and improve patients' quality of life. the main objective of the consensus document is to guide the management of ap in primary care and in community pharmacies. . the most common aetiology of ap is viral. gabhs is the principal bacterial agent. . in general, given the lack of specificity of the signs and symptoms, there is a tendency to over-diagnose streptococcal ap, with the consequent unnecessary over-prescription of antibiotics. . clinical evaluation scales which enable the selection of patients for a rapid diagnostic test are helpful for aetiological diagnosis. . rapid diagnostic tests should be used according to certain criteria, not for all ap. . the strep a test is recommended when the patient presents or more criteria on the centor scale. . the antibiotic of choice for treatment of streptococcal ap is penicillin v, phenoxymethylpenicillin. . the effectiveness of penicillin is proven and no case of resistant gabhs has been described to date. its action spectrum is reduced and, therefore, it selects fewer resistances than other antibiotics. . the association of amoxicillin and clavulanic acid is not is not empirically indicated in the treatment of nonrecurrent streptococcal ap. gabhs does not produce ␤lactamases. . in our country it is necessary to adapt the prescription of antibiotics to the available scientific evidence. . the community pharmacy, as a healthcare service, should manage ap by applying protocols in order to determine the patients who require pharmaceutical care and those requiring medical care. estudio nacional de la infección respiratoria (enir) acute pharyngitis: etiology and diagnosis the rational clinical examination. does this patient have strep throat? outpatient antibiotic use in europe and association with resistance: a cross-national database study the bacterial challenge: time to react. a call to narrow the gap between multidrugresistant bacteria in the eu and the development of new antibacterial agents effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and metaanalysis who's first global report on antibiotic resistance reveals serious, worldwide threat to public health antibiotics for sore throats. potential of antigen detection tests suitability of throat culture procedures for detection of group a streptococci and as reference standards for evaluation of streptococcal antigen detection kits validación de una prueba antigénica rápida en el diagnóstico de la faringitis causada por el estreptococo beta-hemolítico del grupo a clinical practice guideline for the diagnosis and management of group a streptococcal pharyngitis: update by the infectious diseases society of america group a streptococcal diseases and their global burden clinical practice. streptococcal pharyngitis escmid sore throat guideline group. guideline for the management of acute sore throat spanish group for the study of infection in the primary health care setting. resistance to macrolides, clindamycin and telithromycin in streptococcus pyogenes isolated in spain during documento de consenso sobre tratamiento antimicrobiano de la faringoamigdalitis sociedad española de otorrinolaringología y patología cérvico-facial; sociedad española de infectología pediátrica documento de consenso sobre tratamiento antimicrobiano en la faringoamigdalitis aguda documento de consenso sobre el diagnóstico y tratamiento de la faringoamigdalitis aguda precipitating factors in the pathogenesis of peritonsillar abscess and bacteriological significance of the streptococcus milleri group when should patients seek care for sore throat antibiotic prescribing and admissions with major suppurative complications of respiratory tract infections: a data linkage study prescribing of antibiotics and admissions for respiratory tract infections in england antibiotic prescribing in general practice and hospital admissions for peritonsillar abscess, mastoiditis, and rheumatic fever in children: time trend analysis protective effect of antibiotics against serious complications of common respiratory tract infections: retrospective cohort study with the uk general practice research database descarte investigators. predictors of suppurative complications for acute sore throat in primary care: prospective clinical cohort study epiglottitis and necrotizing fasciitis: a life-threatening complication of infectious mononucleosis the diagnosis of strep throat in adults in the emergency room antibiotic prescribing: prescribing of antibiotics for self-limiting respiratory tract infections in adults and children in primary care. guidance london: national institute for health and clinical excellence, n. • prescripción de antibióticos en las infecciones del tracto respiratorio y factores predictores de su utilización streptococcal pharyngitis: optimal site for throat culture the role of the carrier in treatment failures after antibiotic for group a streptococci in the upper respiratory tract impact on antibiotic prescription of rapid antigen detection testing in acute pharyngitis in adults: a randomised clinical trial reflexive culture in adolescents and adults with group a streptococcal pharyngitis antibiotic resistance-the need for global solutions antibiotic prescription strategies for acute sore throat: a prospective observational cohort study diagnosis and management of acute pharyngitis in a paediatric population: a costeffectiveness analysis barcelona: semfyc ediciones antibiotics for sore throat penicillin for acute sore throat: randomised double blind trial of seven days versus three days treatment or placebo in adults once-daily amoxicillin for pharyngitis clinical inquiries. which treatments provide the most relief for pharyngitis pain? relief of sore throat with the anti-inflammatory throat lozenge flurbiprofen . mg: a randomised, doubleblind, placebo-controlled study of efficacy and safety flurbiprofen microgranules for relief of sore throat: a randomised, doubleblind trial efficacy of ambroxol lozenges for pharyngitis: a meta-analysis escenario e identificación de problemas ¿qué papel tiene la otorrinolaringología en la asistencia primaria? un análisis de variación en áreas concretas criterios de derivación ante patología orl guía práctica para el manejo de los procesos otorrinolaringológicos. sociedad andaluza de otorrinolaringología y patología cérvico-facial complicaciones de las infecciones orales y faríngeas libro virtual de formación en orl guia d'actuació farmacèutica en el mal de gola. barcelona: consell de col·legis farmacèutics de catalunya madrid: guía práctica para los servicios de atención farmacéutica en la farmacia comunitaria utilidad del streptotest en la farmacia comunitaria para la discriminación rápida de faringitis bacteriana y vírica en pacientes adultos key: cord- -gkd d k authors: lecky, donna m.; granier, steve; allison, rosalie; verlander, neville q.; collin, simon m.; mcnulty, cliodna a. m. title: infectious disease and primary care research—what english general practitioners say they need date: - - journal: antibiotics (basel) doi: . /antibiotics sha: doc_id: cord_uid: gkd d k background: infections are one of the most common reasons for patients attending primary care. antimicrobial resistance (amr) is perhaps one of the biggest threats to modern medicine; data show that % of antibiotics in the uk are prescribed in primary care. aim: to identify where the perceived gaps in knowledge, skills, guidance and research around infections and antibiotic use lie from the general practitioner (gp) viewpoint. design and setting: an online questionnaire survey. method: the survey, based on questions asked of royal college of general practitioners (rcgp) members in , and covering letter were electronically sent to gps between may and august via various primary care dissemination routes. results: four hundred and twenty-eight gps responded. suspected infection in the elderly, recurrent urinary tract infection (uti), surveillance of amr in the community, leg ulcers, persistent cough and cellulitis all fell into the top six conditions ranked in order of importance that require further research, evidence and guidance. acute sore throat, otitis media and sinusitis were of lower importance than in . conclusion: this survey will help the nhs, the uk national institute for health and care excellence (nice) and researchers to prioritise for the development of guidance and research for chronic conditions highlighted for which there is little evidence base for diagnostic and management guidelines in primary care. in contrast, years of investment into research, guidance and resources for acute respiratory infections have successfully reduced these as priority areas for gps. activity in general practice has increased significantly over the past five years, with the average person visiting their general practice around six times a year [ ] . most primary care consultations ( %) are conducted by a general practitioner (gp) and % of all appointments are face to face [ ] . however, overall patient satisfaction with general practice has declined [ ] . initiatives to improve patient care mean that multiple actions are needed for each patient, e.g., screening, monitoring and other disease management tasks, which presents a challenge to gps working to a -min consultations model. antimicrobial resistance (amr) is perhaps the biggest threat to modern medicine and it will still be even after the covid- pandemic. the majority of antibiotics in england, %, are prescribed in primary care [ ] and is likely to increase during the covid- pandemic due to remotely prescribed and broad-spectrum antibiotics. across the uk, general practice is the first port of call for many people and broad-spectrum antibiotics. across the uk, general practice is the first port of call for many people presenting with an infectious disease [ ] [ ] [ ] ; penicillins are the most commonly prescribed antibiotic group in this setting ( . %) by items prescribed per inhabitants per day, followed by tetracyclines ( %), then macrolides ( . %) [ ] . similar trends have been observed in other uk nations [ , ] . the overprescribing of antibiotics is a major driver for antibiotic resistance. in , research estimated that at least % of antibiotics are prescribed inappropriately in england, many of these for respiratory tract infections (rtis) [ ] . it was found that % of acute cough consultations were prescribed antibiotics when only % were deemed appropriate [ ] . a recent systematic review highlighted diagnostic uncertainty as a contributing factor for overprescribing for acute rtis [ ] . researchers also found that consistently available national guidelines on antibiotic prescribing, were regarded as important by clinicians for their prescribing decision making. as such, this study aims to identify current gaps in knowledge, skills, guidance and research from the gp's point of view as [ , , , ] this will facilitate improved antimicrobial stewardship. in a survey of gps, we found that genital chlamydia infection, antibiotic resistance surveillance, vaginal discharge, leg ulcers, sinusitis, otitis media/externa, dyspepsia/helicobacter pylori, creutzfeldt-jakob disease (cjd) and tonsillitis were the top priorities for improvements to diagnostic tests, and stronger evidence on which to base treatment decisions [ , ] . the present study will also compare findings from the study. of those who opened the online survey, % ( / ) completed all questions, not all participants completed all questions. for those who completed the demographic data section of the survey, % ( / ) of respondents were from england, with % from each of the other devolved administrations (scotland / ; wales / ; northern ireland / ). the response rate by region of england is shown in figure . % ( / ) of respondents self-identified as being from rural practices. in total, % ( / ) of respondents stated that they were from a research practice. a total of % ( / ) reported receiving the survey from the royal college of general practitioners (rcgp), % ( / ) from the crn, % ( / ) from their local ccg, % ( / ) from a colleague, % from rcgp first group ( / ) and % ( / ) from another source. gender, age and years in practice data can be found in table . table demonstrates that there were no differences in the characteristics of gps in the final sample of survey respondents and those of all gps in the sample frame, in terms of age and sex. there was a antibiotics , , of slight over-representation of gps stating they were from a research practice compared with gps in the sample frame and respondents were overrepresented from the south west and underrepresented from the east of england; yorkshire and humber; and london. of the named conditions/illnesses, suspected infection in the elderly ( . %), recurrent urinary tract infection (uti) ( . %), surveillance of antibiotic resistance in the community ( . %), leg ulcers ( . %), and persistent cough ( . %) were the five most highly rated illness/conditions where respondents felt they required more evidence to support their daily practice. weighted scores for all named conditions are shown in figure . ranking did not differ between research and non-research practices (table a ). condition ranking compared to the study can be seen in table . antibiotics , , x for peer review of was a slight over-representation of gps stating they were from a research practice compared with gps in the sample frame and respondents were overrepresented from the south west and underrepresented from the east of england; yorkshire and humber; and london. of the named conditions/illnesses, suspected infection in the elderly ( . %), recurrent urinary tract infection (uti) ( . %), surveillance of antibiotic resistance in the community ( . %), leg ulcers ( . %), and persistent cough ( . %) were the five most highly rated illness/conditions where respondents felt they required more evidence to support their daily practice. weighted scores for all named conditions are shown in figure . ranking did not differ between research and nonresearch practices (table a ). condition ranking compared to the study can be seen in table . condition ranking presented as a percentage of the total possible score for each condition. condition ranking is the total scores for each illness (where = further research unimportant, = further research very important) were converted into a percentage by dividing the total score by the maximum possible score, i.e., as if all respondents indicated that further research into that illness was 'very important'. from the list of named conditions, respondents were asked to identify the top three illnesses/conditions they felt required further research, evidence and guidance. condition ranking is the total scores for each illness (where = further research unimportant, = further research very important) were converted into a percentage by dividing the total score by the maximum possible score, i.e., as if all respondents indicated that further research into that illness was 'very important'. from the list of named conditions, respondents were asked to identify the top three illnesses/conditions they felt required further research, evidence and guidance. table illustrates that the five most frequently named illnesses/conditions by gps that require further research, evidence and guidance, were similar to the top five ranked illnesses/conditions. a total of respondents added both suspected infection in the elderly and surveillance of antibiotic resistance in the community in their top three conditions, resulting in these conditions being ranked joint first place, followed by recurrent uti, persistent cough, cellulitis and leg ulcers, in that order. ranking did not differ between research and non-research practices (table a ) . other conditions participants ( %; / ) identified over 'other' areas that required further research. the most frequently identified areas were mental health ( . %; mentions), pain management ( . %; mentions), skin conditions ( . %; mentions) and chronic fatigue or fibromyalgia ( . %; mentions). table shows rankings for which areas of research (near patient antibiotic resistance test; clinical scores to help inform management; or point of care prognostic tests), evidence (evidence base for antibiotic treatment; evidence base for self-care and non-antibiotic treatment) or guidance (improved treatment guidelines) respondents felt were required for each condition/illness. the top three priorities across all named conditions were the 'need for better evidence base for antibiotic treatment' (exceptions: viral hepatitis and hiv/aids); the 'need for improved treatment guidelines for primary care staff' (exceptions: acute cough and surveillance of amr in the community); and the 'need for better evidence base for self-care and non-antibiotic treatment in primary care' (exceptions: genital chlamydia, lyme disease and suspected infection in the elderly and tuberculosis (tb)). there was little variation between the ranking of the 'need for better clinical scores to help inform management in primary care' (exceptions: viral hepatitis, otitis externa, prostatitis, tonsillitis and tb) and the 'need for better point of care prognostic tests in primary care' (exception: genital chlamydia), with both being ranked in either the th or th position. the need for better near patient antibiotic resistance test in primary care was the lowest ranked respondent priority across all conditions/illnesses (exceptions: amr in returning travelers and genital chlamydia). antibiotics , , of the conditions for which a gp said they wanted more evidence to support their daily practice and require further research, evidence and guidance were: suspected infection in the elderly; recurrent uti; surveillance of antimicrobial resistance in the community; leg ulcers; persistent cough; and cellulitis. the need for a better evidence base for antibiotic treatment in primary care; the need for improved treatment guidelines for primary care staff; and the need for better evidence base for self-care and non-antibiotic treatment in primary care were considered the most important service developments. the need for better point-of-care prognostic test, clinical scores to inform management, and near patient antibiotic susceptibility tests were considered less important. to improve response rates, the survey was disseminated via relevant gp channels in england but we have no information as to how many gps actually received the invitation to participate in the survey. survey site data suggest that internal surveys generally receive a - % response rate compared with - % for external surveys [ , ] , which is in line with our findings regarding how many people opened the survey vs. how many people actually completed it. demographic data indicates that respondents were generally representative of gps in england by age, gender and years in practice distribution. percentage response rates for age and gender were similar to national data [ , ] , and our findings show no differences between gp practice research status and rating of importance of more evidence. we did not collect data on respondent workplace and have assumed independence in all analysis which may be considered a limitation. the provision of a named list of conditions helped reduce seasonal or respondent bias towards specific conditions. the 'other' option allowed respondents to add conditions they felt were important but were not on the main list. the last uk gp survey of this nature was conducted in and found genital chlamydia infection to be the number one priority for 'improvements to diagnostic tests, evidence on which to base treatment, and guidance' [ , ] . interestingly a -fold variation in testing rates across gp practices was observed at this time [ ] . the drop to position for chlamydia, and the drop from the th position to th position for vaginal discharge in the latest survey, may be attributed to the introduction of evidence-based national guidelines and standards for uk specialists in genitourinary medicine [ ] and stis [ ] and the establishment of the national chlamydia screening programme (ncsp) in [ ] ; the latter of which contributed to a reduction in the prevalence and average duration of infections following implementation [ ] . other conditions that have dropped out of the top position since the survey included a range of respiratory tract infections (rtis), suggesting that gps feel the evidence base for diagnosis and treatment of these conditions is adequate. much research has gone into developing evidence-based guidelines for rtis [ , ] and clinical prediction tools in recent years for self-limiting rtis [ ] [ ] [ ] [ ] [ ] . health professional training workshops and toolkits [ ] may also account for the increase in gp confidence to treat these infections. public education campaigns aimed at reducing patient expectations for antibiotics and focussing on rtis have resulted in a decrease in the expectation of antibiotics for these conditions and for consultations with a cough or cold [ ] . venous leg ulcers and persistent sinusitis have remained in the top with the need for improved treatment guidelines a named priority area. a recent systematic review [ ] found only four clinical practice guidelines worldwide (none in england) on venous leg ulcers, between and , considered to be of adequate quality for clinical use. there have been few clinical trials on the antibiotic treatment of leg ulcers; more research has gone into non-antibiotic treatment and the chronic relapsing nature of the condition, highlighting the complexity of treatments for gp staff to follow [ ] . in february , the uk national institute for health and care excellence (nice) developed antibiotic prescribing guidance for leg ulcer infection [ ] . for persistent sinusitis, gps ranked the need for a better evidence base for self-care and non-antibiotic treatment as a priority area. design variation in studies investigating the effects of antibiotic use for chronic rhinosinusitis make drawing firm conclusions in systematic reviews difficult [ ] [ ] [ ] . a cochrane review concluded that there was little evidence that systemic antibiotics are effective in patients with chronic rhinosinusitis and that more research in the field is required [ ] . nice published specific managing common infection guidance for acute sinusitis [ ] of less than four weeks with sudden onset of symptoms, but there is no uk guidance available for persistent sinusitis. an observed increase in the incidence of blood stream infections associated with urinary tract infections (uti) and increasing amr may account for the elevation of recurrent uti to nd place in from th in [ ] . during the time of the survey, nhs england implemented a mandate to reduce inappropriate antibiotic prescribing for uti in primary care [ ] , which may account for the greater interest in the treatment of utis, which represent - % of uk primary care consultations. gps in our survey recorded a 'need for a better evidence base for self-care and non-antibiotic treatment' and 'the need for a better evidence base for antibiotic treatment' as their two priority areas, followed by 'the need for improved treatment guidelines'. although antibiotic prescribing guidelines have been available for suspected bacterial utis in the uk, none focussed on recurrent utis. since this study was conducted, nice have published antimicrobial prescribing guidance for lower, upper, recurrent and catheter-associated uti [ ] . interestingly, gps' ranking of tuberculosis (tb), / (n = ), remains unchanged, with only eight individuals placing it in their top three most important conditions. this is surprising as, due to its resistance to a wide range of antimicrobials, tb is named in the department of health -year strategy [ ] and -year vision [ ] for antimicrobial resistance. the lower priority of tb in this survey may be because tb infections are mostly diagnosed in the london area [ ] , and only % of our respondents were from this region. suspected infection in the elderly, prostatitis, and diverticulitis were ranked in the top of conditions for which gps required evidence to support their daily practice; (ranked first, eighth and ninth respectively). these conditions were not given as an option in the study therefore we cannot compare our findings. for prostatitis and diverticulitis gps ranked the need for a better evidence base for antibiotic treatment and improved treatment guidelines as priority areas. at the time of the survey, there was no antibiotic prescribing guidance for these conditions in england; however, nice have since launched their first antimicrobial prescribing guidance for both acute prostatitis ( ) [ ] and diverticular disease ( ) [ ] . there is still a need for a greater evidence base in both these conditions [ , ] . it is not surprising that suspected infection in the elderly was ranked as the top condition for which gps required evidence to support their daily practice as this group has higher infectious disease morbidity [ , ] . the uk population is also getting older; the number of uk residents aged and over has increased by . million in the past years and is expected to rise by a further . million in the next years [ ] . this increase in life expectancy has a knock-on effect on our health services, with antibiotic prescribing rates being the highest in this age group [ ] . in a recent study, gps used antibiotic treatment both as a diagnostic aid and in an attempt to avoid hospital admission and felt that, in some cases, restrictions on antibiotic use potentially hampered optimal management of infection in this age group [ ] . similar to our findings, authors concluded that research that can fill the gaps in the evidence base is required in order to support gps with their critical antimicrobial stewardship role in this population. over % of bacteraemia occurs in over year olds who have a -fold higher risk of developing sepsis [ ] . the need for a better evidence base for antibiotic treatment and improved treatment guidelines were ranked as the top two gp priorities. an online questionnaire survey, based on a previous survey from [ ] , was used to collect data from gps across the uk. for this study researchers chose to focus on common conditions/illnesses based on their clinical expertise. the survey was designed and tested by researchers, gps and microbiologists at public health england (phe). the survey comprised three sections, with multiple fixed questions and one open question (appendix a): • participant rating of named illnesses/conditions based on how much more evidence they perceive is required to support daily practice. participant selection of the top three illnesses/conditions that they perceive require further research, evidence and guidance, with participant identification of where those improvements are required. • demographic data collection. the survey was implemented using selectsurvey (selectsurvey.netv , classapps llc, kansas city, mo, usa). data were exported from selectsurvey to stata (stata statistical software: release . statacorp lp, college station, tx, usa) for analysis. survey items that asked respondents to rate priorities on a likert scale were given an overall percentage score, which was calculated by dividing a weighted sum of individual responses (coded as very unimportant = , very important = ) by the theoretical maximum score. for the top three illness/condition sections of the survey where different respondents may have rated the same illness/condition in either the number , or position, the total number of respondents selecting a particular illness/condition were added together to give the final overall ranking. statistical comparisons, using the chi-square test (significant at the % level), were made between the survey respondents and all recognised gps in the sample frame during the study period ( table ) . the gp characteristics data for the respondents were taken from their survey responses, while the data for all gps in the sample frame were obtained from nhs digital [ ] . research practices are defined as gp practices that actively take part in research projects. for each condition ordinal logistic regression was used to assess the association between research practice and rating, without adjusting for any other covariate. this association was also assessed after simultaneously adjusting for gender, years, location, rurality and audit, the remaining being omitted due to strong collinearity between them and the other covariates. where this was not possible, a model was developed by means of a forwards stepwise approach wherein non-significant (at the % level), not substantially confounding covariates (a covariate was a substantial confounder if its removal resulted in a greater than % change in the odds ratios (ors) of one or more of the parameters still in the model) were removed, but always retaining research practice. if none of the covariates were found to be significant or confounding, the unadjusted association between research practice and rating is presented. the proportional odds assumption was tested by means of a likelihood ratio test (lrt) and, if significant at the % level, a generalised ordered logit model was fitted wherein the proportionality assumption was relaxed for those parameters not meeting the criterion, as detailed in the reference. the likelihood ratio test lrt was used to obtain determine significance, except when the generalised ordered logit model was used, in which case the p-value was obtained from the wald test. the measure of association for research practice quoted was the odds ratio (or), together with % confidence intervals (cis). this survey has highlighted areas of topic prioritisation for the development of guidance and future research areas. since the survey, investment in research, evidence-based treatment guidelines, training, clinical prediction tools and screening programmes for many of the common infections may have led to the decreased prioritisation of acute rtis by gps. the focus for research to support diagnostic and management guidance now needs to be on less common and chronic infections. we are encouraged that nice and phe have already developed antibiotic prescribing guidance for some of these conditions [ , , , , ] ; however, three of the top conditions where gps required evidence to support their daily practice future were for chronic or recurring conditions, i.e., chronic sinusitis, chronic cough, recurring uti, for which there is currently little or no diagnostic, management or treatment guidelines. on a scale of - , please indicate how much more evidence you would like to see for each of the following conditions to support your daily clinical practice. understanding pressures in general practice the king's fund comparison to other collections english surveillance programme for antimicrobial utilisation and resistance (espaur) surveillance of antimicrobial use and resistance in northern ireland antibacterial usage in primary care in wales research reveals levels of inappropriate prescriptions in england actual versus 'ideal' antibiotic prescribing for common conditions in english primary care antibiotic prescribing for acute respiratory tract infections in primary care: an updated and expanded meta-ethnography phls primary care consultation-infectious disease and primary care research and service development priorities phls laboratory services and primary care needs general practice workforce, final what's a good response rate? available online tips and tricks to improve survey response rate general practice trends in the uk to 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license key: cord- -hip t jx authors: hansford, karl a. title: nontraditional antibiotics—challenges and triumphs date: - - journal: antibiotics (basel) doi: . /antibiotics sha: doc_id: cord_uid: hip t jx the pursuit of nontraditional antibiotics is becoming an increasingly important means to tackle seemingly insurmountable challenges faced by contemporary antibiotic researchers as they overcome the shifting landscape of bacterial pathogenesis, particularly for gram-negative bacteria [...]. the pursuit of nontraditional antibiotics is becoming an increasingly important means to tackle seemingly insurmountable challenges faced by contemporary antibiotic researchers as they overcome the shifting landscape of bacterial pathogenesis, particularly for gram-negative bacteria. defined as therapeutic modalities that do not fit within the traditional direct-acting small molecule paradigm, the scientific merit, translational potential and likely pitfalls of nontraditional approaches was recently reviewed [ ] . encouragingly, there is an unprecedented level of activity around nontraditional therapies based on a recent analysis of the global preclinical antibacterial pipeline [ ] . although the future potential of nontraditional therapies is viewed with cautious optimism, adequate resourcing will be critical to demonstrate clinical impact, especially when many of the translational criteria associated with direct-acting small molecule therapeutics will likely be incongruent with the nontraditional development pathway. this is reinforced by the sobering point that nontraditional therapies will likely be used as adjunctive therapies alongside antibiotics, rather than replacing them, clouding clinical endpoints for regulatory approval [ ] . thus, considerable work is still required to navigate the tortuous pathway to the regulatory approval and future acceptance of nontraditional therapies in clinical practice. this special issue of antibiotics is dedicated to providing a compendium of the latest developments in the field from a diverse cross section of researchers working at the forefront of antibiotic discovery. with a contribution of seven articles (one communication, three reviews, one commentary, one concept paper and one perspective), the authors are sincerely thanked for their efforts. the concept paper by azeredo da silveira and shorr provides an excellent case study on cal , a liposome-derived anti-virulence trap designed to sequester bacterial toxins by acting as a decoy mimic of cellular lipid platforms [ ] . the three review articles by zurawski and mclendon [ ] , nikolich and filippov [ ] , and ghose and euler [ ] give a superb timely survey of how monoclonal antibodies, bacteriophages and lysins, respectively, are currently being explored in the treatment of bacterial infections. the utility and future potential of antibodies to treat bacterial infections is only just being realized now, despite a successful history in other therapeutic areas. similarly, despite widespread use in eastern european countries for decades, bacteriophage therapy is only just being explored in the west. zurawski and mclendon [ ] and nikolich and filippov [ ] provide a contemporary account through the drug development lens, highlighting previous successes and failures, lessons learned and what we might expect in the coming years. bacteriophage endolysins are another product that have been studied intensively, albeit generally against gram-positive organisms due to the gram-negative impermeability barrier. speaking from a commercial drug developer's viewpoint, ghose and euler give a unique detailed account of newly discovered lysins with gram-negative activity currently in the early stages of development [ ] . this will no doubt be of great interest to developers working in the field. turning to small molecule therapeutics, frei's perspective on the untapped potential of metal complexes as antibiotics provides a compelling view that chemical classes often misconstrued as only being useful for certain applications should not be overlooked as potential sources of new chemotypes to fight bacterial infections [ ] . complementing this account is the commentary by quave and marquez, who highlight that it would be remiss to overlook the virtues of medical ethnobotany-the study of how people use plants in medicine-in the quest for new natural products to treat infections, with a particular emphasis on antifungals [ ] . finally, a communication by gajdács and spengler details the role of drug repurposing as a source of new virulence inhibitors [ ] . by testing the utility of a diverse set of pharmacological agents as quorum sensing (qs)-inhibitors, they identified fourteen agents possessing dose-dependent qs-inhibitory activity in vitro, concluding that the qs-based modulation of bacterial virulence is a promising strategy warranting further investigation. as this issue comes to a close, we face an unprecedented global challenge due to the coronavirus covid- pandemic. the world has largely been ill prepared to manage this kind of onslaught, highlighting the catastrophic dangers of unforeseen biological threats. naturally, antibiotics are being used to treat secondary infections in covid- patients, leading to increased pressures on resistance selection, and the potential for critical shortages if supply chains are disrupted. unlike covid- , drug-resistant infections have been on our radar for years. new, effective interventions are needed now, before we reach a tipping point. the articles in this special issue are a snapshot of the incredible work being undertaken by many talented and dedicated developers who choose to remain in the field for the long haul. it should serve to inspire us all. the author declares no conflict of interest. alternatives to antibiotics-a pipeline portfolio review the global preclinical antibacterial pipeline non-traditional antibacterial therapeutic options and challenges critical parameters for the development of novel therapies for severe and resistant infections-a case study on cal , a non-traditional broad-spectrum anti-virulence drug monoclonal antibodies as an antibacterial approach against bacterial pathogens bacteriophage therapy: developments and directions gram-negative bacterial lysins metal complexes, an untapped source of antibiotic potential? antibiotics prevalence and therapeutic challenges of fungal drug resistance: role for plants in drug discovery the role of drug repurposing in the development of novel antimicrobial drugs: non-antibiotic pharmacological agents as quorum sensing-inhibitors key: cord- -hc yo authors: muthanna, abdulrahman; salim, hani syahida; hamat, rukman awang; shamsuddin, nurainul hana; zakariah, siti zulaikha title: clinical screening tools to diagnose group a streptococcal pharyngotonsillitis in primary care clinics to improve prescribing habits date: - - journal: malays j med sci doi: . /mjms . . . sha: doc_id: cord_uid: hc yo this review highlights the clinical scoring tools used for the management of acute pharyngotonsillitis in primary care clinics. it will include the prevalence of group a pharyngotonsillitis among children and adults worldwide and the selective tests employed for diagnosing group a streptococcal pharyngotonsillitis. pharyngotonsillitis is one of the common reasons for visits to primary care clinics worldwide, and physicians tend to prescribe antibiotics according to the clinical symptoms, which leads to overprescribing antibiotics. this in turn may lead to serious health impacts and severe reactions and may promote antibiotic resistance. these significantly add on to the health care costs. the available information from health organisations and previous studies has indicated the need to manage the diagnosis of pharyngotonsillitis to improve prescribing habits in primary care clinics. acute pharyngotonsillitis is the second most commonly diagnosed pediatric illness, with sporadic cases among adults ( ) . group a streptococcal (gas) infection frequently causes significant morbidity and is associated with significant mortality rates worldwide. around the world, more than million cases annually have been diagnosed as pharyngotonsillitis ( ) . serious complications of pharyngotonsillitis caused by streptococcus pyogenes (also known as group a streptococcus) are rheumatic fever, scarlet fever, toxic shock syndrome, and acute glomerulonephritis ( ) . streptococcus pyogenes is responsible for about %- % and about %- % of acute pharyngotonsillitis cases in children and adults, respectively ( ) . clinical signs and symptoms alone cannot be used to rule out or diagnose pharyngotonsillitis, as it can mimic other types of diagnosed infections ( ) . thus, diagnosis of pharyngotonsillitis has always been delayed. ideally, the diagnosis of gas pharyngotonsillitis should be confirmed by throat swab culture, which usually takes two to three days for the bacterial growth to be identified. during this period, the illness might be resolved, or patients might experience several complications ( ) . viral pharyngotonsillitis is treated by a symptomatic relief, whereas gas pharyngotonsillitis may require the prescription of antibiotics such as penicillin, clindamycin, or erythromycin. a specific treatment might be required if complications occur ( , ) . in general, . what are the clinical scoring tools to diagnose group a streptococcal pharyngotonsillitis? . what are the sensitivity and specificity of the centor scoring system? . what are the treatment and diagnosis of group a streptococcal pharyngotonsillitis in primary care practice? pharyngotonsillitis (pharyngitis or tonsillopharyngitis) is one of most common upper respiratory tract infections ( ) . it is an inflammation involving both the pharynx and tonsils most commonly caused by viral or bacterial infection. pharyngotonsillitis can be classified as acute or chronic depending on the causative agent and the patient's immune system efficiency ( ) . the typical symptoms of pharyngotonsillitis are a sore throat, red and swollen tonsils, white or yellow patches on the tonsils, and fever ( ) . the patient's temperature rises to above °c in group a streptococcal pharyngitis ( ) . cough and nasal discharge are more symptomatic of viral infections than bacterial infections. other symptoms may include swollen anterior cervical lymph nodes, headache, painful or difficult swallowing (dysphagia), loss of voice or changes in the voice, abdominal pain in children, and bad breath. symptoms usually begin one to three days after exposure (table ) ( ) . antibiotics are safe but should be prescribed by a physician after a careful clinical assessment. however, antibiotics that are taken unnecessarily may contribute to the development of antibiotic resistance ( ) . the excessive use of antibiotics and an unnecessary antibiotic prescription add an economic burden to the health care system worldwide, as well as to patients and their families ( ) . studies have shown trends of inappropriate prescribing of antibiotics for upper respiratory tract infection (urti) in malaysian primary care, where antibiotic prescribing rates for urti were . % in malaysian primary care settings, and these rates exceed the expected prevalence of group a streptococcus among adults and children ( ) . previous studies have shown that clinical scoring tools have an acceptable specificity and can limit the overprescribing of antibiotics, thereby reducing the emergence of antibiotic resistance and the cost of health care ( , ) . this review has gathered information relevant to pharyngotonsillitis. the sources of the information provided are reliable to an extent owing to the references that have been cited. recent literature has been used, and very few sources of old literature have been used where necessary. in writing this review, answers to the following questions are sought: . what is the prevalence of group a streptococcal pharyngotonsillitis among children and adults worldwide? . what is the principle of management for antibiotic prescription in primary care clinics? and about %- % of acute pharyngotonsillitis cases in children and adults, respectively. it is characterised by inflammation, exudates, fever, leukocytosis and tender cervical lymph nodes ( , ) . groups c and g beta-hemolytic streptococci are a normal flora of the human upper airway, but they can cause pharyngotonsillitis ( ) . occasionally groups b, and f betahemolytic streptococci are responsible for pharyngotonsillitis. haemophilus influenzae cause pharyngotonsillitis in children less than five years old. others bacteria such as moraxella, chlamydia pneumoniae, mycoplasma pneumoniae, corynebacterium diphtheriae, and neisseria gonorrhoeae cause pharyngotonsillitis, rarely ( , ) . candida albicans rarely cause pharyngitis when the normal flora is killed through antibiotics therapy or when the individual is immunosuppressed by disease or drugs ( table ) ( ) . table shows the prevalence of group a pharyngotonsillitis among children and adults. the studies included developing and developed countries around the world. the prevalence of group a pharyngotonsillitis around the world varies from % to . %. most cases of pharyngotonsillitis are caused by viruses and sometimes occur as a part of the common cold or influenza syndromes ( ). the most common viruses that cause uncomplicated pharyngitis are adenoviruses, especially in children ( ) . rhinoviruses cause about % of pharyngitis cases, and there are more than serotypes of rhinovirus ( ) . in addition, pharyngotonsillitis is common in patients with influenza a and constitutes about % of the cases, whereas the proportion is lower in patients with influenza b ( ) . the epstein-barr virus is responsible for % of pharyngotonsillitis cases and usually spreads from adults to infants ( ) . moreover, coxsackieviruses and echoviruses are common enteroviruses that cause pharyngitis ( ) . cytomegalovirus, parainfluenza viruses, coronaviruses, and the measles virus may cause pharyngotonsillitis ( , ) . bacteria cause about %- % of pharyngotonsillitis cases ( ) . the most common and important bacteria that cause acute pharyngotonsillitis belong to streptococcus pyogenes (group a beta-hemolytic streptococcus). streptococcus pyogenes is responsible for about %- % that weaken the immune system, such as diabetes, organ transplant, chemotherapy, and aids ( ) . all racial and ethnic groups are affected by pharyngotonsillitis worldwide and the infection can affect both male and female genders ( ). appearance of streptococcus pyogenes produces a zone of β hemolytic around the colonies and it is sensitive to bacitracin disc on the blood agar, following h of incubation under anaerobic conditions figure shows the wide variation in prevalence of group a pharyngotonsillitis around the world. the highest prevalence of group a pharyngotonsillitis was recorded in the middle east, while the studies in the southeast asian countries has reported the lowest the prevalence. the rate of infection was higher among children than adults. these variations in the prevalence of group a pharyngotonsillitis between the different countries due to several factors such as the study design, sampling technique, cultural, ecological, and others ( ) . furthermore, the incidence pharyngotonsillitis is more common in children, especially in school age because they are in close contact with the pathogens, where infection spreads through close contact with an infected child, when a person inhale droplets of respiratory secretions from the air when an infected person breathes, coughs, or sneezes ( ) . an environment, polluting the environment and the lack of ventilation and air pollution, all of these environmental factors reinforce the spread of infection ( ) . in addition, the peak incidences of pharyngotonsillitis occur in the winter and spring with sporadic cases throughout the year ( ) . other risk factors for pharyngotonsillitis are sickle cell anemia, sinusitis, smoking or exposure to secondary smoke, and any condition s o u t h a f r i c a s a u d i a r a b i a e g y p t i r a n p a k i s t a n a u s t r a l i a j a p a n t h a i l a n d s i n g a p o r e i n d o n e s i a i n d i a y e m e n e t h i o p i a s e r b i a t u r k e y f r a n c e u k u s a c a n a d a b r a z i l a r g e n t i n a ( ) . according to previous studies, rapid antigen detection test has been hindered because it has low sensitivity ( ) . therefore, the centres for disease control and prevention (cdc) and american academy of family physicians (aafp) guidelines have recommended that the negative radt results should be backed up by a swab throat culture to increase the accuracy of the diagnosis ( ). however, radt has a high specificity, this means that the positive radt results do not require to be backed up by a swab throat culture ( ) . more recently, molecular based techniques, such as dna probes and polymerase chain reaction (pcr) have been developed to identify the pathogens that cause pharyngitis. it is a sensitive, and specific method, but it is not used routinely in most of the countries around the world, and usually it is used in epidemiological studies ( ) . anti-streptolysin-o (aso) test is a rapid latex agglutination test to determine antistreptolysin-o antibodies in patient's serum who had a recent β-haemolytic streptococci infection. the titer increases after days of infection and reach the peak after to weeks ( ). clinical tools are a guideline for a quick diagnosis and treatment of group a streptococcal pharyngotonsillitis in patients with complaints of sore throat ( ) . it is a screening method to help physicians determine if the patient needs testing (throat culture or rapid antigen detection test) or not and if the patient needs empiric antibiotic therapy ( ) . all the studies that reported the clinical prediction rules for diagnosing group a streptococcal pharyngotonsillitis among adults and children were eligible to inclusion for the purpose of this review. the clinical prediction rules were defined as a decision-making tool that included two or more variables obtained from the physical examination or the history of the patients. all studies that updated by the original authors only was included ( table ). most of these tools are clinical scores based on the clinical findings which is associated with group a streptococcal infection. previous studies regarding to the accuracy of diagnosis of group a streptococcal pharyngotonsillitis by using these tools have shown that, most of these strategies did not show sufficient accuracy, and were majority of physicians depends on the clinical findings to diagnose pharyngotonsillitis but cannot distinguish between streptococcal from non-streptococcal infections according to the clinical findings ( , ) . in addition, signs and symptoms of pharyngotonsillitis overlay extensively with other infectious, making the diagnosis according only to the clinical findings is inaccurate ( ) . pharyngotonsillitis is manifested by white or gray patches on the tonsils, swelling of the tonsils, and redness, and inflammation of pharyngeal wall. usually there will be swollen anterior lymph nodes in the sides of the neck with group a streptococcus pharyngotonsillitis. in addition, ear and nose inflammation might be occurred where pharyngotonsillitis conferred an increase conferred an increase of ear and nose infections. spreading of bacterial infections from pharynx to the nose and middle ear because they are located in the same cavity might be an explanation of this association ( ) . the gold standard laboratory diagnosis of streptococcal pharyngotonsillitis is culture of throat swab. culture of throat swab is a laboratory diagnostic test to evaluate the presence of a streptococcal infection in the throat ( ) . the sample is collected from the tonsils and the wall of pharynx by swab. presence of streptococcus pyogenes onto blood agar confirm the streptococcal pharyngotonsillitis ( figure ). the results are further identified based on biochemical test such as gram stain and pyrrolidonyl arylamidase test ( ) . the sensitivity and specificity of the throat swab cultures ( . %, and . %, respectively) are more than the sensitivity and specificity of the rapid antigen detection test ( . %, and . %, respectively) ( ) . however, the throat swabs culture is not effective enough because of the relatively long time (two to three days) for the bacterial growth to be identified ( ) . rapid antigen detection test (radt) can be an appropriate alternative test to identify group a streptococcus directly from throat swabs because it is a rapid test and takes few minutes in providing results as compared to throat swab culture. therefore, the physician can make a decision about the therapy at in , centor et al. ( ) have developed set of four criteria which might be used to identify the likelihood of group a streptococcal infection in adult patients complaining of a sore unable to identify patients in a low or high-risk case. however, several studies have shown that centor and macisaac scoring have a sensitivity more than % and a specificity more than % ( , ) . of two or three is require testing by using rapid antigen detection test or throat culture, because the chance of streptococcal infection is around %- % and require anti-microbial therapy only if the result is positive. however, a patient with a score of four should be tested by using rapid antigen detection test or throat culture, and empiric antibiotic therapy is required due to chance of streptococcal infection is high between % and % ( figure ) ( ). previous studies about the accuracy of centor criteria have shown that, the sensitivity of absence of cough and swollen anterior cervical lymph nodes was higher than the specificity (sensitivity %, specificity % and sensitivity %, specificity %, respectively), while the specificity of the presence of fever (≥ °c) and tonsillar exudates was higher than sensitivity (sensitivity %, specificity % and sensitivity % and specificity %, respectively throat. centor criteria including the presence of fever equal to or more than °c, absence of cough, swollen anterior cervical lymph nodes, and tonsillar exudates or swelling, one point is added for each criterion. the centor scores might range from - (table ) ( ). bacterial pharyngotonsillitis is treated by anti-microbials. penicillin, a course of oral penicillin v for days or a single dose of parenteral penicillin g are the best choice to treat group a streptococcal pharyngitis. however, amoxicillin can be used. in penicillin allergic patients, cephalosporins, clindamycin, erythromycin or azithromycin are an acceptable alternative ( ) . in addition, group c and g streptococcal pharyngitis are usually treated with antibiotics, although it lacks the clinical trials ( , ) . to help physicians to prescribe the appropriate antibiotics for children and adults with streptococcus pharyngitis, centres for disease control and prevention (cdc), american academy of family physicians (aafp), and the institute for medical research (imr) have developed the clinical practice guidelines for respiratory tract infections ( , , ) . moreover, the guidelines were compiled by the leading medical organisations ( , ) . according to the cdc, aafp guidelines, and the national antibiotic guideline in malaysia, antibiotics should be prescribed only to patients with group a streptococcal infection (streptococcus pyogenes) which group a streptococcus usually cause symptoms including sore throat, fever more than °c, exudates, nausea, vomiting, headache, stiff and swollen neck, abdominal pain, and tender enlarged cervical lymph nodes. however, cough, nasal discharge, conjunctivitis, and diarrhea are more symptomatic of viral infections than group a streptococcal infections and the viral infections do not treat with antibiotics. the diagnosis must be confirmed by throat culture or rapid antigen detection test ( , , ) . cdc and aafp guidelines recommended antibiotics for patients with sore if the patient is younger than months, diagnosis certain, or in severe illness ( ) . the first-line of antibiotics to treat group a streptococcal infection in children and adults are oral penicillin v for days or a single dose of parenteral penicillin g; however, the alternative therapy for children are amoxicillin, oral cephalosporins, clindamycin, and macrolides. amoxicillin, macrolides, erythromycin, oral cephalosporins, clindamycin in adult patients allergic to penicillin for days. ( ) . in addition, the positive likelihood ratio (lr) of tonsillar exudates was the highest positive likelihood ratio equal . , suggesting it raises the probability of having group a pharyngotonsillitis between % and %, while the positive likelihood ratio (lr) of fever (≥ °c) was . and it raises the probability of having group a pharyngotonsillitis between % and % when present. absence of cough and swollen anterior cervical lymph nodes both decrease the likelihood of having group a pharyngotonsillitis between % and % when absent ( ) . the presence of all four criteria have a positive predictive value between % and % for group a streptococcal pharyngotonsillitis. however, the absence of all criteria have a negative predictive value more than %. therefore, these studies have suggested that the presence of all four criteria discriminates group a streptococcal pharyngotonsillitis from other etiology in patients with sore throat ( ) . furthermore, studies have shown that the centor score has an acceptable sensitivity and specificity (sensitivity %, and specificity %, respectively) in predicting likelihood of group a streptococcal pharyngotonsillitis. applying this to prescribing decision, can limit the over prescription of antibiotics, thus will reduce the emergence of antibiotic resistance as well as the cost of health care but should be used in primary care clinics. however, laboratory confirmation is the gold standard in making an accurate diagnosis ( ) . in addition, centor scoring provides quick diagnosis of group a streptococcal pharyngotonsillitis in adult patients, unlike the tests to confirm a diagnosis of streptococcal pharyngotonsillitis, such as a culture which takes two to three days for the results in order to avoid any complications ( ) . macisaac score are similar to centor score, but it adds one extra point for patient less than years old, because this age group is more susceptible to streptococcal pharyngotonsillitis and subtract one point if the patient age years old or more. therefore, the score might range from − to . a low score on macisaac criteria help to exclude streptococcal pharyngotonsillitis, and higher scores require testing by using rapid antigen detection test or throat culture, and empiric antibiotic therapy ( , ) . with sore throat ( ) . a study that carried out in jordan among patients with sore throat has reported that antibiotics were prescribed for . % of patients with sore throat ( ) . another study done by lauri et al. in the united states of america has reported that the rate of prescribed antibiotics to adults with sore throat was . % ( ) . the centres for disease control and prevention (cdc), american academy of family physicians (aafp), and the national antibiotic guideline in malaysia strongly recommend the strategies of centor scoring to select patients need for antibiotic therapy. the goal of the strategies is to limit unnecessary antibiotic prescribing. these strategies are expected to limit the antibiotic prescribing rates between % and %, lower than current rates which is more than %. in addition, the strategies are expected to administer appropriate analgesics, anti-pyretics and supportive care of patients with pharyngotonsillitis ( , ) . the infectious diseases society of america (idsa) and american college of physicians (acp) guidelines, conversely, have recommended that the diagnostic testing is required (radt or throat culture in all patients at risk) and cannot depend on the clinical diagnosis of gas pharyngotonsillitis alone. idsa and acp guidelines recommend confirmatory for negative radt by throat swab culture in children ( ) . in addition, according to the united kingdom national health service (uknhs), the antibiotic is prescribed only to high-risk and very ill patients ( ) . group a streptococcus (streptococcus pyogenes) and other beta haemolytic streptococci are sensitive to penicillin and cephalosporin as well as rifampin and vancomycin. however, some strains of the bacterium have been found to be resistant to macrolides, tetracycline, and clindamycin ( ) . the excessive take of unnecessary antibiotics led to increase and spread the resistant of anti-microbial in communities around the world. the increasing of antimicrobial resistance has been attributed to combinations of microbial characteristics, selective pressures of anti-microbial use, and societal and technological changes that enhance the transmission of drug-resistant organisms analgesics and antipyretics such as ibuprofen or acetaminophen can be used to reduce the pain ( ) . the national antibiotic guideline in malaysia has recommended amoxicillin mg or phenoxymethylpenicillin mg for days to treat pharyngotonsillitis that are caused by group a streptococcus; however, the alternative therapy is a single dose of benzathine penicillin, azithromycin mg for days or clindamycin mg- mg for days to patients who allergic to penicillin ( ). viral pharyngotonsillitis is treated by a symptomatic relief, such as soothing fluids, aspirin, paracetamol, soothing gargle, and rest with drinking an adequate water and hot fluid ( ) . tonsillectomy or surgery to remove the tonsils is indicated when complications of pharyngotonsillitis (repeated occurrence of acute tonsillitis, peritonsillar abscess or obstruction of the nasal airway) ( ) . antiinflammatory medications such as aspirin for pain or corticosteroids might be required if the complications of group a streptococcal pharyngotonsillitis such as rheumatic fever occur ( ). anti-microbial resistance is driven by many factors, the most significant of which is inappropriate prescribing. this is when patients get a prescription for an antibiotic that they don't really need, or get a prescription for the wrong antibiotic, the wrong dose or the wrong duration. typically, antibiotics are prescribed by physicians to the patients based on clinical symptoms. there are reasons for inappropriate prescriptions are very difficult to curb, including the difficulty of diagnosis of whether a viral or bacterial infection to determine the appropriate treatment and it is known antibiotics can only be given to patients with bacterial infection ( ) . patients play an important role in that issue, because most of the patients insist that physicians to prescribe the antibiotic and that increase demand for a group of antibiotics speeds up the resistance of antibiotics and it becomes useless ( ) . the antibiotic prescription rate in a study at public primary care clinics which was carried out in malaysia was . % among patients . % compared to . % in . for group b streptococci, the resistance to tetracycline, co-trimoxazole and clindamycin have increased in compared to . ceftriaxone resistance was less in ( . %) compared to . % in ( ). the above review has documented that the over prescribing of antibiotics is a global problem. since pharyngotonsillitis is one of the common reasons for visiting care clinics worldwide, over-prescription of antibiotics reason to occur the anti-microbial resistance. although, there is a lack of the data on the above matters, the available studies indicated that, there is an urgent need to reduce the overprescription of antibiotics in the health care centres and clinics. one of the solutions is to follow the strategies that help to diagnose group a streptococcal infection. according to previous studies, the clinical rules for triaging patients who should undergo group a streptococcal testing was poor, however, centor and macisaac scoring have shown high sensitivity and acceptable specificity. further validation studies about the clinical prediction rules are needed to ensure the accuracy and update the clinical strategies. future studies should also aim to detect the accuracy of diagnosis using the rapid antigen detection testing and the gold standard to diagnose group a streptococcal pharyngotonsillitis. none. none. none. none. ( ) . furthermore, the resistance of antimicrobial lead to increase the morbidity and mortality since resistance increases the risk of inappropriate therapy. the risk is that the patients who do not receive appropriate therapy will have a longer period of disease or fatal effect; moreover, morbidity and transmission of the microorganism will increase due to the patients remain infectious for a long period. increased morbidity and mortality was documented in several cases including streptococcal infection ( ). a study in france has estimated that , infections due to multidrug-resistant microorganisms occurred in , including , deaths were associated with these infections ( ). in addition, another study in european countries has reported that , infections due to multidrug-resistant microorganisms were associated with , deaths ( ) . in term of cost, the cost of the consequences of anti-microbial resistance might include hospitalisation for long period, costs of additional laboratory testing and including full health care costs. the costs of antibiotic therapy depend on the dose and duration of treatment and often are expensive due to there are few antibiotics available to treat the multidrugresistant bacteria. in addition to this costs, the costs of the efforts and studies to eradicate the anti-microbial resistance from health care centres. the costs of morbidity and mortality has indirect effects and are not easy to be measured and economically evaluated due to a number of effects such as extension of resistant genes between different species and strains ( ) . however, the morbidity, mortality and economic impact of streptococcal infection has not been elucidated ( , ) . previous studies have shown that there was a high rate of resistance among group a streptococcus and other beta haemolytic streptococci to antibiotics β-lactam, but they were highly susceptible to penicillin vancomycin, ofloxacin, cephalosporin, and clindamycin ( ) . in addition, another study in 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use in patients with sore throat performance of a predictive model for streptococcal pharyngitis in children pragmatic scoring system for pharyngitis in lowresource settings mechanisms and consequences of bacterial resistance to antimicrobial peptides antibiotic resistance threats in the united states mortality and hospital stay associated with resistant staphylococcus aureus and escherichia coli bacteremia: estimating the burden of antibiotic resistance in europe the threat of antimicrobial resistance in developing countries: causes and control strategies epidemiology and antibiotic resistance of group a streptococci isolated from health schoolchildren in korea to fight antibiotic resistance, we need to fight bad prescribing habits the effect of profiling report on antibiotic prescription for upper respiratory tract infection antibiotic prescribing for acute respiratory infections in children in jordan us outpatient antibiotic prescribing variation according to geography, patient population, and provider specialty in practice guidelines for the diagnosis and management of group a streptococcal pharyngitis macrolide and clindamycin resistance in group a streptococci isolated from children with pharyngitis key: cord- -e anaxck authors: mostov, perry d. title: treating the immunocompetent patient who presents with an upper respiratory infection: pharyngitis, sinusitis, and bronchitis date: - - journal: prim care doi: . /j.pop. . . sha: doc_id: cord_uid: e anaxck nan usually diffuse nature. as such, the term uri has come to encompass multiple clinical entities including pharyngitis, sinusitis, and bronchitis, as well as nonspecific respiratory infections, a designation that includes the common cold. the classification scheme based upon the predominate anatomic site of the presenting symptom complex tends to be poorly specific for directing therapy [ ] . these diagnoses and their treatment will be examined relative to the nonspecific uri. determining the evidence-based indications and relative value of antibiotic therapy for each may limit unnecessary use. although a thorough examination of the viral uri is beyond the scope of this article, brief review of the nonspecific or undifferentiated uri and its treatment may provide some context for a discussion of these more specific conditions. the inappropriate use of antibiotics, for respiratory infections in particular, has been implicated in the emergence of antibiotic resistance, especially in streptococcus pneumoniae [ ] . guidelines for diagnosis and treatment of the uri based upon a nonfocal presentation have been developed in an effort to limit the indiscriminate use of antibiotics for what are generally viral illnesses [ ] . the course of the viral uri, also termed acute rhinopharyngitis, is generally self-limited in nature and mild in severity. symptoms may persist for greater than week in duration in more than % of cases, and persist for weeks in % [ ] . the cause is most commonly rhinovirus and to a lesser extent coronavirus (typically in midwinter), and adenovirus (typically in spring to fall). although laboratory identification can be accomplished, the time required to identify the cause may exceed the duration of the illness and the yields may be highly variable [ ] . syndromes involving symptoms of greater severity and more commonly including the lower respiratory tract are caused by influenza, parainfluenza, and respiratory syncitial virus [ ] . there may be some benefit in the prompt identification of influenza to initiate timely neuraminidase inhibitor therapy [ , ] . it appears, however, that neither a rapid influenza test nor a clinical prediction rule is superior to clinical judgment in establishing the diagnosis [ ] . treatment of the uri is essentially symptom-directed, because antibiotic treatment does not appear to contribute to resolution of the illness. their benefit in preventing life-threatening complications, such as meningitis, sepsis, or abscess, in such patients has not been adequately assessed [ ] . bacterial sinusitis may develop as a complication in a minority of patients and is reviewed later. improvement is expected in the uri by the first week, notwithstanding reports that sinus changes may be demonstrated on ct studies in most patients in the first few days of illness [ ] . a recent systematic review of the literature has found insufficient evidence to warrant the use of antibiotics for uris in adults or children [ ] . adults experienced a greater rate of adverse effects with antibiotics than with placebo. patients who have respiratory infections may have certain expectations for antibiotic prescriptions, and physicians may prescribe antibiotics based on their perceptions of these expectations; however, patient satisfaction has been correlated with physician time spent with them and the patient's understanding of their diagnosis to a greater extent than the prescription of an antibiotic [ ] . when patients who had upper respiratory symptoms were randomized to receive immediate antibiotics, or to have antibiotic use delayed by hours, clinical outcomes were not significantly different for most symptoms, although some symptom scores worsened in the delayed use groups who had sore throat and otitis media [ ] . significant variability of symptom scores was noted between these trials. clinical decision support systems, guiding physicians in appropriate antibiotic use for respiratory infections may reduce inappropriate use [ ] . use of oral and topical nasal decongestants provides benefit for shortterm use in adults; there is no evidence supporting their use in children [ ] . studies of treatment with antihistamines alone for the common cold have shown no faster recovery, and only small benefit for sneezing and rhinorrhea at the expense of sedation. in combination with decongestants, no effect was seen in small children, but some benefit in general recovery and nasal symptoms was noted in older children and adults [ ] . intranasal ipratropium decreases rhinorrhea, and may decrease sneezing and promote nasal drying [ ] . evidence for the use of zinc in the treatment of uri is inconclusive [ ] , and echinacea extract showed no significant effects in either infection rates with rhinovirus or symptom severity [ ] . the role of vitamin c in prevention appears to be limited to perhaps those individuals exposed to severe physical or low-temperature stress, and therapeutic benefit was limited or equivocal [ ] . the pharynx is the common portal to the human respiratory and digestive tracts and is exposed to multiple potential pathogens. pharyngitis is predominantly viral in etiology, accounting for as much as % of all cases in adults [ ] . the cardinal feature, sore throat, is also a feature of the common cold. in adenovirus infections it is usually accompanied by adenitis and conjunctivitis, and is associated with erosive stomato-pharyngitis in herpes simplex [ ] . in coxsackie virus infections sore throat is associated with pharyngeal vesicles (herpangina) or with hand and foot vesicles [ ] . epstein-barr virus infection is characterized by the fatigue, functional impairment, and cervical lymphadenopathy of mononucleosis [ ] . bacterial causes of sore throat include group a b-hemolytic streptococcus (gabhs), the most common cause of bacterial pharyngitis, and non-group-a streptococcus. less common causes are mycoplasma pneumoniae, chlamydia pneumoniae, and neisseria gonorrhoeae. a rare cause is arcanobacterium haemolyticum, which is associated with an exanthema that may mimic the rash of scarlet fever [ ] . among these various causes, the only commonly occurring infection for which antibiotic therapy is beneficial is gabhs. the goals of treating gabhs include expediting clinical recovery, decreasing the likelihood of suppurative complications (such as abscess), preventing acute rheumatic fever, and limiting transmission of the disease [ ] . at the same time, by excluding from treatment those patients who have pharyngitis who are not infected by gabhs, the adverse effects of treatment and the emergence of antibiotic-resistant bacteria are avoided [ ] . gabhs may account for % to % of pharyngitis in adults and % to % in school age children, yet in a national survey % of adults [ ] and % of children [ ] who had pharyngitis were treated with antibiotics. the typical symptoms of streptococcal pharyngitis are sudden onset of sore throat accompanied by fever. in children, abdominal pain and vomiting are also reported. the presence of cough and rhinorrhea suggest a non-gabhs etiology. the physical findings may include pharyngeal erythema, tonsillar exudates, and enlarged cervical lymph nodes. fever, palatal petechiae and uvular swelling, none of which are specific for streptococcal infection, are also found. all of these historical and physical features are common to infections by other agents, including group c and group g streptococcus [ ] . because a physician may be unable to clinically distinguish gabhs from the causes of pharyngitis for which antibiotics should be withheld, a laboratory test will in some cases be necessary to confirm the diagnosis [ ] . a throat culture, consisting of a throat swab incubated on blood agar and confirming gabhs growth by the inhibitory effects of bacitracin, has been the standard for diagnosis; however, results of this culture are only available after to hours, with a delay in immediate and appropriate therapy. with this delay, the benefits of timely treatment, which include reducing risk of disease transmission, diminishing symptoms, and speeding recovery, are jeopardized [ ] . rapid antigen detection testing (radt) for gabhs was developed to provide more immediate, albeit more costly results, with a demonstrated specificity exceeding % relative to blood agar culture [ ] . a clinical score based on the cumulative presence or absence of specific clinical features may be used to exclude or entertain the diagnosis of gabhs, thereby reducing the need for both throat cultures and unnecessary antibiotics [ , ] . use of a sore throat score to determine treatment of children and adults in a university-based family practice demonstrated a % reduction in antibiotic prescription compared with usual care [ ] . in a community-based family practice, mcisaac and colleagues [ ] assessed a clinical score for validity that resulted in a reduction in antibiotic prescription of . %, and a reduction in throat cultures of . %. sensitivity and specificity of the score relative to culture was . % and . % respectively ( table ) . a systematic review of the clinical diagnosis of strep throat by ebell and coworkers [ ] showed that the presence of tonsillar or pharyngeal exudates or exposure to strep throat infection in the previous weeks were reliable in predicting the likelihood of gabhs pharyngitis (positive likelihood ratio [lr] of . , . , and . , respectively). the absence of tender anterior cervical nodes, tonsillar enlargement, or exudates were reliable predictors that gabhs was not present (negative lr of . , . , and . , respectively). no single element of the history or physical examination alone was sufficient for excluding or diagnosing strep throat. based on the prevalence of gabhs in a given population, clinical prediction rules can be used to calculate the individual's probability of gabhs pharyngitis ( table ) . the american college of physicians (acp) developed guidelines for the diagnosis of pharyngitis in adults based upon clinical prediction rules [ ] . throat culture is excluded from this diagnostic algorithm because the delay in its result precludes an immediate treatment decision and the potential benefit of symptom relief. an additional concern is the failure of culture to discriminate between infection and the carrier state. instead, recommendations are to assess by radt the patient who have two to three clinical criteria (intermediate risk) and treat only for a positive test. patients who have three or four criteria are treated empirically. all others are neither tested nor treated. this approach acknowledges the chance of undertreatment based on testing only those designated as intermediate to high risk by criteria (both sensitivity and specificity of approximately %), while emphasizing the relatively low likelihood of suppurative complications and acute rheumatic fever. a cost-effectiveness analysis compared five strategies in the diagnosis and management of pharyngitis in adults assuming a gabhs prevalence of % [ ] . a decision model was constructed to evaluate the strategies of observation only, empiric therapy, two-plate throat culture, radt (optical immunoassay) followed by culture to confirm negative results, or radt alone. the findings of this analysis generally supported the acp guidelines, except that a marginal superiority in costs and effectiveness is seen with culture. the other strategies differed little in cost-effectiveness; however, empirical therapy achieved reasonable cost-effectiveness only when very high gabhs prevalence is assumed. guidelines provided by the infectious disease society of america for the diagnosis and management of gabhs pharyngitis calls for laboratory testing based on epidemiological and clinical features and exclusion of those who appear at low risk [ ] . confirmatory culture of negative radt results in adults is not recommended. a confirmatory throat culture is advised for radt negative children and adolescents because there is a higher prevalence of gabhs and acute rheumatic fever. follow-up cultures are not recommended after appropriate therapy in asymptomatic individuals except under circumstances of an epidemic in a closed community or recurrent infection in a household when carriage is suspected. treatment of gabhs is aimed at eradication of the organism from the upper respiratory tract [ ] . a cochrane review [ ] assessed the benefits of antibiotic treatment of sore throat. studies demonstrating a reduction in rheumatic fever with antibiotic therapy found benefits were modest, with large numbers of individuals needed to treat to derive meaningful benefit [ ] . a reduction in symptoms (sore throat, headache, or fever) by about one half was seen with antibiotic therapy at . days of illness. five patients would need to be treated with antibiotics to eliminate one sore throat by day and seven patients would need to be treated to eliminate one sore throat by day . a subgroup analysis of patients evaluated with a throat swab for streptococcus revealed significantly greater symptom reduction with antibiotic treatment in those who had a positive swab than a negative swab. antibiotic therapy resulted in a reduction in the incidence of suppurative complications, including otitis media, sinusitis, and quinsy (peritonsillar abscess) compared with placebo. penicillin is recommended for the treatment of gabhs pharyngitis [ ] . in penicillin-allergic patients, erythromycin is recommended. gabhs resistance to penicillin has not been reported; however, some resistance to macrolides, including erythromycin, has been seen [ ] . first-generation cephalosporins are acceptable alternatives for patients who have a history of non-anaphylactic allergy to b-lactam antibiotics. although a -day course of penicillin is recommended for eradication of gabhs, shorter courses of therapy with other agents have been shown to be effective [ , ] . providing written instructions on the use of the antibiotics for sore throat has improved compliance [ ] . treatment of pharyngitis with corticosteroids has demonstrated inconsistent results. in one study [ ] , a single dose of oral dexamethasone ( . mg/kg) provided greater pain relief than placebo in children who had moderate to severe pharyngitis caused by gabhs and non-gabhs. in a somewhat smaller study with a similar design [ ] , the antigen-positive subset of children reported an improvement in time to onset of pain relief with dexamethasone treatment compared with placebo. no significant decrease in time to onset of pain relief or time to complete pain relief was seen in the antigennegative treatment group compared with placebo. inflammation of the mucosa of the paranasal sinuses, or sinusitis, is among the group of respiratory illnesses (excluding pharyngitis) which was ranked second in frequency of visits to outpatient clinics in [ ] . the term rhinosinusitis may more accurately describe the condition, because inflammation of the nasal mucosa is usually present as well [ ] . although it is usually caused by a viral infection, rhinosinusitis is often attributed by patients and physicians to bacterial cause. noninfectious causes of sinusitis include allergy, foreign body, deviated septum, tumor, polyps, and barotrauma [ ] . although bacterial sinusitis may complicate only . % to % of uris, it accounts for a disproportionate % of antibiotic prescriptions written [ ] . acute bacterial rhinosinusitis (abrs) shares symptoms with the viral uri, including rhinorrhea, nasal congestion, facial pressure, and fever, which may lead the patient to request antibiotics from their physician. though antibiotic therapy may be beneficial for bacterial sinusitis, the definitive diagnosis is made by sinus aspiration, an invasive procedure not typically performed in the office setting. instead the physician must rely on the presentation of a persistent symptom complex, including facial pressure, nasal obstruction, nasal discharge, hyposmia, and fever [ ] . the treatment guidelines for sinusitis have generally been directed at reducing the inappropriate use of antibiotics for viral respiratory infections [ ] . this article addresses the evaluation and therapy of abrs in immunocompetent adults and children aged years and older. the paranasal sinuses typically involved in abrs are the maxillary and ethmoid sinuses. these sinuses are present at birth, having formed in the third and fourth gestational month [ ] . the sphenoid sinus develops through early childhood and the frontal sinuses develop by adolescence. infections of the frontal sinuses typically present with greater intensity and severity and may require hospital admission. bacterial infection typically follows the impairment of mucus clearance and the obstruction of sinus ostia caused by viral respiratory infection. the paranasal sinuses are ordinarily sterile. with infection, the most common microorganisms isolated from maxillary sinuses are s pneumoniae, haemophilus influenzae, and moraxella catarrhalis. sinusitis has been defined as acute when symptom duration is of less than weeks, and chronic when symptoms persist for more than weeks [ ] . complications are potentially quite serious because of the anatomical relationship of the sinuses to the eyes and brain. these complications include orbital cellulitis, orbital abscess, and potentially life-threatening intracranial complications such as cavernous sinus thrombosis, meningitis, and brain abscess. chronic sinusitis is defined by the presence of two major, or one major and two minor criteria. criteria are listed in box [ ] . noninfectious factors such as allergy and irritants appear to initially cause inflammation, and then bacteria may have some role in its persistence. antibiotic therapy for chronic rhinosinusitis has not been shown to improve outcomes in children, whereas the benefits of antibiotic therapy for adult chronic sinusitis have not been studied [ ] . endoscopic surgery may be used in the treatment of chronic rhinosinusitis that has failed to resolve with conservative therapy [ ] . the diagnosis of abrs is complicated by the symptoms it shares with viral uri and by the lack of data correlating these symptoms with sinus aspirate findings [ ] . clinical impression alone may result in % to % accuracy in diagnosis by the primary care physician [ ] . current guidelines provide for a diagnosis of abrs in patients who have duration of illness with typical symptoms of more than to days [ , , ] . patients who have rhinovirus infection may have symptoms from one to days, but most are well by days, and % have resolution of symptoms by days [ ] . evaluation of patients' symptoms and physical features relative to radiological findings has been studied. features associated with significant ct findings (air-fluid levels or complete sinus opacification) included purulent rhinorrhea, erythrocyte sedimentation rate greater than , purulent nasal secretions, and ''double sickening,'' or symptom worsening after an initial resolution [ ] . ct findings are, however, not specific for abrs, and are seen in patients who have uri [ ] . williams and colleagues [ ] used sinus radiographic changes to identify five predictors of abrs, namely, maxillary toothache, poor response to decongestants, history of discolored nasal discharge, mucopurulent nasal discharge on examination, and abnormal transillumination. no single finding had sufficient specificity and sensitivity to be diagnostic [ ] . although transillumination of the sinuses was found to be an independent predictor of sinusitis, its utility is limited to the maxillary and frontal sinuses, it is difficult to perform and is likely unreliable in younger children; its practical use appears limited [ ] . hansen and coworkers [ ] found a relationship between positive bacterial culture of sinus aspirates and unilateral tenderness of the maxillary sinus, maxillary pain, maxillary toothache, and mucopurulent nasal discharge. a study of emergency room patients who had symptoms of sinusitis [ ] , some for more than days, found an increased likelihood of abrs (with purulent sinus aspirate, not cultured) in those who had unilateral predominate purulent nasal discharge and unilateral predominate facial pain by history, bilateral purulent nasal discharge, and pus in the nasal cavity. reviewing the studies to identify clinical signs and symptoms of abrs, it appears that purulent nasal discharge, unilateral maxillary tenderness, and worsening of symptoms after initial improvement predict a higher likelihood of the diagnosis [ ] . radiography has been employed in the evaluation of abrs, but there are significant limitations in its ability to reliably predict this diagnosis. in particular, mucosal thickening lacks specificity as a finding in abrs, and is no more predictive than clinical judgment. patients who had either complete sinus opacification or air fluid levels benefited from treatment for abrs with amoxicillin [ ] . these findings have relatively high specificity, approximately % and % respectively. the sensitivity of a radiographic negative for these three findings is about %, and the normal study can be powerful evidence for excluding abrs [ , ] . management guidelines exclude radiography from the routine evaluation of sinusitis in both children and adults [ ] [ ] [ ] . ct has the ability to visualize the paranasal sinuses and the osteomeatal complex, the anatomic entity central to the diagnosis of abrs. lindbaek and colleagues [ ] found no difference in outcomes for patients who had a clinical diagnosis of sinusitis, but only mucosal thickening on ct treated with either amoxicillin or placebo. in patients undergoing ct examination for reasons other than sinusitis but who had a history of recent uri, % were found to have sinus abnormalities [ ] . the changes seen in ct examination are not sufficiently specific for sinusitis, and ct should be used carefully and within the clinical context. when surgical management is being considered, as in cases of persistent infection or complicated infections, ct may be indicated in planning therapy [ , ] . the rational approach to treatment of abrs is somewhat limited by the diagnostic uncertainties that have been described. nevertheless, guidelines have been published that advocate antibiotic therapy dictated by the severity and duration of symptoms [ ] [ ] [ ] . antibiotic therapy has been shown to shorten the duration of symptoms in patients who have purulent rhinorrhea compared with placebo; however, no difference in overall recovery was seen, and the antibiotic group had a higher frequency of diarrhea [ ] . when study participants were limited to those who had pus in the nasal cavity, facial pressure, or nasal discharge lasting longer than days, the group treated with antibiotics experienced symptom improvement earlier ( versus days), but there was no significant difference in improvement at days [ ] . a cochrane review of antibiotic therapy for persistent (more than days) nasal discharge in children found a reduction in the probability of persistent symptom in the short to medium term, with eight children needed to be treated to achieve one additional cure [ ] . a systematic review of antibiotic therapy for acute maxillary sinusitis in adults included studies with significant variability among them that compared antibiotic to control or antibiotics from different classes [ ] . penicillin improved clinical cures and radiographic outcomes. no significant differences were seen between classes of antibiotics. recommendations of the american college of physicians-american society of internal medicine (acp-sim) are for symptomatic treatment or reassurance for those who have mild to moderate symptoms [ ] . antibiotics are reserved for those who have severe or persistent symptoms of more than days. it is surmised that the modest improvements seen in the studies using relatively nonspecific standards (clinical or radiographic) were caused by the inclusion of patients who have no bacterial infections. the agent with the narrowest spectrum active against the likely pathogens is recommended, and amoxicillin is preferred. the american academy of otolaryngology-head and neck surgery recommends initial therapy of adults who have mild disease and who have not received antibiotics in the previous to weeks with first-line agents such as amoxicillin. those who have mild disease but antibiotic use in the previous to weeks or moderate disease are treated with second-line agents, including fluoroquinolones. failure to respond after hours of therapy should prompt a re-evaluation of therapy [ ] . likewise, for the treatment of children, severity of disease and prior treatment with antibiotics determine therapy choice, excluding fluoroquinolones. efficacy is predicted according to a mathematical model based on the expected pathogens, spontaneous resolution rates, and in vitro activity. the american academy of pediatrics recommends antibiotic therapy for children who have sinusitis meeting the clinical definition and whose symptoms are severe or persistent [ ] . amoxicillin is recommended at usual doses ( mg/kg) in two divided doses for children who have mild to moderate disease and who do not attend day care and have not recently been treated with antibiotics. failure to improve (reduction in respiratory symptoms and in general well-being) within to hours should lead to reconsideration of the diagnosis or changes in therapy. high-dose amoxicillin ( mg/kg) is advised if patients fail to improve with usual doses of amoxicillin, have moderate to severe illness, have been recently treated with antibiotics, or attend day care. alternatives for b-lactam allergic patients include cefdinir, cefuroxime, or cefpodoxime. clarithromycin and azithromycin are recommended in anaphylaxis-type, b-lactam allergic patients. there are few data concerning the use of additional non-antimicrobial therapies for sinusitis. a -day course of prednisone ( . - . mg/kg) combined with cefpodoxime resulted in less pain and nasal obstruction in the first days compared with placebo in adults who have radiograph-or endoscope-documented maxillary rhinosinusitis [ ] . daily hypertonic saline use for months by patients who had a history of sinusitis resulted in improved symptom severity and sinusitis-related disability scores, and less antibiotic use [ ] . the addition of intranasal steroids to antibiotic therapy for acute rhinosinusitis in patients who had [ ] and did not have [ ] a history of chronic or recurrent sinus symptoms achieved a higher and more rapid rate of patient-reported clinical success than placebo. unlike the other diagnostic entities reviewed here, acute bronchitis refers to inflammation of a portion of the lower respiratory tract. like pharyngitis and sinusitis, however, it is a condition that shares a primary symptom, in this case cough, with the nonspecific uri, an illness of viral origin not requiring antibiotic therapy. and as with these other specific conditions, there is evidence for benefit from antibiotic therapy in only the minority of cases. because of its relationship to the viral uri, acute bronchitis, defined as an acute cough illness in an otherwise healthy adult, is included here for review [ ] . acute bronchitis generally refers to an infection of the respiratory tract in which cough is the predominate feature [ ] . when surveyed on the definition of acute bronchitis, there is disagreement among family physicians, some qualifying the cough as purulent, and others indicating that it must only be productive [ ] . although a systematic review found antibiotic therapy for acute bronchitis offers only modest benefit [ ] , it is reported that % to % of office visits for this diagnosis result in a prescription for antibiotics [ ] . treatment guidelines have been developed in an effort to limit unnecessary antibiotic therapy for this condition [ ] . the majority of cases of acute bronchitis are caused by infection by viruses, including influenza, parainfluenza, and respiratory syncytial virus, resulting in lower tract disease; and rhinovirus, coronavirus, and adenovirus, usually resulting in upper tract disease [ ] . an etiological study of adults who had lower respiratory tract infection and controls identified rhinovirus in %, and influenza in % of patients [ ] . noninfectious causes of acute cough include allergy, asthma, environmental exposures, heart failure, gastroesophageal reflux, and tumor [ ] . cough-variant asthma may be difficult to distinguish from uncomplicated acute bronchitis, which may also be associated with transient bronchial hyperresponsiveness but typically resolves after to weeks [ ] . the other causes are identified by unique epidemiological or clinical features (table ). bacterial infection causes fewer than % of the cases of infectious bronchitis; only bordetella pertussis, m pneumoniae, and c pneumoniae, have been identified as primary agents [ ] . pneumonia is a relatively frequent and important cause of cough that must be excluded as a diagnosis because it may be associated with significant mortality. the cough of acute bronchitis may be productive and may be accompanied by wheezing. this reflects hypersensitivity of the bronchial epithelium that can be measured by pulmonary function testing, with abnormalities most prominent or more weeks after infection [ ] . these abnormalities typically persist for to weeks, but may last longer. in a study of patients presenting to a general medical practice who have acute cough, purulent sputum, or abnormal auscultory findings, it was to weeks before most patients were well and able to resume usual activities [ ] . although the productivity of the cough, and in particular the purulence of the sputum, is associated with antibiotic use by physicians [ ] , this feature, a nonspecific sign of inflammation, is not predictive of a bacterial infection [ ] . established criteria for the diagnosis of pneumonia do not include purulent sputum, and only % of patients presenting with purulent sputum have pneumonia [ ] . a rule to exclude the diagnosis of pneumonia without the need for further evaluation is based on the absence of abnormal vital signs (tachycardia, tachypnea, and fever) and the absence of specific adventitious breath sounds (consolidation signs, such as rales, egophony, or fremitus) [ ] . although this may guide the physician in the decision to proceed with radiography, other factors that may influence this decision include the age and comorbidities of the patient, and the likelihood of a seasonal illness such as influenza. the use of c-reactive protein measurement to distinguish bacterial pneumonia from uncomplicated acute bronchitis has been studied but does not appear to offer an advantage in the evaluation of patients who have acute cough [ ] . infection with b pertussis should be considered if there is a history of exposure to an individual who has confirmed pertussis or when cough persists. nasopharyngeal swab for polymerase chain reaction testing is particularly useful for diagnosis in previously vaccinated individuals who less frequently meet clinical criteria for the disease [ ] . increasing reports of pertussis appear to be due to waning vaccine immunity in adolescents and young adults [ ] . use of serology for the diagnosis of pertussis and for diagnosis of infection with m pneumoniae or c pneumoniae is limited, in part because seroconversion may occur in asymptomatic individuals [ , ] . sputum culture is poorly sensitive for these species and is not recommended. m pneumoniae infection commonly produces an influenza-like tracheobronchitis with a self-limited course resolving in to weeks without treatment [ ] . it may also produce an atypical pneumonia. c pneumoniae infection of the respiratory tract is usually asymptomatic, but may be associated with bronchitis or pneumonia. there has been speculation that c pneumoniae may be implicated in adult new-onset asthma based on serological findings in these patients [ ] . therapy treatment guidelines derived from the available evidence recommend against routine antibiotic therapy for uncomplicated acute bronchitis [ ] . systematic reviews have failed to discover more than marginal benefit in treatment with antibiotics of acute bronchitis patients, including smokers [ , ] . although a shorter duration of cough (by . days), productive cough (by . days), and feeling ill (by . days) was noted in the treated group in one review [ ] , there was no difference at follow-up for night cough, productive cough, or activity limitations. in another systematic review [ ] , there were significantly more side effects in the antibiotic treatment group. no trials have specifically examined antibiotic treatment for smokers who have acute bronchitis, but a review of existing data found the same or less benefit for smokers compared with nonsmokers [ ] . in a trial of azithromycin or vitamin c therapy for adults who had acute bronchitis, there was no significant difference in health-related quality of life after days [ ] . antibiotic therapy is recommended for acute bronchitis caused by pertussis [ ] . a cochrane review of antibiotics for pertussis [ ] found that short-term therapy with azithromycin ( days), clarithromycin ( days), or erythromycin ( days) was as effective as long-term therapy with erythromycin in eradicating infection from the nasopharynx with fewer side effects in the short-term treatment. although the clinical course of the illness is not altered, treatment is recommended for individuals who have bronchitis and who have been exposed to documented pertussis in order to decrease spread of the disease [ ] . although there is scant evidence supporting the use of antibiotics for acute bronchitis, the evidence for use in chronic bronchitis and its exacerbation is mixed [ ] . the us food and drug administration (fda) no longer considers antibiotic trials for acute bronchitis warranted because of lack of evidence of benefit [ ] . nevertheless many of the antibiotics with indications for chronic bronchitis are used by physicians for the treatment of acute bronchitis. perhaps this is due in part to the failure to distinguish between the otherwise healthy patients with acute, self-limited cough and the patient who has worsening symptoms associated with irreversible lung disease [ ] . various agents used to provide symptom relief for the patient who has acute bronchitis have been studied. because bronchial hyperresponsiveness with bronchospasm is a feature of the disease in a significant percentage of patients [ ] , it is not surprising that the evidence supports the use of bronchodilators in individuals who demonstrate airflow obstruction [ ] . cough scores did not change after treatment in children who had no airway obstruction. in studies of adults, there was no difference in cough at days for treatment or control groups; however subgroups who had airflow limitation had lower cough scores, and those who had wheezing at baseline had quicker resolution of cough [ ] . there is little evidence to support the use of antitussives specifically for acute bronchitis. guidelines suggest that there may be modest responses to dextromethorphan and codeine preparations [ ] . few studies have evaluated the efficacy of guaifenesin as an expectorant, although its use is widespread. it has been found to inhibit capsaicin-induced cough in patients who have uri [ ] . an herbal agent, pelargonium sidoides (eps ) was studied against placebo in adults who had acute bronchitis and less than days of cough [ ] . a significant decrease in symptom severity scores and in work disability was found in the treatment group, with no difference in adverse effects. the approach to the patient who has acute cough should be to first identify, based on history and physical examination, individuals likely to have pneumonia who require further evaluation and specific therapy (strength of recommendation [sor]: a) in the remaining patients there is a subset for whom treatment with antiviral therapy for influenza may be indicated based upon clinical judgment, and seasonal prevalence. if there is known exposure to pertussis, macrolide therapy should be considered. antibiotic therapy is otherwise not indicated, and is unlikely to provide benefit to the patient. symptomatic therapy, including inhaled-bronchodilators for those who show evidence of airway obstruction, and antitussives for those who have chest discomfort or sleep disturbance from cough, may be added. table evidence-based recommendations for the treatment of uri antibiotics are not indicated in the treatment of a nonspecific uri in adults and children. a delayed antibiotic therapy may decrease use with no effect on outcome except symptom score for otitis media and pharyngitis. oral and topical decongestants are beneficial in adults with uri. a decongestant/antihistamine combinations improve recovery and nasal symptoms in older children and adults with uri. radt for gabhs is recommended if pretest likelihood is intermediate to high. a culture for gabhs is recommended to confirm negative radt in children and adolescents. c penicillin is recommended therapy for gabhs if no allergy history. a oral dexamethasone is recommended to speed pain relief in pharyngitis. b antibiotic therapy does not improve outcomes in children with chronic sinusitis. a radiographs are not recommended for routine evaluation of acute sinusitis in children and adults. antibiotics are recommended for persistent or severe symptoms in acute sinusitis. combination prednisone and antibiotics decrease symptoms in acute sinusitis. antibiotic therapy is not indicated for acute bronchitis unless symptoms persist after pertussis exposure. a bronchodilator therapy is recommended in bronchitis with evidence of airway obstruction. antitussive therapy may improve cough in bronchitis. c patient education on appropriate antibiotic use decreases use of antibiotics for uri. a patient education by the physician on the appropriate treatment of acute bronchitis can result in lower antibiotic usage without affecting clinical outcomes [ ] . these efforts may include providing an informational leaflet, or during the visit reviewing with the patient the following. there is a very high likelihood that the illness will resolve with or without antibiotics. inappropriate antibiotic use is associated with emergence of antibioticresistant bacteria. antibiotic use is associated with risk of adverse events, including serious allergic reactions. avoid terms such as bronchitis that engender fear but have no value in specifying treatment. the patient presenting to the primary care physician with infection of the upper respiratory tract is most likely experiencing a frequent and usually self-limited viral infection. the viral uri is characterized by nonspecific symptoms including sore throat, nasal congestion, and cough that may respond to symptom-targeted measures. in those who have pharyngitis and features typical of streptococcal infection, rapid in-office testing may guide antibiotic treatment and limit their unwarranted use. the appropriate treatment of acute sinusitis is dictated by an assessment of historical and physical features generally not requiring diagnostic imaging. when cough is the predominate symptom in the immunocompetent individual and pneumonia is excluded, then treatment with antibiotics is not indicated. physician responsibility in the judicious use of antibiotics may reduce the emergence of bacterial resistance and also decrease adverse reactions. patient education may mitigate demands for unnecessary therapy and preserve satisfaction with their care. table summarizes the evidence-based recommendations for the treatment of uri. national ambulatory medical care survey: summary bacterial infections of the upper respiratory tract antibiotic prescribing for children with cold, upper respiratory tract infections, and bronchitis antibiotic prescribing for adults with colds, upper respiratory infections, and bronchitis by ambulatory care physicians evaluation and treatment of the patient with acute undifferentiated respiratory tract infection antibiotic resistance and the need for the rational use of antibiotics principles of appropriate antibiotic use for treatment of nonspecific upper respiratory tract infections in adults principles of appropriate antibiotic use for treatment of nonspecific upper respiratory tract infections in adults: background aetiological role of viral and bacterial infections in acute adult lower respiratory tract infection (lrti) in primary care neuraminidase inhibitors for preventing and treating influenza in children neuraminidase inhibitors for preventing and treating influenza in healthy adults performance characteristics of clinical diagnosis, a clinical decision rule, and a rapid influenza test in the detection of influenza infection in a community sample of adults computed tomographic study of the common cold antibiotics for the common cold and acute purulent rhinitis antibiotics and respiratory infections: are patients more satisfied when expectations are met? delayed antibiotics for symptoms and complications of respiratory infections clinical decision support and appropriateness of antimicrobial prescribing nasal decongestants for the common cold antihistamines for the common cold effectiveness and safety of intranasal ipratropium bromide in common colds zinc for the common cold an evaluation of echinacea angustifolia in experimental rhinovirus infections vitamin c for preventing and treating the common cold acute pharyngitis family medicine principles and practice prospective study of the natural history of infectious mononucleosis caused by epstein-barr virus arcanobacterium haemolyticum pharyngitis and exanthema. three case reports and literature review practice guidelines for the diagnosis and management of group a streptococcal pharyngitis principles of appropriate antibiotic use for acute pharyngitis in adults antibiotic treatment of adults with sore throat by community primary care physicians: a national survey antibiotic treatment of children with sore throat clinical symptoms and signs in sore throat patients with large colony variant beta-haemolytic streptococci groups c or g versus group a rapid diagnosis of pharyngitis caused by group a streptococci the diagnosis of strep throat in adults in the emergency room a clinical score to reduce unnecessary antibiotic use in patients with sore throat the validity of a sore throat score in family practice the rational clinical examination. does this patient have strep throat diagnosis and management of adults with pharyngitis antibiotics for sore throat two dosages of clarithromycin for five days, amoxicillin/clavulanate for five days or penicillin v for ten days in acute group a streptococcal tonsillopharyngitis the effect of written information on adherence to antibiotic treatment in acute sore throat effectiveness of oral dexamethasone in the treatment of moderate to severe pharyngitis in children oral dexamethasone for the treatment of pain in children with acute pharyngitis: a randomized, double-blind, placebo-controlled trial national hospital ambulatory medical care survey: outpatient department survey principles of appropriate use of acute rhinosinusitis in adults: background acute community-acquired bacterial sinusitis: the value of antimicrobial treatment and the natural history antimicrobial treatment guidelines for acute bacterial rhinosinusitis principles of appropriate use for acute sinusitis in adults subcommittee on management of sinusitis and committee on quality improvement diagnosis of chronic rhinosinusitis do antibiotics improve outcomes on chronic rhinosinusitis? current concepts in therapy of chronic rhinosinusitis and nasal polyps rhinovirus infections in an industrial population. ii. characteristics of illness and antibody response use of symptoms, signs, and blood tests to diagnose acute sinus infections in primary care: comparison with computed tomography clinical evaluation for sinusitis. making the diagnosis by history and physical examination predicting acute maxillary sinusitis in a general practice population analysis of symptoms and clinical signs in the maxillary sinus empyema randomised, double blind, placebo controlled trial of penicillin v and amoxicillin in treatment of acute sinus infections in adults antibiotic treatment of patients with mucosal thickening in the paranasal sinuses, and validation of cut-off points in sinus ct incidental paranasal sinus abnormalities on ct of children: clinical correlation the role of computed tomography and magnetic resonance imaging in patients with sinusitis with complications does amoxicillin improve outcomes in patients with purulent rhinorrhea? a pragmatic randomized double-blind controlled trial in family practice are antibiotics beneficial for patients with sinusitis complaints? a randomized double-blind clinical trial antibiotics for persistent nasal discharge (rhinosinusitis) in children antibiotics for acute maxillary sinusitis treatment of functional signs of acute maxillary rhinosinusitis in adults. efficacy and tolerance of administration of oral prednisone for days efficacy of daily hypertonic saline nasal irrigation among patients with sinusitis: a randomized controlled trial comparison of cefuroxime with or without intranasal fluticasone for the treatment of rhinosinusitis. the caffs trial: a randomized controlled trial nasonex sinusitis group. effective dose range of mometasone furoate nasal spray in the treatment of acute rhinosinusitis viral infection of the respiratory tract uncomplicated acute bronchitis diagnosis of acute bronchitis in adults: a national survey of family physicians antibiotics for acute bronchitis principles of appropriate antibiotic use for treatment of acute bronchitis in adults acute bronchitis principles of appropriate antibiotic use for treatment of uncomplicated acute bronchitis: background acute bronchitis: course of symptoms and restrictions in patients' daily activities the relation between purulent manifestations and antibiotic treatment of upper respiratory tract infections does this patient have community acquired pneumonia? diagnosing pneumonia by history and physical examination diagnosing pertussis: the role of polymerase chain reaction overview of pertussis: focus on epidemiology, sources of infection, and long term protection after infant vaccination harrison's principles of internal medicine chlamydia pneumoniae as a respiratory pathogen quantitiative systematic review of randomized controlled trials comparing antibiotic with placebo for acute cough in adults antibiotic treatment of acute bronchitis in smokers azithromycin for acute bronchitis: a randomized, double-blind, controlled trial antibiotics for whooping cough (pertussis) antibiotics in chronic obstructive pulmonary disease exacerbations. a meta-analysis beta -agonists for acute bronchitis do inhaled beta-agonists control cough in uri's or acute bronchitis? effect of guaifenesin on cough reflex sensitivity efficacy and safety of an extract of pelargonium sidoides (eps ) in adults with acute bronchitis. a randomized, double-blind, placebocontrolled trial reducing antibiotic use for acute bronchitis in primary care: blinded, randomized controlled trial of patient information leaflet key: cord- - b hm e authors: sariola, salla; gilbert, scott f. title: toward a symbiotic perspective on public health: recognizing the ambivalence of microbes in the anthropocene date: - - journal: microorganisms doi: . /microorganisms sha: doc_id: cord_uid: b hm e microbes evolve in complex environments that are often fashioned, in part, by human desires. in a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. the germ theory of disease cast microbes as enemies of the body and the body politic. antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. public health perspectives such as “precision public health” and “one health” have recently been proposed to further manage microbial populations. however, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. we propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. this perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the “one health” model with the genomic methodologies utilized in the “precision public health” model. in the anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions. the anthropocene marks the end of a period characterized by the human triumph of nature, and nowhere is this more prominent than in public health. the heroic era of microbiology made pasteur, koch, lister, and fleming household names, and few have done more for humanity [ ] [ ] [ ] . the lifespan of a newborn parisian was years in ; and a century later, a newborn parisian could expect to live another years [ ] . much of this increase in life expectancy (as well as the expectation to be healthy) has been due to the ability of public health measures-proper sanitation, food surveillance, antisepsis, and anti-viral vaccination-to remove humans from sources of microbial infection. however, our relationship with microbes and their evolution has changed dramatically since the discovery of antibiotics, and the conquest of polio and other endemic viruses in the s and s. the first part of our changing relationship to microbes involves the western world's manufacturing an environment that is increasingly sterile and characterized by the removal of unplanned and unplannable nature [ , ] . indeed, nature is no longer our "state of nature." rather, we have continually separated ourselves from nature, separating the "who" of human lives from the "what" of other lives. and immune systems of plants and animals and ( ) the microbes' ability to transfer dna horizontally from organism to organism. this article attempts to map out a holobiont perspective to public health. it is important to determine how these new views of microbial evolution-lateral gene transfer and mutualistic symbiosis-might be integrated into public health initiatives. it seems that present initiatives ignore or marginalize these phenomenon and that public health might be served better if they were made more central. two pertinent public health paradigms that have received much publicity in recent years are the "precision public health" (pph) paradigm and the "one health" (oh) paradigm. neither of these appear to take seriously our new appreciation of microbial evolution. precision public health (pph) is the application of genomics technology for population health benefits [ , ] , and it is the attempt to make public health into a genomic science. pph began in , when the office of public health genomics of the cdc was formed to "transform" population health care into a genomic science "by identifying, evaluating, and implementing evidence-based genomics practices to prevent and control the country's leading chronic, infectious, environmental, and occupational diseases" [ ] . pph claims that it would be able to analyze one's genome and then prescribe the appropriate drugs and dietary regimens. however, the original promises that genomic science would find common alleles for common diseases were not fulfilled [ , ] . genome-wide association studies (gwas) for cardiovascular disease showed that that genes played a negligible role in predicting heart attacks and that human genetic variation accounted for roughly % of the variation in blood pressure [ ] . moreover, the prediction that a patient would have a heart attack was better made by the number of pushups a patient could do than by genomic analyses [ ] . the genes thought to be associated with depression were "lost" when large trials were done [ ] ; and deficiencies of the gut microbiome may provide a better account of causation [ ] . worse, for any genomic model of public health, was when the genome of the founder of the human genome project, james watson, was analyzed. his dna sequences predicted him to be deaf, blind, growth retarded, and mentally deficient [ , ] . genes work differently in different people. "phenotypic heterogeneity," wherein the same mutant allele causes different phenotypes in different individuals carrying it, is a well-known phenomenon in medical genetics [ , ] and a gene that is "normal" in one generation can cause disease in another [ ] [ ] [ ] . nevertheless, the pph got a shot in the arm (to use an old public health metaphor) by the "all of us" project begun at the usa's national institutes of health [ ] . its website proclaims this to be a big genome, big data approach to public health, whereby "taking into account individual differences in lifestyle, environment, and biology, researchers will uncover paths toward delivering precision medicine..." pph is getting a shot in the other arm from pharmacogenomics, the study of how responses to drugs are influenced by the genetic makeup of the person receiving the drug. according to kapoor et al. [ ] pharmacogenomics, is "one of the cornerstones of precision medicine" and furthermore, is a "significant innovation in health care that possesses the potential to change the paradigm in the practice of medicine, not solely in the way drugs are prescribed, but also in the way drugs are discovered and developed." indeed, precision pharmacogenetics is being touted as a paradigm for third-world health care [ ] . however, this population-centered model of genomic healthcare delivery has been criticized [ ] as being a salvage attempt to rescue something of value from the numerous extremely expensive genome projects that had been the scientific rage of the late th and early st centuries. reardon and others [ , , ] claim pph is most likely dangerous fantasy, exacerbating global economic differences, taking the "public" out of "public health," and shifting responsibility for health onto the individual citizen [ , ] . pph has also been criticized for not recognizing the contributions of the symbiotic microbial genomes [ ] . symbiotic relationships with microbes, as will be discussed below, provide essential metabolic pathways for phenotype production (including those for drug metabolism) and over ten-fold the number of different genes than the zygote-derived genome. whereas precision public health works from one privileged level-the genome-up to humans and human communities, the one health paradigm is consciously interdisciplinary and multi-species-it attempts to envision people, animals, and environments as partners in each other's health on several levels [ , ] . as gibbs [ ] (p. ) notes, "one health is the collaborative effort of multiple disciplines-working locally, nationally, and globally-to attain optimal health for people, animals, and our environment." the one health paradigm, according to friese and nuyts, provides a theoretical basis for research involving nonhumans in public health and used to re-organize relationships between human medicine and animal veterinary medicine so that these two fields communicate in both knowledge and practice [ ] . with contributions from such disciplines as ecosystem services and soil microbiology, one health approach also recognizes the role of environments and ecologies in how human and animal health is shaped. these contributions see ecosystems (including symbiotic microbiomes) as providing economic infrastructure benefits that can be calculated as part of any managed change to the environment [ ] [ ] [ ] . however, overall, the implementation of one health is still fixed on protecting humans from zoonotic infections [ ] . indeed, the cdc, who, ama, and avma websites stress zoonoses and the fact that most infectious diseases are spread by animals. the environment gets short shrift in these sites, and this deficiency has not gone unnoticed. numerous investigators have documented that the environment does not receive attention or funding in most one health networks [ ] [ ] [ ] [ ] . thus, the three components of the one health model are not equal, and the framework is still used to prioritize protection of humans from zoonotic diseases. while the importance of this goal is made obvious in this coronavirus-infused decade, the anthropogenic deterioration of the environment by humans-such as mountain-top coal removal, anthropogenic deforestation, soil microbial deterioration, and reef depletion-are crucial in and of themselves as well as can have enormous effects on public health and do not appear on the one health agenda. only recently have there been calls to put microbes and global climate change under the one health umbrella [ , ] . some of these initiatives have come under the planetary health [ ] , which emphasizes how critical such ecological perspectives are for human health. the planetary health perspective, however, concentrates on the important issues of politics and economics of global health care in the anthropocene, but it does not address the issues the changes in how we perceive microbes. in contrast to the precision public health and one health paradigms, a recently proposed theory holds that microbes such as bacteria are primarily beneficial symbionts of the human body, and their presence is both expected and necessary for normal human health. while pathogenic microbes can cause enormous damage, they are a distinct minority, and public health needs to recognize the other arm of symbiosis-mutualism. this approach, which could revitalize the community-based one health perspective to public health by using the techniques of the molecularly based pph model, is based on the hologenome theory [ ] . this model has recently received support by private funding, most notably from the bill and melinda gates foundation [ , ] . the hologenome theory [ , ] recasts the individual animal or plant (and other multicellular organisms) as a consortium ("holobiont")-the host plus all its symbiotic microbes. during the past two decades, advances in microbiome research have clearly shown that most animals cannot normally develop, function, or reproduce without the vast numbers of microorganisms that inhabit their bodies [ , ] . microbes are essential for normal animal development and physiological functioning. for instance, bacteria acquired at birth from the female reproductive tract are critical to the construction of the gut capillaries and epithelia in several vertebrates [ ] [ ] [ ] [ ] [ ] as well as being critical for the normal development of the vertebrate enteric and cerebral nervous systems [ ] [ ] [ ] . pediatric geneticist barton childs [ ] postulated that each person's genetic endowment constitutes a "biochemical individuality" conferred upon us by our genes. patterson and turnbaugh [ ] have used the same term to designate the properties of the "hologenome"-the genes we inherit from our parents and our microbes, our germ cells and our germs. while we inherit some , genes from our parents, we inherit about million different genes from our parents' bacteria [ ] . indeed, in some instances, the gut microbiome appears to be critical in drug metabolism. digoxin, cyclophosphamide, and numerous other drugs are each metabolized differently by different populations of microorganisms [ ] [ ] [ ] , giving each person an assortment of genes (and drug-metabolizing phenotypes) that can change with each meal [ ] . even the human immune system, so critical in public health, is a holobiont property, and not merely the agency of the host [ ] [ ] [ ] [ ] [ ] . microbes enter into the body at birth, prior to the maturation of the immune system, and they induce the formation of lymphoid tissues [ ] [ ] [ ] . moreover, these lifelong immune activities are well-regulated only in the continuous presence of microbes, which in turn, constantly regulate the microbes that can stay with the animal [ ] [ ] [ ] [ ] [ ] [ ] [ ] . the immune system is a continuously co-constructed property of the holobiont. holobiont public health recognizes that microbes may be pathogenic or beneficial, and that deficiencies in bacteria can cause developmental, immunological, cognitive, and physiological ailments. for instance, kwashiokor, long seen as a protein deficiency disease, manifests as a wasting and anorexic pathology only when certain bacteria are absent [ ] . asthma and allergies are also seen to be due to the absence of protective bacteria, which normally are present to be induce anti-inflammatory regulators [ , ] . in these studies, hanski and colleagues [ ] explicitly link environmental health, microbial diversity, and human health. indeed, a new field of dysbiosis is now emerging, including not only infection, but also other conditions that may be caused by deficient or aberrant microbiomes. here, the normal symbiotic relationships that maintain physiological or developmental continuity, have been abrogated. in recent years, science has traced these networks from associations to specific causal changes that can be tested. while many of these experiments have been performed in mice, the same pathways are known to be present in humans. these non-contagious diseases include asthma and allergy [ ] , kwashiorkor [ , ] , obesity [ , ] , diabetes [ ] , ulcerative colitis [ ] , depression [ , ] , and parkinson's disease [ , ] . these "microbial deficiency diseases," constitute a new and possibly important category of illness. this is not to say that dysbiosis is the only cause of these conditions, but that it is a public health concern that should be investigated. an important conceptual barrier was recently crossed when the gut microbiomes of pregnant mice were demonstrated to be critical for the intrauterine development of the fetus. short-chain fatty acids (such as butyrate and propionate) are products of the gut microbiome's digestion of cellulose. as no mammalian genome contains genes for cellulose digestion, the breakdown of plant material is almost totally accomplished by enzymes produced by microbes. kimura and colleagues [ ] demonstrated that propionic acid, derived from the breakdown of fiber by maternal gut microbes, was critical for the normal development of the insulin-producing pancreatic beta cells, the sympathetic neurons that project to the heart, and the gut enteroendocrine cells. without the microbe-derived propionic acid, the adult offspring developed a metabolic syndrome characterized by glucose intolerance, obesity, and insulin resistance. since diet can control the prevalence of microbes, the holobiont model can explain the mechanism whereby eating low-fiber, high-calorie diets during pregnancy predisposes offspring to have metabolic syndrome later in life [ ] . to understand the importance of a symbiotic approach to public health, one has to first appreciate the new biological notion of the human body. each of us is a functional entity that includes our zygote-derived cells as well as hundreds of species of microbes. the body is both an organism and a biome containing several ecosystems [ , , ] . once the amnion breaks, and the fetus passes through the birth canal, the newborn becomes colonized by their mother's bacteria [ ] . furthermore, mothers' milk contains a special set of nutrients to promote the survival and growth of those bacteria that are important for symbiosis [ ] [ ] [ ] . these symbiotic bacteria will produce short-chain fatty acids and sphingolipids necessary for intestinal peristalsis and homeostasis, peptidoglycans necessary for normal neuron function, lipopolysaccharides necessary for the actions of the immune system, the tripeptides necessary for cardiac physiology, and the digestive enzymes necessary to metabolize plants [ ] . remarkably, a third of the small metabolites in the blood are produced or induced by bacteria [ ] . nearly all of our peripheral serotonin is induced by gut microbes, where it regulates the maturation of the enteric nervous system and regulates peristalsis [ , ] . even more remarkable is that such critical symbioses are not only present within humans. rather, the development of most organisms appears to be predicated on interactions between hosts and their symbionts. as mentioned in the above section , without microbial symbionts, mice do not form their gut capillaries, their gut-associated lymphoid tissues, their t-and b-cell repertoires, or the proper synaptic connections in their guts and brains. moreover, no vertebrate contains genes that make the enzymes necessary for digesting plant material such as cellulose, hemicellulose, and pectins [ ] . these genes are provided by symbiotic microbes in our guts. in mammalian evolution, the entire family of ruminants is made evolutionarily possible by the ability of gut bacteria (acquired at birth) to build the rumen of the stomach and then to ferment grass and grains [ ] [ ] [ ] [ ] . thus, symbiosis is a paradigm-changing idea in physiology. we are no longer seen as being "individuals." we are holobionts, and our anatomy, development, immunity, and physiology are intimately linked with that of our microbial components. the importance of the holobiont perspective for public health is that absences of particular microbes may cause dysbioses throughout a population. martin blaser and colleagues [ , ] have warned that we may need particular microbes for particular functions, and that our obsession with exterminating microbes may be inadvertently killing those bacteria that we need to survive. their data indicate that microbes that used to be prevalent (those, for instance, in barnyards and horse stalls) are becoming rarer. if these microbes are necessary for normal organ, immune, or cognitive development, we will be impaired. rhesus macaques that are bottle-fed, rather than breast-fed, acquire a different population of gut microbes, and this population is not as adequate to develop a functioning immune system that can repel opportunistic infections [ ] . in zebrafish, a relatively rare species of bacteria is essential for permitting the expansion of insulin-producing pancreatic cells, thereby protecting these fish against diabetes [ ] . this absence of specific bacteria (or their genes) may be crucially important for explaining the increases in allergies and asthma since world war i, and especially, after world war ii. throughout human history, we had constant exposure to barnyard microbes. it was only in the th century that they were displaced. the barnyard was not just an attribute of farms. the nineteenth century city, according to raulff [ ] (p. ) "consisted of rows and rows of urban stables." mid th c. boston had some stables, each having around eight horses. in contemporary america, only % of amish children, whose homes are often adjacent to their barns, have allergy and asthma. about % of the genetically similar hutterites, whose farms are not located close to their homes, have allergies, roughly the same as the american population in general [ ] . similarly, finnish studies have shown that proximity to the barn is a factor in combatting allergies. a recent study shows that children living in urban homes with barnyard bacteria have much less asthma and allergies than those children living in urban homes with urban bacteria [ ] . indeed, two of the bacterial types found in the "rural" homes and missing in "urban" homes were brevibacterium and ruminococaceae, bacteria found in horses and cattle. although the severity of microbiome diversity loss might be most discernable in urban populations [ ] , the importance of soil microbiomes for the maintenance of healthy human intestinal microbiomes has recently been emphasized in studies [ ] showing that even in rural areas, farming techniques have severely reduced soil microbiome biodiversity. bacterial displacement due to urban living and the absence of animals is only one of the ways that anthropogenic microbial displacement can affect public health. caesarian sections disrupt one of the pathways of maternal kinship. babies receive a protective set of symbiotic microbes from mothers when they pass through the birth canal. in caesarean sections, this transmission is abrogated. babies delivered by c-section were found to be deprived of those microbes that otherwise colonize the infant gut. instead, there were the hospital dwelling microbes that included a substantial number of opportunistic pathogens. moreover, a substantial set of these microbes contained genes associated with antimicrobial resistance [ ] . not only were the species of microbes different, but so were their functions. the caesarean-delivered infants had less ability to mount immune responses to common antigens [ ] . this may have strong public health implications concerning elective c-sections. the microbes of our gut are critical for "basic neurogenerative processes such as the formation of the blood-brain barrier, myelination, neurogenesis, and microglia maturation." [ ] . if this is indeed true, then could microbes also be critical for mental health? what if, in addition to protection against allergies and asthma, bacteria were protecting us against mental health conditions such as schizophrenia, bipolar disease, and autism? several studies now indicate that gut microbes appear to be critical for normal brain development and behaviors in mice [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] . first, mice born from germ-free mothers and who are themselves without microbes have a syndrome that includes obsessive self-grooming and asocial behavior [ ] . this behavior is possibly due to the failure of oxytocin-releasing signals from the vagus nerve, and it can be reversed by providing the germ-free mice with lactobacillus reuteri or with microbes from normal mice or from normal humans [ , ] . germ-free mice given microbes from autistic humans do not show improvement of their symptoms. although human cognitive and affective behaviors cannot be extrapolated for those of mice, a pilot uncontrolled fecal transplant study in humans showed that after two years, the acquisition of normal bowel microbes by autism patients significantly improved their symptoms: from % severe autism to % severe autism [ ] . similar studies in mice and humans have shown that the gut microbiome may be critical in protecting humans from depression [ , [ ] [ ] [ ] . there is therefore reason to test the hypothesis that removal or depletion of normal environmental microbes may be responsible for the increasing percentage of the population diagnosed with cognitive dysfunction. while studies of the effects of microbes on mental health lag behind those studies of microbial involvement in physical health, the relationship of symbiotic microbes to cognitive and affective health and disorder is an area that cannot be ignored. public health must acknowledge that we are not monogenomic individuals. we are consortia of dozens of species per person, integrated together in a complex and dynamically changing network that forms who we are at any given moment. this network is altered by the food we eat, by the food our mother ate, the toxins and medications we are exposed to, and by our daily interactions with other holobionts. our health depends upon other species, making the "one health" perspective more than metaphor. the symbiotic networks of the human holobiont are enmeshed in larger symbiotic networks that sustain the planet. public health would be severely affected if any of the many life support systems on which we depend-including pollinators, soils, and bacteria-fail. indeed, symbiosis is the signature of life on earth. the nitrogen in our soil and atmosphere is made available for protein synthesis by symbioses between rhizobacteria and legumes. the interactions of plant roots and mycorrhizal fungi are critical for plant growth, while endophytic fungi are often necessary to protect the plants against dessication [ ] [ ] [ ] . the coral reef ecosystem is dependent on the symbiosis of algae and the ectoderm of corals, while the marine seagrass ecosystems are sustained by symbioses involving clams and their bacteria. reef-building corals survive through the photosynthesis of their algal symbiont, which enters into the ectoderm of its host and transports over % of its photosynthetically derived carbon compounds to the host cells [ ] . however, these symbioses, the very symbioses that define the planet, are at risk. these are the analogues of the microbial displacement and extinction that affect human health. although public health is mainly concerned about "human" public health, one readily finds that we cannot separate ourselves from our ecosystems socially, politically, economically, or biologically. coral reefs, for instance, are thought to support million people across nations and contribute nearly a trillion dollars to the world's economy [ ] . the great barrier reef, alone, brings billion dollars annually to australian commerce. healthy coral reefs absorb over % of a wave's energy, thus protecting the shoreline, preventing nearly a hundred million dollars' worth of flood damage each year. however, the coral that form the critical structure of these reefs must be seen as a holobiont that exists only in a fragile symbiosis between the coral animal and single-celled zooxanthellae algae. the coral animal provides a sunlit, safe, and nutrient-containing environment for the algae; and the algae, living within the animal cells, provide the coral with the sugars it produces by photosynthesis. the coral holobiont can survive only when its symbionts are present to provide the food resources [ , ] . under stress conditions such as high temperatures, the symbionts are expelled from the corals, leaving the corals "bleached" and undernourished. these corals usually die. as a result of global warming, massive bleaching events and coral die-offs have occurred [ , ] . we are writing this essay not only in the coronavirus pandemic of but in the great barrier reef bleaching event of [ ] . over half the corals in the great barrier reef have perished, and some entire reefs have collapsed. the mechanisms for the expulsion of the algal symbiont from its coral host are under investigation, and it appears to be a mutual breakdown of the symbiotic relationship [ ] . one hypothesis is that heat disrupts the photosynthetic apparatus of the algae, causing them to produce dangerous hydrogen peroxide radicals. the coral cells defend themselves by expelling the algae or destroying them. another hypothesis is that warmer temperatures permit algae to get the organic nitrogen that allows them to metabolize their sugars without needing the coral, thereby forcing the coral to rely on their own meager carbon reserves [ , ] . in addition to anthropogenic heating, humans are also affecting symbiosis through domestication. mycorrhizal symbiosis is critical to plant nutrition and, therefore, a necessity for sustainable agriculture. however, artificial fertilization of soil diminishes the mycorrhizal fungi and root symbiosis. martin-robles and colleagues [ ] have linked the loss of symbiotic colonization with plant domestication. indeed, failure to colonize is common, making domesticated strains addicted to artificial fertilization [ , ] . moreover, the lack of myccorhizal fungus may make the domesticated plants more susceptible to pathogenic fungi [ ] . we are integrated into these webs, where our nutrition, oxygen, and environmental temperature depend on global symbioses, and microbes are at the base of each of them. the anthropocene has put these relationships in peril. as deborah bird rose [ ] wrote, "relationships unravel, mutualities falter, dependence becomes a peril rather than a blessing, and whole worlds of knowledge and practice diminish. we are looking at worlds of loss that are much greater than the species extinction numbers suggest." the vectors of disease are following the sun and following airplane and sea lanes. wastewater, tourism, and trade are circulating microorganisms around the world in a scale never before seen [ ] . moreover, global warming is predicted to introduce new microbes from melting permafrost as well as bringing many insect-borne diseases (dengue fever, malaria, lyme disease etc.) into new regions [ ] . here, the vector spreads a pre-existing symbiont. these will undoubtedly cause major public health concerns. however, another mechanism of disease can be predicted: when organisms reach new lands, they are capable of finding new symbiotic partners. there is a new anthropogenic mingling going on. as an example, consider the red turpentine beetle, dendroctonus valens, a minor pest species that routinely infects pine trees that have been damaged by weather or fire. like other bark beetles, it is covered by fungi. these fungi digest tree bark, allowing the beetle to have a home and mate. the fungus associated with d. valens is usually leptographium procerum. however, this beetle was introduced from the pacific northwest of america to shanxi province of china in the s. in china, it met other fungi, which are much more potent at digesting wood than the american fungi [ , ] . these newly acquired fungi can degrade a major host defensive chemical [ ] . as a result, over ten million pine trees have been killed by this fungus in china. american officials are worried about a "boomerang effect" [ ] . the version of the beetle with its chinese fungi may have been re-imported into the usa. however, the public health services of the various states that might be affected claim they do not have the revenue to test whether this is so. organisms are holobionts, and public health must recognize the webs of symbioses uniting different species of organisms into a collective "individual" and uniting these different individual teams into complex ecosystems. symbiosis takes two major forms-mutualism (cooperative) and parasitism (pathogenic). the emergence of antibiotic drug resistance is the anthropocene effect on parasitic symbiosis. just as anthropogenic changes in the environment have changed the populations of microbes involved in mutualistic interactions with humans, so other anthropogenic changes have increased the prevalence and virulence of parasitic microbes. until the early century, the leading cause of death, world over, was infectious disease. crucial to turning this around were sanitation of water, and the discovery of antibiotics. since their discovery in the s, antibiotics have become the key tool against infections caused by microbes, used across different forms of medicine. by this definition, microbes are understood as pathogenic and parasitic, dangerous, dirty, and damaging the host that they reside in. bodies are seen to be 'at war' against harmful outside invaders and entire disciplines have been hinged on this notion-immunology, clinical medicine, and public health just to mention a few. antibiotics have been the miracle weapon that have been used to tackle the looming threats of bacteria and have been said to have developed contemporary medicine to be the success story that it is today [ ] . antibiotics have magnificent power to alleviate symptoms and ensure sterile conditions; they play central roles in basic surgeries, cancer, cesarean birth, and in treating basic infections. they are prescribed against infections by doctors, nurses, pharmacists, dentists, and traditional healers, depending on the contexts, all across the world. there are very few communities left that have not incorporated the use of antibiotics into their basic methods of healing, and research on those communities is tapping to their 'untouched microbiomes' microbiome as an 'oasis' [ ] [ ] [ ] [ ] . literature about antibiotic prescription describes how requests for antibiotics reside on all sides of the patient-health care practitioner dyad: patients say that health care practitioners hand out antibiotics liberally and health care practitioners argue that patients demand them [ ] [ ] [ ] . in addition, antibiotics are bought over the counter from pharmacies, and informal markets [ ] . antibiotic use is a matter of concern as excessive or unregulated use of antibiotics is connected to the development of drug resistance and while there are few new antibiotics in the pipeline, there is a need to ensure the utility of existing ones [ , ] . antibiotic use patterns offer insights into how central antibiotics are to public health, as well as the specific practices and contexts that rely on the use of antibiotics. understanding these dynamics also illuminates the effects of pathogenic thinking as well as the myriad ways in which reliance on antibiotics would need to change in order to make space for a holobiont practice of public health. global statistics about antibiotic use show differences between countries that often follow the guidelines of health system efficiency and general national income. since the s, antibiotic use in low-and middle-income countries has considerably increased, while in high-income countries, particularly with those that rely on public rather than private health care, antibiotic use has been reduced. india, pakistan and china are among those countries where use has increased most [ ] , while data is unavailable in most african countries [ , ] . that said, despite the reduction in the high-income countries, antibiotic use in many european countries and the us is still considerably higher per capita than across many african nations [ , ] . the increase of antibiotic use in low-income countries underscores the utility of antibiotics within lagging health care systems and/or in places where people cannot afford health care. especially in countries where health care access is precarious due to lack of access, poverty, or poorly operating health systems, antibiotics have come to play a central role in how short-term health goals are achieved. for example, work by denyer willis and chandler [ ] shows how antibiotics function as a 'quick fix' for well-being. this fix operates on multiple domains: to ensure productivity of humans, animals and crops; hygiene in settings of minimized resources marked by lack of infrastructures; and good health in landscapes scarred by political and economic violence. in short, antibiotic use has come to stand for development and well-being. while use of antibiotics has played a crucial role in helping to increase life expectancy, implementing invasive surgical procedures, and stand in for health care systems where they are otherwise unavailable, the use of antibiotics has accelerated embodied and ecological havoc. a narrow characterization of microbes solely as parasitic and pathogenic enemies rather than as needed and helpful partners contributes to excessive use of antibiotics for humans and animals, where microbes 'refuse' to remain contained in bodies but shift their form by evolving resistance to antibiotics. the heroic narrative of antibiotics is beginning to crumble as microbes push back. mass scale attempts to eradicate bacteria with antibiotics in humans and animals has led to increase of antimicrobial resistance (amr), making it a quintessential anthropocene problem. indeed, the mass scale of antibiotic production, beginning in the s, "quickly became infrastructural to the production of many other things at scale: more health, more meat, more fruit, more surgery, less death, more fertility, in everything from in vitro embryos cultured in antibiotics to fish farming. the scale of production is also the scale of resistance" [ ] . the higher-than-expected levels of amr put western medicine in its current form-where antibiotics play central roles-at risk. with antimicrobial resistance, global health literature continues to frame microbes as a threat, now an incurable threat. the most comprehensive report about amr and its future impacts, the so-called o'neill report commissioned by the uk government and the wellcome trust, indicated that million people will die due to complications associated with amr [ ] . this report has evoked a flurry of research efforts, systemic interventions, stewardship programmes, and funding to tackle amr. health risks for humans have been extensively documented, with resistance spreading owing to both excessive use of antibiotics for human consumption and the use of antibiotics as part of animal feeding and in husbandry. a key route by which amr spreads is via environmental bacteria that serve as vectors for the resistant genes-lateral gene transfer-which is seen to become a problem when otherwise benign environmental bacteria contribute to the spread of resistance in pathogens [ , , ] . robinson et al. state that this otherwise 'natural' quality of environmental bacteria is exacerbated, for example, by the influx of antibiotic residues from human and animal faeces, and run-offs from hospitals and pharmaceutical manufacturing [ , ] . a global comparison of socio-economic determinants correlated with amr prevalence offers insights into the crucial roles that developmental and social inequalities play in anthropocene ecology. factors predicting high amr rates are not antibiotic consumption, but, rather, differential access to sanitation, education, and public investment in health care services, as well as the level of corruption in society [ ] . the focus, therefore, cannot be simply on clinical bodies, but must broaden to encompass environments including animals and infrastructures on the one hand, and social practices and power on the other. we posit that the notion of plantationocene captures this complexity that transcends the human-more-than-human bodily boundary while taking power structures into consideration. as defined above, the plantationocene constitutes the coercive labor structures and extractive and hierarchical management of planetary resources to feed an ever-growing population [ , ] . the plantationocene acts here both an analytical and a descriptive term. analytically, plantationocene points to transnational circulations of goods, domination and dominion of people over other people and people over nature, hegemonic colonial legacies, systematisation of farming. haraway et al. [ ] point to the historical origins of the term and how relocations of the substances of living and dying around the earth as a necessary prerequisite to their extraction. the logic of the plantation system makes it more efficient to destroy the local labor and import labor from elsewhere. the plantation system is built on the relocation and control of any generative unit, whether plant, animal, microbe, or person [ ] . indeed, plantations were the result of one of the most catastrophic public health events in world history-the columbia exchange. a major part of this exchange resulted in the elimination of a majority (perhaps %) of indigenous american people by the microbes-rubeola, variola, influenza, rubulavirus, rickettsia, salmonella and bordetella-brought across the atlantic ocean by the european settlers. the great migration of people and crops took place to bring workers to areas whose native populations had perished, especially in the caribbean, where the death rate of indigenous people was probably close to % [ ] [ ] [ ] . intensive labour was needed to produce crops in north and south america, and the 'workers' at plantations were slaves shipped from west and central africa-now sites that have the least infrastructure to surveil and control amr, but have the most troubling evidence of amr prevalence [ , ] . these were also sites of resource extraction as well as subjected to structural adjustments in the s by the world trade organisation to privatize health care and social welfare, resulting in poor health care and sanitation infrastructures and overall poverty that now are known to be key factors for the development of amr. the industrial agriculture of the plantationocene may also contribute to the spread of drug resistant microbes. the recent increase in resistant fungicides such as candida auris, that has caused tremendous concern among health practitioners and ecologists alike, is a resistant yeast that has contaminated entire hospitals [ , ] . its spread has environmental vectors-resistance has developed in connection to the use of fungicides in monocropping [ ] . environmental and agricultural practices are thus directly connected to public health concerns. amr with plantationocene underscores that public health needs to re-think its relationships with bacteria and antibiotics-it cannot bracket out environmental extraction, socio-economic injustices and the on-going need for health systems strengthening as factors that create the conditions for why excessive antibiotics are used that lead to antimicrobial resistance. amr by this definition is not an exemplary threat by microbes as is framed in global public health but should be seen as a result of the modernist, eradication approach towards microbes that requires rethinking. health is a negotiation between microbes and hosts. holobiont public health would do well to recognize both the parasitic and the mutualistic branches of symbiosis [ ] it would also recognize the two major changes in our scientific knowledge of microbial evolution that have occurred in this century: ( ) organisms are holobionts composed of several species, wherein microbes help maintain healthy physiology and resilience; and ( ) bacteria can pass genes through horizontal genetic transmission, thereby facilitating the rapid spread of antibiotic resistance through numerous bacterial species. symbionts must be seen as partners and respected as agents with their own agendas. three recent examples of holobiont "management" for public health should be mentioned in this regard. the first concerns the public health against mosquito-transmitted diseases such as dengue, zika, and chikungunya by using wolbachia bacterium to infect aedes egypti mosquitos. wolbachia infects numerous insects, but not these species of mosquitos. however, wolbachia can become a symbiont in these insects, preventing the acquisition or replication of viruses inside their cells. scientists have been able to get wolbachia to grow inside aedes cells, and wolbachia-infected mosquitoes have been released into the wild. where this has happened, there has been significant drops (up to %) in reported cases of the vector-transmitted diseases [ ] [ ] [ ] . the second holobiont-informed type of public health involves seeking alternatives to antibiotics and partnering with microbes capable of keeping pathogens in check. if symbionts help protect hosts from pathogenic bacterial infections, then symbiotic microbes would be a good place to start looking for new antibiotics. this is especially true of antibiotics for gram-negative bacteria. the antibiotics currently in use were developed in the s, and several bacterial species have successfully been evolving resistance to them. certain nematode worms are susceptible to the same types of gram-negative bacteria as humans, so imai and colleagues [ ] sought out the antibiotics made by the symbiotic strains of bacteria found in the nematode guts. by screening chemicals made by these symbionts, they have isolated darobactin, a modified and crosslinked -amino acid peptide. this antibiotic acts by disrupting the cell envelope of the gram-positive pathogens and is largely non-effective in destroying human gut commensals. the experiments further show that this new antibiotic is effective at protecting infected mice given potentially lethal infections of gram-negative bacteria. the third approach recognizes the importance of microbes to the life cycles of parasites and seeks to kill the parasite by killing its symbionts. this approach has worked in eliminating schistosoma mansoni, a filariasis worm that has become resistant to the drugs traditionally used to kill these parasites. a newer treatment strategy has been to use antibiotics (such as doxycyline) against its symbiotic bacteria [ , ] . once the antibiotic destroys the symbiont, the worms' cells undergo apoptosis and the worms die [ ] . a similar strategy is being considered to eradicate the plague locusts that are now devastating east africa. here, a locust-specific fungus might be sprayed on the juvenile locusts as they develop their wings. this fungus would grow inside the maturing insect and consume it from within [ ] . we need to be in symbiosis with bacteria on a social, as well as on a corporal level. like the body, we need to be able to distinguish mutualistic from pathogenic microbes and treat them differently. humanity has been given notice. a paper by the alliance of world scientists [ ] "puts humanity on notice that the impact of climate change will depend heavily on the responses of microorganisms which are essential for achieving an environmentally sustainable future." public health must take note that we humans are never independent of nature and, therefore, must be expanded to preserve environmental health as well as human and animal health. resilience to perturbations is increased by plasticity and the inputs of symbiotic microbes. each human is a biome of many ecosystems. asthma, allergies, and amrs must not be considered the "revenge of nature." rather they are expected consequences of lower resilience to perturbations. public health must see the life on this planet as biology now sees it-as a rich mixture of cooperative and antagonistic interactions, with our bodies in dynamic relations with its hundreds of microbial partners. author contributions: each author contributed to both the planning and the writing of this paper. all authors have read and agreed to the published version of the manuscript. funding: sgf is funded by a swarthmore college faculty research grant. ss is funded by academy of finland, grant number . microbe hunters; hartcourt brace pasterurization of france vaccines through centuries: major cornerstones of global health. front life expectancy in france the technological society missing microbes: how killing bacteria creates modern plagues three dialogues on knowledge we have never been modern the death of 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frederic; cayet, delphine; faveeuw, christelle; carnoy, christophe; sirard, jean-claude title: therapeutic synergy between antibiotics and pulmonary toll-like receptor stimulation in antibiotic-sensitive or -resistant pneumonia date: - - journal: front immunol doi: . /fimmu. . sha: doc_id: cord_uid: cxz hf q bacterial infections of the respiratory tract constitute a major cause of death worldwide. given the constant rise in bacterial resistance to antibiotics, treatment failure is increasingly frequent. in this context, innovative therapeutic strategies are urgently needed. stimulation of innate immune cells in the respiratory tract [via activation of toll-like receptors (tlrs)] is an attractive approach for rapidly activating the body's immune defenses against a broad spectrum of microorganisms. previous studies of the tlr agonist flagellin in animal models showed that standalone tlr stimulation does not result in the effective treatment of pneumococcal respiratory infection but does significantly improve the therapeutic outcome of concomitant antibiotic treatment. here, we investigated the antibacterial interaction between antibiotic and intranasal flagellin in a mouse model of pneumococcal respiratory infection. using various doses of orally administered amoxicillin or systemically administered cotrimoxazole, we found that the intranasal instillation of flagellin (a dose that promotes maximal lung pro-inflammatory responses) induces synergistic rather than additive antibacterial effects against antibiotic–susceptible pneumococcus. we next set up a model of infection with pneumococcus that is resistant to multiple antibiotics in the context of influenza superinfection. remarkably, the combination of amoxicillin and flagellin effectively treated superinfection with the amoxicillin-resistant pneumococcus since the bacterial clearance was increased by more than -fold compared to standalone treatments. our results also showed that, in response to flagellin, the lung tissue generated an innate immune response even though it had been damaged by the influenza virus and pneumococcal infections. in conclusion, we demonstrated that the selective boosting of lung innate immunity is a conceptually advantageous approach for improving the effectiveness of antibiotic treatment and fighting antibiotic-resistant bacteria. bacterial infections of the respiratory tract constitute a major cause of death worldwide. given the constant rise in bacterial resistance to antibiotics, treatment failure is increasingly frequent. in this context, innovative therapeutic strategies are urgently needed. stimulation of innate immune cells in the respiratory tract [via activation of toll-like receptors (tlrs)] is an attractive approach for rapidly activating the body's immune defenses against a broad spectrum of microorganisms. previous studies of the tlr agonist flagellin in animal models showed that standalone tlr stimulation does not result in the effective treatment of pneumococcal respiratory infection but does significantly improve the therapeutic outcome of concomitant antibiotic treatment. here, we investigated the antibacterial interaction between antibiotic and intranasal flagellin in a mouse model of pneumococcal respiratory infection. using various doses of orally administered amoxicillin or systemically administered cotrimoxazole, we found that the intranasal instillation of flagellin (a dose that promotes maximal lung pro-inflammatory responses) induces synergistic rather than additive antibacterial effects against antibiotic-susceptible pneumococcus. we next set up a model of infection with pneumococcus that is resistant to multiple antibiotics in the context of influenza superinfection. remarkably, the combination of amoxicillin and flagellin effectively treated superinfection with the amoxicillin-resistant pneumococcus since the bacterial clearance was increased by more than -fold compared to standalone treatments. our results also showed that, in response to flagellin, the lung tissue generated an innate immune response even though it had been damaged by the influenza virus and pneumococcal infections. in conclusion, we demonstrated that the selective boosting of lung innate immunity is a conceptually advantageous approach for improving the effectiveness of antibiotic treatment and fighting antibiotic-resistant bacteria. keywords: flagellin, toll-like receptor , antibiotic, resistance, streptococcus pneumoniae, pneumonia, superinfection introduction pneumonia constitutes a major cause of death, morbidity and health resource use worldwide. the main causative agents identified in adult patients hospitalized for community-acquired pneumonia (cap) are viruses (in - % of cases, the most common being rhinovirus, influenza and coronavirus) and bacteria ( - % of cases, with a marked predominance of streptococcus pneumoniae infections) ( ) ( ) ( ) . when faced with overt clinical signs of bacterial pneumonia, the standard of care is antibiotic treatment. the combination of a constant rise in antibiotic resistance in recent decades with a decline in the discovery of new drugs has led to an increase in treatment failure and mortality ( ) . in , the world health organization's global action plan highlighted the urgent need to control the emergence of antibiotic resistance ( ) . given this context, a number of new anti-infectious treatment strategies are being developed. the modulation of innate immunity [by targeting immune receptors, such as toll-like receptors (tlrs)] is a promising approach ( , ) . indeed, innate immunity is highly conserved in evolution, and this system constitutes the first line of defense against invading pathogens. moreover, innate immunity triggers a broad range of antimicrobial defense mechanisms and immune cells-thereby greatly reducing the risk of resistance in the pathogens. moreover, activation of tlr signaling has been associated with a favorable outcome in infections with antibiotic-resistant bacteria or colonization resistance by such pathogens ( ) ( ) ( ) . these observations support that stimulation and effector activities of innate immunity are not influenced by the antibiotic resistance mechanisms carried by bacteria. flagellin is the main protein component of the bacterial flagellum and is a natural agonist of tlr ; the latter is expressed at the surface of a many different cell types, including mucosal epithelial cells and immune cells such as dendritic cells, macrophages, and lymphocytes ( ) . various studies in animal models have highlighted the antimicrobial potency of flagellin against a wide variety of bacterial infections [such as intestinal infections caused by salmonella enterica, enterococcus faecium, clostridium difficile, and escherichia coli ( , ( ) ( ) ( ) , respiratory infections caused by pseudomonas aeruginosa and s. pneumoniae ( , ) ], and viral and fungal infections ( ) ( ) ( ) . although most studies have demonstrated the protective effect of flagellin administered before or during exposure to a microbial pathogen, the protein's immunostimulatory efficacy in therapeutic context has not been extensively characterized. using a mouse model of s. pneumoniae lung infection, we recently demonstrated that combination treatment with mucosally administered flagellin and an orally or intraperitoneally administered low-dose (i.e., subtherapeutic) antibiotic is more effective than the antibiotic alone (i.e., with a lower bacterial load in the lung, and a lower mortality rate). furthermore, the combination treatment was also effective in a model of post-flu pneumococcal superinfection ( ) . the effectiveness of these combination therapies depends on tlr signaling as demonstrated using tlr -deficient animals and tlr -mutated recombinant flagellin ( ) . our studies highlighted that the airway epithelium is the main tlr -specific signaling compartment ( ) ( ) ( ) . taken as a whole, these observations are the first to highlight the added value of respiratory delivery of flagellin as an immunomodulatory biologic for the adjunct treatment of bacterial pneumonia (i.e., in addition to the standard of care). our working hypothesis was that simultaneous treatment with an antibiotic and intranasal, i.e., respiratory flagellin constitutes a "double hit" against the pathogen. a combination of two drugs may result in independent actions or specific (i.e., additive, synergistic, or antagonistic) effects that define the biological outcome ( ) ( ) ( ) . an interaction between two drugs is considered to be synergistic when the measured effect of the combination treatment exceeds the predicted cumulative value of the two components given separately. synergy increases treatment efficacy, and is expected to limit the emergence of drug resistance. furthermore, synergy allows the physician to decrease the dose level or the frequency of dosing, which thereby dampens adverse drug reactions and may even enable the rehabilitation of neglected drugs. conversely, an antagonistic combination treatment has a smaller effect than the predicted cumulative value of the two components given separately. most studies of potentially synergistic antimicrobial agents are performed in in vitro systems such as bacterial cultures, using checkerboard assays and increasing doses of each drug ( , ) . unlike antibiotics that directly affect the bacteria, immunomodulatory biologic activity requires sentinel cells for detection, downstream signaling and thus the production of antimicrobial effectors and the recruitment and/or activation of innate immune cells. at present, there are no comprehensive in vitro models of this complicated physiological system. in the present study, we quantified the nature and magnitude of the interactions between antibiotics and intranasal instillation of flagellin with regard to antibacterial effectiveness in a murine model of s. pneumoniae respiratory infections. furthermore, we wanted to assess the efficacy of this novel therapeutic strategy against infection with antibiotic-resistant bacteria, which represents major public health issues today. to this aim, we investigated the combination's effect on antibiotic-resistant s. pneumoniae in a relevant model of post-flu pneumococcal pneumonia, and characterized the immune response induced by the flagellin-mediated protection. serotype s. pneumoniae (sp ; clinical isolate e ) was obtained from the national reference laboratory-ministry of health, uruguay ( ) . serotype s. pneumoniae (sp ; strain ) was provided by the institut pasteur (paris, france); it is a multidrug-resistant clinical isolate from a human bronchial secretion, and is resistant to amoxicillin (amx), cefotaxime, doxycycline, erythromycin, chloramphenicol, streptomycin, and cotrimoxazole (sxt). working stocks were prepared as described previously ( , ) . briefly, fresh colonies grown on bloodagar plates were incubated in todd hewitt yeast broth (thyb) (sigma-aldrich, saint-louis, mo) at • c until the od nm reached . - . units. cultures were stored at − • c in thyb + glycerol % (vol./vol.) for up to months. for infection, working stocks were thawed and washed with sterile dulbecco's phosphate-buffered saline (pbs, gibco, grand island, ny) and diluted to the appropriate concentration. the number of bacteria (as colony forming units [cfus] ) was confirmed by plating serial dilutions onto % sheep blood agar plates. female balb/cj mice, female swiss mice, and male c bl/ j mice ( - weeks old) (janvier laboratories, saint berthevin, france, or envigo, huntingdon, uk) were maintained in individually ventilated cages and handled in a vertical laminar flow cabinet (class ii a , esco, hatboro, pa). all experiments complied with institutional regulations and ethical guidelines (c - , institut pasteur de lille; protocol ). prior to intranasal infection, the mice were anesthetized via the intraperitoneal injection of . mg ( mg/kg) ketamine plus . mg ( mg/kg) xylazine in µl of pbs. for primary infections with sp , - × cfu were inoculated intranasally in µl pbs, as described previously ( ) . the influenza infection model was developed in our laboratory on the c bl/ j mice ( , ) . the sp pneumococcal superinfection model was therefore performed in these animals. briefly, mice were first infected intranasally with µl pbs containing plaque-forming units (pfus) of the pathogenic, murine-adapted h n influenza a virus strain scotland/ / , as described previously ( , ) . seven days later, animals were infected intranasally with cfu of sp in µl pbs. for the determination of bacterial counts in lung and spleen, mice were sacrificed at selected times via the intraperitoneal injection of . mg of sodium pentobarbital in µl pbs. tissues were collected and homogenized with an ultraturrax homogenizer (ika-werke, staufen, germany), and viable counts were determined by plating serial dilutions onto blood agar plates and incubating them at • c for - h. the recombinant flagellin flic − came from s. enterica serovar typhimurium flic and was produced with an histidine tag, as described previously ( , ) . the protein flic − was certified to be immunologically active in reporter cells and in mouse assays, and the residual lipopolysaccharide concentration was determined to be < pg per µg of flagellin ( ) . the treatments' effects on s. pneumoniae lung infection were quantified as the percentage bacterial growth (% growth ), corresponding to the ratio of the mean bacterial load in the lungs of infected, treated mice to the load in infected, nontreated (control) mice. for example, the effect of treatment a was calculated as follows: % growth[a] = (mean cfu [a] /mean cfu [control] ) × . the predicted additive effect (or predicted % growth ) of a combination treatment was calculated as described previously ( ) . briefly, the predicted % growth of a treatment combining compounds a and b is the product of the experimentally defined % growth values for each standalone treatment (predicted% growth[a+b] = % growth[a] × % growth [b] ). if the experimental % growth for the combination treatment is lower or higher than the predicted % growth , then the two drugs are synergistic or antagonistic, respectively. when the experimental and predicted % growth values are identical, the two drugs' effects are additive. total lung rna was extracted with the nucleospin rna plus kit (macherey-nagel, duren, germany) and reverse-transcribed with the high-capacity cdna archive kit (applied biosystems, foster city, ca). the cdna was amplified using sybr greenbased real-time pcr on a quantstudio k pcr system (applied biosystems). relative mrna levels ( − ct ) were determined by comparing first the pcr cycle thresholds (c q ) for the gene of interest and the reference genes actb and b m ( c q ), and then the c q values for infected mice treated with the amx+flagellin combination treatment and with amx alone (control group) ( cq). all the primers used in the study (listed in table ) were validated for efficacy. bronchoalveolar lavage (bal) fluid samples were obtained after intratracheal injection of × ml of pbs supplemented with % fetal calf serum (fcs). lungs were perfused with pbs, excised and finely minced then digested in a solution of rpmi medium (gibco) containing mg/ml collagenase viii (sigma-aldrich) and µg/ml dnase i (sigma-aldrich) for min at • c. after washes, red blood cells were removed using a lysis solution (pharmlyse, bd bioscience). lung cell homogenates were then suspended in a % percoll gradient and centrifuged at , rpm without brake at room temperature for min. the cell pellets were washed with pbs supplemented with % fcs and cells were filtrated before antibody labeling. bal and lung cells were stained with anti-cd -allophycocyanin-cyanine (clone f ), anti-cd b-brilliant violet (clone m . ), anti-siglecf-alexafluor (clone e - ), anti-ly c-peridinin chlorophyll protein-cyanine . (clone hk . ), anti-ly gphycoerythrin (clone a ), anti-cd c-phycoerythrin-cyanine (clone hl ), and ccr -brillant violet (clone sa g ) antibodies. dead cells were excluded from the analysis using propidium iodide. the antibodies were purchased from bd biosciences (san jose, ca) or biolegend (san diego, ca). data were collected on a bd lsr fortessa and analyzed with the bd facsdiva software. concentration of ccl , cxcl , cxcl , il- , il- β, and tnf was determined in bal fluids and lung homogenates by enzymelinked immunosorbent assay (elisa kit from ebioscience, r&d systems or becton dickinson). bal fluids were obtained by intratracheal injection of × ml pbs supplemented with protease inhibitors (roche). lungs were perfused with pbs and collected in t-per reagent (pierce) supplemented with protease inhibitors and debris were eliminated by centrifugation. all samples were stored at − • c. the results were described as the mean ± standard error of the mean (sem) or the median (range), as indicated. intergroup differences were analyzed using the mann-whitney test and the log rank test. all analyses were performed with prism software (version . , graphpad software, la jolla, ca). the threshold for statistical significance was set to p < . . in earlier research, we had shown that the intranasal administration of a combination of flagellin flic − and low-dose antibiotics improved the therapeutic outcome of lung infection with the antibiotic-susceptible sp [minimum inhibitory concentration (mic) amx = . µg/ml] ( ) . given the difficulty of performing in vitro checkerboard assays with immunomodulators, we therefore sought to evaluate the nature of antibiotic-flagellin interactions in vivo. we first defined the dose of flagellin that promoted saturating immune responses in sp -infected mice (figure ) . intranasally administered flagellin was associated with the production of various innate immunity-related components, including chemokines (cxcl , cxcl , and ccl ), inflammatory cytokines (il- β and il- ), and antimicrobial peptides (s a ), along with the recruitment of neutrophils to the airways ( , , , , , ) . mice were treated simultaneously with oral amx ( . mg/kg) and intranasal flagellin flic − (at doses of . µg to mg/kg, i.e., ng to µg per animal). immune responses were analyzed by monitoring the lung transcription of inflammatory genes associated with tlr signaling and by comparing mrna levels to animals that received amx alone. the results showed that doses from to µg per animal saturated the upregulation of transcriptional response for cxcl , cxcl , ccl , il b, and il genes. ultimately, the dose of . µg of flic − was selected as a saturating immunostimulatory dose in the context of pneumococcal infection and lung inflammation. the next set of experiments was designed to characterize the therapeutic interaction between intranasal flagellin flic − and oral amx. mice were infected with sp and treated h later with either a single intranasal instillation of flagellin ( . µg), a single intragastric administration of suboptimal amx doses of µg ( . mg/kg) or µg ( . mg/kg) or the combination treatment. to define the treatments' efficacy, lung bacterial counts were measured at h post-treatment. the results showed that flagellin alone had mostly no antibacterial effect, whereas and µg doses of amx alone were, respectively, associated with -and -fold smaller bacterial loads, relative to untreated mice (figure a) . the combination treatment (amx + flic − ) induced a -fold relative decrease in bacterial counts for µg of amx and a -fold relative decrease for µg of amx-showing that amx-flagellin combination treatment is more effective than the corresponding dose of amx or flagellin as monotherapy (figure a) . the nature of the interactions between flagellin and antibiotics was further analyzed by comparing the bacterial growth upon treatment. the % growth values for the combination treatment ( . % for flagellin + amx µg and . % for flagellin + amx µg) were much lower than the corresponding predicted % growth values for additive effects, calculated as % growth[amx] × % growth[flagellin] ( . % for flagellin + amx µg and . % for flagellin + amx µg) (figure b) . this experiment indicated strong synergy between the two compounds. similar experiments were carried out with the combination of the antibiotic sxt and flagellin (figures c,d) . the antibiotic sxt was administered intraperitoneally at doses of and mg ( and mg/kg, respectively). flagellin ( . µg) significantly improved the therapeutic outcome of sxt treatment, as evidenced by cfu counts in the mice's lungs h after administration of the treatments ( figure c) . the experimental % growth values for the combination treatment were lower than the corresponding predicted % growth values ( vs. . % for sxt mg, and . vs. . % for sxt mg)-reflecting a synergy between flagellin and sxt ( figure d ). taken as a whole, these results show that antibiotics + flagellin had a strong synergistic effect on pneumococcal lung infection in mice. furthermore, the synergy seems to be independent of the type of antibiotic, since it was observed with a compound that inhibits bacterial cell wall (amx) and a pair of compounds that inhibits folic acid synthesis (sxt). next, we looked at whether the combination treatment's effect on an antibiotic-sensitive s. pneumoniae strain was also exerted on antibiotic-resistant bacteria. to this end, a mouse model of infection with a sp strain that is resistant to a wide range of antibiotics including amx (mic amx = µg/ml, i.e., -fold higher than for sp ) was developed. we found that the sp strain failed to induce a lethal infection and other signs of disease (weight loss) in naïve mice-even at high doses of challenge ( or bacteria per animal) (figures a,b) . given that the influenza virus infection increases susceptibility to bacterial infections even after it has been eliminated ( - ), sp infection was assessed in mice that had already been exposed to the virus. briefly, mice were infected first with an intranasal, sublethal dose of h n virus ( pfu) and then infected days later with cfu of sp . this bacterial superinfection induced significant weight loss and was % lethal (figures a,b) . the bacterial counts increased gradually over time, and reached cfu per lung h post-infection ( figure c) . sp was also detected in the spleen-indicating a translocation and systemic dissemination of the bacteria-from h post-infection onwards (figure c ). in conclusion, the antibiotic-resistant sp strain induced effective pneumonia when animals had been previously exposed to experimental flu. in order to test the efficacy of an antibiotic+flagellin combination treatment in the post-influenza sp superinfection model, mice were treated with amx alone, flagellin flic − alone, or a combination of both compounds h after the bacterial infection ( figure a ). due to the high level of amx resistance, the doses of antibiotic used were µg ( mg/kg) and µg ( mg/kg). using this regimen, the serum concentration levels of amx in naïve animals were expected to be close to × mic and × mic, respectively (professor charlotte kloft, personal communication). flagellin treatment alone decreased bacterial counts in the lungs by . -fold, whereas amx treatments decreased bacterial counts by . -fold (for a dose of µg) and . -fold (for a dose of µg). when amx was combined with flagellin, bacterial counts were of , -and , -fold lower for the and µg doses of antibiotic, respectively. these results show a significant therapeutic advantage for the combination treatment, relative to standalone amx or flagellin treatments ( figure b) . we also determined cfu counts in the spleen; both amx and amx + flagellin treatments (either with or µg of the antibiotic) were able to prevent systemic dissemination of the infection (data not shown). comparison of % growth for the observed effect of the combination treatment vs. predicted additive effect ( . vs. . % for amx µg, and . vs. . % for amx µg) demonstrated the synergy of the combination in the context of superinfection and antibiotic resistance ( figure c) . after two administrations of treatments and h after sp superinfection, the flagellin + amx combination was found to significantly improve the survival of mice, relative to standalone treatments ( figure d) . these data strongly suggest that flagellin + amx have synergistic therapeutic effects to control the antibiotic-resistant pneumococcal infections in relevant pathophysiological contexts. since infection by influenza virus induces major changes in lung integrity and immune cell populations, we investigated the immunomodulatory impact of flagellin on post-flu respiratory infections by the antibiotic-resistant sp strain. to this end, c bl/ mice were infected with influenza a virus at day and then challenged with antibiotic-resistant sp at day . treatments with oral amx ( µg) combined or not with intranasal flagellin ( . µg) were administered h after sp infection. lungs were collected h post-treatment for transcriptional analysis using rt-qpcr assays, as described in figure . we observed that despite the superinfection, flagellin still enhanced the transcription of cxcl , cxcl , ccl , il b, il , and s a genes, i.e., surrogate markers of tlr mediated lung stimulation ( figure a) . we next quantified the cytokine/chemokine production after h of treatment both in the bal fluids and lung protein extracts. delivery of flagellin in the lung of amx-treated pneumococcal superinfection significantly increased levels of ccl , cxcl , cxcl , and tumor-necrosis factor (tnf) both in the lungs ( figure b ) and in the bal fluids ( figure c ) in amx+flagellin-treated mice compared with amx+pbs-treated mice. we also observed increased il- production in both compartments although it was not statistically significant. production of il- β (or pro-il- β) was detected only in the lung tissue and was increased in flagellin-treated mice. finally, we used flow cytometry to evaluate immune cell populations in bal fluids and lung tissue collected h posttreatment. the analysis showed that the neutrophil counts were higher in mice having receiving the combination treatment (i.e., tlr stimulation and amx) than in mice having receiving amx alone both in the lung tissues ( figure d ) and the bal fluids ( figure e) . interestingly, the innate response to combination treatment was also detectable in blood since the production of the inflammatory mediators were significantly augmented at h (for il- , ccl , cxcl , and cxcl ) and h (ccl and cxcl ) compared to amx alone treatment (supplementary figure ) . the blood cytokine production then diminished to an undetectable or very low level at h. thus, these observations showed that the mucosal delivery of flagellin does not induce sustained systemic inflammation. overall, the innate immune response to flagellin was effectively stimulated in the context of the influenza immunological imprinting, the superinfection challenge, and the antibiotic treatment. our present results demonstrated the synergistic efficacy of a combination of an antibiotic (amx or sxt) and the local administration of the immunomodulatory biologic flagellin against respiratory infections caused by s. pneumoniae. of note, the efficacy of combined antibiotic + flagellin treatment, previously demonstrated in inbred balb/c and c bl/ mice by porte et al. ( ) , was here extended to outbred swiss mice, showing genetic background independence of the protection. remarkably, flagellin was able to trigger lung innate immune responses in the context of inflammation (i.e., airways damaged by bacterial pneumonia and flu). immunostimulation in the lung was a dose-dependent process that was saturating by microgram-per-animal levels of flagellin. the synergy appeared to be independent of the antibiotic dose level and the antibiotic's target, since amx acts on the bacterial cell wall and sxt inhibits dna synthesis. the present study is also the first to have demonstrated that stimulating innate immunity can treat severe pneumonia induced by antibiotic-resistant pathogenic bacteria; this may open up new avenues for the treatment of pneumonia in the context of growing antimicrobial resistance. it has been demonstrated that intranasal administration of flagellin activates tlr -dependent local innate responses with broad-spectrum antibacterial activity ( , , , , , ) . the pulmonary response includes the production of various antimicrobial peptides (i.e., cathelicidin antimicrobial peptide and the β-defensins), cytokines (tnf, il- β, and il- ), and chemokines (i.e., ccl , cxcl , cxcl , cxcl , and cxcl ). this cytokine and chemokine production is in line with the observed recruitment of phagocytes (and especially neutrophils) in the lung following the intranasal administration of flagellin to naïve mice ( , , ) . flagellin intranasal administration specifically triggers tlr -mediated transcription in the lungs from to h after a pneumococcus infection or from to days after an influenza infection ( ) . here, we demonstrated that the lung innate immune signature induced by intranasal instillation of flagellin is still effective in a highly inflammatory context with associated lung damage (pneumococcal postinfluenza superinfection), and is not influenced by antibiotic treatment (figure ) . interestingly, earlier reports indicated that influenza infections promote the partial but sustained desensitization of tlr-mediated lung innate responses and a reduction in tlr expression ( ) . our observations demonstrate that, in the physiopathological context of superinfection, flagellin is still able to trigger sufficient levels of innate defense and exert synergy with antibiotics (figure ) . airway epithelial cells have been identified as an important component for detection of flagellin and tlr signaling at homeostasis ( , ) . these sentinel cells not only sense danger signals introduced in the conducting airways but also produce factors to directly impair the colonization and growth of pathogens or indirectly mobilize phagocytic and immune cells to clear infection. more generally, airway epithelium tlr signaling represent a key driving force in antibacterial defense ( ). recently, anas et al. demonstrated an essential contribution of epithelial signaling in the respiratory tract in response to flagellin in the context of infection with pseudomonas aeruginosa ( ) . our data showed that several antimicrobial peptides (s a ), cytokines (il- β and tnf), and chemokines (ccl , cxcl , and cxcl ) that were associated to epithelial responses are also upregulated after the administration of the combination treatment in the post-flu superinfection model, suggesting that the epithelium is also an important flagellin-specific driving force in the lung damaged by viral and bacterial infections. targeting epithelium is a serious benefit for immunostimulation since it allows reducing the dose and bypassing systemic adverse effects. our data contribute to highlight the therapeutic potential of the association of two drugs with distinct modes of action: an antibiotic with a direct effect on bacteria, and a tlr specific stimulator of innate immunity with indirect antibacterial activity mobilizing both multiple phagocytic host cells and various antimicrobial factors such as antibacterial peptides, and chemokines and cytokines that mobilize and activate immune cells. besides pathogen killing, the multitargeting of innate immunity by flagellin could impact on bacterial fitness and thereby increase susceptibility to the antibiotic. the innate immune response induced by tlr signaling may also modify the distribution of antibiotic in lung tissues while the antibiotic, by damaging the pathogen, could also enhance the immune signaling. in addition, the pharmacokinetics of the antibiotic and the immunostimulator, i.e., a short-term dose-dependent effect for the antibiotic, and an immediate and long-lasting impact of the immunostimulator due to cell mobilization, are likely complementary. finally, flagellin, by modulating innate immunity in the respiratory tract, has been shown to enhance the mucosal and systemic adaptive immunity ( , ) . such property may be of interest to elicit anti-pathogen immune memory and prevent recurrent/relapse infections. as an opportunistic bacterium, s. pneumoniae frequently colonizes the upper respiratory tract and thus represents lungs were collected h after treatment, and homogenized. after rna extraction, expression levels of selected genes were then analyzed using rt-qpcr assays. the relative expression level for each gene is expressed against that of the reference genes actb and b m and the reference condition amx+pbs (arbitrarily set to a value of ). the data represent the mean ± sem. lungs (b) and bal fluids (c) were collected h after treatment and cytokine (continued) figure | and chemokine levels were measured by elisa. data from amx+flagellin-treated and amx+pbs-treated mice were compared in a mann-whitney test and are represented as individual values and mean. lungs (d) and bals (e) were collected h after treatment. lungs and bal cell suspensions were stained using a mixture of antibodies specific for surface markers before flow cytometry analysis. neutrophils were defined as cd + cd b + ly g + cells after exclusion of dead cells and alveolar macrophages (cd + siglecf + cd c + cells) from the analysis. numbers of neutrophils in the lung parenchyma (d) and bal fluids (e) are shown for individual animal and the line represents the mean. data from amx+flagellin group were compared to those of amx+pbs group in a mann-whitney test. statistical significance is indicated as follows: *p < . , and **p < . . the prime cause of bacterial-associated cap ( ) . however, other microorganisms can cause cap and healthcare-associated pneumonia; they include gram-positive bacteria such as staphylococcus aureus, gram-negative bacteria like p. aeruginosa, klebsiella pneumoniae, haemophilus influenzae, mycoplasma (m. pneumoniae) and intracellular bacteria (legionella pneumophila) ( ). the diagnosis and treatment of cap is complicated by the broad variety of causative agents, and the progression of antibacterial resistance. in this context, immunomodulators such as flagellin are of great interest because they activate a large number of antimicrobial immune mechanisms. indeed, flagellin has already demonstrated its ability to protect against various pathogens including gram-negative and gram-positive bacteria ( , ( ) ( ) ( ) ( ) ( ) ) . furthermore, our present results showed that the therapeutic synergy between antibiotic and intranasal flagellin is independent of the antibiotic's mechanism of actionsuggesting that flagellin can potentially be combined with various antibiotics for a wide range of clinical situations. the synergistic effects of the combined therapy have been determined to be independent of capsule antigenicity (serotype or ) of pneumococcus, suggesting that the general innate immune protecting mechanisms triggered by flagellin could potentially be effective against a large variety of serotypes. given the progression of antibiotic resistance, a model of infection by antibiotic-resistant bacteria would constitute an important tool for developing alternative anti-infectious approaches. we first attempted to develop such a model in immunocompetent animals. the multidrug-resistant clinical isolate of pneumococcus sp was unable to induce a lethal infection, even at high doses. acquisition of antibiotic resistance is often associated with a loss of bacterial fitness ( ) , which might explain the sp 's very low virulence in naïve mice. it is now becoming clear that many cases of bacterial pneumonia result from co-infections or consecutive infections (especially influenza virus infections) ( ) . as shown by figures d,e, , influenza virus infection creates a favorable environment for colonization and invasion by the low-virulence antibioticresistant pneumococcus sp strain. our data demonstrated that the flagellin+amx combination treatment effectively reduces the bacterial burden caused by the sp strain in the lung, and improves the survival rate among treated mice. our proof-of-concept findings may be transposable to the clinic for patients with co-infections and superinfections, which are relevant physiopathological causes of hospitalization and complicated pneumonia. antibiotics constitute the current standard of care for bacterial pneumonia, and the growing threat of antibiotic resistance is a major public health concern. when defining the dosing regiments of antibiotics used to treat a patient, the physician must take account of the antibiotic' pharmacokinetic and pharmacodynamic characteristics. the relationship between in vivo exposure to the drug and in vitro susceptibility of the bacteria conditions not only the treatment's clinical outcome (i.e., clearance of the infection) but also adverse effects or drug toxicity ( ) . thus, the maximum dose of antibiotic that can be administered to a patient may not be enough to totally clear highly resistant bacteria. our data suggest that the antibacterial efficacy of these antibiotic dose levels can be synergistically enhanced by the effect of flagellin on lung innate immunity. taken as a whole, the present results suggest that the selective boosting of innate lung immunity by flagellin improves the therapeutic outcome of antibiotic treatment. in humans, this approach might be a useful generic alternative to the treatment of bacterial pneumonia, thereby reducing the antibiotic dose and regimen as well as the emergence of antibiotic resistance. moreover, such strategy promotes multitarget inhibition through multiple innate immune effectors that should be more resistant to the development of resistance and may restore some antibacterial activity to antibiotic in the context of antibiotic resistance. characterization of flagellin's contribution to the lung antibacterial defenses at the molecular and cellular level and the protein's synergy with antibiotics is likely to open up new avenues for the immunotherapy of respiratory tract infections. all experiments complied with institutional regulations and ethical guidelines (c - , institut pasteur de lille; protocol apafis # - ). the protocols were validated by the ethical committee for animal experiments (comitéd'éthique en expérimentation animale-nord-pas-de-calais ceea ). lm performed all animal, rt-qpcr, and flow cytometry experiments. fc, rp, dc, and cf provided lm with technical assistance. fw analyzed the bacterial species and antibiotic resistance. lm, cc, and j-cs designed experiments and wrote the manuscript. j-cs and cc supervised the experimental work as a whole. the study was funded by inserm, institut pasteur de lille, université de lille, inserm-transfert (grant: copoc innatebiotic r es), and the era-net joint programming initiative on antimicrobial resistance and the agence nationale de la recherche (grant anr- -jamr- - ). lm is a fellow of the innovation pharmaceutique et recherche program. aetiology of lower respiratory tract infection in adults in primary care: a prospective study in european countries community-acquired pneumonia requiring hospitalization among u.s. adults dynamics of lung defense in pneumonia: resistance, 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identifies potent drug combinations against trypanosoma cruzi both influenza-induced neutrophil dysfunction and neutrophil-independent mechanisms contribute to increased susceptibility to a secondary streptococcus pneumoniae infection influenza a inhibits th -mediated host defense against bacterial pneumonia in mice influenza and bacterial superinfection: illuminating the immunologic mechanisms of disease the co-pathogenesis of influenza viruses with bacteria in the lung mucosal administration of flagellin induces innate immunity in the mouse lung flagellin promotes myeloid differentiation factor -dependent development of th -type response lung epithelial cells: therapeutically inducible effectors of antimicrobial defense lung epithelial myd drives early pulmonary clearance of pseudomonas aeruginosa by a flagellin dependent mechanism understanding the pneumococcus: transmission and evolution antibiotic resistance and its cost: is it possible to reverse resistance? clinical applications of population pharmacokinetic models of antibiotics: challenges and perspectives we thank dr. aneesh vijayan for technical assistance in the production and quality control of recombinant proteins. we also thank the bicel flow cytometry core facility and the animal facility at the institut pasteur de lille for technical assistance. the supplementary material for this article can be found online at: https://www.frontiersin.org/articles/ . /fimmu. . /full#supplementary-material key: cord- -zwslhjju authors: brittain-long, robin; westin, johan; olofsson, sigvard; lindh, magnus; andersson, lars-magnus title: access to a polymerase chain reaction assay method targeting respiratory viruses can reduce antibiotics: a randomised, controlled trial date: - - journal: bmc med doi: . / - - - sha: doc_id: cord_uid: zwslhjju background: viral respiratory infections are common worldwide and range from completely benign disease to life-threatening illness. symptoms can be unspecific, and an etiologic diagnosis is rarely established because of a lack of suitable diagnostic tools. improper use of antibiotics is common in this setting, which is detrimental in light of the development of bacterial resistance. it has been suggested that the use of diagnostic tests could reduce antibiotic prescription rates. the objective of this study was to evaluate whether access to a multiplex polymerase chain reaction (pcr) assay panel for etiologic diagnosis of acute respiratory tract infections (artis) would have an impact on antibiotic prescription rate in primary care clinical settings. methods: adult patients with symptoms of arti were prospectively included. nasopharyngeal and throat swabs were analysed by using a multiplex real-time pcr method targeting thirteen viruses and two bacteria. patients were recruited at outpatient units from october through april , and samples were collected on the day of inclusion (initial visit) and after days (follow-up visit). patients were randomised in an open-label treatment protocol to receive a rapid or delayed result (on the following day or after eight to twelve days). the primary outcome measure was the antibiotic prescription rate at the initial visit, and the secondary outcome was the total antibiotic prescription rate during the study period. results: a total sample of patients was randomised. forty-one were excluded, leaving patients for analysis. in the group of patients randomised for a rapid result, . % ( of ) of patients received antibiotics at the initial visit, compared to . % ( of ) (p = . ) of patients in the delayed result group. at follow-up, there was no significant difference between the groups: . % ( of ) in the rapid result group and . % ( of ) in the delayed result group (p = . ), respectively. conclusions: access to a rapid method for etiologic diagnosis of artis may reduce antibiotic prescription rates at the initial visit in an outpatient setting. to sustain this effect, however, it seems necessary to better define how to follow and manage the patient according to the result of the test, which warrants further investigation. trial registration: clinicaltrials.gov identifier: nct . acute respiratory tract infections (artis) represent a major global health burden [ ] , and viruses cause a large proportion of artis. distinguishing bacterial artis that require antibiotic treatment from viral artis not needing an antibiotic prescription can be difficult on clinical grounds alone and causes unnecessary use of antibiotics, with the highest rates occurring in the primary care setting [ , ] . excess use of antibiotics has major implications for health economics and, more importantly, for the development of bacterial resistance [ , ] , as well as for the individual patient in terms of adverse events such as allergic reactions and antibioticassociated diarrhoea [ , ] . the predictive value of vital signs, c-reactive protein (crp) and x-ray findings for diagnosing pneumonia requiring antibiotics is low [ , ] . the treatment of acute bronchitis serves as an illustrative example of the unnecessary use of antibiotics, where the recommended therapy for immune competent adults does not include antibiotic treatment [ , ] , yet antibiotics were found to have been prescribed for this condition at high rates in studies conducted in the united kingdom ( %) [ ] , sweden ( % to %) [ , ] and the united states ( %) [ ] . the use of improved diagnostic methods such as nucleic acid amplification tests (naats), including multiplex real-time polymerase chain reaction (rt-pcr) assays, has increased in recent years. these methods have proven to be equivalent or superior to conventional methods [ ] [ ] [ ] [ ] [ ] and to have a short turnaround time at the laboratory, as well as affording clinicians the ability to analyse several respiratory agents within the same patient sample. it has been suggested that the use of naats, including multiplex pcr methods, for the detection of respiratory pathogens could reduce antibiotic prescription rates [ , ] . the present study was designed to evaluate whether access to a multiplex rt-pcr method targeting thirteen viruses would have an impact on antibiotic prescription rates for arti in a primary care setting. we conducted an investigator-initiated, multicentre, prospective, randomised, controlled trial with adult patients in a primary care setting. eligibility criteria for participants were age ≥ years and a diagnosis of community-acquired arti, defined as having a history of at least two of the following symptoms: coryza/nasal congestion/sneezing, sore throat/odynophagia, cough, pleuritic chest pain, shortness of breath or fever for which the physician found no other explanation, with a duration of less than days. exclusion criteria included confirmed bacterial infection (defined as a positive streptococcus group a quick test and clinical findings corresponding to bacterial tonsillitis, perforated acute otitis media, high suspicion of lobar pneumococcal pneumonia or severe septicaemia, a positive blood culture for a clinically significant bacterial pathogen and clinical findings corresponding to septicaemia) and ongoing antibiotic treatment. patients were recruited at outpatient units (eight primary healthcare centres and four departments of infectious diseases), and samples were collected from october through april . signs and symptoms were recorded in a webbased case report form. patients were enrolled by the treating physician on the day of inclusion and stratified according to duration of symptoms of either ≤ days or > days. open-label (nonblinded) randomisation (ratio : ) was performed by means of a predefined list and using a concealed, central, web-based procedure on the day of inclusion for the treating physician to receive the results from the multiplex pcr analysis either on the day following inclusion (the rapid result cohort) or eight to twelve days later (the delayed result cohort). recruitment was performed from sunday through thursday from am until pm, allowing for the laboratory to report results the following day. nasopharyngeal (flocked nylon swabs; microrheologics, brescia, italy) and throat swab specimens were collected from each patient. the swabs were jointly placed in a sterile container with ml of sodium chloride solution and sent to the laboratory the same day. specimens were either analyzed directly or frozen at - °c for delayed analysis (see randomisation and masking above). the results were communicated through the web-based case report form to a study nurse at each site. additional diagnostic testing, including throat and sputum cultures, crp and x-ray investigations, were left to the discretion of the treating physician and recorded in the case report form. the objective of the study was to evaluate whether access to a rapid etiologic diagnostic method would have an impact on antibiotic prescription. the primary outcome measure was the antibiotic prescription rate at the initial visit (or within hours thereafter), and the secondary outcome measure was the total antibiotic prescription rate during the study period. antibiotic prescription at the initial visit (or within hours thereafter) was recorded and analysed in relation to access to a rapid vs. a delayed result. results in the rapid result group were provided to the treating physician within hours for the majority of patients and within hours for all patients. the final management of all patients and how to act upon the given result of the pcr assay were left to the discretion of the treating physician. all patients were asked to return for a followup visit eight to twelve days after the initial visit, and this time period represents the duration of follow-up in the study. the total antibiotic prescription rate (prescriptions at initial visit, at follow-up visit or between those visits) was recorded and constituted the secondary outcome measure in the study. the prescription of antiviral medications was not recorded. serious adverse events (saes) were defined as death, life-threatening events, hospitalisation or events resulting or threatening to result in persistent or significant disability. the regional ethical review board approved the study, and all patients provided written informed consent to participate in the study. we utilized a rt-pcr procedure based on automated specimen extraction and multiplex amplification adapted for respiratory specimens as previously described [ ] . briefly, nucleic acid from μl of the respiratory specimen was extracted into an elution volume of μl by using a magnapure lc robot (roche molecular systems, mannheim, germany) according to the total nucleic acid protocol and was amplified in an abi real-time pcr system (applied biosystems, foster city, ca, usa) in -μl reaction volumes. after a reverse transcription step, cycles of two-step pcr were performed. each sample was amplified in six parallel reactions containing primers and probes as previously reported [ ] , with the modification of adenovirus being analysed in a separate reaction. included in the panel were parainfluenzavirus (piv) types through , influenza virus a (ifa) and influenza virus b (ifb), human metapneumovirus, respiratory syncytial virus (rsv), human rhinovirus (hrv), enterovirus (ev), adenovirus (adv) and human coronavirus (hcov) types e, oc and nl , along with the bacteria mycoplasma pneumoniae and chlamydophila pneumoniae. the primers and probes of all rt-pcr assays were designed to bind conserved segments of the targeted agents. this is particularly important for adv, hrv and ev, which are characterised by a large number of subtypes. the accuracy of the adv pcr assay has been documented by heim et al. [ ] . the target region for the hrv and ev assays was the conserved segment of the ' untranslated region that allows amplification of all subtypes and which has been used previously by others [ ] [ ] [ ] . the primers and probes used for ifb and piv type were developed by dr lars nielsen, copenhagen, denmark; those for piv types and were previously described by watzinger et al. [ ] ; those for hcov (types nl , e and oc ) were described previously by gunson et al. [ ] ; and those for ifa virus were a modification of a system published by ward et al. [ ] . on the basis of the nature of the primary outcome measure, patients with protocol violations and/or missing data were excluded from the primary analysis. this was predefined in the analysis plan. the χ test was used to compare proportions. p < . was considered statistically significant. the study was scheduled to include at least patients in each group, allowing for a statistical power of % to demonstrate an estimated reduction in antibiotic prescription rate from % to % in the rapid result group. multivariate analysis using backward stepwise (wald test) logistic regression was carried out to analyse factors separately and independently to predict a positive pcr result as well as the prescription of antibiotics. spss version . for macintosh software (spss inc, chicago, il, usa) was used for all statistical analyses. the patient flow according to the study design is shown in figure . the baseline characteristics of the two groups of patients randomised for rapid vs. delayed results are shown in table . in the entire study population, antibiotics were prescribed for . % ( of ) of patients at the initial visit (or within hours thereof). in the group of patients randomised for a rapid result, . % ( of ) of patients received an antibiotic, compared to . % ( of ) of patients in the delayed pcr-based result group (p = . ) (see table ). patients with symptom duration ≤ days in the rapid result group received significantly fewer antibiotic prescriptions than patients in the delayed result group. of the patients who received initial antibiotic treatment, ( %) tested positive for a respiratory virus, comprising three in the rapid result group and eleven in the delayed result group (see table ). a total of ( %) of patients returned for the optional follow-up visit or were available for a telephone appointment (visit, n = ; telephone appointment, n = ), comprising ( %) of patients in the rapid result group and ( %) of patients in the delayed result group. in total, patients ( . %) in the rapid result group and patients ( . %) in the delayed result group received antibiotic treatment at either the initial or follow-up visit. this difference was not statistically significant (p = . ). antibiotic prescriptions outside the study (that is, by other than the study physician) were allowed. at the follow-up visit, two ( %) of nineteen patients in the rapid result group and one ( %) of nine patients in the delayed result group reported ongoing antibiotic treatment prescribed outside the study. the investigators reported no saes. as shown in table , patients ( %) tested positive for one agent on the basis of a multiplex pcr assay performed at the initial visit. in addition, patients ( . %) tested positive for two agents in the same sample. in three of these patients, one virus and one bacterium were detected, and in nine patients, two viruses were detected (see table ). crp levels were recorded in ( %) of patients, and a predefined subgroup analysis revealed that patients ( %) had a crp level ≥ mg/l and that patients ( %) had a crp level > mg/l. of the patients with a crp level ≥ mg/l, patients ( %) received antibiotic treatment at the initial visit, compared to ( %) of patients in the group with a crp level < mg/l (p < . ). in the rapid result group, two ( %) of twenty-four patients with a crp level ≥ mg/l received antibiotics, compared to ( %) of in multivariate analysis of recorded symptoms, fever (odds ratio (or) . , % confidence interval ( % ci) . to . , p = . ) and pleuritic chest pain (or . , % ci . to . , p = . ) remained independently predictive of a positive pcr result (with m. pneumoniae and c. pneumoniae excluded from the analysis). a reported sore throat (or . , % ci . to . , p = . ) was significantly more common among patients with a negative pcr result. vomiting remained the only symptom associated with the prescription of antibiotics at the initial visit (or . , % ci . to . , p = . ) in multivariate analysis. high fever (≥ . °c) was more common in the group of patients randomised for a delayed result ( of patients; . %) than in the group randomised for a rapid result ( of ; . %) (see table ), but no significant difference in the number of antibiotic prescriptions at the initial visit for these groups was noted (see table ). we have shown that access to a rapid result using a method for aetiologic diagnosis of artis in an outpatient setting significantly reduced antibiotic prescriptions at the initial visit. however, this effect was no longer significant at the time of follow-up. in our study, we evaluated the impact of access to a rapid diagnostic tool rather than the impact of the actual test result, which implies that the mere prospect of a rapid aetiologic diagnosis can influence therapeutic decisions made for patients with an indistinct clinical presentation. in the subgroup of patients with a crp level ≥ mg/l, this effect was even more pronounced. among patients with positive pcr results for viruses, significantly fewer patients in the rapid result group received antibiotics than in the delayed result group. our results are in line with the reduction of antibiotic prescriptions when rapid diagnostic tests for ifa virus were used systematically for hospitalised adult patients [ ] and children [ ] , although these studies evaluated the impact of the result of the test and thus are not fully comparable. the limitations of this study include the choice of antibiotic prescription as the primary outcome and its open-label design, which might have led to performance bias; that is, the physicians might have been influenced by the randomisation in making the decision whether to prescribe antibiotics. also, on the basis of the study design with an optional follow-up visit, a large number of patients were lost to follow-up, and because of the relatively short follow-up period, the effect and duration of antibiotic treatment in relation to the diagnosis could not be properly evaluated. to influence antibiotic resistance and adverse events following antibiotic therapy, it is necessary to reduce the total rate of antibiotic prescriptions, which was not achieved in our study. however, at the time of planning for the study, limited prospective data were available on the performance of a multiplex pcr panel for the diagnosis of viral and bacterial artis in clinical practise. it was not possible to define whether patients should be prescribed an antibiotic depending on the test result. we therefore chose antibiotic prescriptions at the initial visit as a straightforward primary outcome measure to evaluate whether access to the test would have any effect on antibiotic prescription rates, and this should be included in future studies of algorithms for the management of patients with artis. systematic testing for bacterial pathogens such as streptococcus pneumoniae, haemophilus influenzae and moraxella catarrhalis was not conducted in this study. these bacteria may act as potential respiratory pathogens (prps) harbouring in the upper respiratory tract, and an extension of the panel to include these bacterial agents might improve the clinical utility of the test. however, the interpretation of the detection of bacterial pathogens in nasopharyngeal samples in heterogeneous syndromes such as artis is unclear. cultured s. pneumoniae from the nasopharynx of adults has been shown to have high specificity but low sensitivity for the diagnosis of pneumococcal pneumonia [ ] . pcr-based detection of s. pneumoniae from the oropharynx and nasopharynx without codetection of other commensal streptococcus spp. poses technical difficulties. lieberman et al. [ ] reported higher sensitivity in using nasopharyngeal washing compared to nasopharyngeal swabs in the detection of prps. to keep sampling simple, nasopharyngeal washing was not used in this study, which may constitute a study limitation. however, we used flocked nasopharyngeal swabs, which probably yield higher detection rates than previously reported in studies in which cotton-tipped nasopharyngeal swabs were used [ ] . the study population consisted of patients with a broad spectrum of clinical manifestations, many of whom had mild symptoms. however, since the prescription of antibiotics for these patients is not uncommon, this was a deliberate study design. previously, oosterheert et al. [ ] investigated the impact of a pcr method for aetiologic diagnosis of lower rtis in adults but failed to show any reduction in the use of antibiotics. however, their study included only hospitalised patients, and the end point was to register a change of ongoing treatment regimen rather than whether to make the initial decision to prescribe antibiotic treatment. at follow-up, our study no longer showed any significant difference in antibiotic use between the two study groups. however, since a large number of patients were lost to follow-up, the selection of patients may have been biased. moreover, physicians outside the study prescribed antibiotics for some patients between the initial visit and the follow-up visit. because of the study design, the accuracy of prescriptions during follow-up could not be properly evaluated. thus, our results must be interpreted with caution. in the absence of an algorithm to determine how to follow the patients and act upon the results of pcr testing, including a predefined antibiotic management plan, the observed reduction of antibiotic use at the initial visit may be lost by the time of followup. however, our study represents a proof of concept that access to a rapid etiologic diagnostic tool may affect therapeutic decision in this setting. the antibiotic prescription rate in our study was low. a recent retrospective study of primary care patients in a comparable swedish region recorded an antibiotic prescription rate of % for all patients with artis, % for patients with acute bronchitis and % for patients with the 'common cold' [ ] . the low prescription rate in our series could be due partly to a tendency to adhere more strictly than usual to current guidelines for the restrictive use of antibiotics. we detected an infectious agent in % of patient samples taken at the initial visit, which is in line with previous studies in which detection rates between % and % in adults have been described [ , ] . detection of a virus does not exclude concomitant bacterial infections or other noninfectious causes. this safety issue was discussed at the beginning of our study, and physicians were encouraged to treat bacterial complications at their own discretion. no saes were reported, but because of the relatively large number of patients lost to follow-up and the short duration of the study, we cannot exclude the possibility that some patients experienced late saes. patient-relevant outcomes, such as the severity of symptoms over time, were not recorded, which is another limitation of this study. we deliberately chose not to include such outcomes, as the primary objective of the study was to evaluate the impact on antibiotic prescription rates at the initial visit. this study design also reduced the resources needed to conduct the study. analysis of crp is frequently used to discriminate viral from bacterial infections [ ] . prescription rates increase with rising crp levels [ , ] . in the group of patients with crp levels > mg/l, approximately one-third carried a respiratory virus, supporting the need for reliable tools for the aetiologic diagnosis of artis. distinguishing a viral from a bacterial aetiology in artis is difficult on clinical grounds alone, and the predictive value of vital signs, crp and x-ray findings is low [ , ] . procalcitonin (pct) has been proven to be useful in reducing antibiotic prescriptions in hospitalised patients with lower rtis [ , ] , whereas in primary care, the evidence of pct for this purpose is more ambiguous. one study of adults with arti (one to twenty-eight days' illness duration) judged to be in need of antibiotics and treated as outpatients reported a positive effect of antibiotic use [ ] , but another study of children with community-acquired pneumonia, a significant proportion of whom were treated in the hospital, showed a negative effect [ ] . no distinct pattern of symptoms that could guide the clinician towards a correct aetiologic diagnosis was identified in our study. vomiting, which was the only independent variable predicting antibiotic use, may be interpreted as a sign of serious illness justifying antibiotic treatment. reducing the unnecessary use of antibiotics in the treatment of patients with artis is of utmost importance and cannot be accomplished by using a single strategy. patient-and physician-oriented educational programmes could play an important role as previously suggested [ ] . however, these programmes do not solve the issue of the lack of an aetiologic diagnosis, which is important not only for adequate use of antibiotics but also for addressing issues such as possible complications, prognosis, antiviral treatment options, surveillance and infection control. in conclusion, we have shown that access to a multiplex rt-pcr assay for the aetiologic diagnosis of artis may reduce the prescription rate of antibiotics at the initial visit in an outpatient setting. to sustain the effect, it seems necessary to define how to follow and manage the patient according to the result of the test, which warrants further investigation. we believe that the implementation of similar methods in routine clinical care may be a useful tool to reduce the overprescription of antibiotics in patients with artis. world health organisation: the global burden of disease: update geneva: world health organisation interventions to improve antibiotic prescribing practices in ambulatory care outpatient antibiotic use in europe and association with resistance: a cross-national database study effect of azithromycin and clarithromycin therapy on pharyngeal carriage of macrolide-resistant streptococci in healthy volunteers: a randomised, double-blind, placebo-controlled study emergency department visits for antibiotic-associated adverse events editorial commentary: antibiotics for treatment of acute respiratory tract infections: decreasing benefit, increasing risk, and the irrelevance of antimicrobial resistance diagnostic value of signs, symptoms and laboratory values in lower respiratory tract infection aetiology and prediction of pneumonia in lower respiratory tract infection in primary care antibiotics for acute bronchitis principles of appropriate antibiotic use for treatment of uncomplicated acute bronchitis: background aetiological role of viral and bacterial infections in acute adult lower respiratory tract infection (lrti) in primary care swedish study group on antibiotic use: antibiotic prescribing in outpatients: a -week diagnosis-prescribing study in counties in sweden use of rapid diagnostic tests and choice of antibiotics in respiratory tract infections in primary healthcare: a -y follow-up study excessive antibiotic use for acute respiratory infections in the united states development and implementation of a molecular diagnostic platform for daily rapid detection of respiratory viruses respiratory viruses and severe lower respiratory tract complications in hospitalized patients enhanced identification of viral and atypical bacterial pathogens in lower respiratory tract samples with nucleic acid amplification tests impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection rapid multiplex nested pcr for detection of respiratory viruses multiplex real-time pcr for detection of respiratory tract infections pring-akerblom p: rapid and quantitative detection of human adenovirus dna by real-time pcr lion t: real-time quantitative pcr assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients detection of human picornaviruses by multiplex reverse transcription-pcr and liquid hybridization real-time rt-pcr detection of respiratory viral infections in four triplex reactions design and performance testing of quantitative real time pcr assays for influenza a and b viral load measurement impact of rapid diagnosis on management of adults hospitalized with influenza impact of the rapid diagnosis of influenza on physician decision-making and patient management in the pediatric emergency department: results of a randomized, prospective, controlled trial nasopharyngeal culture in the pneumonia diagnosis peled n: nasopharyngeal versus oropharyngeal sampling for isolation of potential respiratory pathogens in adults comparison of nasopharyngeal flocked swabs and aspirates for rapid diagnosis of respiratory viruses in children development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex pcr and a fluid microbead-based assay swedish study group on antibiotic use: the use of crp tests in patients with respiratory tract infections in primary care in sweden can be questioned effect of procalcitonin-guided treatment on antibiotic use and outcome in lower respiratory tract infections: clusterrandomised, single-blinded intervention trial prohosp study group: effect of procalcitonin-based guidelines vs standard guidelines on antibiotic use in lower respiratory tract infections: the prohosp randomized controlled trial procalcitonin-guided antibiotic use vs a standard approach for acute respiratory tract infections in primary care serum procalcitonin concentrations in bacterial pneumonia in children: a negative result in primary healthcare settings decreasing antibiotic use in ambulatory practice: impact of a multidimensional intervention on the treatment of uncomplicated acute bronchitis in adults authors' contributions rbl contributed to the study design, data collection, data analysis and the writing of the manuscript and was the main person responsible for database management. jw and lma contributed to the study design, data collection, data analysis and the writing of the manuscript. so and ml contributed to the study design, technical issues and the writing of the manuscript. all authors read and approved the final manuscript. the authors declare that they have no competing interests. key: cord- - h fk qt authors: kaur, rajwinder; yadav, bhoomika; tyagi, r.d. title: microbiology of hospital wastewater date: - - journal: current developments in biotechnology and bioengineering doi: . /b - - - - . - sha: doc_id: cord_uid: h fk qt the study of hospital wastewater (hww) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. this chapter investigates the potential microbes such as bacteria, viruses, fungi, and parasites present in hww along with the diseases associated and methods of treatment used. due to the indiscriminate release of antibiotics from hospitals, hww serves as a hotspot for emergence of antibiotic-resistance genes (args) and antibiotic-resistance bacteria. this chapter discusses the args occurrence in hww, their prevalence in the environment, the molecular tools used for identification, and different mechanisms of horizontal gene transfer. thus better understanding of the microbiology of hww could further help in development of advanced treatment technologies for effective removal of microbes and their bioproducts (toxins and infectious nucleic acid) from hww and contaminated water. wastewater includes any type (e.g., from agriculture, domestic means, industries, human excretion, commercial sectors, pharmaceuticals, healthcare units) of water which quality has been deteriorated under anthropogenic influence [ ] . hospital wastewater (hww) is quite different from the wastewater discharged from other sources and is hazardous and infectious. it consists of wide range of several micro-and macropollutants, discharged from operation (surgery) rooms, wards, laboratories, laundry, polyclinics, research units, radiology, and medicine and nutrient solutions used in microbiology laboratories [ ] . the micro-and macropollutants include radioactive isotopes, pharmaceuticals, stock cultures, heavy metals, media, pathogens, drugs, cotton particles, disinfectants, and chemical compounds [ ] . the contraceptive-rich pharmaceuticals present in hww were reported to be associated with effects of endocrine disruption, for instance, exposure to pharmaceutical waste containing estrogen or androgen caused sex reversals in fishes and thus, reproductive impairment [ ] . the hospital effluent discharged directly into the ponds has caused eutrophication, which is evident by oxygen depletion, dense algal blooms, and death of aquatic animals [ ] . the discharge of wastewater depends upon the capacity of hospital and generally water varying from to l/day/bed is consumed by the hospitals [ ] . the hww with many microbes and emerging infectious particles such as prions, viroids, and toxins is hazardous for the environment, and ultimately human health. however, in many countries, hww is directly discharged into sewage water without pretreatment, it then undergoes treatment along with the municipal wastewater but the treatment could not be sufficient to remove micropollutants from hww [ ] . moreover, the pharmaceutical compounds present in hww undergo biological transformation and form conjugate compounds, those toxicity could be even higher than the present metabolite [ ] . thus wastewater pretreatment methods designed for municipal wastewaters are not able to remove the pharmaceutical-related micropollutants or conjugate compounds, which are generally present in low concentration than other macropollutants (chemical oxygen demand, biological oxygen demand, phosphorus, and nitrogen) and thus, could not be removed using conventional wastewater treatment plant (wwtp) operations [ ] . moreover, the pathogens present in hww could cause microbial population imbalance in existing and operating municipal wwtp and metals or heavy metals present in the hww can affect the biological processes like nutrient removal. the heavy metals are in fact nonbiodegradable as compared with other organic pollutants and thus move to other pollutant sources [ ] . the hww can act as an ideal growth medium for various pathogenic microbes including bacteria, viruses, fungi, and parasites. the wastewaters from hospitals also consist of several resistant bacteria and antibiotic residues as well, which could inhibit the growth of susceptible bacteria, thereby increasing the population of resistant bacteria in the receiving water. resistant bacteria discharged into environment either act as vectors to carry a transmissible gene or as the reservoirs for antibiotic-resistance genes (args) that could pose a threat to public health [ ] . in addition, fungi which have capability to grow at faster rate and can spread their spores to external environment also pose a serious threat to environment and human health [ ] . the absence of specific pretreatment technologies for hww also increased the frequency of gastroenteric viruses in aquatic bodies [ ] . the direct discharge of hww into municipal wastewater containing disease-causing parasites has also increased the risk of skin infections and other harmful diseases in humans [ ] . the specific and advanced technologies are required to be developed for hww treatment to prevent the release of harmful contaminants into the environment. therefore the microbial community analysis of hww is utmost importance to assess the pollution load and to develop the specific treatment methods for protection of the environmental health. thus authors explain about the various pathogens present in hww, args, and tools used to study the args. moreover, metagenomics, a recent approach used to study different microbial communities and gene-specific identification, are also explained in this chapter. in addition, horizontal gene transfer (hgt) approach, which can efficiently contribute to spreading of args, is discussed briefly. the hww poses a serious threat to humans with respect to contagiousness and drastic spread of infective diseases in healthcare units, society, hospital employees, and environment [ ] . different solvents, pharmaceuticals, and radionuclides are used in hospitals for purpose of diagnostics, disinfection, and research. after the drug consumption, various drugs remain nonmetabolized or partially assimilate in the human body and thus excrete as such and end up into wastewater. the residual quantities of disinfectants used for treatment of skin microbial infection and to disinfect instruments and surfaces of hospitals, also end up in the hww, resulting in an increase in the population of pathogenic microbes. the pathogenic microflora present in hwws also come from medical devices, atmosphere, and water used in the hospital practice, and the pathogens are released mainly in the form of excreta of patients [ ] . therefore hww consists of a mixture of pathogenic microbes including bacteria, fungi, yeasts, algae, viruses, protozoa, parasites, and bacteriophages. the effluent from hospitals is usually discharged and treated with domestic wastewaters without any prior treatment [ ] . the pathogens in the receiving water, if untreated, survive for a long time in soil or water and enter into the food chain causing infectious diseases and health risks to human beings [ ] . due to the economic reasons and lack of resources for analysis of actual pathogens, certain bacteria have been used as indicators for contamination of water since decades [ ] (box . ). however, it has to be considered that removal of coliforms, which is indicator of fecal contamination, could not be directly correlated with removal of viruses, pathogens, fungi, protozoa, or other bacteria from water (samples) [ ] . in addition, the indicator bacteria such as escherichia coli and clostridium perfringens when compared with pathogenic bacteria, protozoa and viruses are more sensitive to inactivation through processes such as natural competition, wastewater treatment, and high temperature [ ] . traditional detection of pathogenic bacteria involves selective culture media and biochemical characterization methods. these techniques are inexpensive and simple; however, sampling error, time consumption ( À days), tedious, and monospecific detection (detection of only one type of pathogen) are the major limitations [ ] . the enzyme-linked immuno sorbent assay (elisa) is used for laboratory diagnostics of different pathogens. the polymerase chain reaction (pcr) has been adapted in many ways: nested pcr, multiplex pcr, real-time pcr, fluorescence, and digital pcr [ ] (box . ) for analysis of waterborne pathogens. criteria for selection: • should be present only in contaminated water, not in uncontaminated ones • should not be able to grow and proliferate in water • should be present in intestinal tract of warm blooded animals • should have similar survival pattern as pathogens present outside the host • should be easily detectable • should be useful for all types of water • should be relatively cheap to use total coliforms are higher in number than any other pathogens. the subgroup fecal coliforms indicate fecal contamination of water and thus, indicate the presence of other pathogens as well, which are lower in number, hard to detect. however, lower number of pathogens are enough to cause morbidity and mortality to humans. they are detectable by inexpensive cultural methods and do not pose any health risk to laboratory workers. however, there are few limitations of fecal indicator bacteria, which have been discussed in the text. biochemical tests, pcr, and sequencing [ ] (continued) bed-linens, or through infected patients [ ] . the hospital-acquired infections resulted in increase of methicillin-resistant s. aureus (mrsa) isolates. the mrsa is associated with infections of skin and soft tissues and has been a global threat for human health. in the united states, , cases of mrsa infections were reported in [ ] . e. coli and pseudomonas aeruginosa are also commonly found in hww along with other nosocomial pathogens including candida albicans, klebsiella proteus, and enterobacter species [ ] . most of the times, e. coli is harmless and is important part of human intestinal tract, but some of the strains are pathogenic to humans. the e. coli :h is related to many outbreaks of water and food-borne illness and also responsible for , hemorrhagic colitis (bloody diarrhea) cases in the united states annually [ ] . a study reported on hww of brazil also confirmed the presence of other bacterial species including citrobacter freundii, klebsiella ornithinolytica, proteus mirabilis, pantoea agglomerans, and serratia rubidacea [ ] . many c. freundii infections have been reported in bloodstream such as septic shock, pneumonia, hypothermia, oliguria, and thrombocytopenia [ ] . another bacterium p. mirabilis, which is found in hww, is responsible for urinary tract infections and is further accompanied by development of kidney stones [ ] . p. agglomerans mostly affects plants but also causes opportunistic infections in immunocompromised individuals causing skin infections [ ] . an important prospect about fluctuations of pollution was discussed [ ] , according to which, the microbial load present in wastewater was directly correlated to several hospital activities. the higher microbial load was present in hww during the day period as compared with evening and early morning. another study [ ] was also conducted on hww collected during early hours (eh) and late hours (lh) of the day in abia state, nigeria. the microbiological analysis revealed the presence of higher total bacterial count ( . cfu/ ml) at lh as compared with that ( . cfu/ml) at eh of the day. the similar results were also observed for total coliform count, which was also higher ( . cfu/ml) at lh as compared with that ( . cfu/ml) at eh due to the fact that hospital activities at night time were more restricted than day time. according to the recent study, the hww samples were collected from three hospitals in different cities of romania [ ] . three hospitals (h , h , and h ) were having different numbers of beds and inhabitants. the microbial community analysis results revealed that wastewater from h was dominant by . % of the proteobacteria phylum, while from h was dominant by . % of proteobacteria phyla followed by firmicutes ( . %), bacteroidetes ( . %), and actinobacter ( . %) and from h was dominant by . % of proteobacteria, bacteroidetes ( . %), and firmicutes ( . %) [ ] . the similar taxonomic composition was also reported in various studies using wastewater collected from different hospital facilities, nonhospital medical facilities, and municipal treatment plant [ , , ] . the dominant nature of proteobacteria was correlated to their presence in human feces, long-term survival ability in wastewater, and exposure to several antibiotics present in hww. moreover, the dominant nature of firmicutes could be correlated to their capacity to survive in extreme environmental conditions and high contaminant levels [ ] . in buelow et al. [ ] detected abundant bacterial taxa to be different from urban and suburban wwtp influents and comprised of camphylobacteraceae, aeromonadaceae, and carnobacteriaceae. hww also consisted of several different members of human gut microbiota such as of genus streptococcus and family ruminococcaceae due to the sampling location in close proximity of the hospital sanitation areas as compared with wwtp influent. these microbes are not well suited to survive in such complex environment, which results in progressively decreased levels of these bacteria in urban wwtp influent [ ] . another study compared the relative abundances of the most abundant bacterial orders in wwtp for years and showed that the wwtp environment was dominated by phyla actinobacteria, bacteriodetes, and proteobacteria, and the wastewater community was highly stable and unique to its environment [ ] . hospital sewage also contained high levels of anaerobic bacteria including genera such as bifidobacteriales, clostridales, bacteroidales that were likely to originate from the human gut [ ] . the release of antibiotics from hospitals results in creating a selection pressure on bacteria and as a result, effluents from hospitals contain high numbers of resistant bacteria as well as antibiotic residues. prevalence and spread of antibiotic-resistance bacteria (arb) in the environment are a major problem worldwide due to improper antibiotic usage and lack of effective hww management systems. therefore arb and args are particularly studied among the hospital contaminants. for example, one study reported e. coli from hospital effluent to be multiresistant toward ampicillin, streptomycin, sulfamethoxazole, cephalosporin, ciprofloxacin, and tetracycline [ ] . the hospital water environment includes potable water, faucets, wastewater drainage systems, and effluents can be the reservoir of nosocomial pathogens (arb such as mdr enterobacteriaceae, acinetobacter baumannii, and pseudomonas species), thus, increasingly dominating the hww microbiome [ ] . commonly found isolates such as p. aeruginosa, a. baumannii, and enterobacteriaceace in hospital effluents have shown carbepenem resistance and have disseminated around the globe [ ] . baricz et al. [ ] reported antimicrobial effect of a crude bacterial extract of janthinobacterium lividum against mdr bacteria of both clinical and environmental origin, for example, mrsa, methicillin susceptible s. aureus, enterococci, and enterobacteriaceae [ ] . such studies not only help to provide promising candidates for development of new antimicrobials but also to propose new or improved treatment technologies to reduce the burden of antimicrobial resistance (amr) in environment. the microbiological analysis of several hwws showed the prevalence of fungal species along with bacterial and coliform species. the fungi have simpler nutritional requirements and have higher capability to grow at lower water activity as compared with bacteria [ ] . moreover, the fungal populations can easily spread their spores to external environment, hence affecting the human beings directly [ , ] . this is the reason for its prevalence in hospital and clinical environment because if healthcare facilities are even considered free from fungus, but nature and environment factors such as temperature, moisture, and nutrients could provide easy and favorable conditions for the extensive growth of fungal species in storage containers holding clinical waste. the fungal infections could range from moderate to fatal depending upon the infection site as well as immune system of the affecting individual [ ] . the prevalence of invasive fungal species has been reported to increase since three decades, due to increase in number of immunocompromised patients. the moderate fungal infections include athlete's foot and ring worm infections (cutaneous infections) in immunocompetent patients and life-threating infections include mucosal and systemic infections [ ] . the fungal isolates, associated diseases, and treatment methods reported in various studies are presented in table À . the study reported by neely and orloff [ ] stated the prevalence of aspergillus species in the hospital waste collected from the united states and even worse than that, this species was capable enough to survive for more than a month on the hospital waste. the longer survival of aspergillus can result in reoccurrence of fungi and has higher chance to cause disease. moreover, many spores have capacity to remain dormant under adverse conditions and then again develop into fungi, when conditions become favorable. the other fungal species were also detected but the survival capacity of mucar ( . days), paecilomyces ( days), and fusarium ( days) species was lower than that of aspergillus species. the survival efficiency of different fungal species is related to the presence of specific structure of spores. the spores of aspergillus species are spiny and rough and thus capable enough to adhere to any type of waste and can survive longer time. however, spores of fusarium species are smooth and thus have less capability to adhere and survive. the wastewater collected from nigeria revealed the presence of total fungal count of . cfu/ml during the day time activities in the hospital [ ] . the most prevalence fungal species in the hww were aspergillus ( . %), followed by candida ( . %), cryptococcus ( . %), and penicillium ( . %) species. the fungal diversity ( species) was reported to be higher for waste samples collected from hematology section of malaysia hospital [ ] . moreover, gloves waste consisted of the highest number of fungal species ( species) among all the different types of waste collected from hospital. the high fungal count of cfu/ml was also reported in soil collected from hospital dumpsite, which was correlated with the presence of high organic material present in the hospital waste. the fungi are heterotrophic microorganism, which have capacity to consume organic compounds from the surrounding environment [ ] . the common fungal species identified in hospital waste were penicillium rubrum, penicillium viricadum, trichothecium roseum, rhizopus nigricans, aspergillus flavus, aspergillus parasiticus, microsporum canis, and aspergillus niger. among them, a. niger was found to be dominant fungal species with . % due to the fact that it released variety of enzyme such as amylases, pectinases, and proteases and had capacity to utilize number of organic compounds as a substrate [ ] . a. flavus and a. niger can cause disease named as aspergillosis and are considered as pathogens for both humans and animals. they can cause either bronchopulmonary (coughing and wheezing) or invasive aspergillosis (affects the lungs and could spread to throughout the body) [ ] . more than , cases and %À % mortality rate have been reported for aspergillosis infections worldwide. the nonpathogenic black bread mold called r. nigricans was also found in abundance with . %. m. canis can cause infection in upper and dead layer of skin of domestic animals, including dogs and cats and later on the humans can also get affected by the infection [ ] . other fungal species including t. roseum, p. viricadum, and p. rubrum are nonpathogenic fungus, which can only affect the humans with weak immune system. the curvularia species have also been reported to be present in hospital waste and can cause rare infections in the respiratory tract and cornea of human beings. curvularia lunata is also responsible for eumycetoma disease caused in farmers of chandigarh and rajasthan. most of the agricultural regions use azole fungicides (imidazole, metalaxyl, tebuconazole, and propiconazole). therefore the farmers responded poorly to antifungal treatment and were referred for long-term therapies [ ] . the few fungal species of fusarium ( . %) and trichoderma ( . %) have also been reported in hospital waste, but infection caused by these fungal species is difficult to cure [ ] . over . billion people worldwide are reported to be suffered from several fungal infections and . À million people die due to fungal infections each year, which are far superior than malaria or tuberculosis death rate [ ] . antifungal drugs are mostly used for treatment of fungal infections as they target plasma membrane, sterol biosynthesis, dna biosynthesis, and β-glucan biosynthesis of different fungi. however, since past decades, the increased use of antifungal drugs resulted in development of resistance, leading to increase in morbidity and mortality. the drug resistance could be due to several reasons such as alterations of the drug target site, increased efflux of drugs, and biofilm formation. although several studies have reported, antifungal drugs resistance is not at the same level as resistance in bacteria against antibiotics. other reasons of high mortality rate with fungal infections include availability of limited treatment options against invasive fungal diseases and less susceptibility of immunocompromised patients to antifungal drugs [ ] . for instance, in the united states, until , there were reports of , organ transplants, which resulted in increased susceptibility to fungal infections in immunocompromised patients [ ] . in addition, adverse effects of antifungal drugs and lack of effective antifungal therapies are the other reasons, which necessities the development of novel treatment strategies and next-generations of antifungal drugs. the development of ultrahigh-throughput screening techniques could help in advent of novel antifungal drugs by providing rapid, effective, and economical drug screening. presently, the viral infections are in forefront as compared with pathogenic diseases caused by bacteria, fungi, and parasites (table À ) . moreover, the detection, analysis, characterization, and epidemiology of virus is entirely different from bacteria because the bacterial indicators used to represent water contamination cannot actually represent viral contamination. it has been reported that each of the material present in the hospital waste can carry viruses, and thus, viruses are able to survive for À days [ ] . the viral hepatitis is very common and leading disease. moreover, human immunodeficiency virus infections, hepatitis b, and hepatitis c are among the deadly infectious diseases, transmitted by direct contact of blood from infected to another. however, these are yet easy to prevent, once detected at early stages and obligatory precautions are followed by patients [ ] . the samples collected from different wwtps have been analyzed for detection and characterization, and even research has been focused on removal of viruses from wastewater [ ] . however, in spite of all the health risks associated with viruses, very few research [ ] has been conducted specifically for hww, and thus, requires special attention due to the fact that, it is one of the main sources to spread the pathogenic and deadly viral diseases. the modern techniques of molecular biology including pcr assays offer several advantages such as specificity, sensitivity, and wider data analysis for easy and faster detection of viruses. the occurrence of rotavirus a, norovirus genogroup i and ii, human adenovirus (hadv), and hepatitis were detected in samples collected from two different hospital wwtps. the load of rotavirus and hadv present in hospital wwtp was log cycle higher as compared with that present in urban sewage wwtp [ ] . the hadv consists of double-stranded linear dna (fig. À ) and comes under category of nonenveloped viruses, which makes them resistant to heat, dry, and acidic conditions [ ] . the adenovirus consists of outer capsid and inner core with several histone proteins. the elongated fiber proteins on the surface of the virus interact with receptor of host cell such as coxsackie and adenovirus receptor and mcp and start infection in the host cells. after interaction between virus fiber proteins and host cell receptors, uncoating of virus particles takes place resulting in dissolution of viral protein in the endosome. ultimately, the translocation of adenovirus takes place with microtubules through cytoplasm toward the nucleus [ ] . hadv is mostly profound in patients with weak immune system and acute lower respiratory disease [ ] . seventy-nine types of hadv have been reported [ ] , and out of them, hadv / is mostly prevalent in aquatic systems such as sea water, sewage, rivers, surface water, and drinking water [ ] . the hadv is placed among the contaminant candidate list for drinking water by u.s. environment protection agency and is a real factor of concern for the human health [ ] . it can cause several diseases in humans including ocular infections, conjunctivitis, genitourinary infections, pharyngoconjunctival fever, hemorrhagic cystitis, exanthema, encephalitis, and pneumonia [ ] . the hadv is more frequently found in wastewater than any other enteric virus. the hadv is reported to be transmitted through fecal-oral transmission, aerosol droplets, and contaminated materials. it can survive for the extended period of À weeks in the environment without host. due to its stable and persistence nature in aquatic systems, it could also be considered as an indicator of fecal contamination as suggested by various studies [ , ] . the prevalence of hadv species varies according to the hospital environment. according to prado et al. [ ] , the hadv / (species f) was among the most prevalence genotype found during molecular characterization of viruses, detected during analysis of samples collected from two different hospital wwtps. the species f come from the hospitalized children reported with acute gastroenteritis disease. the other reported hadv strains include species c and d, which are associated with conjunctivitis and respiratory tract infections [ ] . the frequency of hadv has also been tested for the samples ( in number) collected throughout year from hospital wwtp located in tunisia city, tunisia and % samples were detected positive for hadv and most prevalent species were species f (hadv / ) [ ] . in the similar way, the prevalence of hadv was detected in samples collected from different regions of the world such as . % in poland, . %À . % in greece, % in norway, and % in brazil, while samples collected from morocco ( . %), italy ( . %), and taiwan ( . %) consisted of low prevalence of hadv [ ] . the high and low prevalence of hadv reported in various countries could be collaborated by the fact that the circulation of virus varied according to the geographical regions and epidemiological community profile. however, whether it was high or low prevalence, still presence of hadv questions the ability of wwtps to remove the gastroenteric viruses and highlights the urgency for development of effective environmental control programs and innovative hww treatment plants before discharging the hww into the sewage system. the detection of hadv includes cell culture method, antigen detection, and pcr method. serology is also used sometimes to detect adenovirus-specific antibodies. there is no effective treatment against hadv, essential precautions should be taken to control infections, which include washing of hands, disinfection of instruments as well as application of infection control protocol in hospitals against adenovirus to prevent outbreaks [ ] . the rotavirus consists of segmented double-stranded rna and its surface is surrounded by three layers: the outer capsid, inner capsid, and central core. there are seven rotavirus groups that have been reported from a to g and studies have revealed that groups a, b, and c affect both humans and animals, while d to g are reported to cause infection mainly in animals. the dual (binary) classification system has been used for detailed classification of rotavirus on the basis of two outer capsid proteins; the glycoprotein vp and protein vp (fig. À ) , where the glycoprotein vp defines for the stereotype g and protein vp defines for stereotype p [ ] . the viral attachment to the host cell surface is by glycoprotein vp or surface protein vp . after interaction with host cell, calcium-dependent endocytosis takes place and thus, uncoating of the particle occurs, resulting in release of double layer of the viral particle into cytoplasm. further, transcription and translation takes place in the cytoplasm and viral proteins are synthesized by cellular ribosomes. after assembly, virus particle is released from the infected cell through cell lysis, and infection is further spread into the host [ ] . rotavirus is associated with around million cases of acute gastroenteritis in the newborn babies and children across the world, and , À , deaths have been reported for children with age of , years globally. after infection and replication, rotavirus is discharged into surface water, groundwater, drinking water, and wastewater, able to transmit effectively through water due to its stable and resistant nature under adverse environmental conditions [ ] . the rotavirus can survive at ambient temperature of cÀ c and can exist on inanimate objects for days without host. the rotavirus is mostly prevalent in humans and %À % of positive samples are associated with group a rotavirus [ , ] . the detection methods of rotavirus include electron microscopy, elisa, passive particle agglutination tests, polyacrylamide gel electrophoresis, and rt-pcr. the vaccination with safety and efficacy profile for rotavirus a has been developed and licensed in after the withdrawn of first ever vaccination, which was associated to cause intestinal intussusceptions in children [ ] . the prevalence of rotavirus in different seasons (summer, autumn, and winter) was detected by collecting different samples in the period of months from hww located in shiraz, iran. enzyme immunoassays (eias) were performed and positive specimens were further investigated with nested-pcr by various primers. moreover, the virus concentration method such as the pellet and two-phase is reported to enhance the concentration of virus by -to -fold before applying eia. about samples ( %) were found to be positive for rotavirus a and the highest prevalence was detected in autumn with frequency of . % followed by . % and % of prevalence in winter and spring, respectively [ ] . other studies also confirmed the prevalence of rotavirus a in cold weather as compared with other seasons [ ] . the molecular characterization of rotavirus further revealed the predominance of g genotype during various clinical investigations followed by mixed genotype of g g , which is associated with frequent water contamination and further generation of novel strains by genetic reassortment. moreover, various studies have reported the prevalence of rotavirus in treated wastewater as well, which is a real concern for public health [ ] . the studies on rotavirus highlight the significance of environmental surveillance tools for detection of novel genotypes and to further analyze the distribution and treatment of the hazardous effects caused by rotavirus in human beings. the norovirus belongs to the family caliciviridae, and is reported to be nonenveloped and contains a positive sense, single-stranded rna, which is organized into three open reading frames (orfs). the three orfs encode three different proteins; orf is of size kb and encodes nonstructural (ns) polyproteins, orf is having . kb size and encodes structural capsid protein vp , while orf with size of . kb encodes a vp protein to maintain the stability of capsid protein [ ] . the norovirus life cycle has been presented in fig. À . the interaction of norovirus with the host cell surface takes place through histoblood group antigens. after release of the vpg-linked rna genome of the virus into cytoplasm of host cell, the viral rna translation takes place. once the translation of the orf polyprotein is done, further co-and posttranslation processing occurs by ns protease of virus, which results in the release of ns proteins for the formation of replication complex. thereafter the viral replication takes place by rna-dependent rna polymerase using de novo and vpg-dependent mechanism. furthermore, the replicated genomes are translated and further packed into the capsid for assembly of virion and exit [ ] . the norovirus is divided into seven genotypes, among them three genotypes gi, gii, and giv are responsible for infection in humans, and gii with genotype (gii. ) is a predominant infectious virus associated with % of the diarrheal diseases and gastroenteritis infections around the world. in addition to gii. , various other non-gii. containing viral strains are also responsible for gastroenteritis infections, for instance, the gastroenteritis emerged in southeast asia in À was associated with g . viral strain. norovirus is associated with million gastroenteritis cases and , deaths annually around the world [ ] . the emission of waterborne norovirus is caused by contamination of water systems including drinking water, surface water, mineral water, and groundwater [ ] . as the infectious individuals shed the virus into the water system, the samples collected from hww are considered useful for study of norovirus epidemiology at population level [ ] . the transmission of norovirus is through fecalÀoral route from person to person or animal to person by contamination food or water intake. depending on the surface temperature and conditions, the norovirus can survive for longer period outside the host. it has capacity to survive for weeks on the hard surface, until days on contaminated fabrics and for years in the contaminated still water [ ] . the norovirus infection in humans can be detected by real-time pcr, multiplex gastrointestinal platforms, eias, and genotyping as well. the development of real-time pcr for detection of norovirus is considered as significant advancement with various environmental applications. the prevalence of norovirus was studied by ibrahim et al. [ ] , where samples were collected form different basins of hospital wwtp located in tunisia. the % of the samples were positive for norovirus gii followed by norovirus g , which was detected in % of the samples collected from wastewater, while frequency of norovirus was lowered moving from one basin to another. however, there is requirement of tertiary wastewater treatment before recycling of water for bathing and other purposes. different studies have revealed the prevalence of norovirus in different seasons, for instance, studies on hww collected from italy and sweden have showed occurrence of norovirus gii in spring and summer seasons [ , ] . however, the study from china has revealed the prevalence of norovirus in winter conditions, which could be explained by variability in temperature during different seasons, immunity level of the host, humidity as well as socioeconomic conditions of different countries [ ] . the emerging recombinant norovirus has been analyzed by illumine miseq and sanger sequencing technique by collecting different clinical and wastewater samples within australia and new zealand. the prevalence of pandemic variant (gii.pe/gii. ) was found in sydney during and , while decline in pandemic virus was observed in with emergence of five new recombinant strains. these new viruses were held responsible for emergence of gastroenteritis outbreaks during november [ ] . the use of new generation sequencing tools has advanced and reformed the genome sequencing of different pathogens present in wastewater. the norovirus has been responsible for , deaths per year. in world health organization (who) identified norovirus as a priority disease for vaccine development. however, several vaccines are still in trails phase and preclinical stages and no licensed vaccine has been available for norovirus infection treatment. the cost effectiveness, target population, and public acceptance are the major considerations for vaccine development [ ] . the public awareness about the norovirus and prevention measurement should be spread for protection of people from norovirus infection due to lack of treatment available. hepatitis a virus (hav) is a nonenveloped virus, belongs to the picornaviridae family, and has positive sense single-stranded rna (fig. À ) . the rna consists of only one orf, which encodes a large polyprotein [ ] . there are six genotypes of the virus reported and genotype i, ii, and iii are infectious to human population and are further subgrouped into a and b, while iv, v, and vi affects other primates than human beings [ ] . there is a genetic nucleotide variation of . % in each of the subgenotypes, which has been evaluated with pcr by vp /vp a junction present in nucleotide fragment [ ] . the interaction of the hav with host cell involves endocytic pathway. the host cell receptor involved in interaction with virus is tim- (havcr ) and it is reported to cycles between plasma membrane and lysosome of host cell with calthrin-mediated endocytosis. the replication, translation, and assembly of virus occurs inside the cytoplasm of host cell [ ] . the genetic analysis of hav could be correlated with the outbreaks of viral infections and transmission mode as well. the main transmission mode for the virus is fecalÀoral route, which could be directly transmitted through one human to another or indigestion of contaminated food as well [ ] . the hav has capacity to survive for months outside the host body, it can survive through freezing temperature but can be killed, when exposed to high temperature of . c. the geographical distribution of the virus has been mainly present in india, africa, middle east, central america, and south america. the hav is considered as one of the most important food-borne pathogens and is a major cause of hepatitis in humans with reported cases of around . million globally. it has been estimated that half of the hepatitis cases are related to hav. the wastewater coming from the hospital could be emerging source of hav due to the fact that human excretion contains enormous amount of virus; moreover, virus is highly resistant to harsh environmental conditions and is able to survive for longer periods [ ] . the hav is also detected in rivers, raw or treated water, and dam water as well [ ] . these viruses are a real cause of concern for human health; moreover, there are no strict regulations in existence related to monitoring of these viruses in environment and water resources [ ] . the consumption of contaminated food has also been directly linked with outbreak of hav at several places. for instance, there were reported cases of hav in michigan between august to october with fatalities and hospitalization. the outbreak was linked to consumption of raw scallops served in sushi chain. in another case at hawaii, cases suffering with hepatitis a infections were reported between june and october , which were linked to contaminated frozen strawberries [ ] . the prevalence of hav was detected in different clinical samples collected over a period of years from patras and alexandroupolis located in greece. the nested real-time pcr revealed the presence of % genotype- and particularly subgenotype a [ ] . the predominance of genotype- and subgroup a has also been reported in wastewater samples collected from brazil [ ] . the prevalence of virus was also reported to be higher during the lower number of cases reported for hepatitis a, which could be directly correlated to the shedding of virus into feces. the detection of igm antibodies and anti-hav in blood is related to hepatitis a infection. the presence of anti-hav in blood indicates infection or past vaccination. the hav vaccination within weeks of infection is the prevention method for hav infection and includes two-dose series for individuals above age of months. the vaccination includes inactivated virus and is safe for immunocompromised persons [ ] . the hww is heavily loaded with pathogens and discharged directly into aquatic bodies could be directly evident by skin infections and intestinal parasites. around the globe, millions of people are affected by deadly parasites infections, for instance, . million suffer from giardiasis, million from amebic dysentery, million affected by hookworm infections, million detected with trichuriasis, and . billion are infected with ascariasis [ ] . these parasites are mostly transmitted through fecalÀoral route under poor hygienic conditions, contaminated water and food sources, and poor wastewater disposal practices. the parasites in their ineffective stages such as cysts, eggs, and oocysts survive under environmental adverse conditions and through many wastewater treatments processes due to the presence of protective outer layer. therefore parasites have capability to survive in wastewater for extended time period in comparison to viruses and bacteria [ ] . the samples collected from hospital sewage treatment plant located in zaria, nigeria contained several eggs, cysts, and oocytes of various parasites. about eggs, cysts, and oocysts were present per liter of wastewater. ascaris lumbricoides was the common parasite found in hww with eggs per liter ( . %) of wastewater followed by eggs ( . %) of taenia spp., eggs ( . %) of schistosoma spp., eggs of toxocara spp., eggs ( . %) of ancylostoma spp., eggs ( . %) of cryptosporidium parvum, and eggs ( . %) of giardia lambila. moreover, eggs ( . %) of trichuris and hymenolepis spp. were also found in hww. the cysts of entamoeba histolytica and a. lumbricoides were found in many studies and remained viable for longer period of time in pond effluents that was further used to irrigate raw vegetables, thus, entering the food chain and then directly to humans [ ] . c. parvum causes the disease cryptosporiadiasis and g. lambila causes giardiasis, both could be life threatening if found in persons with weak immune system. the children diarrhea in many cases is caused by the cryptosporidium species [ ] . taenia species can cause cysticerocosis in humans that can infect muscles, brain and can ultimately cause onset seizures in adults, while it can also cause bovine cysticerocosis in cattle after consumption of contaminated water. the main symptoms of parasitic infection include nausea, vomiting, malabsorption, diarrhea, and stomach cramps [ ] . therefore the wastewater should be treated before discharge into water bodies otherwise they could be a great risk to public health. antibiotics are one of the most successful and important drugs used in therapeutic applications and the indiscriminate use of these compounds has made their way into the environment. the overuse and misuse of antibiotics not only in human therapeutics but also in veterinary, agriculture, and aquaculture applications [ ] has led to the emergence of args and arb compromising or decreasing the effect of antibiotic compounds as they are becoming resistant to multiple drugs thus, causing a major concern. some studies have shown that resistant bacteria can also be present where antibiotic concentrations are low, saying that subinhibitory concentrations can also promote resistance among bacteria as similar to concentrations found in some aquatic and soil environments [ ] . just as natural antibiotics have existed for billions of years, args are also ancient [ ] . there have been occurrences of args in places where anthropogenic activities are minimal such as genes encoding for β-lactamase in a remote alaskan soil suggesting the environment to be a reservoir of args [ ] . antibiotic-resistant bacteria have been reported from lechuguilla cave, new mexico which has been isolated for more than million years including some strains which were resistant to over different antibiotics [ ] and in ancient permafrost samples where communities harbored resistance mechanisms minimum years ago [ ] . such studies improve our understanding of the prevalence of resistance genes in environments much prior to human use of antibiotics. within past years, pieces of evidence have shown mobilization of these resistance genes from the environment into pathogenic bacteria causing health risks to humans and animals and also, demonstrating a link between environmental and clinical resistance [ ] . moreover, due to the introduction of antibiotics from various human activities, the environment has turned into a reactor of arb and args contributing to the evolution and spreading of resistant genes. the phenomenon of emergence and spread of args has increased so intensely that % of all hospital-acquired infections show resistance toward at least one family of antibiotics. hww represents an important source of args and arb and such effluents are highly hazardous due to its infectious and toxic features [ ] . traditionally, resistance was viewed as a healthcare problem but now nonclinical environment has also been reported as an important factor in the dissemination of resistance genes [ ] . a wide range of antibiotics and args are being released from the hospitals and urban wastewaters which are received by wwtps [ ] . the wwtp also serves as a hotspot in the emergence and spreading of args and arb in the ecosystem [ ] . even after the treatment, some of the antibiotics and args are still not completely removed and being released into the receiving water bodies making aquatic ecosystems an ideal place for acquisition and spread of such genes. commensal bacteria of humans and animals also constitute a reservoir of such resistance genes which can enter the environment through sewer systems or use of animal manure [ , ] . other than wwtp effluents, args can reach the soils, sediments, surface water and groundwater bodies including drinking water systems [ , ] by surface runoff or infiltration of water that has been used for agricultural purpose [ ] . it has been estimated by who that arbs are responsible for , , , , and , deaths per year in european union, the united states, and thailand, respectively [ ] . there has been increasing resistance in many human pathogens such as e. coli, a. baumannii, enterococcus sp., klebsiella pneumonia, s. aureus, p. aeruginosa, serratia marcesens, citrobacter sp., and other enterobacter species, and there have been a great number of growing reports concerning the prevalence and dissemination of these pathogens into various environmental settings [ À ]. knapp et al. [ ] reported args from different major classes of antibiotics tested from to had significantly increased since , along with tetracycline args around times more abundant than in the s [ ] . the resistant gene can be specific to one antibiotic, for example, ciprofloxacin or a group of antibiotics such as β-lactums and as a result, hundreds of args are being detected [ ] . genes resistant to antibiotics are commonly observed for aminoglycoside (aac, aad, aph), chloramphenicol (cat, cml), sulfonamide (suli, sulii, suliii, sula), trimethoprim (dfra, dfrb), quinolone (qnra, b, s), tetracycline (teta-e, g, h, j, y, z, etc.), vancomycin (vana, vanb), macrolide (erma-c, e, f, t, v, x), β-lactum, and penicillin (bla, meca, pena) antibiotics in different environments [ , , ] . infections caused by resistant strains are difficult to deal and have led to increasing rates of infections, higher hospital costs, and high rates of morbidity and mortality, for example, strains producing extended-spectrum β-lactamase (esbl) are responsible for higher rates of mortality [ ] . there is a widespread occurrence of args originating from different settings that has contributed to a web of resistance among humans, animals, and the environment and, even after their treatment, they can be still present and can contribute to their spread in the environment. furthermore, there still exists an unexplored pool of genes that may have the potential to be used as args and may be passed to pathogenic bacteria. various hypothesis have been given for the mechanisms of resistance genes to traverse wwtp and their influence by the treatment process [ ] (fig. À ) . thus antibiotic resistance development includes a broader impact on the environment and human health rather than just a local health issue and has to be addressed. the current risk assessment is inadequate and requires advanced biological risk assessment evaluations to detect the proliferation of args and antibiotics. this includes minimizing the resistance emergence and spread in the environment and their transmission to humans. to achieve this, it is necessary to achieve goals such as defining resistance in environmental samples and standardizing testing in those samples which will further require establishment of more comprehensible databases to combine both environmental and clinical metadata. it would help to understand relationships between resistomes of different settings and would improve the risk assessment of args and arb to further develop control strategies [ ] . the need for screening of args present in bacteria is important for the optimal antimicrobial therapy to treat infections in patients and this need is increasing with increasing resistance among bacteria. detection will also predict the spread of resistant organisms and genes throughout the environment. a diversity of detection methods is available for both phenotypic as well as genotypic determination of args in isolates. antibiotic resistance is a selectable phenotype and can be detected using growth inhibition assays using disc diffusion method, broth dilution, gradient strips, or other methods to determine the minimum inhibitory concentration (mic) of antibiotics [ ] . the mic is calculated for each isolate and based on the results, isolate can either be susceptible or resistant to the antibiotic [ ] . however, there remain certain problems associated with this method, such as gradation of resistance, time-consuming (can take several weeks for slow-growing bacteria such as mycobacterium tuberculosis), and culture-dependent method, relate to only concentration of antibiotics (difficult to detect low-level resistance), and give no information about dissemination of resistance via mobile genetic elements (mges) [ , ] . to overcome these disadvantages, genotypic or molecular characterization methods such as pcr, hybridization techniques including microarray, and whole genome sequence (wgs) are used extensively to determine specific resistance genes and providing results within hours. genotypic characterization has led to the identification of args in fastidious bacteria which expresses few phenotypic features, for example, tropheryma whipplei, that causes whipple's disease showed mutations in gyra and parc gene owning to fluoroquinolones resistance [ ] . the wwtp compartments like influent, activated sludge, effluent consist of contrasting conditions including different concentrations of metals, antibiotics, etc. changing stress concentrations may act as drivers for microbial community and resistomes thus, changing biomass per volume and persistence/enrichment of arb this can result in a strong shift in the whole microbial community composition and antibiotic-resistance subset these changes are expected to correlate with the changes of resistome. contigs analysis allows further identification of marker genes for mobile genetic elements finally, horizontal gene transfer may help in the transfer of resistance genes and may act on evolutionary timescales the use of a plethora of pcrs such as standard, real-time, multiplex pcr to detect the presence of genes encoding resistance to aminoglycoside, chloramphenicol, macrolide, β-lactum, penicillin, trimethoprim, and tetracycline in bacteria is quite common [ , , ] . isothermal amplifications using loop-mediated isothermal amplification [ ] pcrs are very rapid, performed at one constant temperature and have been developed to detect esbls genes and carbapenemases genes in bacteria but they cannot be used in multiplex to detect several genes simultaneously. very recently, a paper-based chip which is integrated with lamp and a switch molecule for fluorescent detection of args has been developed to allow more convenient and efficient detection especially in resource-limited conditions [ ] . many other detecting and genotyping techniques based on the pcr have been developed to identify args such as restriction fragment length polymorphism-pcr, mismatch amplification mutation assay-pcr, or pcr-single strand conformation polymorphism that have been used to detect gyra mutations in quinolone-resistant isolates [ ] . schwartz et al. [ ] used pcr technique to detect vana (vancomycin-resistance gene), meca (methicillin-resistant gene), and ampc (ampicillin-resistant gene) in wastewater, surface water, and drinking water biofilms [ ] . recently both pcr and rt-pcr have been used across europe for detection of plasmid-mediated mcr- genes harboring resistance against colistin [ À ] (table À ) . multiplex rt-pcr has been used to identify staphylococci from blood samples by targeting meca and other species-specific genes [ ] . another example of using multiplex pcr is in the detection of prevalent esbls genes in e. coli that encoded mainly bla shv , bla tem , bla ctx-m , and bla oxa [ ] . it is also possible to devise and use multiplex pcr to detect genetically diverse resistance genes for [ ] tetracycline thus, making it one of the most widely used techniques [ ] . however, these methods have low-throughput, sometimes gives false results, mostly ignore potential reservoirs of resistance that are nonculturable bacteria, and depend on primers that leave less room for discovery of novel genes. molecular hybridization is one of the oldest molecular techniques that have been used to detect the presence of specific args and meanwhile several improvements have been done on probe designs and synthesis. southern hybridization demonstrated tet and class-i integrons can be cotransferred from isolates present in soil to e. coli and/or pseudomonas putida [ ] . pcr-southern blot assays were used frequently and reported tetracycline (tet ) and sulfonamide (sulii) resistance genes in acinetobacter species from fish farms in thailand [ ] . probes can be labeled with a variety of reporters including radioactive and nonradiolabeled systems. one nonradiolabeled method is fluorescence in situ hybridization that has been used for rapid detection of macrolide, clarithromycin, linezolidresistances [ ] . high-throughput dna microarray is another technique that has been successfully used to detect args in the test organism in comparison to a reference strain and works with high speed and high delicacy. in this technique, probes specific to the particular gene are spotted on a solid substrate (e.g., glass slide). dna is labeled and hybridized, and the specific targetprobe duplexes are detected. comparison of genomic diversity in a large number of test isolates can be done for which wgs is not available [ ] . it enables detection of a large number of single genes, mutations, mges and also can characterize strain at the molecular level [ ] . it has been used for antimicrobial genes detection in a diverse range of bacteria [ ] . glass-based microarray has been developed for the detection of tetracyclineresistance genes and one β-lactamase gene in multiple bacteria that used microarray probes c. -base pair pcr products [ ] . perreten et al. [ ] developed a rapid and efficient screening of gram-positive bacteria using microarray for the presence of args which was further improved by additional oligonucleotides for detecting args [ , ] . similarly, alere microarrays have been developed capable of detecting clinically relevant antibiotics and can be used in routine diagnostics laboratories [ ] . some of its disadvantages include, low detection limit, high cost (due to use of platforms with probes of short oligonucleotides or pcr products as well as fluorescent dyes) and problems in dealing with complex samples [ , ] . just like pcr and microarray, wgs is another potential method to detect genes and mutations conferring antibiotic resistance. the main advantage is its ability to use and detect different targets simultaneously and to subtype-specific gene variants. one can possibly add new targets to the database for analysis and can perform rapid in silico reanalysis of sequenced isolates. the presence of args within the wgs data has to be determined for which, comprehensive databases containing relevant target dna is required along with the use of appropriate bioinformatics methods for obtaining information about the wgs data. some of the databases that have been used for detection of args in curated wgs data are resfinder, which is a web server and uses blast for identification of args [ ] , comprehensive antibiotic-resistance database that uses blast and resistance gene identifier as two analysis options [ ] , antibiotic-resistance gene-annotation that gives user an opportunity to use local blast in bio-edit software and analysis can be done without web interface [ ] , and antibiotic-resistance gene database that is a manually curated database unifying publicly available information on args such as resistance profile, ontology, mechanism of action, and much more [ ] . other knowledge resources of amr include antibioticresistance genes online, collection of antimicrobial peptides, database of antimicrobial activity and structure of peptides, antimicrobial peptide database, and bacmet which differ from each other on the basis of the knowledge on molecular level of args they reflect and the scope of resistance mechanism they cover [ ] . however, one major drawback of using molecular techniques for arg detection is that new emerging resistances against some antibiotics may be overlooked as observed for ndm- gene encoding resistance to carbapenem antibiotics which was first isolated using phenotypic methods and then characterized on the basis of genotype [ ] . thus, within the number of both phenotypic and genotypic methods, there are limitations involved with each one and one can perform a combination of these screening methods to monitor resistance. thus the use of all these techniques helps in predicting the resistance genes, setting up control measures in hospital infections, adapt to a specific therapy and using them routine detection tools [ ] . the molecular analysis tools such as pcr, quantitative pcr, and s rrna analysis have provided the in-depth knowledge about microbial communities present in wastewater since decades [ ] . however, requirement of gene-specific primers, and species-specific approach used by these tools limit their activity for detection of certain targeted microbes providing incomplete information about microbial communities present in wastewater [ ] . recently, metagenomics analysis has been introduced, which overcomes the limitations related with conventional molecular analysis tools and is able to generate hundreds to thousands of sequences, providing complete profile of microbial communities present in unknown samples, thus high abundance of potential microbes are detected [ ] . the metagenomics analysis consists of four steps; genetic material isolation followed by genetic material cloning, construction of library, and the analysis of genetic material from the metagenomics library. metagenomics along with search engine for amr [ ] can analyze the unknown samples collected from environment and can provide full-length arg data. the hww has been reported to have two overexpressed β-lactam-resistance genes (bla ges and bla oxa ) as compared with the water collected from other aquatic bodies, which could be correlated with antibiotic usage over the time in hospitals and discharge of the residues of antibiotics in the wastewater [ ] . the hww that is derived from clinical speciality ward is determined to be major spot for the amr. the wastewater derived from different wards of the hospital and the final effluent of hospital was tested and compared for resistance genes. the wastewater has a high abundance of class a β-lactamase resistant genes (i.e., bla kpc , bla ctx-m , bla shv , bla tem ) and the wastewater from clinical ward also consists of high level of bla kpc- genes ( , x/gb), encoding for carbapenem resistance. moreover, there was presence of assembled scaffolds of incq and incf plasmids having quinolone-resistance genes (qnrs , qnrs ) and the class a β-lactamase gene (bla tem- ) in wastewater, which further helps in proliferation of amr [ ] . metagenomic functional selection has been integrated with deep metagenomic sequencing to trace validated args in different environments. studies have identified wwtp resistome consisting of novel args thus, throwing the limelight on wwtp reservoir of uncharacterized resistance genes using these selections. using such metagenomic methods relates the number of clinically relevant resistant genes to overall functional resistant genes and thus, helps in improving the risk classification in environments [ ] . metagenomics strategy also revealed the association of isolated p. aeruginosa from hww with amr frequency. the isolated strain was selected as a bio-indicator, due to its ability to survive and colonize in harsh environments and it was used to assess its viability, antibiotic susceptibility, and diversity in hww. the samples collected during different treatment steps of hww revealed that each treatment step was able to decrease the bacterial population by four logarithm cycle; however, the antibiotic resistance profile did not decrease at each treatment level, while, on the contrary, there was increase in amr microbes and genes as well. the microorganism was able to remain survived in the spore form during different treatment steps and again transform into vegetative form when released into surviving environment [ ] . the healthcare clinics and hospitals, where antibiotic use is more common among the major contributor to disseminate the pathogenic microorganism into the environment. in addition, shortgun metagenomics analysis of hww collected from turkey revealed the presence of more than antibiotic resistance determinants and most common genes belongs to aminoglycosides and β-lactameses. the prediction of high resistome diversity in hww raises an alarm for health concern of human population. an important step in coping with the serious problem of emergence and dissemination of args is to understand the pathways for resistance gene spread. the ability of bacteria to respond to selective pressures and new environments can be explained by the acquisition of new genes by cells using horizontal transfer methods. studies have shown around % of the genes in each genome have been transferred by hgt during evolution [ ] . many resistance genes are located on mges such as plasmids, transposons also known as jumping genes, and integrons that are capable of capturing and expressing gene cassettes [ ] , which are responsible for antibiotic resistance that functions as vectors for their dissemination [ ] . horizontal acquisitions might be neutral or have deleterious effects in the chromosome or confer a selective advantage to the host. other than mutations, hgt has been one of the methods which are most responsible for the dissemination of args among different bacterial species. it has caused the spread of antibiotic resistance from commensal and environmental bacteria to pathogenic species. the args transfer by hgt exists much back before the use of antibiotics by humans, for example, oxa β-lactamase genes that confer resistance against β-lactam antibiotics mobilized from chromosomes to plasmid millions of years ago [ ] . but the rate of the resistance gene transfer has increased tremendously due to selective pressure caused by antibiotic use by humans in the last few decades. bacteria employ three mechanisms for hgt, that is, conjugation, transformation, and transduction (fig. À ) . conjugation is said to have the greatest influence over the spread of args. conjugation requires a physical contact between two cells via pili or adhesions to transfer the genetic material. this mechanism has been found in bacterial cells with an exception of agrobacterium species that uses hgt in plants. the conjugative machinery encoded by the genes on plasmids or by integrative conjugative elements on chromosomes facilitates this process. args are mostly associated with conjugative elements like plasmids and transposons, and the transfer of these elements is most likely to occur by conjugation because it provides a more efficient way to enter the recipient cell and gives better protection in the environment [ ] . conjugation can be of various types such as ( ) transfer of a selftransmissible conjugative plasmid, for example, rp plasmid of e. coli. ( ) mobilization of nonself-transmissible plasmids by the action of conjugative plasmid, for example, incq plasmid rsf . ( ) cointegration of two different circular plasmids to fuse to become one. ( ) conjugated transposons which may facilitate mobilization of plasmids or cointegration. the mges conferring agrs transfer have been found in bacteria ranging from soil, water ecosystems to food, and human pathogens [ ] . the transfer of the conjugative elements between bacteria over distant phylogeny indicates the emergence of multiresistance between different reservoirs [ ] . bla ctx-m esbl genes have been disseminated to various plasmids within enterobacteriaceae and other pathogens and can be found in various geographical locations [ ] . the conjugation of plasmids has caused dissemination of args worldwide that encode resistance to β-lactamases, carbapenemases, quinolones, aminoglycosides, colistin, sulfonamide, tetracyclines, and other classes of drugs. conjugation has been also reported between bacteria and eukaryotic cells and is observed in various environments such as soil, aquatic, marine sediment, wastewater, and activated sludge [ ] . the second mechanism is transformation, in which the cells take up the naked dna from the environment. for transformation to take place, there are certain prerequisites like release and persistence of extracellular dna in the environment, the recipient cells must be competent, and the dna translocated must be stabilized by integration into the genome or by recircularizing into self-replicating plasmids [ ] . the process takes place in two steps: first, the dna substrate is transferred from surface to the cytoplasmic membrane which is mediated by type ii secretion system, type iv secretion system, and type iv pili; and second, is the transport of dna across the cytoplasmic membrane using cytoplasmic membrane channels [ ] . with an exception of neisseria gonorrhoeae that is a naturally transformable bacteria which responds to environmental conditions [ ] , most species develop competence under autoinducers, peptides, or stressful conditions, for example, aminoglycoside and fluoroquinolone antibiotics sublethal concentrations induce competence in streptococcus pneumoniae and legionella pneumophila [ ] . mao et al. [ ] developed a method to extract extracellular and intracellular dna from water and sediments. they obtained a higher concentration of extracellular dna than intracellular dna in sediments from a river basin that serves as a major arg reservoir that could be transferred to indigenous bacteria through natural transformation [ ] . also, it has been shown in pneumococcal genome that the conjugated transposon disseminates via transformation in addition to conjugation [ ] . transduction is the process by which dna is transferred with the help of bacteriophages. bacteriophages can transfer dna sequences like chromosomal dna, mges such as plasmids, transposons and genomic islands that are advantageous to their bacterial hosts as well as serves in improving the survival of bacteriophages [ ] . transduction can be generalized where random host dna is incorporated during cell lysis and specialized, where the prophage excises itself from the host genome and also incorporates flanking host dnas [ ] . args transfer by transduction has also been reported in various bacteria, for example, β-lactamase gene transfers by p -like bacteriophages in e. coli [ ] , erythromycin resistance transfer by phage between clostridium difficile strains [ ] , tetracycline and gentamycin resistance between enterococci [ ] , or transfer of resistance plasmids in msra [ ] . bacteriophages can have broad host range, that is, between different species or among different taxonomic groups [ ] thus, indicating dissemination of args via transduction in the environment, a common mechanism. other mechanisms such as gene transfer agents (gtas) and cell fusion have also been described. gtas are delivery systems that carry random pieces of host genome in capsids and get integrated into the host chromosome. the amount of dna that gta contain is insufficient to encode their proteins counterparts, unable to self-propagate thus, they do not necessarily carry gta-encoding genes that is an important distinction from transduction mechanism [ ] . the first gta discovered was in rhodopseudomonas capsulate called as rcgta and they were able to transfer antibiotic resistance to bacteria by a mechanism similar to transduction which does not require cells contact and was resistant to dnases [ ] . apart from the evidence of gta shown in various members of rhodobacterales, for example, ruegeria pomeroyi which contain a complete rcgta-like cluster of these genes, roseovarious nubinhibens and ruegeria mobilis also showed rates of transfer of antibiotic resistance around -fold higher than rates of transformation and transduction when added to microbial communities [ ] . mcdaniel et al. [ ] reported gta frequencies to be much higher, around a million times higher the frequency of transformation and transduction measured previously in the marine environment [ ] . there are several advantages of gtas over other mechanisms such as protection of dna from environmental factors, transfer not constrained to cellÀcell contact, and they contain random dna from host rather than most of the bacteriophage dna as observed in transduction. another mechanism, cell fusion has been observed in haloferax and sulfolobus species [ , ] . symmetric and bidirectional cell fusion has been observed in haloferax volcanii. studies have shown interspecies gene exchange in halophilic archaea where cells fuse forming a diploid state containing two different chromosomes of parental cells thus, facilitating genetic exchange and recombination followed by separation of hybrid parental cells [ ] . although new mechanisms are continuously being developed by bacteria and identification, mapping of these resistance mechanisms provides us with knowledge of sources of resistance and helps in designing new antimicrobial drugs. the prions are infectious protein particles present in brain, which are responsible for degenerative neurological disorders. in humans, the prnp gene present on chromosome produces the prp protein and prions results in transformation of prp protein into abnormal disease causing isoform [ ] . these pathogenic prions cause the functional disruption of neural cells resulting in cell death and leading to memory problems, trouble with movement and personality changes as well. the prions can result in many infectious diseases such as creutzfeldtjakob disease (cjd), variably protease-sensitive prionopathy, gerstmann-sträussler-scheinker disease, scrapie, variant cjd, fatal insomnia, and kuru. these transmissible disease impacts number of mammalian species, including sheep and goats, cattle, deer, moose, elk, and humans. the scrapie and cjd are of particular concern because they can be transmitted horizontally and they remain infectious in the environment for very long time [ ] . for instance, the scrapie infection was persistent even after burial in soil for years. the cjd disease is most common and deadly human prion disease and can cause infection in three ways: sporadic, genetic, and acquired. most of the times ( %À %), cjd occurs sporadically and approximately À . million people are affected annually, because there is no cure available for cjd and other prion diseases [ ] . the recently developed methods for detection of prion infectivity include protein misfolding cycling amplification, quake-induced conversion, and quantitative tandem mass spectrometric techniques [ ] . however, the study of prions is highly challenging due to the fact that the high-resolution structure of prion isotherm is still to be determined and change in structure directly affect infectivity and pathology of disease. prions are likely to enter through live, infected hosts, and can be shred through saliva, urine, feces, mucus, and blood; and they enter in wastewater through hospital effluents, research facilities, homes, slaughterhouses, and mortuaries [ ] . the wwtps are not able to treat prions, for instance, after entering into municipal wwtp, the prions bind to sewage sludge, survive through anaerobic digestion and are further present in treated biosolids. these biosolids are further used for land application, which results in their introduction into environment. thereafter they can be swept by wind and contaminated water with prions could further migrate into lakes, rivers, and oceans and thus, directly affecting the humans, aquatic life, and animals as well [ ] . viroids are small (b À nucleotides), single stranded, circular rna particles, which are distinguished from viruses by smaller size, lack of capsid and also they do not encode any protein. they have capacity to reproduce and are mostly known to cause infection in plants; however, hepatitis δ, which cause infections in humans, has many similar properties with viroids and could be related to viroids [ ] . a total of viroids species has been identified, which are grouped into avsunviroidae and pospiviroidae. the viroids are mainly infectious for plants such as tomatoes, cucumber, avocados, potatoes, apples, coconut palms, and chrysanthemums and are responsible for million dollars' loss in agriculture revenue each year. the most commonly reported viroid plant diseases caused by viroid include apple fruit crinkle, tomato chloric dwarf, and chrysanthemum chlorotic mottle [ ] . the yellowish curled leaves of plants are due to pairing of viroid rna with messenger rna of plants resulting in interference of proper translation. some of the viroids cause devastating effects, for instance, coconut cadongÀcadong viroid has caused lethal effects in coconut palms in philippines, resulting in loss of million coconut palm [ ] . other reported effects of viroids include epinasty, rugosity, necrosis, chlorosis, stem shortening, color alteration of fruits, flowering, and ripening delays. the microarrays are identified as a significant tool for detection of many viroids simultaneously and even has ability to detect emerging or established viroid in new host. potent protein toxins such as tetanus and botulinum toxins, anthrax toxin, epsilon-toxin, and enterotoxin can cause some most significant diseases in humans and animals. these protein toxins are most common virulence factors encoded by plasmids in clostridium and bacillus species, for example, tetanus toxin plasmid and conjugative toxin plasmid of c. perfringens. extracellular vesicles (evs) are also infectious particles said to be produced by all types of microorganisms. these evs can contain nucleic acids, toxins, lipoproteins, adhesins, nutrient scavenging factors, and enzymes that can play major role in pathogenicity in hww. such vesicles from gram-positive bacteria, mycobacteria, and fungi contain virulence factors that can elicit host immune responses. for example, crytococcus neoformans evs have glucuronoxylomannan (capsular polysaccharide) which is a virulence factor [ ] . evs from gramnegative bacteria originate from outer membrane and are called outer-membrane vesicles which have been associated with cytotoxicity, virulence, invasion of host cells, and antibiotic resistance proteins. in addition to these particles, certain factors and conditions may further increase the virulence of evs, for example, a study indicated the role of iron-limiting conditions in the virulence of mycobacterium evs. these emerging infectious particles are not easily removed by conventional treatment technologies. thus there is a requirement of more novel methods and techniques to deal with such infectious particles. therefore these particles have to be readily analyzed for their presence and have to be studied for their removal from hww due to their potential negative effects on human and animal life. the recent years have witnessed the emphasis toward management of hww and various studies focused on the microbial communities present in wastewater have increased immensely. the pathogenic microbes present in hww have affected the human health since decades and antibiotic resistance microbes are also increasing significantly with time. the development of resistance toward antibiotics has been observed worldwide and has challenged both public and animal health. the use and release of various antibiotic agents in different settings have not only led to the prevalence of args in the environment but also spread and emergence of resistant bacteria. this has caused increased resistance in human pathogens and thus, making infections caused by them difficult to deal with, leading to higher mortality rates. however, the surveillance of its spread and prevalence in environment is limited and has to be expanded more due to the broad impact of antibiotic resistance on human health. various culture-dependent 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viroid (cccvd) in oil palm by reverse transcription loop-mediated isothermal amplification (rt-lamp) key: cord- -j r nq authors: hernando-amado, sara; coque, teresa m.; baquero, fernando; martínez, josé l. title: antibiotic resistance: moving from individual health norms to social norms in one health and global health date: - - journal: front microbiol doi: . /fmicb. . sha: doc_id: cord_uid: j r nq antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. it is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. in this regard, the health of humans, animals, and local antibiotic-resistance–polluted environments should influence the health of the whole interconnected local ecosystem (one health). in addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. consequently, antibiotic resistance is a pandemic that requires global health solutions. social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. in this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human–natural ecosystem interactions. the problem of antibiotic resistance (ar) has been traditionally addressed by focusing on humanlinked environments, typically health care facilities. nevertheless, it is now generally accepted that most ecosystems may contribute to the selection and spread of ar (aminov, ; martinez et al., ; davies and davies, ; martinez, ; berendonk et al., ; larsson et al., ) . a key conceptual point is that, based on cultural, humanitarian, and economic reasons, we have historically preserved the health of individual humans and farming animals. to that purpose, the same families of antimicrobial agents have been used. as a consequence, their positive (healing) and negative (selection of ar, therapeutic failure) effects have influenced the common health of humans and animals in particular locations (one health). the concept one health, first used in early twentieth century, expands the integrative thinking about human and animal medicine, including for the first time ecology, public health, and societal aspects (zinsstag et al., ) . in the case of ar, the one health perspective focuses on the risk assessment of emergence, transmission, and maintenance of ar at the interface between humans, animals, and any other linked (local) environment (robinson et al., ; jean, ) . consequently, the application of one health approaches demands integrative surveillance tools and interventions based on multidisciplinary approaches that include ecological and sociodemographic factors, besides more classic epidemiological models. global health is based on a broad collaborative and transnational approach to establish "health for all humans." in this case, it focuses ar at a general (global) scale, considering that the selection and global spread of antibiotic-resistant bacteria (arbs) and antibiotic resistance genes (args) are a problem that influences the health of human societies with disparate social and economic structures and is linked to many societal and ecological factors (chokshi et al., ) . interventions to reduce ar burden in a global world certainly require common and integrated policy responses of countries, international organizations, and other actors (stakeholders included). its goal is the equitable access to health and minimizing health risks all over the globe. besides its objective aspects (i.e., how travelers, migrating birds, or international commerce may contribute to ar spread), it has important international political aspects. it focuses in how countries and international organizations address the elements connecting and potentially spreading ar among humans, animals, and natural ecosystems at the earth scale (wernli et al., ) . in summary, the problems and the potential solutions concerning ar are not confined to particular regions, but have a global dimension: a problem for all humans, animals, and natural ecosystems, which should be solved with interventions aiming to improve health for all of them koplan et al., ; laxminarayan et al., ) . in the context of ar, a healthy environment would be an environment where ar is low or can be controlled by human interventions (hernando-amado et al., ; andersson et al., ) . of course, the global health concept of "health of an environment" (iavarone and pasetto, ; pérez and pierce wise, ; bind, ; van bruggen et al., ) or, in general, planetary health (lerner and berg, ) , has an unavoidable anthropogenic flavor. in practice, we consider "healthy environments" or "healthy ecosystems" those that minimize their current or their potential harm for the human individual or the society, in our case for ar. in other words, we adopt a selfish strategy, which should be necessarily implemented by the international (global) institutions. selfishness (kangas, ) applies mainly to individuals, but also to societal groups. however, these groups have not enough possibilities to act alone in the case of infectious diseases in general and ar in particular, which may expand worldwide. therefore, individual selfishness for health should be integrated in local one health and also in global health actions. the goal of controlling ar is a highly complex one, and its dimension has been compared to climate change or biodiversity loss, problems where individual actions are not enough for providing a solution, and consequently, individual freedom is confronted with collective responsibility (looker and hallett, ) . the construction of human societies reflects the tension between individual freedom and social rules/laws. the implementation of different social rules/laws for regulating human activities within a society is mainly based on moral (as kant's categorical imperative (kant, ) or religious-based brotherhood (matthew : - ) statements), social stability (as anticrime laws; schiavone, ) , organizative (type of government and how it is formed, group identity), and efficacy (as antitrust laws; ricardo, ) arguments. however, these arguments mainly apply for establishing the socioeconomic organization as well as the individual welfare within a society. the situation concerning human health is somehow different. there are individual diseases, such as cancer or stroke, and social diseases, such as transmissible infections. for the firsts, social norms (as consciousness of the importance of the control of cholesterol, excess sugar uptake, or hypertension levels) are well established, and even laws (non-smoking regulations) had been implemented in occasions. however, the main impact of these regulations is at the individual health level (wikler, ) , because the associated diseases are not physically transmissible. a different situation happens in the case of infectious diseases in general and of ar in particular. for these diseases, everything that happens in a single person affects any one around. further, the fact that an arg emerging in a given geographic area can spread worldwide implies that neither individual norms nor country-based norms have been sufficient until now to counteract the worldwide spread of ar. one important aspect of laws in democratic societies is that they must be well accepted by the community, so that the acceptation of social norms usually comes first than their implementations as rules/laws. actually, the efficiency of democracy for responding to social crisis (as current ar or covid- crises), in opposition to other more autocratic regimens where decisions are implemented top-down, had been the subject of debate from the early beginning of democratic revolutions (tocqueville, ; hobbes, ; rousseau, ; spinoza, ) . in this regard, it is important to remark that one health aspects of ar can be tackled in the basis of countrylevel regulations that are linked to the socioeconomic and cultural aspects of each country (chandler, ; chokshi et al., ) . however, because global earth governance does not exist, global health control of ar is based on recommendations, rather than in rules/laws. consequently, the acceptance of social norms, starting within individuals or small organizations and expanding throughout the whole society (figure ) , is fundamental to provide global solutions to the ar problem (nyborg et al., ; chandler, ) . the acceptance by the community of these social norms, considering that the way of promoting these norms might differ in different parts of the world (cislaghi and heise, ; cislaghi and heise, ) , largely depends on the transfer to the society of the knowledge required to understand the mechanisms and the impact for human health of the emergence and transmission of ar, an information that is discussed below. figure | how the interactions among individual health, one health, global health, and social norms influences antibiotic resistance. the right panel shows the different levels of dissemination of antibiotic resistance. in the left panel, the different types of norms (from individual to global norms) that can impact antibiotic resistance at each level are shown. these norms influence all levels of transmission: the individual promotes (red arrows) his own individual health, but doing it also promotes the health of the group, and the health of the group promotes global health of the human society at large. at each level, there is a positive action (red broken lines) on antibiotic resistance. such dynamics largely depends on social norms (blue arrows) rewarding the individual or the groups whose behavior promotes health. below the left panel, the basic social norm, progress and development, has consequences on the whole ecobiology of the planet (lower panel with bullet points), influencing the undesirable open circulation of antimicrobial resistant bacteria (with their mobile genetic elements) and antibiotic resistance genes. the classic definition of ar is based only on the clinical outcome of the infected patient. an organism is considered resistant when the chances for the successful treatment of the infection it produces are low . this definition, which is the most relevant in clinical settings, presents some limitations for studies based on one health approaches that include the analysis of non-infective organisms, which lack a clinical definition of resistance, as well as analysis of the distribution of args, in several occasions, using non-culture-based methods . even in the case of animal medicine, antibiotic concentration breakpoints defining resistance are still absent for some veterinary-specific antimicrobials and poorly defined for different types of animals with disparate weights, which would influence the availability of the drug inside animal body (toutain et al., ; sweeney et al., ) . to analyze ar beyond clinical settings, the term resistome, understood as the set of genetic elements that can confer ar, irrespectively of the level of resistance achieved, in a given organism/microbiome was coined (d'costa et al., ; wright, ; perry et al., ) . ar acquisition is the consequence of either mutation (or recombination) or recruitment of args through horizontal gene transfer (hgt), transformation included. ar mutations are generally confined to their original genomes, propagating vertically and not spreading among bacterial populations, although some few exceptions of horizontal transfer of chromosomal regions containing ar mutations have been described (coffey et al., ; ferrandiz et al., ; novais et al., ; nichol et al., ) . the set of mutations that confer ar can be dubbed as the mutational resistome. current wholegenome-sequencing methods of analysis can allow defining the mutational resistome in an isolated microorganism (cabot et al., ; lopez-causape et al., ) . however, they are not robust enough yet for determining the mutational resistome in metagenomes. consequently, the impact of these analyses in one health studies is still limited and will not be further discussed in the present review. concerning their relevance for acquiring ar, args can be divided in two categories. the first one comprises the genes forming the intrinsic resistome (fajardo et al., ) , which includes those that are naturally present in the chromosomes of all (or most) members of a given bacterial species and have not been acquired recently as the consequence of antibiotic selective pressure. despite that these genes contribute to ar of bacterial pathogens, they are responsible just for the basal level of ar, which is taken into consideration when antibiotics are developed. in this regard, unless these genes, or the elements regulating their expression mutate, they are not a risk for acquiring resistance and have been considered as phylogenetic markers . further, it has been discussed that these genes may contribute to the resilience of microbiomes to antibiotic injury (ruppe et al., b) , hence constituting stabilizing element of microbial populations when confronted with antibiotics more than a risk for ar acquisition by pathogens. the second category, dubbed as the mobilome, is formed by args located in mobile genetic elements (mges) that can be transferred both vertically and horizontally, hence allowing ar dissemination among different bacteria (frost et al., ; siefert, ; jorgensen et al., ; lange et al., ; martinez et al., ) . while the analysis of the resistome of microbiota from different ecosystems has shown that args are ubiquitously present in any studied habitat (d'costa et al., ; walsh, ; jana et al., ; lanza et al., ; chen et al., b) , the impact of each one of these args for human health is different. indeed, it has been stated that the general resistome of a microbiome is linked to phylogeny and to biogeography, indicating that most args are intrinsic and do not move among bacteria (pehrsson et al., ) . however, some args escape to this rule and are shared by different ecosystems and organisms (forsberg et al., ; fondi et al., ) . these mobile args, frequently present in plasmids (tamminen et al., ; pehrsson et al., ) , are the ones that are of special concern for human health. although not belonging to the antibiotic resistome, genes frequently associated with resistance to other antimicrobials, such as heavy metals or biocides, as well as the genes of the mges backbones, eventually involved in the transmission and selection of args among microbial populations, the mobilome at large, are also relevant to track the emergence and dissemination of ar among different habitats martinez et al., ; baquero et al., ) . hgt processes are recognized as the main mechanisms for transmission of genetic information (baquero, ) . from the ecological point of view, hgt should be understood as a cooperative mechanism that allows the exploitation of common goods as args by different members within bacterial communities. in fact, some studies suggest that the ecological consequences of hgt events in ar evolution are contingent on the cooperation of complex bacterial communities, besides the acquisition of individual adaptive traits (smillie et al., ) . however, the understanding of the ecological causes and consequences of args transmission among organisms and microbiomes is still limited from the one health and global health perspectives. hgt-mediated ar is a hierarchical process (figure ) in which args are recruited by gene-capture systems as integrons and afterward integrated in mges as plasmids, insertion conjugative elements, or bacteriophages (frost et al., ; garcia-aljaro et al., ; gillings et al., ; botelho and schulenburg, ) , which afterward are acquired by specific bacterial clones. selection at each of these levels will also select for all the elements involved in ar spread. for instance, the acquisition of an arg by a clone may promote the expansion of the latter (and of all the genetic elements it contains, other args included) in antibiotic-rich environments, such as hospitals or farms schaufler et al., ) , and vice versa, the introduction of an arg in an already successful clone may increase the chances of this resistance gene for its dissemination even in environments without antibiotics, unless the associated fitness costs are high. in this sense, if arg acquisition reduces the fitness, and this implies a decreased capability for infecting humans (see below), the burden for human health might eventually be lower. nevertheless, it is relevant to highlight that ar transmission cannot be understood just by analyzing the genetic mechanisms involved and the consequences of such acquisition for the bacterial physiology. indeed, as discussed below, there are ecological and socioeconomic elements that strongly influence ar dissemination. the evolution of ar comprises the emergence, the transmission, and the persistence of arbs (martinez et al., ; baquero et al., ) . concerning human health, selection of arbs/args is particularly relevant at the individual health level, whereas transmission is a main element to be taken into consideration at the one health and global health levels (figure ) . indeed, unless ar is transmitted, it will be just an individual problem that would not affect the community at large. it is generally accepted that non-clinical ecosystems are often primary sources of args (davies, ) . as above stated, after their capture and integration in mges (figure ), args and their bacterial hosts can contaminate different ecosystems, which might then be involved in their global spread (martinez, ; fondi et al., ; gillings, ; gillings et al., ) . this means that nearly any ecosystem on earth, along with the humandriven changes produced in it, may modulate evolution of ar. importantly, the huge escalation and worldwide expansion of a limited set of animals, plants, and their derived products, including foods, due to the anthropogenic selection of a few breeds and cultivars for mass production in livestock and agricultural industries (okeke and edelman, ; zhu et al., ) of economic interest have collapsed the variability and biodiversity of animals and plants (seddon et al., ) . because these organisms harbor particular host-adapted bacteria, which are frequently under antibiotic challenge, this situation, together with the ecological similarities of human habitats, might favor ar spread (martiny et al., ; manyi-loh et al., ) . indeed, while in underdeveloped areas of the world food animals are very diverse, intensive farming, common in developed countries, ensures a "shared-stable" environment where only the most productive types prevail (kim et al., ) . the common genetic origin of these types and the process of microbiota acquisition from nearby animals in intensive farming should homogenize also their microbiomes with consequences for ar dissemination. actually, it has been shown that the loss of microbial diversity figure | genetic, ecological, and socioeconomic elements mediating the transmission of antibiotic resistance. args are ubiquitously present in any studied microbiome (a). however, only a few of them are transferred to human/animal pathogens, hence constituting a health problem. the genetics events implied include the acquisition of args by gene-recruiting genetic elements such as integrons (b); the integration of these elements in mges as plasmids, bacteriophages, or frontiers in microbiology | www.frontiersin.org figure | continued insertion conjugative elements (c); and the acquisition of these elements by specific bacterial clones (d). these arbs can share these elements among the members of gene-sharing communities (e) and also move among different ecosystems, including humans, animals (particularly relevant farm animals), and natural ecosystems (with a particular relevance for water bodies). the connection of these ecosystems, as well as the reduced diversity of animals, plants, and in general habitats as the consequence of human activities, allows the different microbiomes to be in contact, favoring args transmission among the microorganism they encompass (f). this transmission is facilitated at the global scale by travel, animal migration, trade of goods, and eventually by meteorological phenomena, climate change included (g), hence producing a global health problem (h). while most studies on the dissemination of args focus on mges (davies, ; muniesa et al., ; lanza et al., ; garcia-aljaro et al., ) , recent works suggest that the contribution of natural transformation (orange arrow), allowing the direct uptake of args by natural competent microorganisms, may have been underestimated (domingues et al., ; blokesch, ) . further, competence can occur due to interbacterial predation (veening and blokesch, ) , a biological interaction that may facilitate the acquisition of beneficial adaptive traits by predator bacterial species (cooper et al., ; veening and blokesch, ) . other hgt mechanisms, such as dna packing in extracellular vesicles (ecv) or transference of dna through intercellular nanotubes, also seem to be relevant in nature (dubey and ben-yehuda, ; fulsundar et al., ) . while the biotic conditions that may enhance hgt have been studied in detail, less is known concerning abiotic modulation of args transfer. under contemporary conditions, at least microorganisms are affected by a freeze-and-thaw cycle, at least are agitated by sand, and at least are subjected to conditions suitable for electrotransformation every year (kotnik and weaver, ) . may favor ar spread (chen et al., a) . note that, beyond the transmission of particular ar spreading clones, ar is expected to spread in farms by the modification (eventually homogenization) of animals' microbiota. notwithstanding, even farm workers are subject to microbiome acquisition from animals, leading to microbiome coalescence sun et al., ) . it is to be noticed, and the recent covid- crisis exemplifies it, that besides economic development, cultural habits are relevant in the use of animals for food, a feature that has not been analyzed in detail, particularly with respect to their role as vectors potentially involved in ar dissemination. despite that the homogenization of hosts may help in ar transmission, the spread of arbs has some constraints, because the differential capability of each bacterial clone for colonizing different hosts may modulate their dissemination. indeed, while some species and clones are able to colonize/infect different animal species, humankind included, several others present some degree of host specificity (price et al., ; sheppard et al., ) . further, it has been shown that the capacity to colonize a new host is frequently associated with a reduction in the capacity for colonizing the former one. the same happens for mobile args; they are encoded in mges that present different degrees of host specificity, which defines the formation of gene-exchange communities, where the interchange of genetic material among members is facilitated (skippington and ragan, ) . conversely, the incorporation of different replicons and modules within plasmid backbones, a feature increasingly reported (douarre et al., ) , would enable arg replication in different clonal/species background and thus modify the community network of args. actually, the risk for humans of animal-based ar seems to be linked in most cases to shuttle, generalist clones able to colonize humans and particular animals (price et al., ; sheppard et al., ) . the understanding of the elements driving the transfer of ar among animals, humans included (figure ) , requires the comprehensive survey of the clones and args that are moving among them (european food safety authority et al., ). tools to track the global epidemiology of antimicrobial-resistant microorganisms such as bigsdb (jolley et al., ) or comprehensive databases of args, ideally providing information of their mobility (zankari et al., ; alcock et al., ) , are fundamental for studying ar transmission at a global level. it is worth mentioning that, because humans constitute a single biological species, the human-associated organisms spread easily among all individuals. in fact, more prominent differences in humans' microbiome composition can be observed between individuals than among ethnic groups, even though, as expected, the resemblance in microbiotas is higher among those groups that are geographically clustered (deschasaux et al., ; gaulke and sharpton, ) . some groups of human population are, however, more prone to acquire arbs, due either to socioeconomic or to cultural factors. in lmics (low-to medium-income countries) and brics (brazil, russia, india, china, and south africa) countries, the combination of wide access to antibiotics, weak health care structures, and poor sanitation defines certainly a dangerous landscape. moreover, the progressive aging of the western population might favor the establishment and further expansion of an elderly reservoir of arbs and args, an issue that deserves further studies. the hypothesis that the microbiome of elder people might be a reservoir of ar is based not only on their cumulative history of antibiotic exposure and contacts with health care centers, but also on the rampant use of antibiotics of this population more prone to suffer from acute, chronic, or recurrent infections. significant worldwide advances in the organization of medical care of the elderly people lead to frequent hospitalizations, but health care centers may also facilitate the selection and further amplification of ar in the community. in addition, this may subsequently favor the entry of high-risk clones and of args in the hospital setting (hujer et al., ) . as stated above, there is a global increasing permeability of the natural biological barriers that have historically prevented bacterial dissemination through different ecosystems. besides local spread of ar in environments shared by animals and humans, which has to be addressed under a one health approach, ar can disseminate worldwide (figure ) by economic corridors that promote the global interchange of goods and trade or human travelers or by natural bridges, such as animal migration paths or natural phenomena such as air and water movements (okeke and edelman, ; baquero et al., ; allen et al., ; overdevest et al., ; kluytmans et al., ; fondi et al., ) . the result is the appearance of similar arbs and args in different geographic areas. as the consequence, ar is a global health problem in the sense that an arb that emerges in a given place can rapidly spread worldwide. indeed, multidrugresistant bacteria, similar to those encountered in clinical settings, have been detected in human isolated populations that were not previously in contact with antibiotic, as well as in wildlife (clemente et al., ) . this indicates that pollution with args is present even in places where antibiotic concentrations are low (kümmerer, ) and might involve mechanisms of transmission that do not require selection. for instance, migrating birds can carry enteropathogenic bacteria resistant to different antibiotics (middleton and ambrose, ; poeta et al., ) , and international travelers, even those not receiving antibiotic treatments, also contribute to ar transfer among different geographic regions (murray et al., ; reuland et al., ) . in the group of long travelers are refugee people, in which dissemination of multidrug-resistant strains is favored by the poor sanitary conditions and overcrowding camps that refugees confront (maltezou, ) . a final issue concerning ar is its stability in the absence of selection. it has been proposed that the acquisition of ar reduces bacterial competitiveness in the absence of antibiotics (fitness costs) (andersson and hughes, ; martinez et al., ) ; certainly, a wishful proposition such as, if true, the reduction in the use of drugs or eventually antibiotic-cycling strategies should decrease ar (beardmore et al., ) . nevertheless, eliminating the use of an antibiotic does not produce a full decline of ar (sundqvist et al., ) . in fact, different studies have shown that ar not always reduces fitness but also can even increase bacterial competitiveness (andersson and hughes, ; schaufler et al., ) . in addition, compensatory mutations or physiological changes that restore fitness can be selected in resistant bacteria (andersson, ; schulz zur wiesch et al., ; olivares et al., ) . it is a fact, however, that although arbs are found nearly everywhere, including wild animals, natural ecosystems, or people from isolated populations without contact with antibiotics, among others (durso et al., ; clemente et al., ; alonso et al., ; fitzpatrick and walsh, ; power et al., ) , ar prevalence is consistently lower when antibiotics are absent, which suggests that pollution may impact ar, a feature that is discussed below. pollution of natural ecosystems is associated with activities that have driven relevant economic transition, in principle favoring human welfare, such as mining, industry, intensive land use, or intensive farming, among others. notwithstanding, globalization of health services, as well as the shift toward intensive farming, besides their positive contribution to human wellbeing, has rendered an increasing pollution by compounds with pharmacological properties of natural ecosystems, particularly water bodies, which may disrupt the stability of these ecosystems (oldenkamp et al., ) . among them, antibiotics are considered the most relevant cause of ar selection. despite regulations for reducing their use (van boeckel et al., ) , a substantial increase in global antibiotic consumption has occurred in the last years, and an even greater increase is forecasted in the next years (klein et al., ) . however, antibiotics are not the unique pollutants that can prime the selection and spread of ar. in this regard, it is important to highlight that heavy metals are one of the most abundant pollutants worldwide (panagos et al., ) . their abundance results from anthropogenic-related activities, such as mining, industry, agriculture, farming, or aquaculture and even for therapeutic use in ancient times. importantly, they may persist in nature for long periods of time. further, likely because metal pollution occurred before the use of antibiotics, heavy metal resistance genes were incorporated to mge backbones before args (mindlin et al., ; staehlin et al., ) . this means that heavy metals may coselect for mges and the args they harbor (partridge and hall, ; staehlin et al., ; zhao et al., a) . even more, the presence of heavy metals, as well as of biocides or sublethal antibiotic concentrations (jutkina et al., ; zhang et al., ) , may stimulate hgt, as well as modify the dynamics of antibiotics, such as tetracyclines, in natural ecosystems (hsu et al., ) . coselection may also occur when a single resistance mechanism, such as an efflux pump, confers resistance to both heavy metals and antibiotics (cross-resistance) (pal et al., ) . although most published works analyze the effect of different pollutants on their capacity to select arbs or args, it is important to highlight that args should also be considered pollutants themselves. actually, a recent work indicates a close relationship between the abundance of args and fecal pollution (karkman et al., ) . in this respect, it is worth mentioning that, differing to classic pollutants, args/arbs are not expected to disappear along time and space, but rather, their abundance may even increase as the consequence of selection and transmission (martinez, ) . while the direct selection of ar by antibiotics or the coselection mediated by other pollutants, as the aforementioned heavy metals, has been discussed (wales and davies, ) , the effect of other types of human interventions on the dissemination of args and arbs through natural ecosystems has been analyzed in less detail. as an example, it has been proposed that wastewater treatment plants, where commensals, arbs, args, and antibiotics coexist, could act as bioreactors favoring the selection and transmission of args between different organisms (rizzo et al., ; su et al., ; manaia et al., ) , although evidences supporting this statement are scarce (munck et al., ; azuma et al., ) . in addition to the aforementioned pollutants with a direct effect in ar selection, it is worth noting that there are other abundant contaminants, such as sepiolite (present in cat litters or used as a dietary coadjuvant in animal feed) or microplastics, present in almost all aquatic ecosystems, which can favor the transmission of args or mges between bacterial species (rodriguez-beltran et al., ; kotnik and weaver, ; arias-andres et al., ) , hence amplifying the ar problem at a global scale. finally, the possible effect of climate change on the spread of ar is worth mentioning. indeed, it modifies the biogeography of vectors (such as flies, fleas or birds) involved in the spread of infectious diseases (fuller et al., ; beugnet and chalvet-monfray, ) . in addition, the increase of local temperatures seems to correlate with an increased ar abundance in common pathogens (macfadden et al., ) . besides, climate change is affecting ocean currents (martinez-urtaza et al., ) , which may allow the intercontinental distribution of arbs and args (martinez, a,b) . although this phenomenon might contribute to the globalization of ar, further research is needed to clearly demonstrate a cause-effect relationship. it is relevant to mention that increased pollution and climate change are the unwanted consequences of human development. it would then be worth discussing how human development in general may impact (positively and negatively) ar, a feature that is analyzed below. human development is a necessity of our human behavior, although different models of development have been and are proposed, each one producing different impacts in the structure of human societies and on the preservation and stability of natural ecosystems (fenech et al., ; farley and voinov, ; seddon et al., ) . nevertheless, even for different socioeconomic models, there are some social norms that tend to be widely accepted, in particular those aiming to improve individual well-being. this implies the establishment of a society of welfare, understood as a right of any human on earth, a feature that depends on the economic development, and can be particularly relevant in the case of transmissible infectious diseases in general and of ar in particular. a continuously repeated mantra in worldwide ar policies is that the abusive consumption of antibiotics for the treatment or prevention of infections in humans and animals constitutes the major driver of ar. however, we should keep in mind that antibiotics constitute an important example of human progress supporting individual and global human health. in fact, the origin of the massive production of antimicrobials was a consequence of the needs resulting from world war ii in the s. this was followed by many decades of human progress, most importantly by the common understanding of equal human rights, which was followed by the economic and social development (including medicine and food industry) of densely populated regions in the planet, including india and china. these countries are currently among the leaders in the production and consumption of antimicrobial agents. notwithstanding, as in any area of economy, progress bears a cost that, in this case, is antibiotic pollution of the environment, globally accelerating the process of the emergence, the transmission, and the persistence of arbs (martinez et al., ; baquero et al., ) . the non-controlled use of antibiotics is facilitated in lmics with disparate economic growth by different factors. heterogeneous regulation of antibiotic sales and prescriptions (often weak or missing) and the increase of online on-bulk sales in recent years contribute to their overuse (mainous et al., ). most of live-saving medicines represent out-of-pocket costs in most lmics, which led to an exacerbated use of cheap (usually old and less effective) antibiotics, phasing out their efficacy and increasing the demands and prices for the most expensive ones, eventually resulting in treatment unavailability (newton et al., ) . further, the cost of treating ar infections is much higher than that of treating susceptible ones, which is increasing the cost of health services (wozniak et al., ) . conversely, the growing economic capability of lmics in the brics category triggers the access of the population to health services and last-resort antibiotics. these countries also face a sudden high demand for meat and thus a prompt industrialization of animal production that has favored the misuse of antibiotics for growth promotion facilitated by their online availability (mainous et al., ). in addition, counterfeit or substandard antibiotics recently become a serious global problem (gostin et al., ) , which is exacerbated in lmics, where they represent up to a third of the available drugs. noteworthy, % of all reports received by the who global surveillance and monitoring system on substandard and falsified medicines worldwide come from africa, and most of them correspond to antimalarials and antibiotics (newton et al., ; gostin et al., ; hamilton et al., ; petersen et al., ) . despite this situation, it is important to highlight that human consumption of antibiotics is an unavoidable need to preserve human health. in fact, most health problems dealing with infections in lmics are still caused by a poor access to antibiotics, not by an excessive use of them. proof of this is the fact that the distribution of antibiotics has reduced endemic illnesses and children mortality in sub-saharan africa (keenan et al., ) . this means that, while a global decline in the use of antibiotics would be desirable to diminish the problem of ar, there are still several parts in the globe where antibiotic use should still increase to correctly fight infections. in fact, our primary goal should not be to reduce the use of antibiotics, but to ensure the effective therapy of infectious diseases for the long term. this does not mean that ar is not a relevant problem in lmics; it means that reducing antibiotic use is not enough to solve the problem. indeed, the current high morbidity and mortality due to infectious diseases (malaria, tuberculosis, low respiratory infections, sepsis, and diarrhea) in lmics will be worsened in the absence or low efficiency of therapeutic treatments. further, ar has economic consequences. according to world bank, . million people could fall into extreme poverty by because of ar, most of them from lmics (jonas and world bank group team, ) . consequently, besides a global health problem, ar has an important economic impact (rudholm, ) , hence constituting a global development problem, endangering not only the achievements toward the millennium development goals but also the sustainable development goals (van der heijden et al., ). world bank estimates that ar could impact the gross domestic product from to . %, which is even higher than what is estimated for the climate change (jonas and world bank group team, ) . these economic foresights are linked to the threads of increased poverty, food sustainability, global health deterioration (associated with both food safety and affordability to health care), and environment protection. all these issues are also impacted by the overuse and misuse of antibiotics, its lack of effectiveness, and the affordability to medicines and health care (van der heijden et al., ) . when talking about reducing antibiotic consumption, it is important to remind that up to two-thirds of overall antibiotic usage is for animal husbandry (done et al., ) . further, recent work states that the use of antibiotics in crops, particularly in lmics, might have been largely underestimated (taylor and reeder, ) . despite that evidences on the presence of common args distributed among animals and humans were published decades ago wegener et al., ; aarestrup, ; aarestrup et al., ) , and although the use of antibiotics as growth promoters has been banned in different countries (cox and ricci, ) , they are still allowed in many others (mathew et al., ) . of relevance is the fast increase of antibiotic consumption for animal food production in china ( % in ) and other brics countries . as stated previously, in these countries, increased income has produced a fast increase in meat products demand, due to changes in diet of their population. in addition, the increasing international competitiveness in meat production of these countries has fostered the rampant development of their industrial farming. together with the fact that legislation on antibiotics use remains weak, this situation increases the risk of emergence of ar linked to animal production. nevertheless, the problem is not restricted only to lmics, because antibiotics consumption rose as well in the highincome countries as the united states ( %) , where approximately % of the antimicrobials purchased in were applied in livestock production as non-therapeutic administration (done et al., ) . the development of intensive methods of fish production has also contributed to the rise in the use of antimicrobials and the selection of resistance determinants that can be shared among fish and human bacterial pathogens (cabello et al., ) . economic development has facilitated as well more global transport, waste disposal, and tourism, favoring ar spread within and between different geographical areas (ruppe et al., a; ruppe and chappuis, ) . however, economic growth can also reduce the ar burden, especially when it enables the development of regulations and infrastructures that might reduce the risks of infection and ar spread. this is particularly relevant in the case of public health interventions on food, water, and sewage. because ar pathogens are mainly introduced in natural ecosystems through the release of human/animal stools (karkman et al., ) , the best way of reducing this impact is through the use of wastewater treatment plants, which are still absent in several places worldwide. indeed, it has been described that drinking water is a relevant vehicle for the spread of arbs in different countries (walsh et al., ; fernando et al., ) and that raw wastewater irrigation used for urban agriculture may increase the abundance of mobile args in the irrigated soil (bougnom et al., ) . notably, the analysis of args in wastewaters has shown that the prevalence of args in the environment in each country might be linked to socioeconomic aspects mainly related to economic development, as general sanitation, particularly the availability of drinking and wastewater treatments, malnutrition, number of physicians and health workers, human overcrowding, or external debt grace period (hendriksen et al., ) . the field of ar has mainly focused in the mechanisms of selection; the main driver for the increased burden of ar would be then the use of antibiotics itself. however, these results indicate that transmission, even in the absence of direct human-to-human contact, might be, at least, equally relevant. in this situation, an important element to reduce the ar burden will be to break the transmission bridges among different ecosystems that could be reservoirs of args. even when wastewater-treatment plants are available, the presence of arbs in drinking, fresh, and coastal waters, as well as in sediments nearby industrial and urban discharges, has been described in several countries (ma et al., ; leonard et al., ) . as in the case of fecal contamination markers, a reduction in the amount of args to non-detectable levels would be extremely difficult even when advanced water treatment procedures are applied. a standard definition of polluting arb/arg markers, as well as their acceptable levels, is then needed. this would be required not only for potable water, but also for water reutilization, as well as for land application and release of sewage effluents, because in all cases the reused water/sewage may carry arbs and args, together with pollutants, such as antibiotics, metals, biocides, or microplastics, which, as above stated, may select for ar (baquero et al., ; moura et al., ; yang et al., ; zhu et al., ; larsson et al., ; imran et al., ; wang et al., ) and may even induce hgt. the examples discussed above justify that human health in general and ar in particular are closely interlinked with economic development (sharma, ) . economic differences are also found at individual level, because there is a positive relationship between economic status and health (tipper, ) . in addition, social behavior might also impact ar, a feature discussed in the following section. different socioeconomic factors can modulate the spread of infective bacteria in general and of ar in particular. among them, the increasing crowding of humans and foodborne animal populations favors transmission at the local level (one health), whereas trade of goods and human travel (figure ) favor worldwide transmission (global health) (laxminarayan et al., ; hernando-amado et al., ) . besides these global changes in social behavior, linked to economic development, more specific socioeconomic factors (income, education, life expectancy at birth, health care structure, governance quality), sociocultural aspects (inequalities, uncertainty avoidance, integration of individuals into primary groups, gender biases, cultural long-term orientation), and personality dimension highly influence antibiotic use and ar transmission (gaygısız et al., ) . for instance, although the governance quality seems to be the most important factor associated with a proper antibiotic use, western countries with distinct national culture patterns show different levels of antibiotics consumption (kenyon and manoharan-basil, ) . a better understanding of human social responses facing ailments, especially epidemics and antibiotic use, requires then a more detailed analysis of the differences between collectivistic (individuals living integrated into primary groups) and individually long-term oriented societies (oriented to future individual rewards) (hofstede, ; gaygısız et al., ; kenyon and manoharan-basil, ) . consistent with the sociological elements of ar, many of the aspects influencing ar reviewed above depend on social norms (figure ) . in the classic view of the psychoanalyst erich fromm presented in his book "escape from freedom" (fromm, ) , human individual behavior is oriented to avoid being excluded from a higher social group. indeed, not following social common rules can be eventually considered as a mental disorder; a sociopathology. a social norm is defined as a predominant behavioral pattern within a group, supported by a shared understanding of acceptable actions and sustained through social interactions within that group (nyborg et al., ) . in democratic societies, laws usually derive from already accepted social norms; otherwise, they would be changed, and in that sense, the establishment of accepted social norms for fighting ar is a prerequisite to implement the global approaches, based on worldwide rules, which are required for tackling this relevant problem. interestingly, the ar problem is a bottom-up process, where small emergent changes (in some type of individual patients, in some groups, in some locations) cumulatively escalate to gain a global dimension. frequently, that occurs by crossing tipping points, that is, points where the local ar incidence becomes significant enough to cause a larger, eventually global, health problem. because of that, the implementation of solutions should be adapted to the control of critical tipping points in the small groups of individuals to disrupt the bottom-up processes. however, as ar spread can occur everywhere and at any time, global surveillance and mechanisms of control should be implemented to prevent a top-down process of global ar expansion. individual selfishness for ar is the cornerstone of social norms. this concept was coined and developed by one of us over a decade ago (baquero, ) . let us imagine that each individual is aware that each consumption of an antibiotic increases the personal risk of himself/herself or for his/her closer relatives (frequently exchanging microorganisms) of dying because of an antibiotic-resistant infection. the situation is analogous to the consumption of cholesterol-rich or highly salted food, or drinks with excess of sugar, concerning individual health. however, in the case of ar, it requires the understanding of the impact of individual actions at the global level. in this respect, anti-ar social actions should resemble more antitobacco and even general pollution/ecological campaigns. at the individual level, there is inertia that precludes changing habits, until a tipping point is crossed and health is compromised. the conclusions of studies mainly based on long-term cohort analysis, such as the framingham program for the influence of diet or smoking on personal cardiovascular disease (mahmood et al., ) , have become social norms that are naturally imposed by the ensemble of individuals. this creates a kind of societal culture, leading to appropriate individual behaviors, in occasions without the need of specific laws (diet), in occasion favoring the implementation of such laws (antismoking). however, we lack similar studies on issues such as these dealing with personalfamiliar risks that have successfully shifted social norms, driven by groups of individuals and based on the promotion of individual behaviors in the case of ar. despite that quantitative models on how individual antibiotic use may impact ar at the population level are still absent, it is worth mentioning that a reduced antibiotic consumption has also begun to occur in a number of countries just as a result of a change in individual behavior (edgar et al., ) , and some tools and indicators to address these changes have been suggested (ploy et al., ) . the "tragedy of the commons" metaphor, first proposed in the xix century (lloyd, ) and later on discussed in (hardin, ) , has been used for addressing the sociology of ar, by showing how individual selfishness promotes antibiotic use, increases resistance, and influences the health of the community by impairing antibiotic efficacy (baquero and campos, ; foster and grundmann, ) . ensuring the prestige of individuals that follow the social rules is needed to counteract the tragedy of the commons. nevertheless, it is important noticing that the tension between individual freedom and social rules that is inherent to the construction of democratic societies (tocqueville, ; hobbes, ; rousseau, ; spinoza, ) also applies here. one example of this situation is vaccination, considered in the last century as one of the most important advances to fight infectious diseases and now being the focus of antivaccination campaigns (megget, ) , a movement that has been considered by the who as one of the top global health threats of . it is commonly accepted that social norms are mainly created by learning and education, a rational path that promotes health (chen and fu, ) . also, the increasing activities of "personalized medicine, " including antibiotic stewardship, follow the same trend (gould and lawes, ) . however, the antivaccination movement is an example of how the narrative, as well as the use of decentralized, social information channels such as the internet search, blogs, and applications to facilitate communication such as twitter, facebook or whatsapp, is of particular relevance in the construction of social norms, not necessarily based on scientific and rational grounds (jacobson et al., ; scott and mars, ) . the impact of social norms goes beyond human societies as human activities alter natural ecosystems; consequently, humans cannot be aliens of nature. we should then shape a socioecological system, linking the individuals, the groups, and the entire society, as well as natural ecosystems, also potentially damaged by ar, in a common multilevel adaptive system based on social norms and policies at the individual, local (one health), and global (global health) scale (levin et al., ) . the recent crisis of covid- illustrates the influence of social norms in the individual behavior. each one of the individuals, protecting himself/herself, also protects the others. a person not wearing on face mask is frowned upon, and on the contrary, somebody attaching to the rules increases reputation. the individual adopts the right behavior being influenced by the judgment. of others. in addition, different political regimes (democracy or autocracy), as well as their organization (centralized, federal), together with the capacity of the health services to support the norms and their efficacy to communicate the chosen policy to the citizenry, may shape the individual responses to social norms (greer et al., ; häyry, ; kavanagh and singh, ) . notwithstanding, two reasons that have been proposed to explain the low prevalence of covid- in japan were related with social norms more than with biological issues. these reasons, which are not common to other countries, were the socially accepted use of face masks and the mandatory vaccination of all the population against tuberculosis, which might protect from sars-cov- infection (iwasaki and grubaugh, ) , a feature that is still to be confirmed. the loss of social prestige of individuals taking antibiotics without prescription, as well as the pharmacies delivering these drugs or do not respect environmental protection, or the overconsumption of antibiotics in hospitals or in farms, or even in certain countries, is progressively constituting a "social norm, " converted in rules able to reduce ar emergence and spread. of course, family and school education, as well as governmental campaigns, including the use of social media (grajales et al., ) reinforces such social norms, which could allow the support of the society for the implementation of different interventions, some of them described below. controlling resistance not only requires establishing local interventions, which could be relatively easily implemented, but would also require global interventions that every country should follow, despite their disparate regulatory systems. local and global interventions are necessarily intertwined; for example, the use of a new drug to treat a single individual depends on regulations at the county level (one health approach), but the worldwide prevalence and transmission of resistance to this drug, as well as the regulations of its use, should be established internationally (global health approach). three main interventions to tackle ar have been historically considered: first, reduction of the antibiotic selective pressure by decreasing antimicrobials use; second, reduction of transmission of arbs using improved hygienic procedures that prevent spread; third, development of novel antimicrobials with limited capacity to select arbs or the design of new treatment strategies based on use of non-antibiotic-based approaches or, more recently, on the exploitation of trade-offs associated with ar evolution (imamovic and sommer, ; gonzales et al., ; barbosa et al., ; imamovic et al., ) . these interventions have been basically limited to local initiatives, applied mainly to hospitals and, more recently, to farms. however, ar has emerged and spread globally, in bacteria from different environments, so the health and dynamics of the global microbiosphere could be affected by antibiotics. in a sense, ar is affecting the planetary health (lerner and berg, ) , and the needed interventions for tackling this problem cannot be restricted to hospital settings (figure ) . the proposed reduction in the use of antibiotics (blaskovich, ) must be compensated with alternative approaches for fighting infectious diseases. in this regard, strategies based on improving the capability of the immune system for counteracting infections (levin et al., ; traven and naderer, ) or the use of non-antibiotic approaches to prevent them, such as vaccines (jansen and anderson, ) , may help to reduce the burden of ar infections. indeed, vaccination against haemophilus influenzae and streptococcus pneumoniae has been demonstrated to be an effective intervention for reducing ar (jansen and anderson, ) . however, while vaccination has been extremely useful to prevent viral infections, it has been less promising in the case of bacterial ones. recent approaches, including reverse vaccinology, may help in filling this gap (delany et al., ; ni et al., ) . moreover, vaccination should not be restricted to humans, because veterinary vaccination can also contribute to animal wealth and farm productivity (francis, ) . besides, the use of vaccines in animal production reduces the use of antibiotics at farms/fisheries, hence reducing the selection pressure toward ar. other strategies to reduce antibiotic selective pressure include the use of bacteriophages (a revitalized strategy in recent years) (viertel et al., ; forti et al., ) , not only in clinical settings, but also in natural ecosystems (zhao et al., b) , as well as the use of biodegradable antibiotics (chin et al., ) or adsorbents, able to reduce selective pressure on commensal microbiome (de gunzburg et al., . besides reducing the chances of selecting arbs, the use of antibiotics adsorbents may preserve the microbiomes, reducing the risks of infections (chapman et al., ) . importantly, the procedures for removing antibiotics should not be limited to clinical settings, but their implementation in wastewater treatment plants would reduce selection of ar in non-clinical ecosystems (tian et al., ) . concerning the development of new antimicrobials (hunter, ) , while there is a basic economic issue related to the incentives to pharmaceutical companies (sciarretta et al., ; theuretzbacher et al., ) , the focus is on the possibility of developing novel compounds with low capacity for selecting ar (ling et al., ; chin et al., ) . for this purpose, multitarget (li et al., ) or antiresistance drugs, such as membrane microdomain disassemblers (garcia-fernandez et al., ) , are also promising. furthermore, antimicrobial peptides, with a dual role as immunomodulators and antimicrobials, may also help fight infections (hancock et al., ) . in fact, some works figure | local and global intervention strategies to tackle ar and knowledge gaps that could help improve existing ones. most interventions for reducing antibiotic resistance are based on impairing the selection of arbs/args, which is just the first event in ar spread. our main goal, as for any other infectious disease, figure | continued would be reducing transmission. this does not mean that selective pressure is not relevant for transmission. indeed, without positive selection, hgt events are not fixed, allowing the enrichment of some args that are consequently more prone to diversification, both because they are more abundant and more frequently subjected to selection (davies, ; martinez, a,b; salverda et al., ) and because they can explore different landscapes when present as merodiploids in multicopy plasmids (rodriguez-beltran et al., ) . therefore, reducing the selective pressure, either due to antibiotics or by other coselecting agents as heavy metals, still stands as a major intervention against ar emergence and transmission. to address this issue, we need to know more on the amount of pollutants, their selective concentrations, and their mechanisms of coselection and cross-selection in different ecosystems. this is a general example illustrating the gaps in knowledge in the ar field that need to be filled as well as strategies that may help in tackling this problem. the figure includes several other examples of the gaps of knowledge (red) that require further studies and the interventions (blue) that may help to tackle ar. have shown that arb frequently present collateral sensitivity to antimicrobial peptides (lázár et al., ) and that, importantly, some antimicrobial peptides present limited resistance or crossresistance (kintses et al., ; spohn et al., ) . from a conservative point of view, based on the use of the drugs we already have, it would be desirable to fight ar using evolution-based strategies for developing new drugs or treatment strategies. regarding this, the exploitation of the evolutionary trade-offs associated with the acquisition of ar, as collateral sensitivity, could allow the rational design of treatments based on the alternation or the combination of pairs of drugs (imamovic and sommer, ; gonzales et al., ; barbosa et al., ; imamovic et al., ) . in addition to interventions that reduce the selective pressure of antibiotics or that implement new therapeutic approaches, reducing transmission is also relevant to fight infections. the development of drugs or conditions (as certain wastewater treatments) able to reduce mutagenesis or to inhibit plasmid conjugation may also help in reducing the spread of resistance (thi et al., ; alam et al., ; lin et al., ; lopatkin et al., ; valencia et al., ; kudo et al., ) . besides specific drugs to reduce the dissemination of the genetic elements involved in ar, socioeconomic interventions to break the bridges that allow transmission between individuals and, most importantly (and less addressed), between resistance entities (hernando-amado et al., ) are needed (figure ) . more efficient animal management, not only allowing less antibiotics use but also reducing animal crowding (and hence ar transmission), as well as improved sanitation procedures, including the universalization of water treatment, will certainly help in this task (berendonk et al., ; manaia, ; hernando-amado et al., ) . notably, wastewater treatment plants are usually communal facilities where the residues of the total population of a city are treated. hospitals are the hotspots of ar in a city; hence, on-site hospital (and eventually onfarm) wastewater treatment may help to reduce the pollution of communal wastewater by antibiotics and arbs (cahill et al., ; paulus et al., ) , hence reducing ar transmission. concerning trade of goods, it is relevant to remark that, although there are strict regulations to control the entrance of animals or plants from sites with zoonotic of plant epidemic diseases (brown and bevins, ) , there are no regulations on the exchange of goods from geographic regions with a high ar prevalence, a feature that might be taken into consideration for reducing the worldwide spread of ar. once arbs are selected and disseminated, interventions based on the ecological and evolutionary (eco-evo) aspects of ar lehtinen et al., ) should be applied to restore (and select for) susceptibility of bacterial populations, as well as to preserve drug-susceptible microbiomes in humans and in animals . eco-evo strategies include the development of drugs specifically targeting arbs. for that, drugs activated by mechanisms of resistance, vaccines targeting high-risk disseminating resistance clones or the resistance mechanisms themselves (kim et al., ; ni et al., ) , or drugs targeting metabolic paths that can be specifically modified in arbs ) might be useful. the use of bacteriovores such as bdellovibrio to eliminate pathogens without the need for antibiotics has been proposed; although its utility for treating infections is debatable, it might be useful in natural ecosystems (shatzkes et al., ) . more recent work suggests that some earthworms may favor the degradation of antibiotics and the elimination of arbs (wikler, ) , a feature that might be in agreement with the finding that arbs are less virulent (and hence might be specifically eliminated when the worm is present) in a caenorhabditis elegans virulence model ruiz-diez et al., ; paulander et al., ; olivares et al., ) . however, the information on the potential use of worms for reducing ar in the field is still preliminary and requires further confirmation. noteworthy, ar is less prone to be acquired by complex microbiomes (mahnert et al., ; wood, ) , a feature that supports the possibility of interventions on the microbiota to reduce ar. among them, fecal transplantation (chapman et al., ; pamer, ) or the use of probiotics able to outcompete arbs (keith and pamer, ) has been proposed as strategies for recovering susceptible microbiomes. the recent crisis of covid- (garrett, ) resembles the pandemic expansion of args and clearly shows that pandemic outbreaks cannot be solved by just applying local solutions. further, unless all population is controlled, and comprehensive public-health protocols are applied to the bulk of the population, such global pandemics will be hardly controlled. the case of covid- is rather peculiar, because we are dealing with a novel virus. very strict interventions have been applied, mainly trying to control something that is a novel, unknown, disease; we have been learning along the pandemic and still ignore what will come further. ar is already a very well-known pandemic affecting humans, animals, and natural ecosystems (anderson, ; verhoef, ) . in this case, we have tools that might predict the outcome, and likely because the degree of uncertainty is lower than in the case of covid- , we have not applied clear, common, and comprehensive procedures to reduce the spread of ar. it is true that we know the evolution of antibiotics consumption and ar prevalence in several countries, and also interventions, mostly based on social norms, have been applied. social norms have reduced the unnecessary prescription of antibiotics, or pharmacy sales without prescription, and the use of antibiotics for fattening animals has been banned in several countries, being still allowed in several others. nevertheless, these actions are not general, and more aggressive, global actions are still needed. coming back to the covid- example, while the aim of health services worldwide is to detect any possible source of sars-cov- , surveillance of infections (eventually by arbs) is not universal. in other words, it does not apply to all citizens in all countries. the reasons can be just political such as the inclusion of immigrants in public health services (scotto et al., ) or the consequence of limited financial resources and technical capacity that countries such as those belonging to the lmic category can face (gandra et al., ) . the problem is not only on citizens, because different non-human reservoirs, such as wastewater, drinking water, or freshwater, may jointly contribute to ar dissemination (hendriksen et al., ) . in this regard, it is important to highlight that low quality of water is regularly associated to poverty. universalization of health services, sanitization, access to clean water, and in general reduction of poverty are relevant step-forward elements for reduction of the burden of infectious diseases in general and of ar in particular. the time has come to tackle ar, and this cannot be done just by taking actions at the individual or even country level, but by taking convergent actions across the globe. as stated by john donne ( ) in his poem, "no man is an island, " written after his recovery from an infectious disease (likely typhus): "no man is an iland, intire of itselfe; every man is a peece of the continent, a part of the maine; if a clod bee washed away by the sea, europe is the lesse, as well as if a promontorie were, as well as if a manor of thy friends or of thine owne were; any mans death diminishes me, because i am involved in mankinde; and therefore never send to know for whom the bell tolls; it tolls for thee." this reflection on how infectious diseases in general should be faced by the society was published at , but the idea behind still applies nowadays, especially for ar. all authors have contributed to the concept of the review and in its writing. jm was supported by grants from the instituto de salud carlos iii [spanish network for research on infectious diseases (rd / / )], from the spanish ministry of economy and competitivity (bio - -r) and from the autonomous community of madrid (b /bmd- ). work in tc and fb laboratory was supported by grants funded by the joint programming initiative in antimicrobial resistance (jpiamr third call, starcs, jpiamr -ac / ), the instituto de salud carlos iii of spain/ministry of economy and competitiveness and the european development regional fund "a way to achieve europe" (erdf) for co-founding the spanish r&d national plan estatal de i + d + i - (pi / ), ciberesp (ciber in epidemiology and public health; cb / / ), the regional government of madrid (ingemics-b /bmd- ) and the fundación ramón areces. the funders did not have any role neither in the design, nor in the writing of the current review. association between decreased susceptibility to a new antibiotic for 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phenomenal contribution to the health and well-being of people throughout the world. in addition to producing many primary metabolites, such as amino acids, vitamins and nucleotides, they are capable of making secondary metabolites, which constitute half of the pharmaceuticals on the market today and provide agriculture with many essential products. this review centers on these beneficial secondary metabolites, the discovery of which goes back years to the time when penicillin was discovered by alexander fleming. back in , alexander fleming began the microbial drug era when he discovered in a petri dish seeded with staphylococcus aureus that a compound produced by a mold killed the bacteria. the mold, identified as penicillium notatum, produced an active agent that was named penicillin. later, penicillin was isolated as a yellow powder and used as a potent antibacterial compound during world war ii. by using fleming's method, other naturally occurring substances, such as chloramphenicol and streptomycin, were isolated. naturally occurring antibiotics are produced by fermentation, an old technique that can be traced back almost years, initially for beverages and food production. beer is one of the world's oldest beverages, produced from barley by fermentation, possibly dating back to the sixth millennium bc and recorded in the written history of ancient egypt and mesopotamia. another old fermentation, used to initiate the koji process, was that of rice by aspergillus oryzae. during the past years, penicillium roqueforti has been utilized for cheese production, and for the past years soy sauce in asia and bread in egypt has represented examples of traditional fermentations. natural products with industrial applications can be produced from primary or secondary metabolism of living organisms (plants, animals or microorganisms). owing to technical improvements in screening programs, and separation and isolation techniques, the number of natural compounds discovered exceeds million. among them, - % are produced by plants (alkaloids, flavonoids, terpenoids, steroids, carbohydrates, etc.) and % have a microbial origin. of all the reported natural products, approximately - % show biological activity, and of these approximately % have been obtained from microbes. furthermore, from the biologically active compounds that have been obtained so far from microbes, % are produced by actinomycetes, % by fungi and % by unicellular bacteria. the increasing role of microorganisms in the production of antibiotics and other drugs for treatment of serious diseases has been dramatic. however, the development of resistance in microbes and tumor cells has become a major problem and requires much research effort to combat it. drugs of natural origin have been classified as (i) original natural products, (ii) products derived or chemically synthesized from natural products or (iii) synthetic products based on natural product structures. evidence of the importance of natural products in the discovery of leads for the development of drugs for the treatment of human diseases is provided by the fact that close to half of the best selling pharmaceuticals in were either natural products or their derivatives. in this regard, of the top-selling drugs reported in , % were natural products or their derivatives and of these, % were antibiotics. today, the structures of around secondary metabolites have been elucidated. it is important to understand that many chemically synthesized drugs owe their origin to natural sources. applications of chemically synthesized natural metabolites include the use of a natural product derived from plant salicyclic acid derivatives present in white willow, wintergreen and meadowsweet to relieve pain and suffering. concoctions of these plants were administered by hippocrates back in the year bc, and even earlier in egypt and babylonia, for fever, pain and childbirth. synthetic salicylates were produced initially by bayer in , and later in , arthur eichengrun at bayer discovered that an acetyl derivative (aspirin), reduced acidity, bad taste and stomach irritation. these plant-based systems continue to play an essential role in health care, and it has been estimated by the world health organization (who) that approximately % of the world's inhabitants rely mainly on traditional medicines for their primary health care. other synthesized compounds originating from natural products include a nonapeptide, designated teprotide, which was isolated from the venom of the brazilian pit viper bothrops jararaca. this led to the design and synthesis of angiotensin-converting enzyme (ace) inhibitors such as captopril, which was the first marketed, orally active ace inhibitor. enalapril, another ace inhibitor used in the treatment of cardiovascular disease, was approved for marketing by the food and drug administration (fda) in . the alkaloid quinine, the active constituent of the 'fever tree' cinchona succirubra, has been known for centuries by south american indians to control malaria. during the twentieth century, massive programs to synthesize quinoline derivatives, based on the quinine prototype, were carried out. the first of the new quinolones to be used clinically as an antibacterial agent was nalidixic acid, which emerged as part of a large chemical synthesis program developed at the sterling winthrop research institute. , the program was begun when -chloro- , -dihydro- -ethyl- -oxoquinolone- -carboxylic acid was obtained as a side product during purification of chloroquine and found to have antibacterial activity. the best compound found in the program was nalidixic acid, which had remarkable activity against gram-negative bacteria and was shown to be an inhibitor of dna gyrase. its discovery led to a whole series of synthetic quinolone and fluoroquinolone antibiotics (pefloxacin, norfloxacin, ciprofloxacin, levofloxacin, ofloxacin, lomefloxacin, sparfloxacin, etc.), which have been very successful in medicine and have achieved major commercial success (table ) . it is important to appreciate that all quinolones, though synthetic, are based on the structure of the natural plant product quinine. secondary metabolites have exerted a major impact on the control of infectious diseases and other medical conditions, and the development of pharmaceutical industry. their use has contributed to an increase in the average life expectancy in the usa, which increased from years in to years (in men) and years (in women) in . probably, the most important use of secondary metabolites has been as anti-infective drugs. in , the market for such antiinfectives was us$ billion (table ) and in it was us$ billion. table shows that, among the anti-infective drugs, antivirals represent more than % of the market. two antivirals that are chemically synthesized today were originally isolated from marine organisms. they are acyclovir (active against the herpes virus by inhibition and inactivation of dna polymerase) and cytarabine (active against non-hodgkin's lymphoma). both compounds are nucleoside analog drugs, originally isolated from sponges. other antiviral applications of natural compounds are related to human immunodeficiency virus (hiv) treatment. in the pathogenesis of this disease, hiv- , similar to other retroviruses, depends on its stable integration into the host genome to facilitate efficient replication of the viral rna and maintenance of the infected state. therefore, de novo viral dna synthesized during reverse transcription is immediately integrated into the host cell dna (through the integration step), allowing for further transcription of viral rna. in the late phase of hiv viral replication, the large precursor polyprotein (gag-pol precursor, pr ) must be appropriately cleaved by a viral protease. the cleavage of the gag precursor protein of hiv is critical for the maturation and infectivity of the viral particle. without the appropriate cleavage of the precursor polyproteins, non-infectious viral particles are generally produced. to confront this problem, a tremendous effort has been made at the us national cancer institute (nci), in search of natural metabolites capable of inhibiting hiv reverse transcriptase and hiv protease. chemically synthesized derivatives of these compounds are the main agents now used against hiv. furthermore, reports have been published on natural product inhibitors of hiv integrase obtained from among the marine ascidian alkaloids; that is, the lamellarins (produced by the mollusk lamellaria sp.), and from terrestrial plants (baccharis genistelloides and achyrocline satureioides). the most consistent anti-hiv activity was observed with extracts prepared from several baccharis species. in addition, nci has been evaluating the hiv- inhibitory activity of pepstatin a, a small pentapeptide produced by several streptomyces species. it contains a unique hydroxyamino acid, statine, that sterically blocks the active site of hiv- protease. , reasons for developing new antibiotics new antibiotics that are active against resistant bacteria are required. bacteria have lived on the earth for several billion years. during this time, they encountered in nature a wide range of naturally occurring antibiotics. to survive, bacteria developed antibiotic resistance mechanisms. therefore, it is not surprising that they have become resistant to most of the natural antimicrobial agents that have been developed over the past years. this resistance increasingly limits the effectiveness of current antimicrobial drugs. the problem is not just antibiotic resistance but also multidrug resistance. in , more than % of pathogenic bacteria were estimated to be resistant to at least one of the currently available antibiotics. the so-called 'superbugs' (organisms that are resistant to most of the clinically used antibiotics) are emerging at a rapid rate. s. aureus, which is resistant to methicillin, is responsible for many cases of infections each year. the incidence of multidrug-resistant pathogenic bacteria is increasing. the infectious disease society of america (idsa) reported in that in us hospitals alone, around million people acquire bacterial infections each year (http://www.idsociety.org/content.aspx?id¼ ). s. aureus is responsible for half of the hospital-associated infections and takes the lives of approximately patients each year in the usa alone. the bacteria produce a biofilm in which they are encased and protected from the environment. biofilms can grow on wounds, scar tissues and medical implants or devices, such as joint prostheses, spinal instrumentations, catheters, vascular prosthetic grafts and heart valves. more than % of the bacterial species producing such biofilms are likely to be resistant to at least one of the drugs commonly used in anti-infectious therapy. called 'nosocomial bacteria.' more than % of sepsis cases in hospitals are caused by gram-negative bacteria. among them, pseudomonas aeruginosa accounts for almost % of these opportunistic infections. they represent a serious problem in patients hospitalized with cancer, cystic fibrosis and burns, causing death in % of cases. other infections caused by pseudomonas species include endocarditis, pneumonia and infections of the urinary tract, central nervous system, wounds, eyes, ears, skin and musculoskeletal system. this bacterium is another example of a natural multidrug-resistant microorganism. although many strains are susceptible to gentamicin, tobramycin and amikacin, resistant forms have also developed. these multidrug-resistant bacteria make hospitals ''dangerous places to be, especially if you are sick, but even if not.'' although we are seeing a steady increase in resistance in almost every pathogen to most of the current antibiotics over time, not all the antibacterial agents show the same rate of resistance development. for example, antimicrobials such as rifampicin, which targets single enzymes, are most susceptible to the development of resistance, whereas agents that inactivate several targets irreversibly generate resistance more slowly. in addition to the antibiotic-resistance problem, new families of anti-infective compounds are needed to enter the marketplace at regular intervals to tackle the new diseases caused by evolving pathogens. at least new diseases emerged in the s and s and they are growing in incidence. emerging infectious organisms often encounter hosts with no prior exposure to them and thus represent a novel challenge to the host's immune system. several viruses responsible for human epidemics have made a transition from animal host to humans and are now transmitted from human to human. hiv, responsible for the acquired immunodeficiency syndrome (aids) epidemic, is one example. although it has not been proven, it is suspected that severe acute respiratory syndrome (sars), caused by the sars coronavirus, also evolved from a different species. in the early s, after decades of decline, the incidence of tuberculosis began to increase. the epidemic took place owing to inadequate treatment regimens, a diminished public health system and the onset of the hiv/aids epidemic. the who has predicted that between and , nearly billion people will become infected with mycobacterium tuberculosis and that this disease will cost the lives of million people. sexually transmitted diseases have also increased during these decades, especially in young people (aged - years). the human papillomavirus, chlamydia, genital herpes, gonorrhea and hiv/aids are examples. hiv/aids has infected more than million people in the world. together with other diseases such as tuberculosis and malaria, hiv/aids accounts for over million illnesses and more than million deaths each year. additional evolving pathogens include the (i) ebola virus, which causes the viral hemorrhagic fever syndrome with a resultant mortality rate of %; (ii) the bacterium legionella pneumophila, a ubiquitous aquatic organism that lives in warm environments, which causes legionnaire's disease, a pulmonary infection; (iii) the hantavirus, which can infect humans with two serious illnesses: hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome; (iv) at least three species of bacteria from the genus borrelia, which cause lyme disease, an emerging infection. in this case, the infection is acquired from the bite of ticks belonging to several species of the genus ixodes. borrelia burgdorferi is the predominant cause of lyme disease in the us, whereas borrelia afzelii and borrelia garinii are implicated in most european cases. the disease presentation varies widely, and may include a rash and flu-like symptoms in its initial stage, followed by musculoskeletal, arthritic, neurologic, psychiatric and cardiac manifestations. in the majority of cases, symptoms can be eliminated with antibiotics, especially if the treatment begins early in the course of illness. however, late or inadequate treatment can lead to 'late-stage' lyme disease that can be disabling and difficult to treat. (v) other evolving pathogens include the escherichia coli :h (enterohemorrhagic e. coli), a strain that causes colitis and bloody diarrhea by producing a toxin called shiga toxin, which damages the intestines. it is estimated that this bacterium causes infection in more than patients a year in the usa. another example is (vi) cryptosporidium, an obligate intracellular parasite commonly found in lakes and rivers. cryptosporidium parvum is one of the common species affecting the digestive and respiratory organs. intestinal cryptosporidiosis is characterized by severe watery diarrhea. pulmonary and tracheal cryptosporidiosis in humans is associated with coughing and is frequently a low-grade fever. people with severely weakened immune systems are likely to have more severe and more persistent symptoms than healthy individuals. in the developing world, nearly % of the infectious disease deaths are caused by six diseases or disease processes: acute respiratory infections, diarrhea, tuberculosis, hiv, measles and malaria. in both the developing and developed nations, the leading cause of death by a wide margin is acute respiratory disease. in the developing world, acute respiratory infections are attributed primarily to seven bacteria: bordetella pertussis, streptococcus pneumoniae, haemophilus influenzae, staphylococcus aureus, mycoplasma pneumoniae, chlamydophila pneumoniae and chlamydia trachomatis. in addition, the major viral causes of respiratory infections include respiratory syncytial virus, human parainfluenza viruses and , influenza viruses a and b, as well as some adenoviruses. these diseases are highly destructive in economic and social as well as in human terms and cause approximately million deaths per year, and innumerable serious illnesses besides affecting the economic growth, development and prosperity of human societies. morse identified six general factors in the emergence of infectious diseases: ecological changes, human demographics and behavior, international travel, technology and industry, microbial adaptation and change, and breakdown in public health measures. one additional reason for developing new antibiotics is related to their own toxicity. as with other therapeutic agents, the use of antibiotics may also cause side effects in patients. these include mild reactions such as upset stomach, vomiting and diarrhea (cephalosporins, macrolides, penicillins and tetracyclines), rash and other mild and severe allergic reactions (cephalosporins and penicillins), sensitivity to sunlight (tetracyclines), nervousness, tremors and seizures (quinolones). some side effects are more severe and, depending on the antibiotic, may disrupt the hearing function (aminoglycosides), kidneys (aminoglycosides and polypeptides) or liver (rifampin). during recent decades, we have seen an increasing number of reports on the progressive development of bacterial resistance to almost all available antimicrobial agents. in the s, the major problem was the multidrug resistance of gram-negative bacteria, but later in the s the gram-positive bacteria became important, including methicillin-resistant staphylococci, penicillin-resistant pneumococci and vancomycin-resistant enterococci. in the past, the solution to the problem has depended primarily on the development of novel antimicrobial agents. however, the number of new classes of antimicrobial agents being developed has decreased dramatically in recent years. the advent of resistant gram-positive bacteria has been noticed by the pharmaceutical, biotechnology and academic communities. some of these groups are making concerted efforts to find novel antimicrobial agents to meet this need. a new glycopeptide antibiotic, teicoplanin, was developed against infections with resistant gram-positive bacteria, especially bacteria resistant to the glycopeptide vancomycin. in another instance, the approach involved the redesign of a mixture of two compounds, called streptogramin, into a new mixture, called pristinamycin, to allow administration of the drug parenterally and in higher doses than the earlier oral preparation. the two components of streptogramin, quinupristin and dalfopristin, were chemically modified to allow intravenous administration. the new combination, pristinamycin, was approved by the fda for use against infections caused by vancomycin-resistant enterococcus faecium. additional moves against resistant microorganisms are the glycylcyclines developed to treat tetracycline-resistant bacteria. these modified tetracyclines show potent activity against a broad spectrum of gram-positive and gram-negative bacteria, including strains that carry the two major tetracycline-resistance determinants, involving efflux and ribosomal protection. two of the glycylcyline derivatives, dmg-mino and dmg-dmdot, have been tested against a large number of clinical pathogens isolated from various sources. the spectrum of activity of these compounds includes organisms with resistance to antibiotics other than tetracyclines; for example, methicillin-resistant staphylococci, penicillin-resistant s. pneumoniae and vancomycin-resistant enterococci. tigecycline was approved by the fda in as an injectable antibiotic. among the novel class of antimicrobial agents used in treating resistance to gram-positive infections, we can also mention the cyclic lipopeptide antibiotic daptomycin produced by streptomyces roseosporus. this compound was approved in by the fda for skin infections resulting from complications following surgery, diabetic foot ulcers and burns. it represents the first new natural antibiotic approved in many years. its mode of action is distinct from any other approved antibiotic: it rapidly kills gram-positive bacteria by disrupting multiple aspects of bacterial membrane function (by binding irreversibly to the bacterial cell membrane, causing membrane depolarization, destroying the ion concentration gradient and provoking the efflux of k + ). it acts against most clinically relevant gram-positive bacteria (staphylococcus aureus, streptococcus pyogenes, streptococcus agalactiae, streptococcus dysgalactiae subsp. equisimilis and enterococcus faecalis), and retains in vitro potency against isolates resistant to methicillin, vancomycin and linezolid. traditionally, these infections were treated with penicillin and cephalosporins, but resistance to these agents became widespread. [ ] [ ] [ ] [ ] daptomycin seems to have a favorable side effect profile, and it might be used to treat patients who cannot tolerate other antibiotics. telithromycin, a macrolide antibiotic, is the first orally active compound of a new family of antibacterials named the ketolides. it shows potent activity against pathogens implicated in communityacquired respiratory tract infections, irrespective of their b-lactam, macrolide or fluoroquinolone susceptibility. some of the microorganisms susceptible to this antibiotic are pneumococci, h. influenzae and moraxella catarrhalis, including b-lactamase-positive strains. in addition, telithromycin has a very low potential for selection of resistant isolates or induction of cross-resistance found with other macrolides. clavulanic acid, first detected in streptomyces clavuligerus, contains a bicyclic b-lactam ring fused to an oxazolidine ring with an oxygen in place of a sulfur, a b-hydroxyethylidene substituent at c- and no acylamino group at c- . it was first described in and shown to be a potent inhibitor of the b-lactamases produced by staphylococci and plasmid-mediated b-lactamases of e. coli, klebsiella, proteus, shigella, pseudomonas and haemophilus. although it is a broad-spectrum antibiotic, clavulanic acid possesses only very low antibacterial activity. therefore, the molecule has been combined, as a b-lactamase inhibitor, with a variety of broad-spectrum semisynthetic penicillins. for example, when administered with amoxicillin, it is used for the treatment of infections caused by b-lactamase-producing pathogenic bacteria. it has world sales of over us$ billion, and in it was the second largest selling antibacterial drug. clavulanic acid can also be combined with ticarcillin, which is a penicillin effective against organisms such as e. coli, proteus, salmonella, haemophilus, pseudomonas and s. aureus. it is normally used in hospitals for treating severe infections affecting blood or internal organs, bones and joints, upper or lower airways or skin and soft tissue. the combination extends ticarcillin antimicrobial activity by inhibiting the action of the b-lactamases produced by certain bacteria. mycosis is a condition in which fungi pass the resistance barriers of the human or animal body and establish infections. these organisms are harmless most of the time, but sometimes they can cause fungal infections. in most cases, these infections are not life threatening. however, when they are deeply invasive and disseminated, they lead to more serious infections, particularly in critically ill patients, elderly people and those who have conditions that affect the immune system (by disease or through the use of immunosuppressive agents). in addition, the use of antineoplastic and broad-spectrum antibiotics, prosthetic devices and grafts, and more aggressive surgery has increased invasive fungal infections. patients with burns, neutropenia, pancreatitis or after organ transplantation ( % of liver transplants, - % of heart transplants and % of kidney transplants) are also predisposed to fungal infection. approximately % of death from nosocomial infections are caused by fungi, and % of these are caused by candida and aspergillus, although cryptococcus spp., fusarium spp., scedosporium spp., penicillium spp. and zygomycetes are increasingly involved. pulmonary aspergillosis is the main factor involved in the death of recipients of bone marrow transplants, and pneumocystis carinii is the leading cause of death in aids patients from europe and north america. the rising incidence of invasive fungal infections and the emergence of broader fungal resistance have led to the need for novel antifungal agents. amphotericin b is the first-line therapy for systemic infection because of its broad spectrum and fungicidal activity. however, considerable side effects limit its clinical utility. echinocandins are large lipopeptide molecules that inhibit the synthesis of , -b-dglucan, a key component of the fungal cell wall. three echinocandins (caspofungin, micafungin and anidulafungin) have reached the market. caspofungin is also known as pneumocandin or mk- . this compound was the first cell-wall-active antifungal approved as a new injectable antifungal; this was in . it irreversibly inhibits , -b-d-glucan synthase, preventing the formation of glucan polymers and disrupting the integrity of fungal cell walls. it is more active and less toxic than amphotericin b and shows a broad spectrum of activity against candida (including fluconozole resistance), aspergillus, histoplasma and p. carinii, the major cause of hiv death. micafungin is licensed for clinical use in asian countries and in the us. this compound exhibits extremely potent antifungal activity against clinically important fungi, including aspergillus and azole-resistant strains of candida. in animal studies, micafungin is as efficacious as amphotericin b with respect to improvement of survival rate. it is characterized by a linear pharmacokinetic profile and substantially fewer toxic effects. anidulafungin is currently licensed in the us. although several new antifungal drugs have been developed in the past years, some patients remain resistant to treatments. the main reasons for this include intrinsic or acquired antifungal resistance, organ dysfunction preventing the use of some agents and drug interactions. in addition, some drugs penetrate poorly into sanctuary sites, including the eye and urine, and others are associated with considerable adverse events. however, there has been some progress. posaconazole is a new member of the triazole class of antifungals. it has shown clinical efficacy in the treatment of oropharyngeal candidiasis and has potential as a salvage therapy for invasive aspergillosis, zygomycosis, cryptococcal meningitis and a variety of other fungal infections. it is available as an oral suspension and has a favorable toxicity profile. the wide spectrum of posaconazole activity in in vitro studies, animal models and preliminary clinical studies suggests that it represents an important addition to the antifungal armamentarium. in addition to the screening programs for antibacterial activity, the pharmaceutical industry has extended these programs to other disease areas. , microorganisms are a prolific source of structurally diverse bioactive metabolites and have yielded some of the most important products of the pharmaceutical industry. microbial secondary metabolites are now being used for applications other than antibacterial, antifungal and antiviral infections. for example, immunosuppressants have revolutionized medicine by facilitating organ transplantation. other applications include antitumor drugs, enzyme inhibitors, gastrointestinal motor stimulator agents, hypocholesterolemic drugs, ruminant growth stimulants, insecticides, herbicides, coccidiostats, antiparasitics vs coccidia, helminths and other pharmacological activities. further applications are possible in various areas of pharmacology and agriculture, developments catalyzed by the use of simple enzyme assays for screening before testing in intact animals or in the field. in the year , approximately million new cases of cancer were diagnosed in the world, resulting in million cancer-related deaths. the tumor types with the highest incidence were lung ( . %), breast ( . %) and colorectal ( . %). microbial metabolites are among the most important of the cancer chemotherapeutic agents. they started to appear around with the discovery of actinomycin and since then many compounds with anticancer properties have been isolated from natural sources. more than % of the current compounds with antineoplasic activity were originally isolated as natural products or are their derivatives. among the approved products deserving special attention are actinomycin d, anthracyclines (daunorubicin, doxorubicin, epirubicin, pirirubicin and valrubicin), bleomycin, mitosanes (mitomycin c), anthracenones (mithramycin, streptozotocin and pentostatin), enediynes (calcheamycin), taxol and epothilones. actinomycin d is the oldest microbial metabolite used in cancer therapy. its relative, actinomycin a, was the first antibiotic isolated from actinomycetes. the latter was obtained from actinomyces antibioticus (now streptomyces antibioticus) by waksman and woodruff. as it binds dna at the transcription initiation complex, it prevents elongation by rna polymerase. this property, however, confers some human toxicity and it has been used primarily as an investigative tool in the development of molecular biology. despite the toxicity, however, it has served well against wilms tumor in children. the anthracyclines are some of the most effective antitumor compounds developed, and are effective against more types of cancer than any other class of chemotherapy agents. they are used to treat a wide range of cancers, including leukemias, lymphomas, and breast, uterine, ovarian and lung cancers. anthracyclines act by intercalating dna strands, which result in a complex formation that inhibits the synthesis of dna and rna. it also triggers dna cleavage by topoisomerase ii, resulting in mechanisms that lead to cell death. in their cytotoxic effects, the binding to cell membranes and plasma proteins plays an important role. their main adverse effects are heart damage (cardiotoxicity), which considerably limits their usefulness, and vomiting. the first anthracycline discovered was daunorubicin (daunomycin) in , which is produced naturally by streptomyces peucetius. doxorubicin (adriamycin) was developed in . another anthracycline is epirubicin. this compound, approved by the fda in , is favored over doxorubicin in some chemotherapy regimens as it appears to cause fewer side effects. epirubicin has a different spatial orientation of the hydroxyl group at the ¢ carbon of the sugar, which may account for its faster elimination and reduced toxicity. epirubicin is primarily used against breast and ovarian cancer, gastric cancer, lung cancer and lymphomas. valrubicin is a semisynthetic analog of doxorubicin approved as a chemotherapeutic drug in and used to treat bladder cancer. bleomycin is a non-ribosomal glycopeptide microbial metabolite produced as a family of structurally related compounds by the bacterium streptomyces verticillus. first reported by umezawa et al. in , bleomycin obtained fda approval in . when used as an anticancer agent (inducing dna strand breaks), the chemotherapeutic forms are primarily bleomycins a and b . mitosanes are composed of several mitomycins that are formed during the cultivation of streptomyces caespitosus. although the mitosanes are excellent antitumor agents, they have limited utility owing to their toxicity. mitomycin c was approved by the fda in , showing activity against several types of cancer (lung, breast, bladder, anal, colorectal, head and neck), including melanomas and gastric or pancreatic neoplasms. recently, mitomycin dimers have been explored as potential alternatives for lowering toxicity and increasing efficiency. mithramycin (plicamycin) is an antitumor aromatic polyketide produced by streptomyces argillaceous that shows antibacterial and antitumor activity. it is one of the older chemotherapy drugs used in the treatment of testicular cancer, disseminated neoplasms and hypercalcemia. it binds to g-c-rich dna sequences, inhibiting the binding of transcription factors such as sp , which is believed to affect neuronal survival/death pathways. it may also indirectly regulate gene transcription by altering histone methylation. with repeated use, organotoxicity (kidney, liver and hematopoietic system) can become a problem. streptozotocin is a microbial metabolite with antitumor properties, produced by streptomyces achromogenes. chemically, it is a glucosamine-nitroso-urea compound. as with other alkylating agents in the nitroso-urea class, it is toxic to cells by causing damage to dna, although other mechanisms may also contribute. the compound is selectively toxic to the b-cells of the pancreatic islets. it is similar enough to glucose to be transported into the cell by the glucose transport protein of these cells, but it is not recognized by the other glucose transporters. as b-cells have relatively high levels of glucose permease, the relative streptozotocin toxicity for these b-cells can be explained. in , fda granted approval for streptozotocin as a treatment for pancreatic islet cell cancer. pentostatin (deoxycoformycin) is an anticancer chemotherapeutic drug produced by s. antibioticus. it is classified as a purine analog, which mimics the nucleoside adenosine and thus tightly binds and inhibits adenosine deaminase (k i of . Â À m). it interferes with the cell's ability to process dna. pentostatin is commonly used to treat hairy cell leukemia, acute lymphocytic leukemia, prolymphocytic leukemia (b-and t-cell origin), t-cell leukemia and lymphoma. however, it can cause kidney, liver, lung and neurological toxicity. the fda granted approval for pentostatin in . calicheamicins are highly potent antitumor microbial metabolites of the enediyne family produced by micromonospora echinospora. their antitumor activity is apparently due to the cleavage of double-stranded dna. they are highly toxic, but it was possible to introduce one such compound into the clinic by attaching it to an antibody that delivered it to certain cancer types selectively. this ingenious idea of the wyeth laboratories avoided the side effects of calicheamicin. in this regard, gemtuzumab is effective against acute myelogenous leukemia (aml). calicheamicin is bound to a monoclonal antibody against a transmembrane receptor (cd ) expressed on cells of monocytic/myeloid lineage. cd is expressed in most leukemic blast cells, but in normal hematopoietic cells the intensity diminishes with maturation. it was approved by the fda for use in patients over the age of years with relapsed aml who are not considered candidates for standard chemotherapy. a successful non-actinomycete molecule is taxol (paclitaxel), which was first isolated from the pacific yew tree, taxus brevifolia, but is also produced by the endophytic fungi taxomyces andreanae and nodulisporium sylviforme. this compound inhibits rapidly dividing mammalian cancer cells by promoting tubulin polymerization and interfering with normal microtubule breakdown during cell division. the drug also inhibits several fungi (pythium, phytophthora and aphanomyces) by the same mechanism. in , taxol was approved for refractory ovarian cancer, and today it is used against breast and advanced forms of kaposi's sarcoma. a new formulation is available in which paclitaxel is bound to albumin. taxol sales amounted to us$ . billion in for bristol myers-squibb, representing % of the company's pharmaceutical sales and its third largest selling product. currently, taxol production uses plant cell fermentation technology. the epothilones (a name derived from its molecular features: epoxide, thiazole and ketone) are macrolides originally isolated from the broth of the soil myxobacterium sorangium cellulosum as weak agents against rust fungi. they were identified as microtubulestabilizing drugs, acting in a similar manner to taxol. , however, they are generally - times more potent than taxol in inhibiting cell growth in cultures. five analogs are now undergoing investigation as candidate anticancer drugs, and their preclinical studies have indicated a broad spectrum of antitumor activity, including taxol-resistant tumor cells. with the best currently available therapies, the median survival time for patients with metastatic breast cancer is only - years, and many patients develop resistance to taxanes or other chemotherapy drugs. one epothilone, ixabepilone, was approved in october by the fda for use in the treatment of aggressive metastatic or locally advanced breast cancer no longer responding to currently available chemotherapies. in tumor cells, p-glycoprotein reduces intracellular antitumor drug concentrations, thereby limiting access of chemotherapeutic substrates to the site of action. the epothilones are attractive because they are active against p-glycoprotein-producing tumors and have good solubility. epothilone b is a -membered polyketide macrolactone with a methylthiazole group connected to the macrocycle by an olefinic bond. testicular cancer is the most common cancer diagnosis in men between the ages of and years, with approximately cases detected in the united states annually. the majority ( %) of testicular neoplasms are germ cell tumors, which are relatively uncommon carcinomas, accounting for only % of all male malignancies. remarkable progress has been made in the medical treatment of advanced testicular cancer, with a substantial increase in cure rates from approximately % in the early s to almost % today. , this cure rate is the highest of any solid tumor, and improved survival is primarily due to effective chemotherapy. a major advance in chemotherapy for testicular germ cell tumors was the introduction of cisplatin in the mid- s. two chemotherapy regimens are effective for patients with a good testicular germ cell tumor prognosis: four cycles of etoposide and cisplatin or three cycles of bleomycin, etoposide and cisplatin. of the latter three agents, bleomycin and etoposide are natural products. enzyme inhibitors have received increasing attention as useful tools, not only for the study of enzyme structures and reaction mechanisms but also for potential utilization in medicine and agriculture. several enzyme inhibitors with various industrial uses have been isolated from microbes. the most important are ( ) clavulanic acid, the inhibitor of b-lactamases discussed above in the section 'moves against antibiotic resistance development in bacteria,' and the statins, hypocholesterolemic drugs presented below in the section 'hypocholesterolemic drugs.' some of the common targets for other inhibitors are glucosidases, amylases, lipases, proteases and xanthine oxidase (xo). acarbose is a pseudotetrasaccharide made by actinoplanes sp. se . it contains an aminocyclitol moiety, valienamine, which inhibits intestinal a-glucosidase and sucrase. this results in a decrease in starch breakdown in the intestine, which is useful in combating diabetes in humans. amylase inhibitors are useful for the control of carbohydratedependent diseases, such as diabetes, obesity and hyperlipemia. , amylase inhibitors are also known as starch blockers because they contain substances that prevent dietary starches from being absorbed by the body. the inhibitors may also be useful for weight loss, as some versions of amylase inhibitors do show potential for reducing carbohydrate absorption in humans. , the use of amylase inhibitors for the treatment of rumen acidosis has also been reported. examples of microbial a-amylase inhibitors are paim, obtained from culture filtrates of streptomyces corchorushii, and tai-a, tai-b, oligosaccharide compounds from streptomyces calvus tm- . lipstatin is a pancreatic lipase inhibitor produced by streptomyces toxytricini that is used to combat obesity and diabetes. it interferes with the gastrointestinal absorption of fat. the commercial product is tetrahydrolipstatin, which is also known as orlistat. in the pathogenic processes of some diseases, such as emphysema, arthritis, pancreatitis, cancer and aids, protease inhibitors are potentially powerful tools for inactivating target proteases. examples of microbial products include antipain, produced by streptomyces yokosukaensis, leupeptin from streptomyces roseochromogenes and chymostatin from streptomyces hygroscopicus. leupeptin is produced by more than species of actinomycetes. xo catalyzes the oxidation of hypoxanthine to uric acid through xanthine. an excessive accumulation of uric acid in the blood, called hyperuricemia, causes gout. the inhibitors of xo decrease the uric acid levels, which result in an antihyperuricemic effect. a potent inhibitor of xo, hydroxyakalone, was purified from the fermentation broth of agrobacterium aurantiacum sp. nov., a marine bacterial strain. fungal products are also used as enzyme inhibitors against cancer, diabetes, poisonings, alzheimer's disease, etc. the enzymes inhibited include acetylcholinesterase, protein kinase, tyrosine kinase, glycosidases and others. immunosuppresants suppressor cells are critical in the regulation of the normal immune response. an individual's immune system is capable of distinguishing between native and foreign antigens and of mounting a response only against the latter. a major role has been established for suppressor t lymphocytes in this phenomenon. suppressor cells also play a role in regulating the magnitude and duration of the specific antibody response to an antigenic challenge. suppression of the immune response either by drugs or by radiation, to prevent the rejection of grafts or transplants or to control autoimmune diseases, is called immunosuppression. a number of microbial compounds capable of suppressing the immune response have been discovered. cyclosporin a was originally introduced as a narrow-spectrum antifungal peptide produced by the mold, tolypocladium nivenum (originally classified as trichoderma polysporum and later as tolypocladium inflatum), by aerobic fermentation. cyclosporins are a family of neutral, highly lipophilic, cyclic undecapeptides containing some unusual amino acids, synthesized by a non-ribosomal peptide synthetase, cyclosporin synthetase. discovery of the immunosuppressive activity led to its use in heart, liver and kidney transplants and to the overwhelming success of the organ transplant field. cyclosporin was approved for use in . it is thought to bind to the cytosolic protein cyclophilin (immunophilin) of immunocompetent lymphocytes, especially t lymphocytes. this complex of cyclosporin and cyclophilin inhibits calcineurin, which under normal circumstances is responsible for activating the transcription of interleukin- . it also inhibits lymphokine production and interleukin release and therefore leads to a reduced function of effector t cells. sales of cyclosporin a have reached us$ . billion per year. other important transplant agents include sirolimus (rapamycin) and tacrolimus (fk ), which are produced by actinomycetes. rapamycin is especially useful in kidney transplants as it lacks the nephrotoxicity seen with cyclosporin a and tacrolimus. it is a macrolide, first discovered in as a product of s. hygroscopicus, and was initially proposed as an antifungal agent. however, this was abandoned when it was discovered that it had potent immunosuppressive and antiproliferative properties. this compound binds to the immunophilin fk -binding protein (fkbp ), and this binary complex interacts with the rapamycin-binding domain and inactivates a serine-threonine kinase termed the mammalian target of rapamycin. the latter is known to control proteins that regulate mrna translation initiation and g progression. the antiproliferative effect of rapamycin has also been used in conjunction with coronary stents to prevent restenosis, which usually occurs after the treatment of coronary artery disease by balloon angioplasty. rapamycin also shows promise in treating tuberous sclerosis complex (tsc), a congenital disorder that leaves sufferers prone to benign tumor growth in the brain, heart, kidneys, skin and other organs. in a study of rapamycin as a treatment for tsc, university of california, los angeles (ucla) researchers observed a major improvement in mice regarding retardation related to autism. as rapamycin has poor aqueous solubility, some of its analogs, rad (everolimus), cci- (tensirolimus) and ap (ariad), have been developed with improved pharmaceutical properties. everolimus is currently used as an immunosuppressant to prevent the rejection of organ transplants. although it does not have fda approval in the usa, it is approved for use in europe and australia, and phase iii trials are being conducted in the us. everolimus may have a role in heart transplantation as it has been shown to reduce chronic allograft vasculopathy in such transplants. everolimus is also used in drug-eluting coronary stents as an immunosuppressant to prevent rejection. cci- is a rapamycin ester that can be converted to rapamycin in vivo. rad is a rapamycin analog currently being investigated in phase ii trials for recurrent endometrial cancer as a single agent, and in phase i/ii trials for the treatment of glioblastoma in combination with the inhibitor of certain epidermal growth factor receptor and vascular endothelial growth factor receptor family members. ap is a novel non-prodrug rapamycin analog with a nonlinear pharmacokinetic behavior that has demonstrated antiproliferative activity against several human tumor cell lines in vitro and against experimental tumors in vivo. this agent is currently under evaluation in phase i-ii trials, including patients with different tumors. two additional small-molecule rapamycin analogs, ap and ap , are currently in preclinical development for the treatment of bone metastases and primary bone cancer. tacrolimus (fk ) was discovered in in japan. it is produced by streptomyces tsukubaensis. however, its use was almost abandoned because of dose-associated toxicity. dr thomas starzl (university of pittsburgh) rescued it by using lower doses, realizing that it was approximately times more active as an immunosuppressive than cyclosporin a. it was introduced in japan in , and in it was approved by the fda for use as an immunosuppressant in liver transplantation. furthermore, its use has been extended to include bone marrow, cornea, heart, intestines, kidney, lung, pancreas, trachea, small bowel, skin and limb transplants, and for the prevention of graft-vs-host disease. topically, it is also used against atopic dermatitis, a widespread skin disease. in the laboratory, tacrolimus inhibits the mixed lymphocyte reaction, the formation of interleukin- by t lymphocytes, and the formation of other soluble mediators, including interleukin- and interferon g. recently, it has been reported that tacrolimus inhibits tumor growth factor-b-induced signaling and collagen synthesis in human lung fibroblastic cells. this factor plays a pivotal role in tissue fibrosis, including pulmonary fibrosis. therefore, tacrolimus may be useful for the treatment of pulmonary fibrosis, although its use in the acute inflammatory phase may exacerbate lung injury. hypocholesterolemic drugs atherosclerosis is generally viewed as a chronic, progressive disease characterized by the continuous accumulation of atheromatous plaque within the arterial wall. the past two decades have witnessed the introduction of a variety of anti-atherosclerotic therapies. the statins form a class of hypolipidemic drugs used to lower cholesterol by inhibiting the enzyme hmg-coa reductase, the rate-limiting enzyme of the mevalonate pathway of cholesterol biosynthesis. inhibition of this enzyme in the liver stimulates low-density lipoprotein (ldl) receptors, resulting in an increased clearance of ldl from the bloodstream and a decrease in blood cholesterol levels. through their cholesterol-lowering effect, they reduce the risk of cardiovascular disease, prevent stroke and reduce the development of peripheral vascular disease. in addition, they are anti-thrombotic and antiinflammatory. currently there are a number of statins in clinical use. the entire group of statins reached an annual market of nearly us$ billion before it became a generic pharmaceutical. the first member of the group (compactin; mevastatin) was isolated as an antibiotic product of penicillium brevicompactum and later from penicillium citrinum. although not of commercial importance, compactin's derivatives achieved overwhelming medical and commercial success. an ethylated form, known as lovastatin (monacolin k; mevinolin), was isolated in the s in the broths of monascus ruber and aspergillus terreus. lovastatin, the first commercially marketed statin, was approved by the fda in . a semisynthetic derivative of lovastatin is simvastatin, a major hypocholesterolemic drug, selling for us$ billion per year before becoming generic. another statin, pravastatin (us$ . billion per year), is made through different biotransformation processes from compactin by streptomyces carbophilus and actinomadura sp. other genera involved in the production of statins are doratomyces, eupenicillium, gymnoascus, hypomyces, paecilomyces, phoma, trichoderma and pleurotus. a synthetic compound, modeled from the structure of the natural statins, is atorvastin, which has been the leading drug of the entire pharmaceutical industry in terms of market share (approximately us$ billion per year) for many years. an insecticide is a pesticide used against insects in all developmental forms. they include ovicides and larvicides used against the eggs and larvae of insects, respectively. insecticides are used in agriculture, medicine, industry and households. the use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the twentieth century. synthetic insecticides pose some hazards, whereas natural insecticides offer adequate levels of pest control and pose fewer hazards. microbially produced insecticides are especially valuable because their toxicity to non-target animals and humans is extremely low. compared with other commonly used insecticides, they are safe for both the pesticide users and consumers of treated crops. the action of microbial insecticides is often specific to a single group or species of insects, and this specificity means that most microbial insecticides do not naturally affect beneficial insects (including predators or parasites of pests) in treated areas. the spinosyns (a group) are a group of natural products produced by saccharopolyspora spinosa that were discovered in . the researchers isolated spinosyn a and d, as well as minor analogs. they are active on a wide variety of insect pests, especially lepidopterans and dipterans, but do not have antibiotic activity. the compounds attack the nervous system of insects by targeting two key neurotransmitter receptors, with no cross-resistance to other known insecticides. the spinosyns are a family of macrolides with carbon atoms, containing four connected rings of carbon atoms at their core to which two deoxysugars (forosamine and , , , tri-o-methylrhamnose, which are required for bioactivity) are attached. novel spinosyns have been prepared by biotransformation, using a genetically engineered strain of saccharopolyspora erythraea. a mixture of spinosyn a ( %) and d ( %) (spinosad) is being produced through fermentation and was introduced to the market in for the control of chewing insects on a variety of crops. spinosyn formulations were recently approved for use on organic crops and for animal health applications. recently, a new naturally occurring series of insect-active compounds was discovered from a novel soil isolate, saccharopolyspora pogona nrrl . the culture produced a unique family of over new spinosyns. they have a butenyl substitution at the position on the spinosyn lactone and are named butenyl-spinosyns or pogonins. herbicides are chemicals marketed to inhibit or interrupt normal plant growth and development. they are widely used in agriculture, industry and urban areas for weed management. approximately kinds of weeds are widely distributed in the world; yield losses caused by kinds of weeds are approximately . % of total crop production every year. herbicides provide cost-effective weed control with a minimum of labor. most are used on crops planted in large acreages, such as soy, cotton, corn and canola. there are numerous classes of herbicides with different modes of action, as well as different potentials for adverse effects on health and the environment. over the past century, chemical herbicides, used to control various weeds, may have caused many serious side effects, such as injured crops, threat to the applicator and others exposed to the chemicals, herbicide-resistant weed populations, reduction of soil and water quality, herbicide residues and detrimental effects on non-target organisms. for example, alachlor and atrazine were reported to cause cancer in animal tests. with increasing global environmental consciousness, bioherbicides, which are highly effective for weed control and environmentally friendly as well, are very attractive both for research and for application. microbial herbicides can be divided into microbial preparations (microorganisms that control weeds) and microbially derived herbicides. the first microbial herbicide was independently discovered in germany and japan. in , the zähner group in germany isolated phosphinothricin tripeptide, a peptide antibiotic consisting of two molecules of l-alanine and one molecule of the unusual amino acid l-phosphinothricin; that is, n( [hydroxyl(methyl)phosphinoyl]homoalanyl)alanylalanine. they isolated it from streptomyces viridochromogenes as a broad-spectrum antibacterial including activity against botrytis cinerea. in japan, it was discovered at the meiji seiki laboratories in from s. hygroscopicus and named bialaphos. the bioactive l-phosphinothricin is a structural analog of glutamic acid, acting as a competitive inhibitor of glutamine synthetase, and has bactericidal (gram-positive and gram-negative bacteria), fungicidal (b. cinerea) and herbicidal properties. glufosinate (dl-phosphinothricin) (without ala-ala) was developed as a herbicide. therefore, the agent acts as a herbicide with or without ala-ala. bialaphos has no influence on microorganisms in the soil and is easily degraded in the environment, having a half-life of only h. this low level of environmental impact is of great interest to environmentalists. in , the global animal health market was valued at us$ billion, of which % was derived from parasiticides. parasites are organisms that inhabit the body and benefit from a prolonged, close association with the host. antiparasitics are compounds that inhibit the growth or reproduction of a parasite; some antiparasitics directly kill parasites. in general, parasites are much smaller than their hosts, show a high degree of specialization for their mode of life and reproduce more quickly and in greater numbers than their hosts. classic examples of parasitism include the interactions between vertebrate hosts and such diverse animals as tapeworms, flukes, plasmodium species and fleas. parasitic infections can cause potentially serious health problems and even kill the host. parasites mainly enter the body through the mouth, usually through ingestion of tainted food or drink. this is a very common problem in tropical areas, but is not limited to those regions. there are varieties of parasites in four major categories: protozoa, trematoda, cestoda and nematoda. the major groups include protozoans (organisms having only one cell) and parasitic worms (helminths). each of these can infect the digestive tract, and sometimes two or more can cause infection at the same time. the who reported that approximately % of the world's population is infected with roundworms. in addition, a major agricultural problem has been the infection of farm animals by worms. the predominant type of antiparasitic screening effort over the years was the testing of synthetic compounds against nematodes, and some commercial products did result. certain antibiotics were also shown to possess antihelmintic activity against nematodes or cestodes, but these failed to compete with the synthetic compounds. although merck had earlier developed a commercially useful synthetic product, thiabendazole, they had enough foresight to examine microbial broths for antihelmintic activity, and found a non-toxic fermentation broth that killed the intestinal nematode nematosporoides dubius in mice. the streptomyces avermitilis culture, isolated by Ō mura and coworkers at the kitasato institute in japan, produced a family of secondary metabolites (eight compounds) with both antihelmintic and insecticidal activities. these compounds, named 'avermectins,' are pentacyclic, -membered macrocyclic lactones, that harbor a disaccharide of the methylated sugar, oleandrose, with exceptional activity against parasites, especially nemathelminthes (nematodes) and arthropod parasites ( times higher than any known synthetic antihelmintic agent). surprisingly, avermectins lack activity against bacteria and fungi, do not inhibit protein synthesis and are not ionophores. instead, they interfere with neurotransmission in many invertebrates, causing paralysis and death by neuromuscular attacks. the annual market for avermectins surpasses us$ billion. they are used against both nematode and arthropod parasites in sheep, cattle, dogs, horses and swine. a semisynthetic derivative, , -dihydroavermectin b ('ivermectin') is times more active than thiabendazole and is a commercial veterinary product. the efficacy of ivermectin has made it a promising candidate for the control of human onchocerciasis and human strongyloidiasis. another avermectin, called doramectin (or cyclohexyl avermectin b ), produced by 'mutational biosynthesis' was commercialized for use by food animals. a semisynthetic monosaccharide derivative of doramectin called selamectin is the most recently commercialized avermectin, and is active against heartworms (dirofilaria immitis) and fleas in companion animals. although the macrocyclic backbone of each of these molecules (ivermectin, doramectin and selamectin) is identical, there are different substitutions at pharmacologically relevant sites such as c- , c- , c- , and c- . the avermectins are closely related to the milbemycins, a group of non-glycosidated macrolides produced by s. hygroscopicus subsp. aureolacrimosus. these compounds possess activity against worms and insects. coccidiostats are used for the prevention of coccidiosis in both extensively and intensively reared poultry. coccidiosis is the name given to a common intestinal disease caused by the invading protozoan parasites of the genus eimeria that affects several different animal species (cattle, dogs, cats, poultry, etc.). the major damage is caused by the rapid multiplication of the parasite in the intestinal wall and the subsequent rupture of the cells of the intestinal lining, leading to high mortality and severe loss of productivity. coccidia are obligate intracellular parasites that show host specificity; only cattle coccidia will cause disease in cattle; other species-specific coccidia will not. for many years, synthetic compounds were used to combat coccidiosis in poultry; however, resistance developed rapidly. a solution came on the scene with the discovery of the narrow-spectrum polyether antibiotic monensin, which had extreme potency against the coccidian. made by streptomyces cinnamonensis, monensin led the way for additional microbial ionophoric antibiotics, such as lasalocid, narasin and salinomycin. all are produced by various streptomyces species. they form complexes with the polar cations k + , na + , ca + and mg + , severely affecting the osmotic balance in the parasitic cells and thus causing their death. the widespread use of anticoccidials has revolutionized the poultry industry by reducing the mortality and production losses caused by coccidiosis. of great interest was another extremely valuable application of monensin; that is, growth promotion in ruminants. synthetic chemicals had been tested for years to inhibit wasteful methane production by cattle and sheep and increase fatty acid formation (especially propionate) to improve feed efficiency; however, they failed. the solution was monensin, which became a major success as a ruminant growth enhancer. for more than years, certain antibiotics have been used in foodanimal production to enhance feed utilization and weight gain. from a production standpoint, feed antibiotics have been consistently shown to improve animal weight gain and feed efficiency, especially in younger animals. these responses are probably derived from an inhibitory effect on the normal microbiota, which can lead to reduced intestinal inflammation and improved nutrient utilization. pigs in the usa are exposed to a great variety of antibiotics. these include b-lactam antibiotics (including penicillins), lincosamides and macrolides (including erythromycin and tetracyclines). all these groups have members that are used to treat infections in humans. in addition, bacitracin, flavophospholipol, pleuromutilins, quinoxalines and virginiamycin are utilized as growth stimulants. flavophospholipol and virginiamycin are also used as growth promoters in poultry. as described above, cattle are also exposed to ionophores such as monensin to promote growth. the animal health institute of america has estimated that without the use of growth-promoting antibiotics, the usa would require an additional million chickens, million more cattle and million more pigs to reach the levels of production attained by the current practices. considering that animal health research and the development of new anti-infective product discovery have decreased, the discovery of new antibiotics has decreased over the past years, with few new drug approvals. therefore, it will be incumbent on veterinary practitioners to use the existing products in a responsible manner to ensure their longevity. it remains to be seen what effects the dearth of new antibiotics for veterinary medicine will have on the future practice of veterinary medicine, production agriculture, food safety and public health. since the eu decision to prohibit antibiotic use for foodanimal growth promotion, four antibiotic growth promoters have been banned, including the macrolide drugs tylosin and spiramycin. although macrolides are no longer formally used as 'growth promoters,' their use under veterinary prescription has risen from tons in to tons in , which suggests that more of them are being used now than before the prohibition. it is well known that the most effective route for feeding is via the gastrointestinal tract. many critically ill patients who accept early feeding improve their health. in some post-operative patients, gastric stasis and excessive volumes in the stomach increase the risk of aspiration and subsequent pneumonia. on account of the importance of achieving early and adequate nutritional intake, it is common practice in many intensive care units to use drugs to improve gastrointestinal motility. erythromycin is a macrolide antibiotic with a broad spectrum of activity. it is well recognized that when prescribed, either intravenously or orally, it causes side effects, such as diarrhea, nausea and vomiting. these side effects are, in part, due to the action of erythromycin at motilin receptors in the gut. this makes this antibiotic very attractive to be used in ill patients with gastrointestinal motility problems. there have been some developments on erythromycin analogs that lack antibiotic action but retain action at motilin receptors. these have been named 'motilides.' , recently, an orally active erythromycinderived motilin receptor agonist (mitemcinal) has been tested in patients with idiopathic and diabetic gastroparesis. in both cases, an improvement of gastroparetic symptoms was observed. the -year contribution of microorganisms to medicine and agriculture has been overwhelming. however, antibiotic resistance in microbes has created a dangerous situation and the need for new antibiotics is clear. unfortunately, most of the large pharmaceutical companies have abandoned the search for new antimicrobial compounds. owing to the economics, they have concluded that drugs directed against chronic diseases offer a better revenue stream than do antimicrobial agents, as for the latter the length of treatment is short and government restriction is likely. some small pharmaceutical and biotechnology companies are developing antibiotics, but most depend on venture capital rather than sales income, and with the present regulations, they face huge barriers to enter the market. these barriers were raised with the best intentions of ensuring public safety, but will have the opposite effect if they terminate antibiotic development while resistance continues to increase. however, there are some bright possibilities. one of the most promising is the utilization of uncultivated microorganisms. considering that % of the bacteria and % of the fungi have not been cultivated in the laboratory, putting efforts into finding means to grow such microorganisms are proceeding and succeeding. furthermore, researchers are now extracting bacterial dna from soil and marine habitats, cloning large fragments into, for example, bacterial artificial chromosomes, expressing in a host bacterium and screening the library for new antibiotics. this metagenomic effort is allowing access to a vast untapped reservoir of genetic and metabolic diversity, , which could result in the discovery of new and useful natural products. in addition to these two relatively new techniques, the chemical and biological modification of old antibiotics could still supply new and powerful drugs. these comments also apply to non-antibiotics such as antitumor agents and other microbial products. bioactive microbial metabolites. a personal view natural products in drug discovery and development natural products and design: interrelated approaches in drug discovery design of angiotensin converting enzyme inhibitors antibiotics: where did we go wrong? natural and synthetic substances related to human health the future of cephalosporins business infectious history oceans: medicine chests of the future? inhibitors of hiv- replication that inhibit hiv integrase medicinals for the millennia. the historical record natural products based anti-hiv drug discovery and development facilitated by the nci developmental therapeutics program the end of an era? where have all the antibiotic patents gone? barriers on the road to new antibiotics cycling may be bad for your health the microbial rosetta stone database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents sherris medical microbiology th edn health of nations: combating infectious diseases the public health threat of emerging viral disease the future challenges facing the development of new antimicrobial drugs jr problems with antimicrobial resistance in gram-positive cocci recent progress in the field of antibacterial pristinamycins recent developments in tetracycline antibiotics case studies in current drug development: 'glycylcyclines' development of daptomycin for gram-positive infections lipopeptides, focusing on daptomycin, for the treatment of gram-positive infections daptomycin-a novel antibiotic against gram-positive pathogens overcoming antimicrobial resistance: profile of a new ketolide antibacterial, telithromycin biosynthesis and molecular genetics of clavulanic acid invasive aspergillosis in organ transplant recipients: new issues in epidemiologic characteristics, diagnosis, and management invasive fungal infections: a review of epidemiology and management options antifungal resistance trends towards the year . implications for therapy and new approaches caspofungin acetate: an antifungal agent antifungals targeted to cell wall: focus on b- , -glucan synthase role of micafungin in the antifungal armamentarium posaconazole: a new broad-spectrum antifungal agent signal-transduction cascades as targets for therapeutic intervention by natural products thiolactomycin and related analogues as novel anti-mycobacterial agents targeting kasa and kasb condensing enzymes in mycobacterium tuberculosis the combinatorial chemistry of nature anticancer drug discovery and development throughout the world actinomyces antibioticus, a new soil organism antagonistic to pathogenic and non-pathogenic bacteria anthracyclines: molecular advances and pharmacologic developments in antitumor activity and cardiotoxicity new antibiotics, bleomycin a and b the fam ( -fluorouracil, adriamycin, mitomycin c) and smf (streptozotocin, mitomycin c, -fluorouracil) chemotherapy regimens mitomycin dimers: polyfunctional cross-linkers of dna identification of two genes from streptomyces argillaceus encoding glycosyltransferases involved in transfer of a disaccharide during biosynthesis of the antitumor drug mithramycin glut in pancreatic islets: crucial target molecule in diabetes induced with multiple low doses of streptozotocin in mice improved production of pentostatin and identification of fermentation cometabolites pentostatin in t-non-hodgkin's lymphomas: efficacy and effect on cd + t lymphocytes cleavage behavior of calicheamicin gamma and calicheamicin t approval summary: gemtuzumab ozogamicin in relapsed acute myeloid leukemia study on the preparation and regeneration of protoplast from taxol-producing fungus nodulisporium sylviforme natural products as sources of new drugs over the last years epothilons a and b: antifungal and cytotoxic compounds from sorangium cellulosum (myxobacteria): production, physico-chemical and biological properties epothilones, a new class of microtubulestabilizing agents with a taxol-like mechanism of action activities of the microtubule-stabilizing agents epothilones a and b with purified tubulin and in cells resistant to paclitaxel (taxol) epothilones: mechanism of action and biologic activity curing metastatic testicular cancer medical treatment of advanced testicular cancer refining the optimal chemotherapy regimen for good-risk metastatic nonseminomatous germ-cell tumors: a randomized trial of the genito-urinary group of the french federation of cancer centers (getug t bp) enzyme inhibitors of microbial origin chemistry and biochemistry of microbial a-glucosidase inhibitors gastrointestinal and metabolic effects of amylase inhibition in diabetics enzyme inhibitors of marine microbial origin with pharmaceutical importance effect of an a-amylase inhibitor on body weight reduction in obese women effect of a purified amylase inhibitor on carbohydrate metabolism after a mixed meal in healthy humans treatment of rumen acidosis with alpha-amylase inhibitors european patent inhibitory properties of an a-amylase inhibitor, paim, from streptomyces corchorushii novel amylase inhibitors united states patent lipstatin, an inhibitor of pancreatic lipase, produced by streptomyces toxytricini progress towards the discovery of xanthine oxidase inhibitors agar plate method, a new assay for chitinase inhibitors using a chitin-degrading bacterium fungal enzyme inhibitors as pharmaceuticals, toxins and scourge of pcr history of the discovery of cyclosporin and of its early pharmacological development rapamycin, an mtor inhibitor, disrupts triglyceride metabolism in guinea pigs reversal of learning deficits in a tsc +/À mouse model of tuberous sclerosis everolimus for the prevention of allograft rejection and vasculopathy in cardiac-transplant recipients targeting mtor signaling for cancer therapy therapeutic targets: mtor and related pathways targeted mtor in human gynecologic cancers fk- , a novel immunosuppressant isolated from a streptomyces. . fermentation, isolation, and physico-chemical and biological characteristics correlation of rejection episodes with fk dosage, fk level and steroid following primary orthotopic liver transplant use of tacrolimus, a potent antifibrotic agent, in bleomycin-induced lung fibrosis statins, high-density lipoprotein cholesterol, and regression of coronary atherosclerosis mevinolin, a highly potent competitive inhibitor of hydroxylmethylglutaryl-coenzyme a reductase and a cholesterol-lowering agent a two-component-type cytochrome p- monooxygenase system in a prokaryote that catalyzes hydroxylation of ml- b to pravastatin, a tissue-selective inhibitor of -hydroxy- -methylglutaryl coenzyme a reductase a new hydroxylase system in actinomadura sp. cells converting compactin to pravastatin production and purification of statins from pleurotus ostreatus (basidiomycetes) strains evaluation and development of spinosyns to control ectoparasites on cattle and sheep engineered biosynthesis of novel spinosyns bearing altered deoxyhexose substituents butenyl-spinosyns, a natural example of genetic engineering of antibiotic biosynthetic genes research progress on microbial herbicides weed control for the preservation of biological diversity control of problem vegetation: a key to ecosystem management metabolic products of microorganisms. . phosphinothricin and phosphinothricyl-alanyl-analine studies on a new antibiotic, sf- . i. isolation and physicochemical and biological characterization of sf- substances biosynthetic gene cluster of the herbicide phosphinothricin tripeptide from streptomyces viridochromogenes tu avermectins, antiparasitic lactones produced by streptomyces avermitilis isolated from a soil in japan avr- encodes a chloride channel subunit that mediates inhibitory glutamatergic neurotransmission and ivermectin sensitivity in caenorhabditis elegans efficacy of ivermectin against strongyloides stercoralis in humans doramectin-a potent novel endectocide comparison of ivermectin, doramectin, selamectin, and eleven intermediates in a nematode larval development assay a new family of macrolide antibiotics. structure determination of milbemycins d polyether antibiotics: versatile carboxylic acid ionophores produced by streptomyces the determination of anticoccidial drugs (nicarbazin, lasalocid, monensin, salinomycin and narasin) in animal livers and eggs by liquid chromatography linked with tandem mass spectrometry (lc-ms-ms) the role of enteric antibiotics in livestock production (national association for crop production and animal health antibiotics as growth promotants: mode of action antibiotic resistance back in the news antibiotic development pipeline runs dry the future of anti-infective products in animal health the european ban on growth-promoting antibiotics and emerging consequences for human and animal health bioactive metabolites of em and em , erythromycin derivatives having strong gastrointestinal motor stimulating activity erythromycin as a gastrointestinal prokinetic agent clinical trial: effect of mitemcinal (a motilin agonist) on gastric emptying in patients with gastroparesis-a randomized, multicentre, placebocontrolled study the need for new antibiotics isolating 'uncultivable' microorganisms in pure culture in a simulated natural environment fulfilling the promise of biotechnology new antibiotics from bacterial natural products we thank beatriz ruiz and marco a ortiz for their assistance during the development of this review. key: cord- - p wbd h authors: mark, c. title: screening figures date: - - journal: br dent j doi: . /s - - -y sha: doc_id: cord_uid: p wbd h nan nhs dentistry in england in and . the number of antibiotics dispensed each month by community pharmacists in england relating to nhs dental prescription forms from january to may is given in figure . this shows antibiotic use in may was a clear outlier compared to the previous months being . % higher than in may (n = , and , respectively). interestingly, antibiotic use in april was slightly higher than the previous april but still within the normal range for the period of study. this is despite the significantly poorer access to dentistry (only around , patients were seen at designated urgent dental centres [udcs] across england) compared to may when the capacity of these centres increased and saw over , patients. a range of non-clinical factors are known to be associated with dentists' decision-making about antibiotics prescription for acute conditions. antibiotics may have been used: • as a 'quick fix' to avoid the life-time impact of an unnecessary extraction, in anticipation that agps might soon be permissible in general dental practices • because dentists felt pressured by some patients for antibiotics, irrespective of their efficacy or appropriateness for treating toothache • because of difficulties diagnosing a patient's condition remotely prompting a 'just in case' approach through concerns of life-threatening deterioration without treatment • as some udcs were requiring patients to have tried antibiotics before accepting referral for face-to-face care, highlighting system and process impact on antibiotic prescribing. finally, the nhs may have seen an influx in patients who might otherwise receive care privately, resulting in an increase in nhs dental prescriptions as, anecdotally, not all practices were open for telephone triage during april and may . examination of figures for the remainder of will reveal any enduring impact that covid interventions may have on dental antibiotic prescribing and in identifying optimisation of future dental antibiotic stewardship. v sir, pre-covid, dentists were responsible for about % of all antibiotic prescribing worldwide. at the onset of the pandemic most dental practices were restricted to giving advice, analgesia and antibiotics (aaa). reduced access to dental care and an inability for dentists to provide dental procedures increases dental antibiotic prescribing. a large increase in dental antibiotic use in england during april and may was widely anticipated and so we undertook a rapid analysis comparing antibiotic use across sir, the pre-visit triage, which practices are advised to do, will preclude any proven or probable covid- patients from attending a practice, leaving only the possible, undiagnosed cases as posing a risk of bringing this infection into a practice. our city council produces weekly updates of new cases, which gives a good indication of the level of infection in the population which our practice serves. when this figure is combined with the average number of patients that we have seen each week, since lockdown was eased, and the local population, this enables us to quantify the risk of us seeing an undiagnosed covid- patient in the practice. last week, this indicated that the average risk of seeing such a patient was one every , weeks, or one every . years. there are plenty of generalisations used in that calculation but it is certainly food for thought. povidone iodine covid- : povidone-iodine intranasal prophylaxis in front-line healthcare personnel and inpatients (piippi). clinicaltrials.gov practical use of povidone-iodine antiseptic in the maintenance of oral health and in the prevention and treatment of common oropharyngeal infections stable compositions of uncomplexed iodine and methods of use references . fdi. antibiotic stewardship in dentistry -fdi policy statement: fdi world dental federation factors associated with prescribing of systemic antibacterial drugs to adult patients in urgent primary health care, especially dentistry personal communication re: dr re: request for information key: cord- -hnbgaxft authors: krishnamurthy, a.; palombo, e. title: current therapeutics and prophylactic approaches to treat pneumonia date: - - journal: the microbiology of respiratory system infections doi: . /b - - - - . - sha: doc_id: cord_uid: hnbgaxft bacterial pneumonia caused by streptococcus pneumoniae, haemophilus influenzae, staphylococcus aureus, mycoplasma pneumoniae, and klebsiella pneumoniae represents a frequent cause of mortality worldwide. the increased incidence of pneumococcal diseases in both developed and developing countries is alarmingly high, affecting infants and aged adult populations. the growing rate of antibiotic resistance and biofilm formation on medical device surfaces poses a greater challenge for treating respiratory infections. over recent years, a better understanding of bacterial growth, metabolism, and virulence has offered several potential targets for developing therapeutics against bacterial pneumonia. this chapter will discuss the current and developing trends in treating bacterial pneumonia. the mucosal epithelium of the nasopharynx is a well-recognized primary site of bacterial colonisation including the opaque and transparent phenotypes of the pneumococcus. the pneumococcus can traverse down to the lung upon aspiration and start adhering to the alveolar type ii cells to initiate bacterial infection. the progress to pneumonia can occur more rapidly if there is a preexisting respiratory viral infection or increased bacterial adherence facilitated by viruses or cytokines. the different stages of pneumococcal pneumonia are well known. the first stage is characterized by a bulge or engorgement due to the bacterial presence and serous exudate in the alveoli which provides nutrients to the bacteria and facilitates further infection in the lung. the next stage is the intense inflammatory reaction involving leakage of erythrocytes into the alveoli (red hepatisation), followed by the migration of leukocytes into the consolidated area (gray hepatisation), and surface phagocytosis by the leukocytes. due to the intact immune system of the host, normally the type-specific antibodies and the polymorphonuclear leukocytes phagocytise the pneumococci and the lung returns to its normal state. however, in patients with a compromised immune system having certain complement deficiencies or hypogammaglobulinemia (absence of type-specific antibodies), bacteremia can occur and the pneumococcus with its virulence factors (mostly cell wall components such as peptidoglycan, techoic acid, and proteins such as pneumolysin) induce inflammation causing subsequent tissue damage. since the early s, the lrti caused by s. pneumoniae in certain developing countries, such as ghana and south africa, have been reported at > - % of all cases in children less than years of age, and per population of adults per year, and has remained at equivalent rates even a decade later. [ ] [ ] [ ] the incidence of pneumonia in children less than years of age was higher in regions such as south-east asia, africa and western pacific countries in comparison with those in the developed countries like the americas and europe. more recently, the incidence of childhood pneumonia has been estimated to be > million globally, of which ∼ % progressed to severe disease with % vaccination mortality in children < years of age. the risk factors for childhood pneumonia, especially in the developing countries, include nutrition deficiencies, lack of breastfeeding, indoor air pollution due to passive smoking, hiv infection, and substandard housing and living conditions. the etiological agents causing pneumonia include both bacteria and respiratory viruses. certain vaccine studies have indicated the predominant bacterial agent causing pneumonia to be s. pneumoniae resulting in almost - % severe cases and - % mortality, followed by h. influenzae accounting for % of severe cases and % of deaths. influenza virus remains the dominant viral etiological agent responsible for % of the severe cases and % of deaths. , s. pneumoniae is also well-recognized to cause community-acquired pneumonia (cap) in children with lower fatality rates of . %. in addition to these etiological agents, bacteria such as staphylococcus aureus, klebsiella pneumoniae, and respiratory viruses such as rsv, rhinovirus, human metapneumovirus, human bocavirus and parainfluenza viruses are the other commonly identified agents that contribute to the burden of childhood pneumonia. , community-acquired pneumonia (cap) is an increasing health problem and the third most common reason for hospitalization for adults, especially the elderly aged > years. the prevalence of cap has been reported as - cases per population with an increase from % in - year olds to % in - year olds, and % in > year olds. , several predisposing factors such as impaired immunity and lung function, dysfunctional nasal mucociliary clearance, lung and heart diseases, smoking have been identified as independent predictors for cap in adults and the elderly. certain studies have reported s. pneumoniae, legionella species, h. influenzae, moraxella catarrhalis, and s. aureus as the predominant pathogens in cap. although the role of respiratory viruses has been well-recognized in cap in children and infants, it is not well understood in adults and the elderly. it is still unclear whether a virus by itself can cause pneumonia or whether the virus can act in conjunction with other respiratory pathogens. one study has reported that respiratory viruses such as influenza virus, rsv, adenovirus, and rhinovirus were commonly isolated as part of a co-infection, especially with s. pneumoniae. thus, viral agents in adults with cap most often seem to be part of a mixed infection, usually with s. pneumoniae as the co-pathogen. the world health organisation (who) recommends routine childhood immunization programs that include vaccines that offer protection from various respiratory disease such as pneumonia, influenza (flu), measles, and pertrussis. the haemophilus influenzae type b (hib) vaccine and the pneumococcal conjugate vaccines are increasingly available in both developed as well as developing countries, especially the -and -valent pneumococcal conjugate vaccines which have shown effectiveness in reducing the incidence and severity of pneumonia and other lower respiratory infections in children. currently, there are three vaccines in the childhood routine immunization schedule; measles, hib, and the pneumococcal conjugate vaccine that is well-recognized to reduce childhood mortality from and related to pneumonia. vaccination remains the primary preventative strategy for pneumonia, including cap in the elderly. the hib vaccine has a proven efficiency of > % against invasive meningitis and bacteremia and noninvasive pneumonia caused by h. influenzae type b. , this impressive efficiency has resulted in the introduction and addition of the hib vaccine worldwide into national immunization programs, and has resulted in a significant reduction in the vaccination gap between developed and developing countries. a recent review from several randomized controlled trials (from s to ) from different developing countries indicated a significant reduction of severe pneumonia by %, pneumonia-associated mortality by %, and reduction of radiological confirmed cases of pneumonia by %. based on the preventative approach of pneumonia and pneumonia-related mortality with effective vaccination, a certain modeling-based study has estimated that if implemented at present annual rates of increase in developing countries, the vaccine could save up to % of pneumonia deaths by at a cost saving of us$ . billion. high coverage of the hib vaccine immunization in children less than years of age could reduce childhood pneumonia resulting in decreased incidence of severe pneumonia. the -valent polysaccharide vaccine (ppv ) and the -valent protein-conjugated polysaccharide vaccine (pcv ) are the two vaccines that offer protection against pneumococcal disease, and have replaced the -valent conjugate vaccine (pcv ). as the polysaccharide vaccine (ppv) is t-cell independent, it does not boost immunological memory and the immunity offered may not last for a long time. for this reason, this vaccine is not offered to infants aged < years of age, but is provided to children aged > years and to elderly people who are at risk (> years of age) for developing pneumonia. in contrast, the conjugate vaccines stimulate a t-cell dependent response and are more effective in infants and children < years of age. the different pneumococcal vaccines, serotypes covered, and the conjugate protein used are mentioned in table . pcv and pcv are offered for children aged from weeks to years of age, whereas pcv is given to children aged between weeks and years, and to adults aged > years of age. since the introduction of the pcv vaccine in , its efficacy against invasive meningitis, pneumonia, and otitis media is well documented. [ ] [ ] [ ] the subsequent vaccines, pcv and pcv , have also demonstrated comparable immunogenicity to pcv in several clinical trials. [ ] [ ] [ ] although ppv covers serotypes of s. pneumoniae, and is recommended for adults aged > years of age, its effectiveness in reducing invasive pneumococcal disease remains uncertain. , as pcv has equal or greater immunogenicity than ppv , and has greater immunological memory, the use of pcv is now recommended for adults in addition to ppv , particularly the elderly and high risk individuals. in addition to this, newer pcv's have been shown to reduce the number of healthy carriers of the pathogen in the community because of "herd immunity" where unvaccinated people are protected from the pathogen. since the introduction of pcv's as a part of "herd immunity", the incidence of invasive pneumococcal diseases was shown to decline by almost % among vaccinated children < years of age, and by % in adults aged - years, and by % in the elderly aged > years of age, who were not previously vaccinated. the classification of antibiotics is based on the cellular component that they affect, as well as on whether they can induce cell death (bactericidal) or inhibit cell growth (bacteriostatic). antibiotic-mediated cell death is a complex process involving physical interaction between a drug molecule and its bacterial-specific target, and/or modulation of the affected bacterium at the biochemical, molecular, and ultrastructural levels. fig. . summarizes the different drug targets and mechanism of actions of various antimicrobials such as; inhibition of cell wall synthesis, inhibition of protein synthesis, injury to cytoplasmic membrane, and inhibition of nucleic acid synthesis and replication. dna synthesis and cell division are well-recognized processes that involve modulation of chromosomal supercoiling through topoisomerase-catalyzed strand breakage and rejoining reactions. antimicrobials such as quinolone target enzymes like dna gyrase (topoisomerase ii) and topoisomerase iv (topoiv) that are required for bacterial dna synthesis and replication, and prevent dna strand rejoining. peptidoglycan, a covalently cross-linked polymer matrix composed of peptide-linked β-( - )-n-acetyl hexosamine, is the main component of bacterial cell walls that contributes towards the structural integrity of the bacterial cell. the peptidoglycan layer is maintained through the activity of transglycosylase and transpeptidase enzymes, which add disaccharide pentapeptides to extend the glycan strands of existing peptidoglycan molecules and cross-link adjacent peptide strands of immature peptidoglycan units, respectively. βlactams and glycopeptides are among the classes of antibiotics that interfere with cell wall biosynthesis resulting in changes to bacterial cell shape and size and induction of cellular stress responses that leads to bacterial cell lysis. the process of protein synthesis via mrna translation involves the ribosome that is composed of two major components, the s and s subunits. drugs that inhibit protein synthesis are divided into two subclasses: the s inhibitors and s inhibitors. the s ribosome inhibitors include the macrolide, lincosamide, streptogramin, amphenicol, and oxazolidinone classes of antibiotics. the s inhibitors include the tetracycline and aminocyclitol families of antibiotics. the mortality caused due to pneumonia can be avoided through cost-effective and life-saving treatment from antibiotics for bacterial pneumonia, thereby significantly increasing the patient's chances of survival. the pneumonia management strategy with the use of appropriate antibiotics and supportive care including oxygen systems remains an effective cornerstone in the treatment and management of children suffering from pneumonia. the who integrated management of childhood illness program has consistently reported a reduction of childhood mortality rates by approximately %, while certain community based management strategies have reported a decrease in % mortality due to the usage of oral antibiotics such as amoxicillin. [ ] [ ] [ ] the four types of antibiotics recommended for children < years of age for the treatment of pneumonia are; cotrimoxazole, amoxicillin, cephalosporins, and macrolides, with oral amoxicillin ( mg/kg/dose) used for days (nonsevere pneumonia) and days for children with severe pneumonia. during severe pneumonia, the first line of treatment is often parenteral ampicillin (penicillin) and gentamicin, followed by ceftriaxone if the first line of treatment is not effective. various randomized controlled studies from the cochrane database of systemic reviews have shown a multitude of available treatments for pneumonia in children with ( ) cefpodoxime proving to be more effective than amoxicillin, ( ) amoxicillin more effective than chloramphenicol, ( ) amoxicillin being an effective alternative to cotrimoxazole for cap patients, ( ) coamoxyclavulanic acid and cefpodoxime as alternative second-line drugs of choice, and ( ) penicillin/ampicillin plus gentamicin more effective than chloramphenicol for children hospitalized with severe cap. a -year pediatric study of the susceptibility of s. pneumoniae isolates, including serotype a, using antibiotics such as second-and third-generation cephalosporins showed significant efficacy against - % of the isolates, with clindamycin susceptibility of - %, levofloxacin %, and ceftriaxone > %. the american thoracic society and the european respiratory society recommend that hospitalized patients with cap are preferably treated with a respiratory fluoroquinolone or combination therapy with a β-lactam and a macrolide. the success rates of incorporating the fluoroquninolone or combination with a macrolide based on the clinical, bacteriological, or radiological examinations ranged from - %. vancomycin or clindamycin (based on local susceptibility data) should also be provided in addition to β-lactam therapy if clinical, laboratory, or radiological characteristics are consistent with infection caused by s. aureus. although nonsevere and severe cap have been managed by many antimicrobials as a result of various studies from developing countries that compared different types of antibiotics, there is need for more studies and larger clinical trials for better management of pneumonia in developed countries. another major health concern is the continual rise in antibiotic resistance with approximately % of the isolates being resistant to macrolides including erythromycin, azithromycin, and clarithromycin. the introduction and inclusion of the hib vaccine over the past years has resulted in almost complete elimination of h. influenzae in children, therefore it is not considered as a pathogen in cap. nontypeable h. influenzae is also not considered as a pathogen in pediatric pneumonia unless detected in lung disease or copd. when detected as a true pathogen in cap, oral amoxicillin is considered effective against β-lactamase negative strains, and for β-lactamase producing strains, amoxicillinclavulanate, cefuroxime, cefdinir, cefixime, cefpodoxime are all considered effective therapies, while children allergic to oral β-lactam agents are only given fluoroquinolones. although an infrequent cause of cap, group a streptococcus may cause severe necrotizing pneumonia. penicillin g at the dosage of , - , u/kg/day in - divided doses is used to treat patients suffering from cap due to group a streptococcus. as macrolide resistance is greater in streptococcal infections, along with lower tolerability by tissues, erythromycin and other macrolides are not administered. s. aureus capable of causing pneumonia are usually methicillin-sensitive and are treated with either a β-lactamase stable penicillin (oxacillin or nafcillin) or a first-generation cephalosporin, like cefazolin. community-associated methicillin-resistant s. aureus (mrsa) represents > - % of the clinical isolates in some region of the united states, but are shown to be susceptible to vancomycin, clindamycin, and linezolid. however, children intolerant to vancomycin and clindamycin could be treated with linezolid. however, severe adverse effects, including suppression of platelets and neutrophils, nerve injury, mean that this drug should be used with caution. in situations where mycoplasma pneumoniae and chlamydophila pneumoniae are of significant consideration upon diagnostic evaluation, empiric combination therapy with a macrolide and a β-lactam antibiotic is considered. children with moderate to severe cap consistent with influenza virus infection during widespread local circulation of influenza viruses should be administered with influenza antiviral therapy. the susceptible strains of influenza a virus are commonly treated with adamantanes and neuraminidase inhibitors. as the occurrence of genetic variations is highly substantial among influenza strains, resistance to either class of antiviral agents may develop quickly. however, the dosages of antiviral agents currently recommended for seasonal influenza are developed for fully susceptible strains and evaluated in clinical trials mandating the requirement of treatment within days of the onset of symptoms. early antiviral treatment has been shown to provide maximal benefit, and treatment should not be delayed until confirmation of positive influenza test results. negative results of influenza diagnostic tests, especially the rapid antigen tests, do not conclusively exclude influenza disease. therefore, treatment after h of symptomatic infection may still provide some clinical benefit to those with more severe disease. the efficacy of ribavirin for the treatment of rsv cap in infants is debatable, as certain in vitro studies have shown activity of ribavirin against rsv, but its usage for rsv infection is not routinely recommended in the management of lower respiratory tract disease because of the high cost, aerosol administration, and possible toxic effects among healthcare providers. palivizumab (synagis), a humanised murine monoclonal antibody is another effective prophylaxis for rsv infection that is administered intramuscularly. although parainfluenza virus, adenovirus, metapneumovirus, rhinovirus, coronavirus, and bocavirus are associated with pediatric cap, there are no prospective, controlled studies for antiviral therapy against these viruses. since the introduction of penicillin in s, it has been the first choice for treating pneumococcal pneumonia. during the early s, infants and children were successfully treated with amoxicillin ( - mg/kg/day divided into equal doses) because of the susceptible nature of the strains at that time. resistance to the commonly used antibiotics poses a major problem and concern for health practitioners while choosing an empirical therapy against bacterial pneumonia, and there are large geographical variations indicating different resistance patterns. in the s with the widespread pneumococcal resistance to penicillin, the dosage was increased to ∼ mg/kg/day given twice daily for treating children with acute otitis media. a recent review has highlighted advances in the understanding of the various mechanisms by which bacteria acquire resistance to antibiotics, how they prevent access to different drug targets, and modulate or inactivate antibiotics. the introduction of pneumococcal conjugate vaccine and the changes in antimicrobial usage have both significantly altered the resistance patterns of s. pneumoniae. the decreased degree of penicillin resistance further prompted a decrease in amoxicillin dosage compared to that administered in the prevaccine era. over the last decade, a certain multicentre clinical trial study has reported a significant decrease in the susceptibility rates of the commonly used antibiotics such as amoxicillin/clavulante, penicillin, and ceftriaxone from . % to . %, . % to . %, and . % to . %, respectively. the susceptibility rates of macrolides such as erythromycin and clindamycin were also reported to be decreased from . % to . % and from . % to . %, respectively. recently, increasing resistance against macrolides has been reported in several european countries, including the united kingdom. a -year surveillance study involving clinical isolates reported around % and % increase in the rates of ampicillin and trimethoprim/sulfamethoxazole resistance against h. influenzae, respectively, while antibiotics such as ceftaroline, ceftriaxone, amoxicillin/clavulante, and levofloxacin showed - % susceptibility. this study also showed increasing resistance of penicillin ( . %) towards m. catarrhalis, because of the prevalence of β-lactamase that is known to reduce the susceptibility to penicillins. the resistance to macrolides against m. pneumoniae in children and adults with cap has been increasingly emerging in countries like japan, france, denmark, united states, and china, with rates as high as % in japan, % in china, and - % in the europe and the united states. , community-acquired mrsa, although primarily associated with skin and soft tissue infections, are now being recognized to cause invasive infections including cap, with almost % mortality rates reported in the united states and europe. , there are certain ways by which resistance to antimicrobials can be minimized, such as: limiting the exposure to any antibiotic, whenever possible; limiting the spectrum of usage of antimicrobials to that specifically required to treat the identified pathogen; using the proper dosage of antimicrobial to achieve a minimal effective concentration at the site of infection; treatment for the shortest effective duration that will minimize the exposure of both pathogens and normal microbiota to antimicrobials and further minimize the selection for resistance. the increasing incidence of antimicrobial resistance remains one of greatest challenges against emerging bacterial infections and has resulted in some bacteria being essentially untreatable with the current available treatment options. as a result, newer antimicrobials with novel modes of action against multidrug resistant strains are being developed. a recent review has highlighted how combinations of drugs can offer synergistic and antagonistic drug interactions, and how these drug interactions can provide opportunities for discovery of newer drugs. in recent years, the availability of new antimicrobials for human consumption has been lower than in the recent past, with no new classes of antimicrobials developed since the introduction of nalidixic acid ( ) and linezolid ( ) . the availability of antimicrobials in recent years has mostly been the result of modification of existing molecules. one of the reasons for this is that the development of any new antimicrobial agent is very expensive and time consuming, with research and development of infective drugs taking around - years, and costing around us$ million, with further additional costs for bringing the new drug into the market. there is a strong need for newer unexploited targets and strategies for the next generation of antimicrobial drugs against drug resistant and emerging pathogens. some of the new antimicrobial agents that are in the clinical development stage are listed in table . . some of the new antibiotics that have shown promising results in the treatment of pneumonia and cap are as follows: ceftaroline: a fifth generation cephalosporin known to bind to penicillin-binding proteins and preventing synthesis of bacterial cell walls. it is a novel broad-spectrum antibiotic effective against mrsa, penicillin and cephalosporin resistant s. pneumoniae, vancomycin-intermediate s. aureus (visa), and vancomycin-resistant s. aureus (vrsa). it is also active against many gram-negative pathogens but inactive against extended-spectrum β-lactamase (esbl) producing bacteria. it has been approved for the treatment of cap. different randomized, double-blind, multicentre trials have demonstrated the efficacy (> % clinical cure) and safety of ceftaroline (intravenous, mg twice daily) for the treatment of cap. ceftobiprole: another newer cephalosporin that has a broad-spectrum activity against mrsa, penicillin-resistant s. pneumoniae, p. aeruginosa and enterococci. a randomized trial consisting of hospitalized adults with severe cap who were administered ceftobiprole (intravenous, mg over min every h) showed no significant differences between the treatment groups but found adverse events including nausea and vomiting in % of the patients. telavancin: a semi-synthetic lipoglycopeptide derivative of vancomycin known to disrupt peptidoglycan synthesis and alter cell membrane function. it has been in use for treating complicated skin infections caused by s. aureus, and hospital-acquired bacterial pneumonia, including ventilator-associated bacterial pneumonia caused by susceptible isolates of s. aureus. telithromycin: the first ketolide to enter clinical use for the treatment of cap, chronic bronchitis and acute sinusitis. telithromycin is a protein synthesis inhibitor blocking the progression of the growing polypeptide chain by binding to the s subunit of the bacterial ribosome. it exhibits times higher affinity to the subunit s subunit than erythromycin. in addition, telithromycin strongly binds simultaneously to two domains of s subunit of the s ribosomal subunit; older macrolides bind to only to one domain and weakly to the second domain. an in vitro study showed activity of telithromycin against s. pneumoniae and, compared with clarithromycin and azithromycin, was found to maintain its activity against macrolide-resistant strains of s. pneumoniae and s. pyogenes. it is formulated as mg tablet for oral administration with good absorption and bioavailability. however, the fda withdrew its approval in the treatment of cap in due to its safety concerns involving hepatotoxicity, myasthenia gravis exacerbation, and visual disturbances. cethromycin: a -keto, , carbamate derivative of erythromycin a with an o- linked aromatic ring. it binds strongly to the s ribosomal subunit and inhibits bacterial protein synthesis. cethromycin displays in vitro activity against streptococci, including strains of s. pneumoniae that are resistant to penicillins and macrolides. its activity was greater than telithromycin against macrolide-resistant streptococci and is more potent than macrolides and fluoroquinolones against penicillin-resistant streptococci. it also displays comparable in vitro activity to azithromycin against respiratory gram-negative organisms including β-lactamase-producing h. influenzae and m. catarrhalis. it was shown to be more potent than erythromycin and clarithromycin but less potent than fluoroquinolones against β-lactamase-producing h. influenzae. , it showed similar potency against β-lactamase-producing m. catarrhalis. solithromycin: a new macrolide, and the first fluoroketolide in clinical development, with proven activity against macrolide-resistant bacteria. solithromycin is being developed in both intravenous and oral formulations for the treatment of cap, which should allow both oral therapy and i.v.-to-oral stepdown therapy in appropriate patients. a recent multicentre, double-blind, randomized phase ii study consisting of patients with moderate to severe cap administered with oral solithromycin ( -mg loading dose and mg maintenance dose/ days) showed efficacy comparable to that of levofloxacin in the treatment of cap, with a favorable safety and tolerability profile. nemonoxacin: a novel nonfluorinated quinolone with proven in vitro and in vivo activity against cap pathogens including multidrug resistant s. pneumoniae. a randomized multicentre trial consisting of cap patients treated with an oral administration of nemonoxacin ( and mg/ days) showed a remarkable - % clinical and bacteriological success rate, which was comparable tolevofloxacin therapy. a recent comprehensive review has well documented all the data available on the pharmacodynamics, the pharmacokinetics, and the clinical treatment studies of this antimicrobial agent. zabofloxacin: is being developed as a new fluoroquinolone antibiotic that is a potent and selective inhibitor of the essential bacterial type ii topoisomerases and topoisomerase iv and is indicated for community-acquired respiratory infections due to gram-positive bacteria. two dosing regimens of zabofloxacin (zabofloxacin hydrochloride mg capsule andzabofloxacin aspartate mg tablet) were well-tolerated with no adverse effects. jnj-q and kpi- : two novel fluoroquinolones that are being developed for the treatment of bacterial pathogens responsible for respiratory infections including cap, and other skin infections. both agents have demonstrated increased potency when compared with the marketed fluoroquinolones, thus encouraging further clinical development. , bc- : a recent semisynthetic pleuromutilin antibiotic with excellent antibacterial activity against skin pathogens such as s. aureus, β-haemolytic streptococci, viridans streptococci, and enterococcus faecium as well as against respiratory pathogens. its activity against respiratory pathogens has also been confirmed in various murine models of infection using s. pneumoniae, h. influenzae, s. aureus, and mrsa (nosocomial and community-associated), with better drug penetration, strongly supporting its potential use in the treatment of bacterial respiratory tract infections. although there are a wide variety of clinically efficacious antibiotics in use today, the development of bacterial resistance has rendered them less effective, with most being bacteriostatic, and acting by either protein or cell wall synthesis inhibition. further research is needed in the design of novel antibacterial agents with new targets. one approach could be to design antibiotics that can be used against novel drug targets such as the bacterial enzymes β-ketoacyl-acyl-carrier-protein synthase i/ii which are required for fatty acid biosynthesis. platensimycin is one such drug undergoing preclinical trials and is known to block these enzymes that are involved in the biosynthesis of essential fatty acids by gram-positive bacteria. it has potent antibacterial activity against gram-positive bacteria including multidrug resistant staphylococci and enterococci. another approach worth investigating could be to combine β-lactam antibiotics with naturally occurring β-lactamase enzymes in the gastrointestinal microbiota. these enzymes are shown to hydrolyse various antibiotics including penicillin, ampicillin, and piperacillin. p a protein ( kda) is one such example of having both structural and functional similarities to the β-lactamase enzyme. the emergence of resistant microbes can be significantly reduced by taking advantage of combining this naturally occurring hydrolysis of the antibacterial drug with currently available β-lactam drugs. a phase ii trial for the treatment of serious respiratory infections which incorporated treatment with p a (β-lactamase product) and ampicillin showed only a % change in gut microbiota compared to % change in patients treated with ampicillin alone. apart from antimicrobials, strategies involving immunomodulation of inflammatory responses (targeting pattern recognition receptor signaling, corticosteroids, complement inhibitors etc.), improving pulmonary barrier function (using adrenomedullin, angiopoietin etc.) during pneumonia and its associated complications could add a new dimension in providing better therapeutics for patients. despite great advances in management and preventative approaches, pneumonia still remains a major burden of mortality and morbidity in young children and the elderly, especially in the developing and under-developed countries. prevention by means of vaccination is critical for reducing pneumonia mortality in children < years of age, and an effective antibiotic therapy is important for the elderly. the widespread emergence of antimicrobial resistance is a well-recognized cause of the ineffectiveness of the large number of the currently used antimicrobials. although numerous efforts have been made to combat this, newer targets need to be identified for the generation of the next level of effective antimicrobials. in addition, a complete understanding of the various aspects of drug resistance in microbes is essential to assist us in designing better targets and help us discover new antibacterial drugs. in the near future, the next challenge will be to identify newer agents for the treatment of multidrug resistant pathogens which are emerging at a rapid rate. the constant and unpredictable nature of pneumococcal pathogens can outpace technological and drug development strategies. therefore, it is critical for researchers, pharmaceutical companies, and governments and other funding bodies to continue making progress in developing new strategies and antimicrobials towards respiratory infections, including pneumonia. the continuing challenge of lower respiratory 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in streptococcus pneumoniae cells in vitro activity of abt- , a new ketolide, against recent clinical isolates of streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis in vitro activity of abt- versus macrolides and quinolones against resistant respiratory tract pathogens randomized, double-blind, multicentre phase study comparing the efficacy and safety of oral solithromycin (cem- ) to those of oral levofloxacin in the treatment of patients with community-acquired bacterial pneumonia efficacy and safety of nemonoxacin versus levofloxacin for community-acquired pneumonia review of nemonoxacin with special focus on clinical development comparison of pharmacokinetics between new quinolone antibiotics: the zabofloxacin hydrochloride capsule and the zabofloxacin aspartate tablet activity of jnj-q , a new fluoroquinolone, tested against contemporary pathogens isolated from patients with community-acquired bacterial pneumonia advances in antibiotic therapy for community-acquired pneumonia antimicrobial activity of the novel pleuromutilin antibiotic bc- against organisms responsible for community-acquired respiratory tract infections (cartis) platensimycin, a new antibiotic and "superbug challenger" from nature p a recombinant beta-lactamase prevents emergence of antimicrobial resistance in gut microflora of healthy subjects during intravenous administration of ampicillin therapeutic strategies in pneumonia: going beyond antibiotics key: cord- - q xkld authors: shengchen, d.; gu, x.; fan, g.; sun, r.; wang, y.; yu, d.; li, h.; zhou, f.; xiong, z.; lu, b.; zhu, g.; cao, b. title: evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial date: - - journal: clin microbiol infect doi: . /j.cmi. . . sha: doc_id: cord_uid: q xkld objectives: the primary objective was to evaluate whether a molecular point-of-care test (poct) for viral and atypical pathogens added to routine real-time pcr could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (lrti) compared with routine real-time pcr. methods: in this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with lrti. patients were randomized to an intervention group (poct filmarray panel for viruses, atypical pathogens and bacteria plus routine real-time pcr) or a control group (routine real-time pcr for ten pathogens). the primary outcome was duration of intravenous antibiotics during hospitalization. the secondary outcomes included length of stay, cost of hospitalization and de-escalation within hours and between hours and days. intention-to-treat analysis was used. results: between october and july , we enrolled eligible patients ( in the intervention group and in the control group). duration of intravenous antibiotics in the intervention group was shorter than in the control ( . days (interquartile range (iqr) . – . ) versus . days (iqr . – . ); p < . ). length of hospital stay in the intervention group was significantly shorter ( . days (iqr . – . ) versus . days (iqr . – . ; p < . ) and the cost of hospitalization in the intervention group was significantly lower ($ . (iqr . – . ) versus $ . (iqr . – . ); p . ) than control group. more patients in the intervention group achieved de-escalation within hours ( . %, / versus . %, / ; p . ) and between hours and days ( . %, / versus . %, / ; p . ). conclusions: use of molecular poct testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized lrti patients. clinical trial registration: clinicaltrials.gov identifier: nct . lower respiratory tract infection (lrti) is the leading infectious disease in the world [ ] . it is also the fourth commonest cause of death globally, accounting for about . million deaths worldwide in [ ] . viral infection is one of the most important causes of lrti [ ] . because of large overlap in symptoms and clinical presentation between bacterial and viral lrti, antibiotics are inappropriately prescribed to patients with viral infection. this may result in potential risks of antimicrobial resistance with a corresponding financial burden and environmental pollution [ ] . furthermore, inappropriate prescription of antibiotics is even more critical in china, which ranks as the world's most frequent user of antibiotics [ , ] . overuse of intravenous antibiotics in patients hospitalized with lrti constitutes an important part of the inappropriate prescription of antibiotics [ ] . in one retrospective study in a teaching hospital in beijing [ ] , the median duration of intravenous antibiotics was days (interquartile range e days) among hospitalized individuals with mild to moderate communityacquired pneumonia (cap). diagnostic uncertainty regarding the lack of microbiological evidence may be one of the most important reasons. laboratory-developed pcr testing is highly accurate for the diagnosis of microbial aetiology, with the turnaround time generally being e days [ e ]. however, experienced specialists are required for this test and the instruments have to be installed in a central laboratory. filmarray respiratory panel (biofire; salt lake city, ut, usa) is a new molecular point-of-care test (poct) platform, which can simultaneously detect viruses and atypical pathogens and provide results in about hour [ , ] . the sensitivity and specificity of this new molecular poct for detecting pathogens were high, with the sensitivity and specificity ranging from . % to . % and . % to . %, respectively [ , ] . a recently published randomized controlled trial showed that use of the filmarray respiratory panel was associated with reduction in proportion of antibiotic use among patients with acute exacerbation of chronic obstructive pulmonary disease (aecopd) and asthma [ ] . we speculated that molecular poct for the detection of viruses might reduce the duration of antibiotic use in adult lrti patients [ , ] . considering predominant overuse of intravenous antibiotics in china, the aim of this study was to evaluate whether combination of poct and routine real-time pcr for pathogen detection could reduce duration and improve deescalation of intravenous antibiotics in individuals with lrti compared with routine real-time pcr only. this was a single-centre, open-label, parallel randomized controlled study that took place between october and july in the chinaejapan friendship hospital (cjfh), beijing, china (clinicaltrials.gov identifier: nct ). cjfh is a large teaching hospital with beds. patients were recruited from the general ward of the department of pulmonary and critical care medicine, department of traditional chinese medicine lung disease and department of infectious disease in cjfh. hospitalized patients aged ! years who were preliminarily diagnosed as radiographically confirmed cap, aecopd or acute exacerbation of bronchiectasis were recruited on the day of hospitalization. patients were excluded if they were < years old, pregnant, had hospitalacquired pneumonia, or lung tuberculosis. we also excluded patients with human immunodeficiency virus infection, haematological cancer or solid tumour treated with chemotherapy or radiotherapy in the previous months, organ or bone marrow transplantation, splenectomy, or autoimmune diseases including systemic lupus erythematosus, rheumatoid arthritis, rheumatic polymyalgia and interstitial lung disease treated with immunosuppressive therapy for > weeks. in addition, patients with any other condition that may have increased serum procalcitonin levels, including severe burns, major surgical procedures, major trauma, long-term or severe cardiogenic shock, invasive fungal infection, or an acute attack of plasmodium falciparum, were also excluded. this study was conducted in accordance with the declaration of helsinki. the study was approved by the ethics committee of cjfh ( - ). written informed consent was obtained from each participant after meeting inclusion criteria and before randomization. random allocation sequence was generated using spss . software (statistical product and service solutions, ibm co. ltd, armonk, ny, usa) with a fixed random seed. simple randomization was conducted subsequently by sealing the group allocation cards into envelopes according to the sequence number. each envelope was opened only when patients met inclusion criteria and signed informed consent, with allocation of patients to intervention or control group accordingly. study participants, research staff and clinical care providers were not blinded to the group allocations. allocation of patients was blinded to data analysts. demographics and clinical characteristics were collected on enrolment. before the study commenced, research personnel were trained on how to take nasopharyngeal swabs and how to operate the filmarray respiratory panel instrument. routine diagnosis, treatment and microorganism detection of cap, aecopd and acute exacerbation of bronchiectasis followed chinese guidelines and consensus for these diseases [ e ]. in the intervention group, research staff took nasopharyngeal swabs from patients according to standard protocols within hours of admission. the samples were analysed immediately using the filmarray respiratory panel. the panel can detect viruses (influenza a (h and h ) virus, influenza b virus, respiratory syncytial virus, rhinovirus or enterovirus, human metapneumovirus, parainfluenza virus types , coronaviruses (oc , e, hku and nl ) and adenovirus), two atypical pathogens (chlamydia pneumoniae and mycoplasma pneumoniae) and one bacterium (bordetella pertussis). the results were reported and explained to physicians via telephone, sending text messages (with mandatory feedback) or face-to-face communication on the day of admission. in both the intervention and control groups, routine real-time pcr assays for the detection of viral pathogens (including influenza a (h n , h n ) virus, influenza b virus, respiratory syncytial virus, parainfluenza virus, adenovirus, epsteinebarr virus, herpes simplex virus and human cytomegalovirus) were performed in the cjfh microbiology laboratory with sputum or nasopharyngeal swab samples (see supplementary material, table s ). the results were reported and explained to physicians once obtained. other diagnostic tests such as blood gas analysis, c reactive protein, erythrocyte sedimentation rate, procalcitonin and routine microbiological testing were prescribed by physicians in both groups. the responsible attending physicians decided on antibiotic administration (including moxifloxacin, levofloxacin, types i/ii/iii/ iv generation cephalosporin, carbapenem, b-lactamase/b-lactamase-inhibitors, macrolide, penicillins, tetracycline), de-escalation or cessation of use in both groups without intervention of the research staff. management system and technical support framework for antimicrobial stewardship have been established in china. the medical department and pharmacy department regularly assess of the use of antibiotics in cjfh. all data were collected on a standard case report form and then input into an electronic medical database by an authorized assistant. the primary outcome was the duration of intravenous antibiotics during hospitalization. duration of intravenous antibiotics was defined as the total number of calendar days when one or more than one dose of intravenous antibiotics was used. the secondary outcomes included the proportion of patients who received intravenous antibiotics, the proportion of patients with antibiotics deescalation within the first hours and between hours and days, length of hospital stay, cost of intravenous antibiotics and cost of hospitalization. de-escalation of antibiotics was defined as reduction of antibiotic types, change from intravenous antibiotics to oral antibiotics, or from broad-spectrum antibiotics to narrowerspectrum antibiotics (see supplementary material, table s ). cost of hospitalization from the perspective of the hospital before deduction of benefits consist of six parts, including laboratory test (radiation, pathology and blood biochemistry test), medical care (oxygen therapy and doctor visit), surgery, blood storage or processing, drug and other (such as medical material) costs (see supplementary material, table s ). all outcomes were measured until discharge from hospital. participants were followed up in person at day by trained research staff if the length of hospitalization was < days, with six participants in the intervention group and eight participants in the control group lost to follow up. adverse outcomes included admission to intensive care unit (icu), death during hospitalization, readmission within days, and death within days. according to findings of branche et al. [ ] , we assumed that a day reduction of antibiotics use in the intervention group would be clinically significant. we estimated that patients would be required in each group to yield a statistical power of % to detect a -day reduction in antibiotic use in the intervention group at a significance level of p . . we further assumed that %e % of the study participants would be non-adherent or lost to follow up and set a total target recruitment number of patients in each group. data analyses were performed according to intention-to-treat analysis. per-protocol analysis by excluding participants whose diagnosis was ascertained not to be lrti after randomization or who were withdrawn for refusing nasopharyngeal swab was also performed. baseline characteristics were expressed as numbers (proportion), median (interquartile range) or mean ± standard deviation and comparisons were made using the c test, wilcoxon rank-sum test or student's t-test where appropriate. the median and interquartile range of the primary outcome (duration of intravenous antibiotics) and secondary outcomes, including length of hospital stay, cost of intravenous antibiotics and cost of hospitalization, were calculated and the difference between intervention and control group was compared using the wilcoxon rank-sum test. for other secondary outcomes (proportion of intravenous antibiotic use, de-escalation within the first hours and de-escalation between hours and days), any significant differences in the proportions calculated with the c test and unadjusted odds ratios calculated with a logistic regression model were used to look for differences between the intervention and control groups. differences and % cis involved in this study were absolute differences expressed as means or proportions. data analyses were performed using sas version . (sas institute inc.,). between october and july , we assessed patients for eligibility, and of them were eligible to participate in the study (fig. ) . a total of patients were randomly assigned ae, acute exacerbation; aecopd, acute exacerbation of chronic obstructive pulmonary disease; cap, community-acquired pneumonia; curb- , a pneumonia severity score calculator (measured by risk factors in total, with point for each criterion satisfied: confusion defined as an abbreviated mental test score ; blood urea nitrogen ! mmol/l; respiratory rate ! bpm; systolic blood pressure < mmhg or diastolic blood pressure mmhg; age ! years). data are presented as mean ± sd (standard deviation) or as median (interquartile range) for continuous variables and as percent for categorical variables. categorical variables were compared using c tests, and continuous variables were compared using wilcoxon rank-sum test or student's t-test. a the denominator is the number of community-acquired pneumonia. b the denominator is the number of study participants that received the procalcitonin test. to the intervention group and to the control group and included in the intention-to-treat analysis, with patients in the intervention group and patients in the control group who were ascertained not to have lrti after randomization or who were withdrawn for refusing nasopharyngeal swab. baseline characteristics of study participants in intervention and the control group included in intention-to-treat analysis and perprotocol are shown in table and the supplementary material (table s ) , respectively. all patients in the intervention group were tested using the filmarray respiratory panel and . % ( / ) of patients were also tested using routine real-time pcr, whereas . % ( / ) of patients in the control group were tested using routine real-time pcr for viral pathogens (see supplementary material, tables s and s ). the median duration of intravenous antibiotic treatment in the intervention group was significantly shorter than in the control group ( . days ( . e . days) versus . days ( . e . days); difference e . days, % ci e . to e . days; p < . ) ( table ). the proportion of participants who were given intravenous antibiotics was high in both the intervention and control groups, but with no significant differences observed between the two groups ( . %, / versus . %, / ; difference e . %, % ci e . % to . %; p . ). patients in the intervention group stopped having intravenous antibiotics earlier compared with the control group (p < . for log-rank test) (fig. ) . eight patients in the intervention group stopped intravenous antibiotic use on the same day as receiving the poct test result (data not shown). more patients in the intervention group achieved de-escalation within hours ( . %, / versus . %, / ; difference . %, % ci . %e . %; p . ) and between hours and days ( . %, / versus . %, / ; difference . %, % ci . % to . %; p . ) than in the control group. the per-protocol analysis also showed shorter intravenous antibiotic treatment and earlier de-escalation of intravenous antibiotics in the intervention group compared with the control group. the median length of hospital stay in the intervention group was significantly shorter than in the control group ( . days ( . e . days) versus . days ( . e . days)]; difference e . days, % ci e . to e . days; p < . ). the median cost of intravenous antibiotics and hospitalization were also significantly less in the intervention group ($ . ( . e . ) versus $ . ( . e . ); p < . and $ . ( . e . ) versus $ . ( . e . ); p . ). the per-protocol analysis also showed shorter length of hospital stay and lower cost of intravenous antibiotics and hospitalization in the intervention group compared with the control group. the proportions of adverse outcomes, including icu admission, death during hospitalization, readmission within days, and death within days were not found to be significantly different between intervention and control groups (all p ! . ) ( table ). in our study adding poct to routine real-time pcr testing shortened the duration of intravenous antibiotic treatment, reduced the length of stay and cost of hospitalization, and improved early de-escalation of intravenous antibiotics compared with routine real-time pcr assays in hospitalized lrti patients. admission to the icu and fatality rates were similar between groups. the efficacy of this new poct has been evaluated in retrospective studies [ , e ] , but most of them were conducted among paediatric patients [ e ] . a few randomized controlled trials have explored the impact of poct among adults, but with small samples [ , ] . one recent randomized controlled trial with a relatively large sample size evaluated the effect of the filmarray respiratory panel among adult patients with acute respiratory illness [ ] . however, only half of them were diagnosed with lrti, including pneumonia and aecopd. the heterogeneity of the study population, including asthma and upper respiratory infections, limited extrapolation to lrti. the advantage of our study is that only individuals with lrti were enrolled, excluding acute upper respiratory infection and non-infectious respiratory illness. another advantage of our study is that we enrolled patients throughout four consecutive seasons. in this study, we focused on duration of antibiotics, but not on withdrawal of antibiotics once the poct result was available. it is easy to understand that physicians can safely stop antibiotics as soon as they know the positive viral results for patients with upper respiratory infections or asthma, as demonstrated in the study by brendish et al. [ ] . however, for patients with pneumonia and other kinds of lrti, most chinese physicians refer to local clinical guidelines for duration of antibiotics, such as e days for cap [ ] , e days for cap with atypical pathogen [ ] , e days for aecopd [ ] and days for acute bronchiectasis [ ] . although it is difficult to exclude bacterial co-infection, the knowledge of viral aetiology will help physicians to decide whether to stop intravenous antibiotics earlier [ ] . considering that length of hospital stay for lrti patients was directly related to duration of intravenous antibiotics, we finally chose duration of intravenous antibiotics as the primary outcome. with the median cost around $ per hospital-day for patients with lrti, day less of intravenous antibiotics and day less of hospitalization could save billions of dollars in china. there are a number of limitations in our study. first, it was a single-centre study, the results of which need to be verified by future multicentre studies. second, the cost of the filmarray respiratory panel was not considered in the total costs of hospitalization since the filmarray respiratory panel is not commercially available in china. our post-hoc analysis indicated that the cost during hospitalization in the intervention group would be lower than, or at least equal to, that in the control group if the filmarray respiratory panel test cost less than $ . third, because the proportion of patients who received intravenous antibiotic therapy was high and duration of intravenous antibiotics was relatively long in both groups, extrapolation of our results should be carefully interpreted. fourth, the study was conducted in general wards, data are presented as per cent for categorical variables. difference between intervention and control group was compared using c tests and logistic regression model was used to calculate unadjusted odds ratios. a the denominator is the number of study participants that were followed up at day . without including patients from icus. the effect of poct needs further rigorous evaluation in patients who are more severely ill, including icu patients. in conclusion, this study found the addition of molecular poct testing to routine real-time pcr testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in lrti patients without resulting in adverse outcomes. more multicentre studies will be required to verify these findings. we declare that we have no competing interests. the content of the manuscript has not been published, or submitted for publication elsewhere. the abstract has been accepted for presentation at the ats international conference. this work was supported by the national science grant for distinguished young scholars (grant number /h ) and chinese academy of medical science innovation fund for medical sciences ( -i m- - ). biom erieux provided, free-ofcharge, filmarray panel punches and filmarray instruments. they did not participate in the design, conduction and analysis of the study. bc conceived and designed the trial, supervised the trial and allocated staff, had full access to all of the data in the study and takes responsibility for the content of the manuscript. sd and dy participated in the recruitment of patients and data acquisition. the randomization of participants into intervention or control group according to random sequence number was done by rs, and allocation of patients was finished by hl and yw. xg and gf performed the data analysis. sd, bc and xg drafted and revised the manuscript, and zx and bl ensured the quality control and running environment of the filmarray instrument. all authors reviewed the manuscript and contributed to the study report during the whole progress. all authors approved the final version of the manuscript. world health report: the ten most common infections fact sheet : the top causes of death available at: www.who.int/influenza/patient_care/clinical/brave/en 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antimicrobial use fil-marray, an automated nested multiplex pcr system for multi-pathogen detection: development and application to respiratory tract infection comparison of the biofire filmarray respiratory panel, seegene anyplexii rv , and argene for the detection of respiratory viruses serum procalcitonin measurement and viral testing to guide antibiotic use for respiratory infections in hospitalized adults: a randomized controlled trial impact of early detection of respiratory viruses by multiplex pcr assay on clinical outcomes in adult patients diagnosis and treatment of community-acquired pneumonia in adults: clinical practice guidelines by the chinese thoracic society, chinese medical association expert consensus on acute exacerbation of chronic obstructive pulmonary disease in the people's republic of china impact of multiplex polymerase chain reaction testing for respiratory pathogens on healthcare resource utilization for pediatric inpatients impact of a rapid respiratory panel test on patient outcomes the rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs the potential of molecular diagnostics and serum procalcitonin levels to change the antibiotic management of community-acquired pneumonia we thank all the patients and clinical staff in the general wards of the respiratory critical medical department, traditional chinese medicine lung disease department, infectious disease department and laboratory of clinical microbiology and infectious diseases in the chinaejapan friendship hospital, including physicians, nurses and laboratory technicians. supplementary data to this article can be found online at https://doi.org/ . /j.cmi. . . . key: cord- -aoz jbf authors: bartlett, john g. title: why infectious diseases date: - - journal: clin infect dis doi: . /cid/ciu sha: doc_id: cord_uid: aoz jbf infectious diseases is a broad discipline that is almost unique in contemporary medicine with its ability to cure and prevent disease, to identify specific disease causes (microbes), and to deal with diverse, sometimes massive outbreaks. the value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. infectious disease careers have great personal rewards to the practitioner based on these observations. it is unfortunate that we have been so effective in our work, but relatively ineffective in convincing the healthcare system of this value. students of medicine have multiple career options with various attractions and concerns. so it is with the discipline of infectious diseases. as with all medical specialties, infectious diseases has unique features that are important to highlight: among medical specialties, this one is consistently changing, often unpredictable, usually exciting, and incredibly rewarding for health impact. it is also often challenging and seemingly underappreciated, at least until needed. these facts appear to be relatively idiosyncratic to this discipline with a menu of priority pathogens that is in constant flux and weaponry that will change in unpredictable ways. the extraordinary kinetics and ability to intervene successfully using public health, preventive vaccines, and disease-limiting antimicrobials are its great strengths. the following are some of the highlights and unique features of a career in the science and practice of infectious diseases. the menu includes the litany of epidemics, heroic efforts to conquer disease, our expectations with antimicrobials, vaccines and public health, and challenges that may lead to transformative interventions. the field of infectious diseases is kinetic, unpredictable, and layered with surprises that sometime require heroic efforts from a diverse field of scientists and practitioners. • on october , a patient with fever and confusion was seen at a florida medical center by dr larry bush, an infectious disease physician. he examined the cerebrospinal fluid, saw boxcar gram-positive rods, diagnosed anthrax, and predicted bioterrorism [ ] . this was strong stuff at a time no one had thought much of bioterrorism anywhere in decades and especially in an obscure, small town in florida. the ensuing epidemiologic investigation showed anthrax spores in this patient's workplace, the local postal service, and a letter received by the patient. this was the index case of the anthrax bioterrorism epidemic that shook the country in .the result was a major national preparedness response to not only bioterrorism, but also preparedness for natural disasters, epidemics, and other major public health threats. • in , dr alan steere, a rheumatologist from yale school of medicine, led an investigation of an outbreak of arthritis involving children and adults in connecticut. most of the patients had asymmetric swelling and pain of large joints, especially knees, and some also had an erythematous, annular rash [ ] . it was initially called "lyme arthritis," but most physicians thought it was simply juvenile rheumatoid arthritis. dr steere was convinced it was an infection and moreover, that it was arthopod-born based on epidemiology and clinical features. his relentless pursuit of the pathogen was finally rewarded with the discovery of the newly recognized spirochete in the blood and in typical skin lesions [ ] . the specific agent was subsequently defined in a another extraordinary effort, this time by dr willie bergdorfer, who had spent much of his career studying the microbiology of the hindgut of ticks; he successfully isolated the pathogen that he considered his last and most important scientific project [ , ] . that agent is named in his honor: borrelia burgdorferi [ ] . • dr robin warren, a pathologist in australia, made the historic discovery that gastric biopsies from patients with gastritis showed a large burden of curved bacteria. no one paid attention until a young gastroenterologist, dr barry marshall, agreed to study the association. this pairing was considered an "odd couple"; dr warren was described as quiet, thoughtful, and persistent whereas dr marshall was self-described as brash and determined [ ] . subsequent studies consistently showed the association between this curved microbe with gastritis and peptic ulcer disease, but there was almost uniform opposition from both gastroenterologists and infectious disease physicians. larry altman, noted medical editor for the new york times, wrote that never in his experience had he witnessed such fierce opposition from the medical community to the possibility that peptic ulcer disease was caused by a microbe (l. altman, personal communication, may ) [ ] . this prompted proponents, drs barry marshall and alan morris, to perform the ultimate experiment-they swallowed a flask of helicobacter pylori (and suffered from the experience; l. altman, personal communication, may ) [ ] . the long-term result of this unrelenting battle is now well known: h. pylori is accepted as the cause of peptic ulcer disease and its sequela, guidelines for diagnostic testing and treatment are based on h. pylori as the pathogen, this agent is listed as a class carcinogen, and nobel prizes were awarded to drs warren and marshall [ ] . • in early september , dr april pettit, an infectious disease physician in tennessee, saw a patient with aspergillus meningitis following an epidural steroid injection [ ] . this prompted her to notify dr marion kainer at the tennessee health department, who then set up shop with a sleeping cot in the health department to facilitate a nonstop investigation [ ] . this was the beginning of the infamous national epidemic of exserohilum rostratum meningitis associated with the contaminated steroids that led to cases and deaths in states. credit here is to dr pettit for recognition and prompt notification, to dr kainer for her aggressive response on behalf of the victims, and to the centers for disease control and prevention (cdc) for the hasty intervention. (somewhat disappointing is the fact that compounding pharmacies are still unregulated.) • in , dr anthony fauci read the july edition of morbidity and mortality weekly report [ ] describing gay men with kaposi sarcoma or pneumocystis carinii pneumonia in california. for the first time in his life, dr fauci had what he called "chill pimples" ("chill bumps"), and this led to a career change to find the cause, treatment, and prevention of aids. this must be now viewed as possibly the most remarkably successful attack on an important infectious disease since fleming discovered penicillin. • in february , severe acute respiratory syndrome (sars) was a newly described, severe disease in humans that was often fatal and appeared to travel by air routes, but had no established pathogen or treatment. dr klaus stohr at the world health organization (who) identified the finest virology laboratories in the world and asked them to collaborate to define the pathogen with the condition that all information would be shared on the internet and there was no ownership of the data. the participating labs with varying skills were spread throughout the world, so the daily conference calls started with "good morning, good afternoon, and good evening." the etiologic agent was described in an unauthored "global alert" on april and in the lancet with "multicentre collaborative network" as the authors (see [ ] ). this unselfish collaboration under strong leadership is credited with the rapid solving of a global crisis that eventually showed cases with deaths in countries. • these anecdotal experiences (bioterrorism, lyme disease, peptic ulcer disease, iatrogenic fungal meningitis, human immunodeficiency virus [hiv]/aids, and sars) illustrate the unpredictable challenges and some of the unique responses that have left a major imprint on medicine. it is noteworthy that all started with strong leadership and came to closure with either elimination or successful management. epidemics of infections are predictable to occur, but largely unpredictable in time, place, microbe, and consequences. the following highlights some of the recent epidemic records and surprises in this category: • west nile virus was first reported in new york city in and reached a -year zenith for reported cases in with cases, including % with the dreaded neuroinvasive form of the disease [ ] . • coccidioidomycosis: the total number of reported cases increased -fold in years, from in to in [ ] . • malaria reported in us travelers reached a record high of cases in [ ] . • chikungunya virus reached a record number of cases in the caribbean with > reported cases, including in us travelers to st martin [ ] . this pathogen is highlighted because global warming is expected to make it endemic in the southern united states and because of its substantial morbidity with possible long-standing arthritic complications [ ] . • measles: the largest number of annual reported cases in the united states in years was noted during - . it now appears that will be worse [ ] . measles was declared eradicated in but has now become a problem, primarily in those refusing vaccination, but also in some with documented vaccination [ ] . measles continues to be an important infectious disease challenge due, in part, to the extraordinary public health issues that cost one health system $ to deal with the potential epidemiologic consequences of a single case [ ] . • pertussis: this infection is resurgent in the united states and europe, with increased cases including epidemics in children and adults and involving both vaccinated and unvaccinated individuals [ ] . this is thought to reflect waning immunity to the acellular vaccine and the need for a new vaccine [ ] . • meningitis: - reporting showed outbreaks of neisseria meningitidis meningitis, on college campuses and among gay men in new york city and los angeles [ ] . • influenza: this is a continual concern based on the everpresent threat of pandemics with devastating consequences ( - , - , - , - , - ) that seem difficult to predict or control [ , ] . limitations of current expertise were illustrated with influenza a(h n ) swine flu, as the standard concept based on historic precedent is that new influenza epidemics come from asia in the wintertime, but this one came in the eastern hemisphere in the summertime [ ] . the more recent threats that could pose serious consequences are influenza a(h n ) and influenza a(h n ) [ ] [ ] [ ] . both show high mortality rates, but little evidence so far of that single critical mutation permitting attachment to the hemagglutinin antigen to permit sustained person-to-person transmission [ ] . • middle east respiratory syndrome (mers) coronavirus: this coronavirus is a major global concern with analogies to the sars coronavirus in terms of its perceived potential to become a global epidemic with high mortality and no apparent treatment [ , ] . of immediate importance in the united states is recognition of risk with appropriate diagnostic testing, isolation, and management of persons with severe, unexplained pneumonia associated with recent travel to the arabian peninsula (mers) [ ]. • foodborne disease: widespread foodborne epidemics are now a common consequence of the massive food distribution system that permits contaminated beef or lettuce from mexico to reach stomachs in distant multistate areas, with medical consequences involving hundreds or thousands of people. this includes the more recent emergence of the gii. sydney strain of norovirus. these outbreaks seem likely to continue, with unpredictable pathogens in unpredictable places [ ] [ ] [ ] . • heartland virus: a recently encountered tick-borne disease in tennessee and missouri with cases and deaths [ ] . • polio-like virus infection with extremity paralysis has been recently reported in and possibly children in california [ ] . • ebola virus: who has reported an outbreak in guinea involving a new clade of this usually fatal infection [ ] . this listing could continue almost indefinitely. the point is that epidemics are the domain of infectious diseases and public health, with the expectation for management or prevention of outbreaks with requirements for detection, reporting, isolation, and case management. the listing here includes diverse pathogens, some life-threatening diseases, infections with important public health implications, an upsurge of pediatric infections in adults, many travel-related infections, multiple public health threats, and the continuous concerns for influenza and foodborne disease. the major weaponry of the infectious disease catalog includes antibiotics, vaccines, and public health. these categories are remedial reading, but some facets are worthy of emphasis. the value of antibiotics seems obvious. the first patient to receive penicillin was a young woman with β-hemolytic streptococcal bacteremia with fever of . °c- . °c daily for weeks. she received penicillin intravenously starting march , promptly recovered, and survived to age years [ ] . this would appear to be "evidence-based medicine" with an n = . the following statement from dr walsh mcdermott in summarizes this breakthrough especially well: "penicillin gave more curative power to a barefoot, itinerant care provider in the deepest reaches of africa than the collective powers of all physicians in new york city" [ ] . the more recent experience with bacterial resistance and sparse pipeline threatens this miracle, but antiviral development is quite different, primarily for hiv and hepatitis c virus (hcv). it now appears that patients with hiv can achieve near-normal longevity [ ] . hcv infection is even more impressive in terms of speed of progress and ability to cure. the hcv treatment story reflects the efficiency of basic science to define targets, pharmaceutical skills of industry, well-organized trial networks, and a regulatory agency (us food and drug administration [fda]) that facilitated product development [ ] . the impact of vaccines is also impressive. a comparison of annual incidence of vaccine-preventable diseases in the united states reported for the period prior to availability of the designated vaccine compared with its incidence in shows the decrease in polio as %; diphtheria, %; rubella, . %; mumps, . %; invasive type b haemophilus influenzae, . %; and pertussis, a disappointing %. a recent report concluded that the global total for lives saved by vaccines exceeds million [ ] . the impact could be substantially greater with more global access, fewer refusals, and a better pertussis vaccine. a recent cdc analysis of annual costs associated with major nosocomial infections totaled $ . billion per year in the united states with the following rank order by median cost/case: central line bacteremia, $ ; ventilator-associated pneumonia, $ ; surgical site infection, $ ; clostridium difficile infection, $ ; and catheter-associated urinary tract infection, $ . this illustrates the challenge and the priorities [ ] . another challenge is epidemics involving nosocomial pathogens, as shown with the klebsiella pneumoniae carbapenemaseproducing bacteria (kpc) in the national institutes of health (nih) clinical center. this began with a patient transferred from a new york city hospital with a kpc infection and became the source of an institutional outbreak that required extraordinary efforts to control, including a wall constructed to isolate cases, removal of plumbing (as a possible source), use of matrix-assisted laser desorption/ionization time-of-flight (maldi-tof) molecular diagnostics to detect cases and carriers, hydrogen peroxide room aerosols, and "whole house" surveillance cultures. the epidemic was finally halted, but the toll was cases and fatalities over months [ , ] . another kpc epidemiologic investigation showed widespread distribution of this microbe from a long-term acute-care facility in the chicago area [ ] , and others have demonstrated distribution of kpc by air travel from india to europe [ ] . these epidemics require extensive resources and specialized skills; they will be expected to increase substantially in the era of "bad bugs." there is no specialty field in medicine that demonstrates shifting priorities like infectious diseases. to illustrate this point, i have summarized the "hot topics" discussed in the "what's hot in infectious diseases" presentation to the annual meeting of the american college of physicians in , compared with the presentation in , to illustrate the nearly complete change of priorities in a relatively short time. avian influenza, rabies (first survival without vaccine), west nile virus, bioterrorism, transfusion-associated jacob-creutzfeldt disease, usa strain of methicillin-resistant staphylococcus aureus (mrsa), sars, and chlamydia pneumoniae and its role in coronary artery disease and influenza. carbapenemase-producing gram-negative bacilli, colistin, constant infusion of β-lactam antibiotics, molecular diagnostics, a litany of epidemics, new pathogens (mimivirus, borrelia miyamotoi, emmonsia species, and bradyrhizobium enterica), c. difficile gene sequencing, the microbiome, and hcv. note that the -year interval resulted in a completely new agenda for what was considered timely and important in the field based on rapid changes in topical microbes, new epidemics, and new diagnostics, (but not new antimicrobials). it is impossible to predict the menu for . it is now known that genes for resistance to antimicrobial agents were well established in bacteria at least million years before evidence of human life [ ] . the use of antibiotics has selected for these genes by mendelian laws, making it increasingly difficult to control previously treatable infections. this problem was predicted by the father of antibiotics, alexander fleming, who, in , wrote that ". . . the public will demand the drug and . . . then will begin an era . . . of abuses. the microbes are educated to resist penicillin and a host of penicillin-fast organisms is bred out which can be passed to another individual and perhaps from there to others until they reach someone who gets a septicemia or a pneumonia which penicillin cannot save. in such a case, the thoughtless person playing with penicillin treatment is morally responsible for the death of the man who finally succumbs to an infection with penicillin-resistant organisms. i hope this evil can be averted" [ ] . also of note is the prediction by nobel laureate joshua lederberg: "the future of humanity and microbes will likely evolve as . . . episodes of our wits vs their genes" [ ] . it now appears that fleming's prediction is a harsh reality and evolutionary microbial resistance genes are gaining the upper hand, reflecting the combination of massive antibiotic use and lack of new pharmacologic agents. the result is the alarming escalation of antibiotic resistance that is global and applies to nearly all categories of treatable pathogens, leading some to predict "the postantibiotic era." this resistance has been declared a "crisis" by the infectious diseases society of america, the cdc, who, the us congress, and the us president. a disturbing observation in the united states is the conspicuous absence of a national plan to deal with resistance, including the lack of a living record of antibiotic consumption and resistance correlated by location and trajectory. this is in sharp contrast to the european union, which includes countries with official languages and diverse cultures, but has systematically collected data on antibiotic consumption and microbial resistance patterns for years [ , ] . this has resulted in multiple publications with data reviews, studies of interventions, messages to consumers such as an ebug internet program for students, a european antibiotic awareness day, standardized methods to collect data [ ] and a recent -point plan with budget to address the issue [ ] . their data are striking in showing the dramatic association between per capita antibiotic use and national resistance patterns. for example, antibiotic consumption in greece is nearly times that of the netherlands, so we expect more resistance problems in greece, but the magnitude of this difference is alarming: bacteremic carbapenemase strains among all bacteremic k. pneumoniae isolates appear to be about times more common in greece, and mrsa as a percentage of all s aureus isolates is about times higher [ ] . the european union appears to have a mature and substantive model to learn from, with the important caveat that it functions well because there is no claimed ownership, as there are equal partners. there are also some good national programs that have successfully addressed specific problems to learn from: • eu data for showed that france had embarrassingly high antibiotic use rates, accompanied by increasing resistance by s. pneumoniae. this prompted a national campaign targeting prescribers and consumers on antibiotic abuse and its consequences. the goal was a % reduction in antibiotic prescriptions for the entire country; they achieved a % reduced resistance [ ] and also achieved the largest decrease in per capita antibiotic consumption for any nation in the history of the global antibiotic fund [ ] . • a recent report from israel showed a national campaign to reduce the incidence of kpc. analysis of their results with a prevention bundle showed a reduction from per patient-days to . per patient-days [ ] . • the united kingdom addressed the issue of the epidemic nap- strain of c. difficile through gene sequencing and aggressive antibiotic control. the result was a national % reduction in c. difficile infection rates [ ] . the examples given are based on national data addressing major challenges with impressive results. in the united states, this remains a unanswered challenge, but is also an opportunity for the skills of the infectious disease discipline in terms of data collection, evaluation, interventional trials, and policy implementation into practice, primarily in the form of antibiotic stewardship. recent reports using gene sequencing suggest that conventional methods of infection control could substantially improve this effort. examples: ( ) results from the united kingdom have largely disproven conventional teaching regarding the epidemiology of c. difficile infection [ ] ; ( ) this technology also appears to contradict some contemporary concepts about transmission patterns of s. aureus [ ] ; and ( ) it has proven to be a valuable tool in outbreak investigation of kpc infections in a hospital [ ] and in a large community outbreak of kpc involving multiple facilities [ ] . it seems clear that as this technology gets faster and cheaper, it will be embraced as an infection control standard [ ] , although there needs to be caution and skill in interpreting results [ ] . this work in developing countries is another attractive career option based on need, probability of impact, and unique special programs such as the president's emergency plan for aids relief, the bill & melinda gates foundation, and others. some of this is direct patient care, but possibly very attractive targets for impact are the development and implementation of innovative programs that deal with the vast need combined with minimal resources [ ] . the new healthcare system should value infectious disease expertise based on its important role in addressing resistance and costs associated with nosocomial infections. nevertheless, it is feared that the current structure and payment system are not constructed as a good fit to prioritize infectious disease skills. specifically, there is no code for preventing infections, conserving antibiotic use, or preventing resistant pathogens. this might be an erroneous conclusion, or the situation may change as the system matures and becomes serious about addressing the crisis. "bundles" to deal with healthcare efficiencies are in vogue and could be a strength of infectious diseases. an example is the -step central line bacteremia prevention bundle that proved effective in trials [ ] . generalized adoption of this bundle was predicted to save lives and $ . billion per year in us hospitals [ ] , and subsequent actions by clinicians, regulatory agencies, and stakeholders have resulted in an estimated % decline in central line bacteremia rates [ ] . • stewardship: solving or reducing the problem of antibiotic resistance largely depends on antibiotic development and reducing antibiotic abuse. the major on-site forces for improving smart antibiotic use at the point of care are antibiotic stewards-preferably infectious disease or pharmacy personnel trained in this skill to improve the speed of detecting resistant or epidemic pathogens. the tools are obvious to infectious diseases-trained clinicians, but often require methods that are not well inculcated into hospital or clinic practice. methodology with proven value for antibiotic conservation include shortcourse regimens (virtually always wins or ties in trials), use of procalcitonin to facilitate decisions on when to start or stop antibiotics, use of molecular diagnostics to improve pathogentargeted antibiotic decisions, outpatient infusion therapy to reduce inpatient risk (and cost), optimal use of the agents we have, waiting room with notices that the doctor will prescribe antibiotics only according to guidelines, acknowledgement of possible microbiome harm, and possible use of social network media [ , ] . nevertheless, there must be caution: the new us healthcare system represents socialized medicine largely managed by capitalists, which invites both quality and chicanery. for example, the centers for medicare and medicaid services' " -hour rule" for treating community-acquired pneumonia had improved outcome advantages, but also led to overprescribing, declined use of diagnostics, perceived antibiotic abuse, and increases in c. difficile infections. given the priority of cost containment and its relevance to infectious diseases, infectious disease training should probably include attention to the business of medicine. • molecular microbial diagnostics: these are rapidly being developed and introduced into clinical use for detection of epidemic pathogens or resistance genes with advantages of speed, precision, and sensitivity. most polymerase chain reaction (pcr)-based tests define a specific pathogen with extraordinary sensitivity within minutes. the fda has approved these pcr tests to detect at least viruses and bacteria [ ] . these tests may also be useful for early detection of epidemic pathogen or resistance genes [ ] . it seems clear that the introduction of molecular tests for general use may be difficult to interpret in the context of clinical care, so these new tests will require a substantial stewardship from the infectious disease community. this was illustrated in a trial to guide antibiotic decisions based on results of a pcr-based diagnostic to detect mrsa in purulent soft tissue infections that had no significant impact on antibiotic selection [ ] . gene sequencing will be a new and important role for the infectious diseases-trained clinician as it becomes more readily available for defining transmission patterns to inform infection control practice. • microbiome: study of the microbiome at various anatomical sites represents a major nih-sponsored initiative that could possibly translate into important opportunities to treat or prevent multiple conditions [ , ] . this work is at the dawn of development, but the early reads suggest a potential role in obesity, allergies, autoimmune disease, cancer, diabetes, heart disease, and other conditions [ , ] . it is also apparent that antibiotics have a profound and long-lasting impact on the microbiome [ ] . this field requires a transformation in our conventional understanding of infectious diseases, as the "pathogens" are communities of microbes that communicate in contrast to the koch postulate of "one microbe, one infection." an example is a recent report showing that volunteers fed steak and eggs (lecithin) have conversion by gut flora to trimethylamine-n-oxide, which is a marker of atherosclerosis [ ] . this microbial interaction could be altered with antibiotics. the long-term goal is to define associations and intervene possibly with antibiotics and probiotics; this work may also illustrate potential harm to redefine risk-benefit ratios for antibiotics. • bundles: another potentially important role for infectious diseases-trained clinicians is the development of bundles that prevent infectious disease complications. an example is central line bacteremia, as described above [ ] [ ] [ ] . that experience can now be applied to multiple iatrogenic infection risks associated with specific patients or procedures, possibly prioritizing those with the greatest healthcare consequences as described above. the role of infectious diseases is to define the bundle, design the study, and then implement them when results are convincing or even mandated. specialized skills in the management and study of infectious diseases are an increasingly important specialty in contemporary medicine. the roles of practitioners in the discipline are diverse, usually important, and sometimes critical, but commonly undervalued by contemporary priorities in healthcare systems and healthcare reform. it would be difficult to find another discipline in medicine that has such extraordinary diversity, surprises, value in patient care, and clinical relevance for both domestic and international applications. for many trained in medicine, joining the field of infectious diseases is simply the right thing to do. supplement sponsorship. this article was published as part of a supplement titled "the john bartlett festschrift: celebrating a career in medicine," sponsored solely by the department of medicine of the johns hopkins school of medicine in recognition of john bartlett's contributions to medicine. potential conflicts of interest. author certifies no potential conflicts of interest. the author has submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. index case of fatal inhalation anthrax due to bioterrorism in the united states lyme arthritis: and epidemic of oligoarticular articular arthritis in children and adults in three connecticut communities the spirochetal etiology of lyme disease interview with willie bergdorfer, ph.d. interview by vicki glaser lyme disease-a tick-borne spirochetosis? how the discovery of borrelia bergdorferi came about nobel prize winners robin warren and barry marshall two win nobel prize for discovering bacterium tied to stomach ailments long-term follow-up of voluntary ingestion of helicobacter pylori 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intestinal microbial metabolism of phosphaditylcholine and cardiovascular risk key: cord- -e hd iuu authors: maillard, jean-yves; bloomfield, sally f.; courvalin, patrice; essack, sabiha y.; gandra, sumanth; gerba, charles p.; rubino, joseph r.; scott, elizabeth a. title: reducing antibiotic prescribing and addressing the global problem of antibiotic resistance by targeted hygiene in the home and everyday life settings: a position paper date: - - journal: am j infect control doi: . /j.ajic. . . sha: doc_id: cord_uid: e hd iuu antimicrobial resistance (amr) continues to threaten global health. although global and national amr action plans are in place, infection prevention and control is primarily discussed in the context of healthcare facilities with home and everyday life settings barely addressed. as seen with the recent global sars-cov- pandemic, everyday hygiene measures can play an important role in containing the threat from infectious microorganisms. this position paper has been developed following a meeting of global experts in london, . it presents evidence that home and community settings are important for infection transmission and also the acquisition and spread of amr. it also demonstrates that the targeted hygiene approach offers a framework for maximizing protection against colonization and infections, thereby reducing antibiotic prescribing and minimizing selection pressure for the development of antibiotic resistance. if combined with the provision of clean water and sanitation, targeted hygiene can reduce the circulation of resistant bacteria in homes and communities, regardless of a country's human development index (overall social and economic development). achieving a reduction of amr strains in healthcare settings requires a mirrored reduction in the community. the authors call upon national and international policy makers, health agencies and healthcare professionals to further recognize the importance of targeted hygiene in the home and everyday life settings for preventing and controlling infection, in a unified quest to tackle amr. the global impact is already profound and expected to intensify, particularly among the poorest nations. , the main driver is overuse and misuse of antibiotics in medicine and agriculture including unregulated over-the-counter sales, while global spread of resistant bacteria or resistance genes is attributed to poor infection prevention and control in healthcare facilities, and sub-optimal hygiene and sanitation in communities, confounded by poor infrastructure and weak governance. in the us, between - % of the volume of human antibiotic use occurs in the outpatient setting, with nearly % considered to be inappropriate or unnecessary. without prompt action, it is estimated that rates of amr to commonly-used antibiotics could exceed - % in some countries by , and by , around million people could die each year as a result of resistance to antibiotics and other antimicrobial agents. almost million of these will be in africa and asia. in , an alliance of the who, the food and agriculture organization of the united nations interventions." the gap emphasizes the need for society-wide engagement, with a clear focus on "prevention first." one of the five strategic objectives is a reduction in the incidence of infection through improved sanitation, hygiene, and infection prevention. at least countries have finalized national action plans, with the plans of more than other countries under development. what is striking is that the gap and national plans discuss infection prevention and control primarily in the context of healthcare facilities. (see https://www.who.int/antimicrobialresistance/national-action-plans/library/en/). by contrast, the latest uk national action plan, which sets out a -year vision and a -year plan for how the uk will contribute to controlling amr by , offers guidelines on infection prevention in healthcare settings, but also highlights the role of the community, noting that, when it comes to infections in the community, the public have a huge part to play. in recent years, demographic changes and changes in health service structure mean that the number of people living in the community needing special care, because they are at greater risk of infection, has significantly increased. the largest proportion of these are the elderly, who generally have reduced immunity to infection which is often exacerbated by other illnesses like diabetes and malignant illnesses. a decrease in immunity usually starts from years old. other infection-susceptible groups include the very young, patients recently discharged from hospital, and family members with invasive devices such as catheters, as well as those whose immune competence is impaired as a result of chronic and degenerative illnesses (including hiv/aids) or because they are receiving immunosuppressant drugs or other therapies. immunosuppressed individuals are often also on other medications such as antibiotics, to help protect them from infection but can further increase susceptibility to infections such as clostridium difficile. home and everyday life settings provide multiple opportunities for spread of infection. everyday life settings include locations where normally there is no mandated hygiene policy as is typically found in clinical and educational settings; for example: work places, public transport, gyms, child day-care facilities, and shopping centers. poor hygiene is considered a major factor in the transmission of community-based infections, including gastrointestinal (gi) and respiratory tract (rt) infections such as colds and influenza, and skin infections caused by s. aureus. for the elderly, communal living environments, combined with problems of fecal incontinence, create an environment in which enteric and foodborne pathogens are easily spread. as a result, the incidence of salmonellosis and campylobacter diarrhea appears to be higher among the elderly in these situations. more vulnerable 'at risk' members of society are now being looked after outside hospital settings. for example, in germany, it is estimated that approximately three quarters of all people in need of care are currently being cared for at home. in the community the immunocompromised are also at risk from opportunistic pathogens such as e. coli, klebsiella spp., and pseudomonas aeruginosa, which are considered as hospital related. the key steps in preventing the spread of infection, known as breaking the chain of infection, are the same regardless of setting. in the home, pathogens may have been brought home from hospital settings or enter the home via colonized or infected people, pets/domestic animals, or through contaminated food and water. , pathogens and other microbes are shed constantly from these sources, with rapid transmission around the home mainly via hands, hand and food contact surfaces, cleaning utensils and in the air ( figure ). respectively. for campylobacter, counts of > and > were isolated from and . % respectively. this is a concern, since it is estimated that % of salmonella infections originate in the home, and a uk study detected campylobacter spp. in % of chilled retail chickens, with % of samples containing > colony forming units (cfu)/g of skin. the infectious dose of campylobacter is estimated at < cfu. chaidez et al. demonstrated that the risk of salmonella transmission from cleaning cloths via hands to mouth was far higher than the guideline levels for acceptable risk. since most pathogenic organisms die relatively rapidly, particularly on dry surfaces, the greatest risk of human exposure presents immediately after shedding from an infected or contaminated source. however some species, including s. aureus, e. coli, and other organisms such as fungal species, rhinovirus, and norovirus can survive for long periods even on dry surfaces. audit studies suggest that some gram-negative organisms can form permanent reservoirs or secondary sources of contamination, particularly where moisture is present such as in sinks and drains, kitchen cleaning cloths and sponges. the dose also depends on host susceptibility and mode of entry, and may be lower for at-risk groups in the community such as children, the elderly, and people with compromised immunity. although care of increasing numbers of patients in the community, including at home can help alleviate over-burdened health systems, it can be undermined by inadequate infection control in the home and urgent focus is now needed on infection transmission in homes and community settings in addition to healthcare settings. although multidrug-resistant (mdr) bacteria (i.e. bacteria that have acquired resistance to at least one agent in three or more antimicrobial classes) are typically hospital-acquired, since , we have seen the emergence of new "community acquired" strains of mrsa (ca-mrsa). while healthcare-associated strains are mainly a risk to vulnerable people, for ca-mrsa, any family member is at risk and it is more prevalent among children and young adults where they cause infections of cuts, wounds and abrasions. us experience suggests the risk is greatest among those engaging skin-to-skin contact activities and contact with contaminated objects such as towels, sheets and sports equipment. transmission is common in settings such as prisons, schools and sports teams. a study assessing the transmission of ca-mrsa in a university in the us, found multidrug resistant usa responsible for diseases including necrotizing pneumonia, severe sepsis and necrotizing fasciitis, on common touch surfaces at the university, student homes and local community settings. this suggests transfer between different locations within the community. enterobacterales are a common cause of community-associated infections, including urinary tract infections and bacteremia as well as gastrointestinal infections. kitchen sponges not only act as reservoirs of microorganisms, but also as disseminators over domestic surfaces, which can lead to cross-contamination of hands and food, which is considered a main cause of foodborne disease outbreaks. carbapenem-resistant enterobacteriaceae (cre) are also on the rise globally, but, to date, most cre infections in the us and europe have been healthcare-associated. , although data from asia is sparse, carbapenemases have been found in bacteria recovered from drinking water in india and in food-producing animals in china. , , in european studies during the s, vancomycin-resistant enterococci (vre) were detected in the stools of healthy volunteers. [ ] [ ] [ ] [ ] [ ] however, rates of vre, carbapenem resistance in acinetobacter infections, and mdr p. aeruginosa are thought to be low in individuals living in the community. overall, the evidence suggests that mdr strains of bacteria, like any other strains of bacteria, can enter the home or other settings via people who are infected or colonized or via contaminated food and can be spread to other members of the family via hands and contaminated surfaces. if implemented effectively, home and everyday life hygiene has the potential to reduce rates of infection and the need for antibiotic prescriptions, thereby reducing the selective pressure for the development and subsequent dissemination of resistance. microbiological data , suggest that the surfaces that are most often responsible for spread of harmful microbes, at key moments include the hands themselves, hand contact surfaces, food contact surfaces, and cleaning cloths and other cleaning items ( figure ). these surfaces are referred to as critical surfaces or critical control points. clothing, household linen, toilets, sinks and bath surfaces may also contribute to establishing a chain of infection, however, the risks associated with these surfaces are typically lower as they rely on the hands and other "chain links" to disseminate infectious microbes to cause human exposure. an important aspect of targeted hygiene is hygienic cleaning -as opposed to visible cleaningto break the chain of infection. this is achieved using hygiene procedures (products plus process) to reduce pathogenic microorganisms on critical surfaces to a level where they are no longer harmful to health -thereby preventing ongoing spread. , several methods exist to achieve such reduction in potential pathogens: mechanical/physical removal using dry wiping, soap or detergent-based cleaning together with adequate rinsing, inactivation or eradication using a disinfectant on hard surfaces or an alcohol-based sanitizer on the hands, or a physical process such as heating (to ≥ °c/ °f) or ultraviolet treatment. most frequently, a combination of these approaches is likely to be used. , when developing hygiene procedures aimed at breaking the chain of infection, the goal should be to ensure that each procedure is appropriate to its intended use. in recent years, risk modelling has been developed in order to achieve this. quantitative microbial risk assessment (qmra) was originally developed for ensuring water quality and is increasingly being used to develop infection prevention control strategies in other settings, including healthcare. , qmra is a scientifically-validated approach that uses published data to model the chain of infection and estimate safe residual level of contamination at critical points in the chain. , this information is then used to estimate the log reduction required to reduce contamination to a safe level. based on these estimates, tests modelling use conditions can be used to develop effective hygiene procedures to achieve the required reduction. the approach is set out in more detail by bloomfield et al. in the past, recommendations on selection of hygiene procedures for home and everyday life were based on the health status of family members, and it is still argued by some that disinfectants should only be used in situations where people are infected or at increased risk of infection. although there is data to show that hygiene is important in preventing transmission of mrsa colonization and infection in the domestic environment, further investigation is required to demonstrate the full extent to which poor home hygiene may contribute to the burden of foodborne infection associated with antibiotic resistant strains. quantifying the impact of hygiene on the burden of infection in home and everyday life is challenging because of the large population sizes required to generate significant results, and difficulties in conducting studies involving multiple interventions. most data have been generated from single intervention studies -primarily hand hygiene -where meta-analyses show a positive impact on gi and rt infections. [ ] [ ] [ ] children who attend day-care centers have significantly more infections than those who do not. the most common are rt and gi infections, and the risk of otitis media is almost twice that of children remaining at home. studies in day-care centers and schools in which hand hygiene was combined with cleaning and/or disinfection of environmental surfaces indicate a positive impact on illness rates and reduction in the use of antibiotics. [ ] [ ] [ ] [ ] in an intervention study reduction of antibiotic prescriptions for rt infections in a group who used hand sanitizers compared with a control group. another intervention study found that children were prescribed antibiotics for significantly fewer weeks in day care centers using specific disinfecting products and cleaning protocols than centers that continued to use their standard procedures and products (rr= . [ % ci . , . ]; p= . ) -a relative risk reduction of almost onethird. to the best of our knowledge, only one study on the impact of targeted hygiene in the home has been conducted. this study, conducted among low-income communities in cape town, south africa, evaluated the impact of hygiene education alone and education in combination with hand washing with soap at critical times, bathing at least three times a week, cleaning/disinfecting household surfaces at critical times, and proper waste disposal. qmra is also now being used to estimate the impact of hygiene interventions on infection in community settings. haas et al. concern has been expressed as to whether expanding use of microbicidal products, in the home and everyday life may contribute to the rise in amr. sub-lethal levels of microbicides can induce stress on bacterial cells, causing expression of mechanisms that reduce the biocide concentration at the bacterial target site further and allow the bacterial cell to repair. , these include overexpression of an efflux system, membrane regulatory changes, and changes in membrane permeability and composition. these same mechanisms can produce changes in the susceptibility profile to unrelated antimicrobials. in other words, the use of microbicides may cross-select for antibiotic resistance and be associated with reduced antibiotic susceptibility to clinically significant levels (recently reviewed by maillard ). factors inherent to the microbicide (i.e. concentration, formulation, mechanism of action), the microorganisms (i.e. type/strain, metabolism, resistance mechanisms), and product usage (e.g. concentration, exposure time), all impact on product efficacy. decreases in efficacy, for example, following shorter contact time or product dilution, will lead to bacterial survivalantimicrobial damage caused by a sub-lethal concentration of a microbicide is likely to be repairable. a number of expert reports commissioned in the last years have highlighted laboratory studies linking microbicide use with reduced antibiotic susceptibility. however, these reports conclude that there is little evidence for this effect occurring in real-life clinical practice, and have called for further research into whether microbicide use influences antibiotic resistance in the community. - rutala et al. ( ) found that the frequency of occurrence of antibiotic resistance in environmental isolates from homes was much lower than for clinical isolates from a hospital intensive care unit and an outpatient setting where there was routine extensive use of antibiotics. two studies were carried out to investigate whether antibiotic resistant strains were more likely to be found in homes where antibacterial products were used, compared with homes where they were not. , samples were collected from houses in the usa and uk of users and nonusers of antibacterials. susceptibility tests against antibiotics and antibacterial agents (triclosan, pine oil, bac and para-chloro-meta-xylenol) were carried out on the bacteria isolated. the authors concluded that there was no evidence that antibiotic resistant strains occurred more frequently in user homes compared with non-user homes. a -year study by aiello et al ( ) also showed that household use of antibacterial cleaning products was not a significant risk factor for occurrence of antibiotic resistant isolates from hands. despite more than years of research, there is still no conclusive resolution to the question of whether and to what extent; microbicides might contribute to amr in clinical practice. in light of laboratory data, which indicates that microbicide-induced amr is biologically plausible for some types of microbicides, it is concluded that use of microbicides needs to be prudent and appropriate and that the products containing them must be used at recommended concentrations and with the appropriate contact time. targeted hygiene works to ensure that use of disinfectants and hand sanitizers (i.e. microbicides used at the correct concentration and contact time) are confined to situations where there is identifiable risk of spread of harmful microorganisms, ensuring that they play an essential role in tackling amr. the need for antibiotic prescribing may in fact increase if disinfectants and hand sanitizers are not used as indicated, due to the increased risk of infection and survival of bacteria bearing amr determinants. these could potentially spread to other areas in the home and on into the community. it is important to note also that preventing viral infections as well as bacterial infections, such as those that cause respiratory and gi infections, can also have a role in reducing amr as this will eliminate the potential for mis-prescribing or misuse of antibiotics. in in , an estimated million people around the world were drinking from unimproved water sources, and . billion had no access to improved sanitation -the vast majority of these were in sub-saharan africa and south asia. it is estimated that . billion people lack the use of sanitation facilities which are not shared with other households, as with studies conducted in hics, the highest levels of contamination in lmics are typically found in moist locations such as kitchen sponges and dishcloths. [ ] [ ] [ ] the key question, however, is whether, and to what extent, the incidence and levels of potentially harmful pathogens (and thus infection risks) are higher in homes without access to adequate water and sanitation. sinclair and gerba monitored fecal coliforms, total coliforms, e. coli and heterotrophic plate count bacteria on household surfaces in homes that had improved latrines (i.e. a pour-flush latrine) in a rural village of cambodia, and compared the results with similar data from homes in the us and japan. fecal coliform levels in cambodia were found to be highest in moist locations such as the plastic ladle used for sink water, the toilet seat surface, and the cutting board surface. for e. coli, the mean log cfu per cm ranged from . to . , with highest counts found on the top of the squat toilet, the wash basin, and the floor around the toilet. fecal coliform levels were -fold higher on these surfaces in cambodia than on equivalent surfaces in the us and japanese studies. in lmics, due to a lack of basic sanitation, good hand hygiene is of vital importance. globally, it has been estimated that only % of the population washes its hands with soap after contact with excreta. observations show that hand washing with soap is undertaken in an ad hoc manner, with many households having no access to handwashing facilities. unsurprisingly, studies in lmics have reported high levels of fecal indicator bacteria on the hands of household members, [ ] [ ] [ ] with one study correlating presence of fecal contamination on the hands with the prevalence of gastrointestinal and respiratory symptoms within the household. a cochrane review showed that improving hand washing practices probably reduces diarrhea episodes in child day-care centers in both high income countries and among communities living in low to middle income countries by as much as %. the evidence set out in this paper suggests that, if combined with measures ensuring clean water and adequate sanitation, targeted hygiene practices in home and everyday life settings could make a significant contribution to tackling amr through infection prevention and a consequential reduction in antibiotic prescribing. this is true in all areas of the world including low-income countries. additionally, the evidence suggests that hygiene promotion would contribute to preventing the transmission of resistant bacteria from the home and everyday life settings, into healthcare settings, and back into the community. further research is still needed to evaluate the extent to which this might occur, especially in communities in low income countries. to be effective, hygiene interventions need to consider all aspects that are likely to affect the outcome. this includes a reduction of antibiotics from the food chain and the environment, improved hygiene education and availability of appropriate products as well as the provision of clean water and improved sanitation. based on these findings, the authors of this paper issue a call to action to national and international health policy makers, health agencies, and healthcare professionals to give greater recognition to the importance of hygiene in the home and everyday life and development and promotion or more effective codes of practice for hygiene in the home and everyday life as part of national action plans to tackle amr. although the precise impact of hygiene on transmission of infection between community and healthcare settings needs further investigation, it is important to recognise, that reducing the need for antibiotic prescribing and the circulation of amr strains in healthcare settings cannot be achieved without also reducing circulation of infections and amr strains in the community. we cannot allow hygiene in home and everyday life settings to become the weak link in the chain. the development of this position paper was supported by an educational grant from reckitt benckiser who fund the activity of the global 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