# ent

id: cord-000364-ikq38rm1
type: PROTEIN
entity:
  Puumala hantavirus nucleocapsid protein monoclonal antibody A1C5 Progen Biotechnik GmbH Heidelberg Germany For viral antigen


id: cord-006450-si5168pb
type: TAXON
entity:
  viruses herpes simplex virus HSV 1 n 27 cytomegalovirus CMV n 23 Epstein Barr virus EBV n 18 human herpesvirus HHV 6 n 12 respiratory syncytial virus RSV n 3 rhinovirus n 1


id: cord-006302-pnnkfid0
type: ORG
entity:
  the Ethics Committees of Korinthos General Hospital Korgialeneion Benakeion General Hospital ATTIKON University Hospital


id: cord-025861-nsrs6dmc
type: DNA
entity:
  Haemophilus influenzae Streptococcus pyogenes Staphylococcus aureus and Streptococcus pneumoniae 18 S pneumoniae


id: cord-025861-nsrs6dmc
type: ORG
entity:
  the European Organization for Research and Treatment of Cancer Invasive Fungal Infections Cooperative Group


id: cord-006714-q7wy76e2
type: GGP
entity:
  Delannoy P Y Boussekey N Devos P Alfandari S Turbelin C Chiche A Meybeck A Georges H Leroy O title Impact of combination therapy with aminoglycosides on


id: cord-006714-q7wy76e2
type: WORK_OF_ART
entity:
  the Simplified Acute Physiology Score SAPS II 12 and the Sepsisrelated Organ Failure Assessment SOFA


id: cord-006714-q7wy76e2
type: ORG
entity:
  Spanish Collaborative Group for Infections in Intensive Care Units of Sociedad Espanola de Medicina Intensiva


id: cord-010959-sigw7yxk
type: DISEASE
entity:
  influenza A H1N1 pdm09 56 This study was a small n 52 randomised trial of patients treated in community One patient in the single dose group and one in the double dose group developed oseltamivir resistance


id: cord-321455-ooouqna7
type: PROTEIN
entity:
  procollagen type 1 amino terminal propeptide osteocalcin N terminal thyroid stimulating hormone growth hormone and insulin like growth factor binding protein 3


id: cord-321455-ooouqna7
type: GGP
entity:
  procollagen type 1 amino terminal propeptide osteocalcin N terminal thyroid stimulating hormone growth hormone


id: cord-293710-f1tzt6jb
type: WORK_OF_ART
entity:
  Karolyi M Pawelka E Omid S Kelani H Mader T Baumgartner S Laferl H Traugott M Seitz T Zoufaly A Wenisch C


id: cord-274567-xd37wxxf
type: DNA
entity:
  Ev1 5 GATTGTCACCATAAGCAGC 3 EV2 5 CCCCTGAATGCGGCTAATC 3 and Ev probe 5 FAM CGGA ACCGACTACTTTGGGTGTCCGT TAMRA Phosphor 3 13


id: cord-274567-xd37wxxf
type: PROTEIN
entity:
  T4 gene 32 protein Amersham France 1 25 IU MuLV PE Applied Biosystems 5 IU AmpliTaq Gold PE Applied Biosystems 20 IU RNasin Promega France and 1


id: cord-349562-ivu632j2
type: DISEASE
entity:
  influenza B viruses respiratory syncytial virus and parainfluenza viruses 1 2 3 and 4 Real time reverse transcriptase PCR


id: cord-283399-iz4l9i0d
type: DNA
entity:
  C O Gorman E McHenry P V Coyle Regional Virus Laboratory Royal Group of Hospitals Trust Belfast BT126BA


id: cord-321284-0y69n1ea
type: DNA
entity:
  El Kholy A A Mostafa N A Ali A A Soliman M M S El Sherbini S A Ismail R I El Basha N Magdy R I El Rifai N Hamed D H


id: cord-321284-0y69n1ea
type: TAXON
entity:
  coronavirus 229E CoV 229E coronavirus NL63 CoV NL63 coronavirus OC43 CoV OC43 and enterovirus HEV Nucleic acid


id: cord-321284-0y69n1ea
type: GGP
entity:
  Flu B 2 Some 6 12 of all children use healthcare services every year because of influenza 12 Additionally many cases of


id: cord-348840-s8wjg4ar
type: ORG
entity:
  Healthcare Infection Control Practices Advisory Committee s Guidelines for Environmental Infection Control


id: cord-338070-y8zi8iz9
type: PROTEIN
entity:
  Monocyte chemotactic protein 1 MCP 1 granulocyte colony stimulating factor G CSF chemokine C X C motif ligand 1


id: cord-346726-u7dhbmht
type: TAXON
entity:
  pathogens adenovirus coronavirus HKU1 coronavirus NL63 coronavirus 229E coronavirus OC43 hMPV rhinovirus enterovirus


id: cord-346726-u7dhbmht
type: DISEASE
entity:
  influenza virus rhinovirus adenovirus respiratory syncytial virus RSV human coronavirus and parainfluenza virus cause infections


id: cord-269726-z0frgm7s
type: DISEASE
entity:
  cardiomyopathy atrial fibrillation diabetes mellitus type 2 alcoholic cirrhosis myelodysplastic syndrome


# bib

id: cord-000364-ikq38rm1
author: Rasmuson, J.
date: 2011-01-15
txt: ./txt/cord-000364-ikq38rm1.txt
cache: ./cache/cord-000364-ikq38rm1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075397/
doi: 10.1007/s10096-010-1141-6
summary:
  Lung computer tomography (CT) on admission revealed pronounced diffuse bilateral interstitial infiltrates with pulmonary oedema, dependant atelectasis, and moderate pleural effusions (Fig. 1 ) which were later drained (>800 ml). Hantavirus infection was verified with the detection of PUUV RNA in plasma (630,000 copies/ml) on the day of admission, while IgM and IgG were negative. Consecutive plasma samples were analysed for PUUV RNA with declining viral copy numbers until negative 16 days post onset of Fig. 1 Chest CT-scans of two European patients with hantavirus pulmonary syndrome. Concerning the cases of European hantavirus infection in our present report, there was only mild or no renal impairment at the time of admission, whereas the respiratory involvement was early and severe, consistent with acute respiratory distress syndrome (ARDS), fulfilling criteria of HPS according to CDC case definition [19] .

title:
  Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus

abstract:
  Hantaviruses have previously been recognised to cause two separate syndromes: hemorrhagic fever with renal syndrome in Eurasia, and hantavirus pulmonary syndrome (HPS) in the Americas. However, increasing evidence suggests that this dichotomy is no longer fruitful when recognising human hantavirus disease and understanding the pathogenesis. Herein are presented three cases of severe European Puumala hantavirus infection that meet the HPS case definition. The clinical and pathological findings were similar to those found in American hantavirus patients. Consequently, hantavirus infection should be considered as a cause of acute respiratory distress in all endemic areas worldwide.


id: cord-004967-4523cwwi
author: Hsueh, P.-R.
date: 2013-10-18
txt: ./txt/cord-004967-4523cwwi.txt
cache: ./cache/cord-004967-4523cwwi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087826/
doi: 10.1007/s10096-013-1989-3
summary:
  This study is to evaluate the efficacy of bacteria killing nanotechnology Bio-Kil on reducing bacterial counts in an intensive care unit (ICU). In this study, we analyzed whether Bio-Kil when applied to different materials in the ICU, such as sheets, bedding, and clothing, desktops and the surfaces of instruments and equipment, reduces or eliminates bacteria in the environment, on the surfaces of surrounding items, and in the air. Routine textile washing and replacement as well as infection control practices for nurses, physicians, visitors, and disinfection of environments and instruments in these two rooms were performed according to hospital regulations. Bacterial culture results for patients admitted to the rooms during the study period Bacteria grown from textiles, the environment, and air samples were not identified to the species level and testing of susceptibility to antimicrobial agents was not performed. In conclusion, we found that Bio-Kil nanotechnology can significantly reduce the bacterial burden in the environment (textiles, environmental surfaces, and air) and the bacterial density of microbial infections or colonization among patients in the ICU.

title:
  Bacteria killing nanotechnology Bio-Kil effectively reduces bacterial burden in intensive care units

abstract:
  A contaminated hospital environment has been identified as an important reservoir of pathogens causing healthcare-associated infections. This study is to evaluate the efficacy of bacteria killing nanotechnology Bio-Kil on reducing bacterial counts in an intensive care unit (ICU). Two single-bed rooms (S-19 and S-20) in the ICU were selected from 7 April to 27 May 2011. Ten sets of new textiles (pillow cases, bed sheets, duvet cover, and patient clothing) used by patients in the two single-bed rooms were provided by the sponsors. In the room S-20, the 10 sets of new textiles were washed with Bio-Kil; the room walls, ceiling, and air-conditioning filters were treated with Bio-Kil; and the surfaces of instruments (respirator, telephone, and computer) were covered with Bio-Kil-embedded silicon pads. Room S-19 served as the control. We compared the bacterial count on textiles and environment surfaces as well as air samples between the two rooms. A total of 1,364 samples from 22 different sites in each room were collected. The mean bacterial count on textiles and environmental surfaces in room S-20 was significantly lower than that in room S-19 (10.4 vs 49.6 colony-forming units [CFU]/100 cm(2); P < 0.001). Room S-20 had lower bacterial counts in air samples than room S-19 (33.4–37.6 vs 21.6–25.7 CFU/hour/plate; P < 0.001). The density of microbial isolations was significantly greater among patients admitted to room S-19 than those to room S-20 (9.15 vs 5.88 isolates per 100 patient-days, P < 0.05). Bio-Kil can significantly reduce bacterial burden in the environment of the ICU.


id: cord-005057-deq5tv1d
author: Bergström, T.
date: 1990
txt: ./txt/cord-005057-deq5tv1d.txt
cache: ./cache/cord-005057-deq5tv1d.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088202/
doi: 10.1007/bf02184688
summary:
  Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-1-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirulence by assaying the LD(50) after nose and intracerebral (i.c.) inoculation of mice. Vahlne t Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-l-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirnlence by assaying the LDs0 after nose and intracerebrai (i.c.) inoculation of mice. No correlation between high neurovirulence (defined as low LDs0 for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neuruvirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields.

title:
  Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system

abstract:
  Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-1-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirulence by assaying the LD(50) after nose and intracerebral (i.c.) inoculation of mice. HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only. No correlation between high neurovirulence (defined as low LD(50) for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neurovirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields. After nose inoculation, a highly neuroinvasive HSV-1 laboratory reference strain replicated to high titers in nose tissue, the trigeminal ganglia and brainstem, while a strain with low neuroinvasiveness but high i.c. virulence replicated less well in the brainstem. Neuroinvasiveness of the virus strain might be one factor of relevance in the pathogenesis of HSV-1 encephalitis in man.


id: cord-006174-xrhqisii
title: IFITM3 and severe influenza virus infection. No evidence of genetic association
author: López-Rodríguez, M.
date: 2016-08-04
txt: ./txt/cord-006174-xrhqisii.txt
cache: ./cache/cord-006174-xrhqisii.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100079/
doi: 10.1007/s10096-016-2732-7
summary:
  In the present study, we assessed whether the IFITM3 rs12252-C allele is associated with susceptibility to and severity of influenza virus infection (IVI) among a white Spanish population. We performed a case-control genetic association study aimed to analyze the role of the IFITM3 rs12252 polymorphism in the susceptibility and severity of IVI. When the different groups of patients were compared according to severity of infection (development of PVP, ARDS or acute respiratory failure, need of ICU admission or hospital mortality), no significant associations were found (data not shown). [9] found three homozygous individuals for the variant rs12252-C among 53 patients from the United Kingdom hospitalized with influenza (89.5 % H1N1pdm), resulting in a significant overrepresentation when compared with Europeans. These studies suggested that homozygosity for the IFITM3 rs12252-C allele was associated with a populationattributable risk for severe influenza of 5.4 % in Northern Europeans and 54.3 % for severe H1N1pdm infection in Chinese [9, 12] .

abstract:
  Influenza virus infection (IVI) is typically subclinical or causes a self-limiting upper respiratory disease. However, in a small subset of patients IVI rapidly progresses to primary viral pneumonia (PVP) with respiratory failure; a minority of patients require intensive care unit admission. Inherited and acquired variability in host immune responses may influence susceptibility and outcome of IVI. However, the molecular basis of such human factors remains largely elusive. It has been proposed that homozygosity for IFITM3 rs12252-C is associated with a population-attributable risk of 5.4 % for severe IVI in Northern Europeans and 54.3 % for severe H1N1pdm infection in Chinese. A total of 148 patients with confirmed IVI were considered for recruitment; 118 Spanish patients (60 of them hospitalized with PVP) and 246 healthy Spanish individuals were finally included in the statistical analysis. PCR-RFLP was used with confirmation by Sanger sequencing. The allele frequency for rs12252-C was found to be 3.5 % among the general Spanish population. We found no rs12252-C homozygous individuals in our control group. The only Spanish patient homozygous for rs12252-C had a neurological disorder (a known risk factor for severe IVI) and mild influenza. Our data do not suggest a role of rs12252-C in the development of severe IVI in our population. These data may be relevant to recognize whether patients homozygous for rs12252-C are at risk of severe influenza, and hence require individualized measures in the case of IVI.


id: cord-006302-pnnkfid0
author: Ioakeimidou, A.
date: 2017-04-28
txt: ./txt/cord-006302-pnnkfid0.txt
cache: ./cache/cord-006302-pnnkfid0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101577/
doi: 10.1007/s10096-017-2988-6
summary:
  We studied the follow-up changes of circulating vasoactive peptides and cytokines until the improvement or the worsening of a patient and progression into specific organ dysfunctions. In a prospective study, concentrations of tumor necrosis factor-alpha (TNFα), interleukin (IL)-6, IL-8, IL-10, interferon-gamma (IFNγ), endocan and angiopoietin-2 (Ang-2) were measured in serum by an enzyme immunoassay in 175 patients at baseline; this was repeated within 24 h upon progression into new organ dysfunction (n = 141) or improvement (n = 34). Our aims were to monitor the changes of circulating levels of pro-inflammatory and antiinflammatory cytokines and of vasoactive peptides of critically ill patients at well-defined time-points of the clinical course and to understand how these changes mediate progression to organ dysfunction in an individualized way. When pair-wise comparisons between baseline and follow-up measurements were done within the subgroups of patients developing new organ dysfunctions, it was found that the only parameters significantly changing were endocan and Ang-2.

title:
  Increase of circulating endocan over sepsis follow-up is associated with progression into organ dysfunction

abstract:
  How circulating inflammatory mediators change upon sepsis progression has not been studied. We studied the follow-up changes of circulating vasoactive peptides and cytokines until the improvement or the worsening of a patient and progression into specific organ dysfunctions. In a prospective study, concentrations of tumor necrosis factor-alpha (TNFα), interleukin (IL)-6, IL-8, IL-10, interferon-gamma (IFNγ), endocan and angiopoietin-2 (Ang-2) were measured in serum by an enzyme immunoassay in 175 patients at baseline; this was repeated within 24 h upon progression into new organ dysfunction (n = 141) or improvement (n = 34). Endocan and Ang-2 were the only parameters that were significantly increased among patients who worsened. Any increase of endocan was associated with worsening with odds ratio 16.65 (p < 0.0001). This increase was independently associated with progression into acute respiratory distress syndrome (ARDS) as shown after logistic regression analysis (odds ratio 2.91, p: 0.002). Changes of circulating cytokines do not mediate worsening of the critically ill patients. Instead endocan and Ang2 are increased and this may be interpreted as a key-playing role in the pathogenesis of ARDS and septic shock. Any increase of endocan is a surrogate of worsening of the clinical course.


id: cord-006308-s5le8ugm
author: Dimopoulos, G.
date: 2007-05-25
txt: ./txt/cord-006308-s5le8ugm.txt
cache: ./cache/cord-006308-s5le8ugm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101586/
doi: 10.1007/s10096-007-0316-2
summary:
  The purpose of this study was to compare the risk factors, clinical manifestations, and outcome of candidemia in immunocompromised (IC) and nonimmunocompromised (NIC) critically ill patients. No study to date has been specifically designed to compare risk factors, manifestations, and outcome of candidemia in IC and NIC critically ill patients. Thus, we performed the present study to assess possible clinically significant differences between IC and NIC patients with candidemia receiving care in the ICU setting. The investigational work-up for invasive candidiasis in our patients (other than blood cultures, esophageal endoscopy, and oral scrapings) included (a) identification of predisposing factors, (b) surveillance cultures to detect possible colonization, (c) eye exam, and (d) CT scans of the suspected site of infection. The NIC patients in our study developed candidemia during their ICU hospitalization, and none manifested esophageal candidiasis, although one developed oral thrush.

title:
  Candidemia in immunocompromised and immunocompetent critically ill patients: a prospective comparative study

abstract:
  The purpose of this study was to compare the risk factors, clinical manifestations, and outcome of candidemia in immunocompromised (IC) and nonimmunocompromised (NIC) critically ill patients. Data were collected prospectively over a 2-year period (02/2000–01/2002) from patients in a 25-bed, medical–surgical intensive care unit (ICU). Eligible for participation in this study were patients who developed candidemia during their ICU stay. Patients under antifungal therapy and with a confirmed systemic fungal infection prior to the diagnosis of candidemia were excluded. Cultures of blood, urine, and stool were performed for all patients in the study, and all patients underwent endoscopy/biopsy of the esophagus for detection of Candida. Smears and/or scrapings of oropharyngeal and esophageal lesions were examined for hyphae and/or pseudohyphae and were also cultured for yeasts. During the study period, 1,627 patients were hospitalized in the ICU, 57% for primary medical reasons and 43% for surgical reasons. After application of the study’s inclusion and exclusion criteria, 24 patients with candidemia (9 IC and 15 NIC) were analyzed. Total parenteral nutrition was more common in IC than in NIC patients (9/9 [100%] vs 8/15 [53%], p = 0.02). Oropharyngeal candidiasis was detected in 5 of 9 (55.5%) IC patients and in 1 of 15 (6.5%) NIC patients (p = 0.015). Esophageal candidiasis was also more common in IC than in NIC patients (4/9 [44%] vs 0/15 [0%], p = 0.012). Among the 9 IC patients, all except 2 died, resulting in a crude mortality of 78%; among the 15 NIC patients, 9 died, resulting in a crude mortality of 60% (p > 0.05). Autopsy was performed in two IC and in six NIC patients, with disseminated candidiasis found in one IC patient. Oropharyngeal and esophageal candidiasis are frequent in IC patients with candidemia. In contrast, this coexistence is rare in NIC critically ill patients with Candida bloodstream infections. A high mortality was noted in both IC and NIC critically ill patients with candidemia.


id: cord-006325-3no74e74
title: Microorganisms associated with respiratory syncytial virus pneumonia in the adult population
author: Jeannoël, M.
date: 2018-10-23
txt: ./txt/cord-006325-3no74e74.txt
cache: ./cache/cord-006325-3no74e74.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101617/
doi: 10.1007/s10096-018-3407-3
summary:
  A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France

abstract:
  Respiratory syncytial virus (RSV) has been recognized as responsible for severe respiratory illness in adults, especially in the elderly. While pneumonia is commonly observed during RSV infection, the burden and epidemiology of bacterial superinfection is poorly understood. The aim of this study was to identify microorganisms associated with RSV-positive pneumonia in adults. A retrospective study was conducted during three consecutive winters (October to April 2013–2016) in the University Hospital of Lyon, France. During RSV circulation periods, a systematic RSV screening was performed by reverse-transcription PCR on all respiratory samples collected from adults. Records of RSV-positive patients were subsequently analyzed to identify radiologically confirmed pneumonia cases. Bacteria were identified by standard bacteriology cultures or urinary antigen screening and classified as potentially causative of pneumonia if quantification was above the specific threshold as defined by the European Manual of Clinical Microbiology. Overall, 14,792 adult respiratory samples were screened for RSV detection by PCR. In total, 292 had a positive RSV detection (2.0%) among which 89 presented with pneumonia including 27 bacterial superinfections (9.3%) with Streptococcus pneumonia, Haemophilus influenza, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis. Most patients were elderly (55.6%) and patients with comorbidities (77.8%). A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia.


id: cord-006335-j74hnoag
author: Clement, J.
date: 2011-11-09
txt: ./txt/cord-006335-j74hnoag.txt
cache: ./cache/cord-006335-j74hnoag.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101631/
doi: 10.1007/s10096-011-1456-y
abstract: nan
summary:
  The Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, propose a total of eight distinctive clinical criteria for its "Hantavirus Pulmonary Syndrome Case Report Form" [9] : (1) fever, (2) thrombocytopaenia, )3) elevated haematocrit (Hct), (4) elevated serum creatinine, (5) left shift leukocytosis with a high percentage of "atypical lymphocytes", (6) need for supplemental oxygen, (7) need for intubation (and mechanical ventilation), and (8) chest Rx showing unexplained bilateral infiltrates or being suggestive of acute respiratory distress syndrome (ARDS). The first isolation in Europe of a murine HTNV-like hantavirus (in hindsight, probably DOBV) and dated 1986, was from the urine of a 21-year-old Greek soldier, infected during manoeuvres in Porogia (northern Greece) and suffering from acute pulmonary oedema, and later from acute renal failure (ARF), prompting both life-saving ventilation and acute dialysis [17] .

title:
  A unifying hypothesis and a single name for a complex globally emerging infection: hantavirus disease


id: cord-006344-de4dhv4b
author: Seitsonen, E.
date: 2006-03-21
txt: ./txt/cord-006344-de4dhv4b.txt
cache: ./cache/cord-006344-de4dhv4b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101642/
doi: 10.1007/s10096-006-0117-z
summary:
  title: Corticosteroids combined with continuous veno-venous hemodiafiltration for treatment of hantavirus pulmonary syndrome caused by Puumala virus infection Reported here are two cases of hantavirus pulmonary syndrome caused by Puumala virus infection, which rapidly resolved after initiation of corticosteroid treatment combined with continuous veno-venous hemodiafiltration. We describe two cases of PUU-associated HPS, in which administration of intravenous corticosteroids combined with continuous veno-venous hemodiafiltration (CVVHDF) was followed by rapid clinical improvement. On day 5 POS the lung infiltrates had increased considerably (Fig. 3a,b) , and the patient required continuous ventilation with a positive airway pressure mask. We describe two cases of PUU-infected patients who presented with both renal and respiratory failure requiring renal replacement therapy and mechanical ventilation. High levels of cytokineproducing cells in the lung tissues of patients with fatal hantavirus pulmonary syndrome High levels of viremia in patients with the Hantavirus pulmonary syndrome

title:
  Corticosteroids combined with continuous veno-venous hemodiafiltration for treatment of hantavirus pulmonary syndrome caused by Puumala virus infection

abstract:
  Reported here are two cases of hantavirus pulmonary syndrome caused by Puumala virus infection, which rapidly resolved after initiation of corticosteroid treatment combined with continuous veno-venous hemodiafiltration. These cases emphasize the role of the inflammatory response in the pathogenesis of hantavirus pulmonary syndrome.


id: cord-006448-elfroq6f
title: Severe adenovirus pneumonia in immunocompetent adults: a case report and review of the literature
author: Hakim, F. A.
date: 2007-11-21
txt: ./txt/cord-006448-elfroq6f.txt
cache: ./cache/cord-006448-elfroq6f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101838/
doi: 10.1007/s10096-007-0416-z
summary:
  We report a case of severe adenovirus pneumonia in a young immunocompetent male who presented with sudden onset respiratory distress that progressed rapidly to respiratory failure and made a successful recovery on supportive measures. Systematic review of the literature identified 14 cases of severe adenovirus pneumonia (defined as respiratory failure requiring ventilatory support at any point during the course of illness) in otherwise healthy immunocompetent adults both in epidemic and community settings. We report a case of severe adenovirus pneumonia in a previously healthy immunocompetent male who presented to us with rapidly developing respiratory failure and made a successful recovery on supportive measures. We defined severe adenovirus pneumonia if associated with respiratory failure requiring ventilatory support at any point during the course of illness and immunocompetent adults as individuals with no acquired or congenital immunodeficiency state with or without associated premorbid conditions.

abstract:
  Adenovirus is a frequent cause of mild self-limiting upper respiratory tract infection, gastroenteritis, and conjunctivitis in infants and young children. Fatal infections (severe pneumonia progressing to respiratory failure, septic shock and/or encephalitis) are rare among immunocompetent adults. We report a case of severe adenovirus pneumonia in a young immunocompetent male who presented with sudden onset respiratory distress that progressed rapidly to respiratory failure and made a successful recovery on supportive measures. Systematic review of the literature identified 14 cases of severe adenovirus pneumonia (defined as respiratory failure requiring ventilatory support at any point during the course of illness) in otherwise healthy immunocompetent adults both in epidemic and community settings. We describe the clinical characteristics, radiological features, and outcome of identified cases.


id: cord-006450-si5168pb
title: Which patients should be tested for viruses on bronchoalveolar lavage fluid?
author: Jouneau, S.
date: 2012-12-14
txt: ./txt/cord-006450-si5168pb.txt
cache: ./cache/cord-006450-si5168pb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101843/
doi: 10.1007/s10096-012-1791-7
summary:
  The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). The variables significantly associated with positive viral tests on univariate analysis were immunosuppression (i.e., HIV infection, corticosteroids >10 mg/day for ≥3 weeks, and/or other immunosuppressive therapy), ground-glass attenuations on chest CT scans, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) ICU stay, and (iii) mechanical ventilation before BAL was performed (p<0.01 for each comparison). This advocates for the systematic use of PCR techniques for viral tests in BALF, in accordance with previous studies [27, 28] , in the situations where viruses may reasonably be suspected (i.e., acute lower tract respiratory disease in immunocompromised patients and/or patients with unexplained bilateral ground-glass attenuations on CT scan).

abstract:
  Bronchoalveolar lavage (BAL) is a major diagnostic tool in lung diseases, including viral respiratory infections. We aimed to better define the situations where viral tests should be performed on BAL fluid (BALF). We retrospectively studied all cases where viral tests [immunofluorescence, immunocytochemistry, viral culture, and/or polymerase chain reaction (PCR)] were performed on BALF during a period of 1 year (2008) in our institution. We compared the characteristics of patients with virus-positive versus virus-negative BALF. Of the 636 BALF samples sent to the microbiology laboratory, 232 underwent viral tests. Of these, 70 (30 %) were positive and identified 85 viruses: herpes simplex virus (HSV)-1 (n = 27), cytomegalovirus (CMV, n = 23), Epstein–Barr virus (EBV, n = 18), human herpesvirus (HHV)-6 (n = 12), respiratory syncytial virus (RSV, n = 3), rhinovirus (n = 1), and adenovirus (n = 1). The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). On multivariate analysis, only immunosuppression [odds ratio (OR) 6.4, 95 % confidence interval (CI) [2.8–14.3], p < 0.0001] and ground-glass attenuations (OR 3.7, 95 % CI [1.8–7.7], p = 0.0004) remained associated with virus-positive BAL. None of the viral tests performed on BALF for the initial assessment of diffuse infiltrative lung disease (n = 15) was positive. PCR improved the diagnostic yield of viral tests on BALF by 50 %. Testing for viruses on BALF should be mostly restricted to immunocompromised patients with acute respiratory diseases and/or patients with unexplained ground-glass attenuations on CT scanning.


id: cord-006478-qkw1ik4e
author: Blahová, J.
date: 1999
txt: ./txt/cord-006478-qkw1ik4e.txt
cache: ./cache/cord-006478-qkw1ik4e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101884/
doi: 10.1007/s100960050247
abstract: nan
summary:
  title: High-Frequency Transduction of Antibiotic Resistance in Pseudomonas aeruginosa by a Wild-Type Bacteriophage with Restricted Specificity for Recipient Strains Bartoníková Antibiotic resistance can be transferred among strains of Pseudomonas aeruginosa by conjugation [1] , transduction by wild-type phages as well as by generalised transducing phages, such as F-116 or G-101 [2] [3] [4] [5] , or by transposition of integrons [6] . In contrast to other wild-type phages isolated from multiple-drug-resistant nosocomial strains of Pseudomonas aeruginosa [3, 5, 9] , the phage lysate of Pseudomonas aeruginosa 103 showed a lytic reaction when added, in dilution of up to 10 -12 , to the recipient strain Pseudomonas aeruginosa PAO 1670 (Figure 1 ) but not to the other strains. Transduction of antibiotic resistance including imipenem resistance in nosocomial Pseudomonas aeruginosa strains by wild-type phages Transduction of imipenem resistance by wild-type bacteriophages from three Pseudomonas aeruginosa strains from a single clinical source

title:
  High-Frequency Transduction of Antibiotic Resistance in Pseudomonas aeruginosa by a Wild-Type Bacteriophage with Restricted Specificity for Recipient Strains


id: cord-006490-jo8dhtb0
author: Maillet, M.
date: 2013-08-30
txt: ./txt/cord-006490-jo8dhtb0.txt
cache: ./cache/cord-006490-jo8dhtb0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101903/
doi: 10.1007/s10096-013-1960-3
summary:
  All positive Pj qPCR [targeting the major surface glycoprotein (MSG) gene] obtained in respiratory samples from immunocompromised patients presenting pneumonia at the Grenoble University Hospital, France, were collected between August 2009 and April 2011. qPCR targeting the MSG gene can be helpful to discriminate PCP from Pj colonization in immunocompromised patients, using two cut-off values, with a gray zone between them. The aim of this study was to use Pj real-time quantitative PCR (qPCR) in order to differentiate PCP and Pj colonization in immunocompromised patients. A receiver operating characteristic (ROC) curve for copy numbers was constructed and used to define cut-off values in order to discriminate the definite and probable PCP groups from the colonized group (possible PCP group and other diagnosis). In conclusion, our study shows that our qPCR targeting the MSG gene in respiratory samples can help discriminate PCP from pneumonia with Pj colonization in immunocompromised patients, using two cut-off values of 3,160 and 31,600 copies/ml, with a gray zone between them.

title:
  Pneumocystis jirovecii (Pj) quantitative PCR to differentiate Pj pneumonia from Pj colonization in immunocompromised patients

abstract:
  Conventional polymerase chain reaction (PCR) in respiratory samples does not differentiate between Pneumocystis pneumonia (PCP) and Pneumocystis jirovecii (Pj) colonization. We used Pj real-time quantitative PCR (qPCR) with the objective to discriminate PCP from Pj colonization in immunocompromised patients. All positive Pj qPCR [targeting the major surface glycoprotein (MSG) gene] obtained in respiratory samples from immunocompromised patients presenting pneumonia at the Grenoble University Hospital, France, were collected between August 2009 and April 2011. Diagnoses were retrospectively determined by a multidisciplinary group of experts blinded to the Pj qPCR results. Thirty-one bronchoalveolar lavages and four broncho aspirations positive for the Pj qPCR were obtained from 35 immunocompromised patients. Diagnoses of definite, probable, and possible PCP, and pneumonia from another etiology were retrospectively made for 7, 4, 5, and 19 patients, respectively. Copy numbers were significantly higher in the “definite group” (median 465,000 copies/ml) than in the “probable group” (median 38,600 copies/ml), the “possible group” (median 1,032 copies/ml), and the “other diagnosis group” (median 390 copies/ml). With the value of 3,160 copies/ml, the sensitivity and specificity of qPCR for the diagnosis of PCP were 100 % and 70 %, respectively. With the value of 31,600 copies/ml, the sensitivity and specificity were 80 % and 100 %, respectively. The positive predictive value was 100 % for results with more than 31,600 copies/ml and the negative predictive value was 100 % for results with fewer than 3,160 copies/ml. qPCR targeting the MSG gene can be helpful to discriminate PCP from Pj colonization in immunocompromised patients, using two cut-off values, with a gray zone between them.


id: cord-006517-845w9r6l
author: Lalueza, A.
date: 2017-05-13
txt: ./txt/cord-006517-845w9r6l.txt
cache: ./cache/cord-006517-845w9r6l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101956/
doi: 10.1007/s10096-017-2998-4
summary:
  The aim of the present study was to assess the frequency and clinical impact of hematological abnormalities in the range of those accepted by the Histyocite Society for the suspicion of HPS [19] in patients who were admitted to the hospital with a confirmed influenza virus infection. In Beutel''s study of 25 critically ill patients with influenza A (H1N1) pdm09 virus associated hemophagocytic syndrome, the absence of steroid therapy in the early phase of the infection might have contributed to the high incidence of HPS (9 out of 25 patients) and the rather poor outcomes [18] . Significant hematological abnormalities are frequently seen in patients with influenza virus infection who required hospital admission and are associated with a poor outcome.

title:
  Impact of severe hematological abnormalities in the outcome of hospitalized patients with influenza virus infection

abstract:
  Although hematological abnormalities have been described among patients with influenza virus infection, little is known about their impact on the outcome of the patients. The aim of this study was to assess the frequency and clinical impact of severe hematological abnormalities in patients with confirmed influenza virus infection. This was an observational retrospective study including all adult patients with diagnosis of influenza virus infection hospitalized from January to May 2016 in our institution. Influenza virus infection was diagnosed by means of rRT-PCR assay performed on respiratory samples. Poor outcome was defined as a composite endpoint in which at least one of the following criteria had to be fulfilled: (a) respiratory failure, (b) SOFA ≥2, or (c) death. Two hundred thirty-nine patients were included. Applying the HLH-04 criteria for the diagnosis of hemophagocytic syndrome, cytopenias (hemoglobin ≤9 g/dl, platelets <100,000/μl or neutrophils <1,000/μl) were present in 51 patients (21%). Patients with hematological abnormalities showed higher SOFA scores, respiratory failure, septic shock and in-hospital mortality than the remaining patients. The composite endpoint was present in 33.3% in the cytopenias group vs. 13.3% in the group without cytopenias (p=0.001). In a multivariate analysis, variables associated with the composite endpoint were: use of steroids prior to present admission (OR: 0.12; 95% CI: 0.015–0.96, p=0.046), presence of any hematological abnormality (OR: 3.54; 95% CI:1.66–7.51, p= 0.001), and LDH>225 U/l (OR:4.45; CI:1–19.71, p=0.049). Hematological abnormalities are not uncommon among hospitalized patients with influenza virus infection, and they are associated with a poorer outcome.


id: cord-006561-w4s0k75p
title: Blood culture fluorescence rates predict severity and mortality of invasive pneumococcal pneumonia
author: Fink, D.
date: 2015-05-02
txt: ./txt/cord-006561-w4s0k75p.txt
cache: ./cache/cord-006561-w4s0k75p.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102030/
doi: 10.1007/s10096-015-2386-x
summary:
  Comorbidity was defined as the presence of one of the following chronic conditions: immunocompromise (defined as primary immunodeficiency or secondary immunodeficiency due to splenectomy, haematological malignancy, autoimmune disorder, chemotherapy or radiotherapy within 4 weeks prior to admission), diabetes mellitus (defined as receiving any oral or subcutaneous therapy for diabetes mellitus), COPD (defined as the presence of airflow limitation due to chronic bronchitis or emphysema), current smoker (any number of cigarettes/day), heart disease (defined as prior elective or emergency percutaneous coronary intervention or coronary artery bypass grafting, or New York Heart Association classes III or IV symptoms of heart failure), liver disease (defined as biopsy-proven cirrhosis or past medical history of complications of portal hypertension, including upper gastro-intestinal bleeding, encephalopathy, spontaneous bacterial peritonitis or more Fig. 1 The standard curve for Streptococcus pneumoniae (NCTC 12977 strain) was generated by plotting the mean of at least four samples of each ten-fold dilution (log 10 CFU/ml) against the corresponding fluorescence rate (FR).

abstract:
  Invasive pneumococcal pneumonia is associated with high rates of mortality. Clinical assessment tools have poor sensitivity for predicting clinical outcomes. Molecular measurements of bacterial load correlate closely with clinical outcome but require specialist facilities and expertise. This study describes how routine blood culture testing can estimate bacterial load and predict clinical outcome for invasive pneumococcal pneumonia. Between December 2009 to March 2014, clinical and laboratory data were collected for 50 patients with Streptococcus pneumoniae bacteraemia secondary to community-acquired pneumonia. Fluorescence rates (FR) were calculated from growth curves generated by BACTEC blood culture analysers by dividing change in fluorescence units (FU), measured at the first point of detectable fluorescence and at the point of automated BACTEC positivity, by time in hours. The mean age of the patients was 70.6 years (49.6–86.3). Forty patients survived invasive pneumococcal disease and ten patients died. These two groups did not significantly differ by demographic or clinical characteristics. The mean FR for the non-survival group (3.62 × 10(−3) FU/h) was significantly higher (p < 0.001) than that of the survival group (1.73 × 10(−3) FU/h). FR did not vary by serotype. We determined that an FR of 2.59 × 10(−3) FU/h might represent a useful threshold for predicting high mortality risk with a sensitivity of 91 % and a specificity of 97 %. Our FR calculation uses cheap and accessible routine blood culture techniques to predict mortality in a small retrospective cohort study. In patients admitted to hospital with pneumococcal bacteraemia and, potentially, other organisms, this single tool could guide early escalation of clinical care.


id: cord-006581-f957o5z3
author: Gizzi, M.
date: 2013-05-14
txt: ./txt/cord-006581-f957o5z3.txt
cache: ./cache/cord-006581-f957o5z3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102061/
doi: 10.1007/s10096-013-1885-x
summary:
  The most important pathogens are Hantaan virus and Seoul virus in the Far East (>90 % of worldwide infections), Puumala virus (PUUV) and Dobrava-Belgrade virus in Europe and Russia, and, finally, Sin Nombre virus and Andes virus in the Americas [1, 2] Until recently, two clinical syndromes were classically described: hantavirus (cardio-)pulmonary syndrome (HPS or HCPS) described since 1994 in the Americas [4] and hemorrhagic fever with renal syndrome (HFRS) or its milder form nephropathia epidemica (NE), known in Eurasia since the early 1930s. The history of our patient fulfills most of the eight clinical findings specified in the "Hantavirus Pulmonary Syndrome Case Report Form", as issued by the Centers for Disease Control and Prevention (CDC), Atlanta, GA [13] : (1) fever, (2) thrombocytopenia, (3) elevated hematocrit, (4) elevated serum creatinine, (5) left shift leukocytosis with "atypical lymphocytes", (6) need for supplemental oxygen, (7) need for intubation (and mechanical ventilation), and (8) chest radiograph showing unexplained bilateral infiltrates or being suggestive of adult respiratory distress syndrome (ARDS).

title:
  Another case of “European hantavirus pulmonary syndrome” with severe lung, prior to kidney, involvement, and diagnosed by viral inclusions in lung macrophages

abstract:
  Puumala virus (PUUV) is considered a classic Old World etiologic agent of nephropathia epidemica (NE), or hemorrhagic fever with renal syndrome (HFRS). HFRS is considered to be distinct from hantavirus (cardio-)pulmonary syndrome (HPS or HCPS), described in the New World. Here, we report a severe case, which fulfilled most, if not all, Centers for Disease Control and Prevention (CDC) criteria for HPS, needing non-invasive ventilation and subsequent acute hemodialysis. However, the etiological agent was PUUV, as proved by serological testing, real-time polymerase chain reaction (PCR), and sequencing. Viral antigen was detected by specific anti-PUUV immunostaining, showing, for the first time, greenish intracytoplasmic inclusions in bronchoalveolar lavage (BAL) macrophages. This case definitely confirms that HPS can be encountered during PUUV infections. Interestingly, special findings could render the diagnosis easier, such as greenish homogeneous cytoplasmic inclusions, surrounded by a fine clear halo in BAL macrophages. Therefore, although the diagnosis remains difficult before the onset of renal involvement, the occurrence of severe respiratory failure mimicking community-acquired pneumonia must alert the clinician for possible HPS, especially in endemic areas.


id: cord-006714-q7wy76e2
title: Impact of combination therapy with aminoglycosides on the outcome of ICU-acquired bacteraemias
author: Delannoy, P.-Y.
date: 2012-02-15
txt: ./txt/cord-006714-q7wy76e2.txt
cache: ./cache/cord-006714-q7wy76e2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102278/
doi: 10.1007/s10096-012-1568-z
summary:
  Our study supports the hypothesis that combination short-term antibiotherapy with an aminoglycoside for ICU-acquired bacteraemias could increase survival. Meta-analysis failed to demonstrate improved outcomes in patients treated with antibiotic combinations over those receiving monotherapy [1] [2] [3] [4] and resulted in a decreased use of combination therapy. We performed a retrospective study to evaluate the impact of AGs in antimicrobial combination on ICU-acquired bacteraemia in our universityaffiliated ICU [8] [9] [10] [11] . The aim of the study was to evaluate the impact of AGs in antibiotic combination on the outcome of patients with ICU-acquired bacteraemia. We found a survival benefit with the use of combination therapy with AGs for ICU-acquired bacteraemias. In the ICU, inadequate empirical antibiotic therapy is associated with an increased mortality risk in patients with ventilator-associated pneumonia and bacteraemia. Our study suggests that short-term combination beta-lactams plus AGs therapy in intensive care unit (ICU)-acquired bacteraemia could reduce mortality.

abstract:
  Pharmacodynamic studies report on the rapid bactericidal activity of aminoglycosides, conferring them as being of theoretical interest for bacteraemia treatment. We assessed this issue in a retrospective study of patients with intensive care unit (ICU)-acquired bacteraemias. To determine the impact of aminoglycosides in antimicrobial combination on the outcome of patients with bacteraemia, we performed a monovariate analysis and a logistic regression analysis comparing patients treated with or without aminoglycosides. Forty-eight bacteraemias in 48 patients were included. Eighteen patients received aminoglycosides. Baseline characteristics as well as adaptation and adequation of antibiotherapy did not differ in patients who did or did not receive aminoglycosides. Patients who received aminoglycosides had longer time alive away from the ICU (11.3 ± 8.9 (10 [0–20]) vs. 3.2 ± 6.6 (0 [0–2] days; p = 0.002) and free from mechanical ventilation (12.5 ± 9.3 (14 [0–21] vs. 5.5 ± 9.2 (0 [0–10] days; p = 0.02) on day 28. The ICU mortality was 16% in the aminoglycoside group versus 46% (p = 0.03). In the multivariate analysis, patients treated with aminoglycosides were 6 times less likely to die than those treated without aminoglycosides (confidence interval [CI] = [1.3–28.9]; p = 0.02). Our study supports the hypothesis that combination short-term antibiotherapy with an aminoglycoside for ICU-acquired bacteraemias could increase survival.


id: cord-006766-u31go6xi
author: Lepur, D.
date: 2011-01-29
txt: ./txt/cord-006766-u31go6xi.txt
cache: ./cache/cord-006766-u31go6xi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102361/
doi: 10.1007/s10096-011-1184-3
summary:
  The aim of this study was to assess the cerebrovascular CO 2 R measured by TCD using the breath-holding method in patients with inflammatory central nervous system (CNS) diseases. The following parameters were recorded in a database: age, gender, physical and neurological signs, mechanical ventilation (MV), cerebrospinal fluid (CSF) characteristics, microbiological findings in CSF and blood, mean arterial pressure (MAP), Glasgow Coma Scale (GCS) score, Glasgow Outcome Scale (GOS) score, and the mean breath-holding index (BHI m ). Non-bacterial inflammatory CNS disease (NBM) was diagnosed on the basis of present encephalopathy with at least one of the following: fever, seizures, focal neurological findings; pleocytosis with increased protein concentration in the CSF; and a positive CSF or blood culture (fungal meningitis); virus detection by PCR assay in CSF samples; proved intrathecal antibody production and electroencephalographic or neuroimaging findings consistent with encephalitis or acute disseminated encephalomyelitis (ADEM). This prospective study assessed cerebrovascular reactivity (CO 2 R) by TCD using the breath-holding method in patients with inflammatory CNS diseases.

title:
  Prospective observational cohort study of cerebrovascular CO(2) reactivity in patients with inflammatory CNS diseases

abstract:
  The purpose of this study was to evaluate the significance of cerebrovascular CO(2) reactivity (CO(2) R) in the course and outcome of inflammatory central nervous system (CNS) diseases. Sixty-eight patients with inflammatory CNS diseases and 30 healthy volunteers were included in this prospective observational cohort study. The observational period was between January 2005 and May 2009. The CO(2) R was measured by transcranial Doppler (TCD) ultrasound using the breath-holding method. We compared patients with normal CO(2) R (breath-holding index [BHI(m)] ≥ 1.18 = BHI(N) group) with patients who showed impaired CO(2) R (BHI(m) < 1.18 = BHI(R) group). We also analyzed the association of impaired CO(2) R with the etiology, severity, and outcome of disease. When compared to the BHI(N) group, the patients from the BHI(R) group were older, had a heavier consciousness disturbance, experienced more frequent respiratory failure, and, subsequently, had worse outcomes. There were no fatalities among the 28 patients in the BHI(N) group. The comparison of subjects with bacterial and non-bacterial meningitis revealed no significant differences. The unfavorable outcome of disease (Glasgow Outcome Scale [GOS] score 1–3) was significantly more common in subjects with impaired CO(2) R (62.5% vs. 10.7%). Logistic regression analysis was performed in order to establish the prognostic value of BHI(m). The outcome variable was unfavorable outcome (GOS 1–3), while the independent variables were age, Glasgow Coma Scale (GCS) score, and BHI(m). The age and BHI(m) showed the strongest influence on disease outcome. A decrease of BHI(m) for each 0.1 unit increased the risk of unfavorable outcome by 17%. Our study emphasizes the importance of CO(2) R assessment in patients with inflammatory CNS diseases.


id: cord-010959-sigw7yxk
title: Influenza and antiviral resistance: an overview
author: Lampejo, Temi
date: 2020-02-13
txt: ./txt/cord-010959-sigw7yxk.txt
cache: ./cache/cord-010959-sigw7yxk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223162/
doi: 10.1007/s10096-020-03840-9
summary:
  Resistance to neuraminidase inhibitors has remained at low levels to date and the majority of resistance is seen in influenza A H1N1 pdm09 infected immunocompromised individuals receiving oseltamivir but is also seen less frequently with influenza A H3N2 and B. This potential for vast genetic variability within influenza viruses and their highly error-prone RNA dependent RNA polymerase does raise concerns regarding the possible emergence of treatment resistant strains and generates further questions regarding their viral fitness and transmissibility as well as which strategies to employ in rapidly identifying and effectively treating these resistance variants. Neuraminidase inhibitor susceptibility testing should be considered particularly in young children and immunocompromised patients being treated with a neuraminidase inhibitor for influenza (especially H1N1 pdm09), who are not responding to treatment and/or have persistently high viral loads (low cycle threshold values using RT-PCR) and/or exposed to a suspected or confirmed resistant case.

abstract:
  Influenza affects approximately 1 billion individuals each year resulting in between 290,000 and 650,000 deaths. Young children and immunocompromised individuals are at a particularly high risk of severe illness attributable to influenza and these are also the groups of individuals in which reduced susceptibility to neuraminidase inhibitors is most frequently seen. High levels of resistance emerged with previous adamantane therapy for influenza A and despite no longer being used to treat influenza and therefore lack of selection pressure, high levels of adamantane resistance continue to persist in currently circulating influenza A strains. Resistance to neuraminidase inhibitors has remained at low levels to date and the majority of resistance is seen in influenza A H1N1 pdm09 infected immunocompromised individuals receiving oseltamivir but is also seen less frequently with influenza A H3N2 and B. Rarely, resistance is also seen in the immunocompetent. There is evidence to suggest that these resistant strains (particularly H1N1 pdm09) are able to maintain their replicative fitness and transmissibility, although there is no clear evidence that being infected with a resistant strain is associated with a worse clinical outcome. Should neuraminidase inhibitor resistance become more problematic in the future, there are a small number of alternative novel agents within the anti-influenza armoury with different mechanisms of action to neuraminidase inhibitors and therefore potentially effective against neuraminidase inhibitor resistant strains. Limited data from use of novel agents such as baloxavir marboxil and favipiravir, does however show that resistance variants can also emerge in the presence of these drugs.


id: cord-011417-a5q15dq1
title: The epidemiology of invasive meningococcal disease and the utility of vaccination in Malta
author: Pace, David
date: 2020-05-16
txt: ./txt/cord-011417-a5q15dq1.txt
cache: ./cache/cord-011417-a5q15dq1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229431/
doi: 10.1007/s10096-020-03914-8
summary:
  Similarly, a strategy using a conjugate MenACWY vaccine targeting 9-month to 4-year-old children to control MenW disease in Chile provided direct protection to the vaccinated group but did not result in a herd immune effect [17] . In European countries, the highest MenB and C disease burden is similarly seen in infants (although the incidence rate reached 5.4/100,000 and 2.1/100,000 infants for MenB and C, respectively, much less when compared with the mean incidence rate of 9.66/100,000 and 6.72/100,000 infants for the corresponding capsular groups in Malta), with children less than 5 years old and adolescents and young adults being more affected than other age groups [1, 31] . Furthermore, a MenB immunization programme consisting of a 2 dose prime and boost MenB infant vaccine schedule in addition to MenB adolescent vaccination at 12 years of age would also be projected to provide direct protection and reduce the incidence of MenB, which is responsible for the highest meningococcal disease burden in Malta.

abstract:
  Invasive meningococcal disease (IMD) is a vaccine-preventable devastating infection that mainly affects infants, children and adolescents. We describe the population epidemiology of IMD in Malta in order to assess the potential utility of a meningococcal vaccination programme. All cases of microbiologically confirmed IMD in the Maltese population from 2000 to 2017 were analysed to quantify the overall and capsular-specific disease burden. Mean overall crude and age-specific meningococcal incidence rates were calculated to identify the target age groups that would benefit from vaccination. Over the 18-year study period, 111 out of the 245 eligible notified cases were confirmed microbiologically of which 70.3% had septicaemia, 21.6% had meningitis, and 6.3% had both. The mean overall crude incidence rate was 1.49/100,000 population with an overall case fatality rate of 12.6%. Meningococcal capsular groups (Men) B followed by C were the most prevalent with W and Y appearing over the last 6 years. Infants had the highest meningococcal incidence rate of 18.9/100,000 followed by 6.1/100,000 in 1–5 year olds and 3.6/100,000 in 11–15 year old adolescents. The introduction of MenACWY and MenB vaccines on the national immunization schedule in Malta would be expected to reduce the disease burden of meningococcal disease in children and adolescents in Malta.


id: cord-025861-nsrs6dmc
author: Waldeck, Frederike
date: 2020-06-03
txt: ./txt/cord-025861-nsrs6dmc.txt
cache: ./cache/cord-025861-nsrs6dmc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7266735/
doi: 10.1007/s10096-020-03923-7
summary:
  We aimed to describe prognostic factors for influenza-associated IA (IAA) and poor outcome and mortality in critically ill patients in Switzerland. Aspergillus is a common superinfection in critically ill influenza patients associated with poor outcome and longer duration of organ supportive therapies. Since no data on IAA was available from Switzerland, we retrospectively analysed all patients with severe influenza infection needing treatment in two large Swiss ICUs during the 2017/2018 influenza season with regard to predictors of IAA, mortality and poor outcome. In this retrospective cohort study, sixteen ICUs of tertiary hospitals in Switzerland were asked if they had observed cases of IAA and severe influenza and routinely looked for IAA based on clinical suspicion with galactomannan and fungal cultures in BAL; only two of them met the criteria (Cantonal Hospital of St. Gallen and University Hospital of Geneva). IAA is a severe and relatively frequent complication affecting 11% of patients with influenza treated in two Swiss ICUs. Aspergillus represented the most frequent respiratory co-infection of influenza in this cohort.

title:
  Influenza-associated aspergillosis in critically-ill patients—a retrospective bicentric cohort study

abstract:
  Influenza was recently reported as a risk factor for invasive aspergillosis (IA). We aimed to describe prognostic factors for influenza-associated IA (IAA) and poor outcome and mortality in critically ill patients in Switzerland. All adults with confirmed influenza admitted to the ICU at two Swiss tertiary care centres during the 2017/2018 influenza season were retrospectively evaluated. IAA was defined by clinical, mycological and radiological criteria: a positive galactomannan in bronchoalveolar lavage or histopathological or cultural evidence in respiratory specimens of Aspergillus spp., any radiological infiltrate and a compatible clinical presentation. Poor outcome was defined as a composite of in-hospital mortality, ICU length of stay (LOS), invasive ventilation for > 7 days or extracorporeal membrane oxygenation. Of 81 patients with influenza in the ICU, 9 (11%) were diagnosed with IAA. All patients with IAA had poor outcome compared to 26 (36%) patients without IAA (p < 0.001). Median ICU-LOS and mortality were 17 vs. 3 days (p < 0.01) and 3/9 (33%) vs. 13/72 (18%; p = 0.37) in patients with vs. without IAA, respectively. Patients with IAA had significantly longer durations of antibiotic therapy, vasoactive support and mechanical ventilation. Aspergillus was the most common respiratory co-pathogen (9/40, 22%) followed by classical bacterial co-pathogens. IAA was not associated with classical risk factors. Aspergillus is a common superinfection in critically ill influenza patients associated with poor outcome and longer duration of organ supportive therapies. Given the absence of classical risk factors for aspergillosis, greater awareness is necessary, particularly in those requiring organ supportive therapies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03923-7) contains supplementary material, which is available to authorized users.


id: cord-028379-ghudhac6
author: Eichenberger, Emily M.
date: 2020-07-04
txt: ./txt/cord-028379-ghudhac6.txt
cache: ./cache/cord-028379-ghudhac6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334117/
doi: 10.1007/s10096-020-03955-z
summary:
  Complement and cytokine levels were measured in serum samples from 20 hospitalized patients with SAB, 20 hospitalized patients with GNB, 10 non-infected hospitalized patients, and 10 community controls. Low C4 and C3 levels were associated with septic shock and 30-day mortality in patients with GNB, and elevated C3 was associated with a desirable outcome defined as absence of (1) septic shock, (2) acute renal failure, and (3) death within 30 days of bacteremia. We evaluated complement and cytokine levels in patients with Staphylococcus aureus and Gram-negative bacteremia as compared to non-bacteremic hospitalized patients and community controls and explored potential associations between levels of these immune components and clinical outcome of the source patients. The BSIR collects and stores both clinical data and biological specimens from non-neutropenic hospitalized patients aged 18 years or older who have culture-confirmed monomicrobial bloodstream infections caused by either Staphylococcus aureus or Gram-negative bacteria.

title:
  Complement levels in patients with bloodstream infection due to Staphylococcus aureus or Gram-negative bacteria

abstract:
  The complement system is a vital component of the innate immune system, though its role in bacteremia is poorly understood. We present complement levels in Staphylococcus aureus bacteremia (SAB) and Gram-negative bacteremia (GNB) and describe observed associations of complement levels with clinical outcomes. Complement and cytokine levels were measured in serum samples from 20 hospitalized patients with SAB, 20 hospitalized patients with GNB, 10 non-infected hospitalized patients, and 10 community controls. C5a levels were significantly higher in patients with SAB as compared to patients with GNB. Low C4 and C3 levels were associated with septic shock and 30-day mortality in patients with GNB, and elevated C3 was associated with a desirable outcome defined as absence of (1) septic shock, (2) acute renal failure, and (3) death within 30 days of bacteremia. Low levels of C9 were associated with septic shock in patients with GNB but not SAB. Elevated IL-10 was associated with increased 30-day mortality in patients with SAB. Complement profiles differ in patients with SAB and those with GNB. Measurement of IL-10 in patients with SAB and of C4, C3, and C9 in patients with GNB may help to identify those at higher risk for poor outcomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03955-z) contains supplementary material, which is available to authorized users.


id: cord-255785-wqlp6ogb
author: Liu, Wen-Kuan
date: 2019-09-05
txt: ./txt/cord-255785-wqlp6ogb.txt
cache: ./cache/cord-255785-wqlp6ogb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-019-03693-x
doi: 10.1007/s10096-019-03693-x
summary:
  title: Paramyxoviruses respiratory syncytial virus, parainfluenza virus, and human metapneumovirus infection in pediatric hospitalized patients and climate correlation in a subtropical region of southern China: a 7-year survey To investigate the features of paramyxovirus respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (HMPV) infection and determine the effect of meteorological conditions in Guangzhou, a subtropical region of southern China. In this study, we analyzed paramyxovirus infection among children hospitalized with ARI over a 7-year period in Guangzhou, and we collected local meteorological data for climate correlation analysis. In the present study, we sought to analyze the features of paramyxovirus infection and correlation with meteorological conditions in a subtropical region of southern China, by collecting respiratory samples from pediatric patients (≤ 14 years old) hospitalized with ARI in Guangzhou and testing for RSV, PIV, HMPV, and other common respiratory pathogens.

title:
  Paramyxoviruses respiratory syncytial virus, parainfluenza virus, and human metapneumovirus infection in pediatric hospitalized patients and climate correlation in a subtropical region of southern China: a 7-year survey

abstract:
  To investigate the features of paramyxovirus respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (HMPV) infection and determine the effect of meteorological conditions in Guangzhou, a subtropical region of southern China. We collected 11,398 respiratory samples from hospitalized pediatric patients with acute respiratory illness between July 2009 and June 2016 in Guangzhou. The samples were tested simultaneously for 18 respiratory pathogens using real-time PCR. Local meteorological data were also collected for correlation analysis. Of 11,398 patients tested, 5606 (49.2%) patients tested positive for one or more pathogens; RSV, PIV, and HMPV were the first, sixth, and ninth most frequently detected pathogens, in 1690 (14.8%), 502 (4.4%), and 321 (2.8%) patients, respectively. A total 17.9% (4605/5606) of patients with positive results had coinfection with other pathogens. Significant differences were found in the prevalence of RSV, PIV, and HMPV among all age groups (p < 0.001). RSV and HMPV had similar seasonal patterns, with two prevalence peaks every year. PIV appeared alternatively with RSV and HMPV. Multiple linear regression models were established for RSV, PIV, and HMPV prevalence and meteorological factors (p < 0.05). RSV and PIV incidence was negatively correlated with monthly mean relative humidity; RSV and HMPV incidence was negatively correlated with sunshine duration; PIV incidence was positively correlated with mean temperature. We described the features of paramyxovirus infection in a subtropical region of China and highlighted the correlation with meteorological factors. These findings will assist public health authorities and clinicians in improving strategies for controlling paramyxovirus infection.


id: cord-265729-prgj36g0
title: Probiotics in respiratory virus infections
author: Lehtoranta, L.
date: 2014-03-18
txt: ./txt/cord-265729-prgj36g0.txt
cache: ./cache/cord-265729-prgj36g0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24638909/
doi: 10.1007/s10096-014-2086-y
summary:
  Due to the lack of confirmatory studies and varied data available, more randomized, double-blind, and placebo-controlled trials in different age populations investigating probiotic dose response, comparing probiotic strains/genera, and elucidating the antiviral effect mechanisms are necessary. Many experimental studies in vitro and in animals show that specific strains of probiotics are capable of providing protection against virus infections by stimulating antiviral, cytokine, and chemokine responses in the respiratory and gastrointestinal epithelial cells or immune cells. Lactobacillus GG in the prevention of gastrointestinal and respiratory tract infections in children who attend day care centers: a randomized, double-blind, placebo-controlled trial Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial Consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114001 reduces the duration of respiratory infections in the elderly in a randomised controlled trial

abstract:
  Viral respiratory infections are the most common diseases in humans. A large range of etiologic agents challenge the development of efficient therapies. Research suggests that probiotics are able to decrease the risk or duration of respiratory infection symptoms. However, the antiviral mechanisms of probiotics are unclear. The purpose of this paper is to review the current knowledge on the effects of probiotics on respiratory virus infections and to provide insights on the possible antiviral mechanisms of probiotics. A PubMed and Scopus database search was performed up to January 2014 using appropriate search terms on probiotic and respiratory virus infections in cell models, in animal models, and in humans, and reviewed for their relevance. Altogether, thirty-three clinical trials were reviewed. The studies varied highly in study design, outcome measures, probiotics, dose, and matrices used. Twenty-eight trials reported that probiotics had beneficial effects in the outcome of respiratory tract infections (RTIs) and five showed no clear benefit. Only eight studies reported investigating viral etiology from the respiratory tract, and one of these reported a significant decrease in viral load. Based on experimental studies, probiotics may exert antiviral effects directly in probiotic–virus interaction or via stimulation of the immune system. Although probiotics seem to be beneficial in respiratory illnesses, the role of probiotics on specific viruses has not been investigated sufficiently. Due to the lack of confirmatory studies and varied data available, more randomized, double-blind, and placebo-controlled trials in different age populations investigating probiotic dose response, comparing probiotic strains/genera, and elucidating the antiviral effect mechanisms are necessary.


id: cord-267533-nmgtan4e
author: Hu, Zhigang
date: 2020-10-29
txt: ./txt/cord-267533-nmgtan4e.txt
cache: ./cache/cord-267533-nmgtan4e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33123934/
doi: 10.1007/s10096-020-04085-2
summary:
  By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin.

title:
  Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19

abstract:
  Coronavirus disease 2019 (COVID-19) with the infection of SARS-CoV-2 has become a serious pandemic worldwide. However, only few studies focused on risk factors of prolonged SARS-CoV-2 RNA detection among patients with COVID-19. We included 206 adult patients with laboratory-confirmed COVID-19 from two hospitals between 23 Jan and 1 April 2020. Least absolute shrinkage and selection operator (LASSO) analysis was used to screen out independent risk factors of SARS-CoV-2 RNA detection. By multivariate binomial logistic regression analysis and Cox regression analysis, we further determined the associations between SARS-CoV-2 RNA detection and potential risk factors. All patients had two negative SARS-CoV-2 tests with 33 days of median duration of SARS-CoV-2 RNA detection (interquartile range: 25.2–39 days). LASSO and binomial logistic regression analyses suggested that delayed hospital admission (adjusted OR = 3.70, 95% CI: 1.82–7.50), hypokalemia, and subpleural lesion (adjusted OR = 4.32, 95% CI: 1.10–16.97) were associated with prolonged SARS-CoV-2 RNA detection. By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. Early hospital admission shortened 5.73 days of mean duration of SARS-CoV-2 RNA detection than delayed hospital admission after adjusting confounding factors. Our study demonstrated that delayed hospital admission and subpleural lesion were associated with prolonged SARS-CoV-2 RNA detection among patients with COVID-19. The use of high-dose corticosteroids should be interpreted with extreme caution in treating COVID-19.


id: cord-268750-kox3uah2
author: Wong, S. F.
date: 2004-01-08
txt: ./txt/cord-268750-kox3uah2.txt
cache: ./cache/cord-268750-kox3uah2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14712366/
doi: 10.1007/s10096-003-1068-2
abstract: nan
summary:
  When the operations were performed, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga., USA) had not yet prepared guidelines for the prevention of SARS transmission during Caesarean sections. For the three Caesarean sections performed on mothers with SARS, the number of healthcare workers was limited to a minimum, with only those personnel essential to carry out the operation, neonatal resuscitation, and cleanup being involved (i.e., 2 senior obstetricians, 2 senior neonatologists, 1 senior anaesthetist, 1 theatre assistant, a team of 4 senior midwives, and 2 cleansing staff). The participating HCWs wore appropriate PPE according to the hospital''s guidelines prior to the arrival of the patient from the intensive care unit. In conclusion, the procedures described above were sufficient to prevent our healthcare workers from contracting SARS while performing these very high-risk operations.

title:
  Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures


id: cord-269726-z0frgm7s
author: Gidari, Anna
date: 2020-10-10
txt: ./txt/cord-269726-z0frgm7s.txt
cache: ./cache/cord-269726-z0frgm7s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-04057-6
doi: 10.1007/s10096-020-04057-6
summary:
  Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) .

title:
  Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature

abstract:
  Can a patient diagnosed with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) be infected again? This question is still unsolved. We tried to analyze local and literature cases with a positive respiratory swab after recovery. We collected data from symptomatic patients diagnosed with SARS-CoV-2 infection in the Italian Umbria Region that, after recovery, were again positive for SARS-CoV-2 in respiratory tract specimens. Samples were also assessed for infectivity in vitro. A systematic review of similar cases reported in the literature was performed. The study population was composed of 9 patients during a 4-month study period. Among the new positive samples, six were inoculated in Vero-E6 cells and showed no growth and negative molecular test in culture supernatants. All patients were positive for IgG against SARS-CoV-2 nucleoprotein and/or S protein. Conducting a review of the literature, 1350 similar cases have been found. The presumptive reactivation occurred in 34.5 days on average (standard deviation, SD, 18.7 days) after COVID-19 onset, when the 5.6% of patients presented fever and the 27.6% symptoms. The outcome was favorable in 96.7% of patients, while the 1.1% of them were still hospitalized at the time of data collection and the 2.1% died. Several hypotheses have been formulated to explain new positive respiratory samples after confirmed negativity. According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo.


id: cord-271781-cfv0ta10
title: Transmission of SARS-CoV-2: an update of current literature
author: Patel, Kishan P.
date: 2020-07-07
txt: ./txt/cord-271781-cfv0ta10.txt
cache: ./cache/cord-271781-cfv0ta10.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-03961-1
doi: 10.1007/s10096-020-03961-1
summary:
  To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] .

abstract:
  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent for the 2019 coronavirus disease (COVID-19) pandemic, has caused a public health emergency. The need for additional research in viral pathogenesis is essential as the number of cases and deaths rise. Understanding the virus and its ability to cause disease has been the main focus of current literature; however, there is much unknown. Studies have revealed new findings related to the full transmission potential of SARS-CoV-2 and its subsequent ability to cause infection by different means. The virus is hypothesized to be of increased virulence compared with previous coronavirus that caused epidemics, in part due to its overall structural integrity and resilience to inactivation. To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. Additionally, the receptor by which the virus gains cellular entry, ACE2, has been found to be expressed in different human body systems, thereby potentiating its infection in those locations. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Understanding these different routes is important as they pertain to clinical practice, especially in taking preventative measures to mitigate the spread of SARS-CoV-2.


id: cord-272943-q09i8fqu
author: Dalhoff, A.
date: 2014-12-17
txt: ./txt/cord-272943-q09i8fqu.txt
cache: ./cache/cord-272943-q09i8fqu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-014-2296-3
doi: 10.1007/s10096-014-2296-3
summary:
  Surprisingly, the use of fluoroquinolones in indications other than bacterial infections has never been exploited, although not only nalidixic acid and its congener chloroquine exerts pleiotropic actions but, e.g., β-lactams and aminoglycosides are characterized by a broad range of biological activities too [47, 48] , so that a multitude of antimicrobial effects would not have been unusual. Fluoroquinolones inhibit not only enzymic activity of viral topoisomerases/helicases, but inhibit in vitro human immunodeficiency virus (HIV) reverse transcriptase as well; complete inhibition was observed at concentrations of ciprofloxacin and ofloxacin of 3 μM and norfloxacin of 1 μM, respectively [71] [72] [73] . Fluoroquinolones like ciprofloxacin, amifloxacin, enoxacin, norfloxacin, ofloxacin, pefloxacin, grepafloxacin, trovafloxacin, and 16 additional commercially available quinolones exhibit marked in vitro activity and in vivo efficacy against Plasmodium spp.

title:
  Antiviral, antifungal, and antiparasitic activities of fluoroquinolones optimized for treatment of bacterial infections: a puzzling paradox or a logical consequence of their mode of action?

abstract:
  This review summarizes evidence that commercially available fluoroquinolones used for the treatment of bacterial infections are active against other non-bacterial infectious agents as well. Any of these fluoroquinolones exerts, in parallel to its antibacterial action, antiviral, antifungal, and antiparasitic actions at clinically achievable concentrations. This broad range of anti-infective activities is due to one common mode of action, i.e., the inhibition of type II topoisomerases or inhibition of viral helicases, thus maintaining the selective toxicity of fluoroquinolones inhibiting microbial topoisomerases at low concentrations but mammalian topoisomerases at much higher concentrations. Evidence suggests that standard doses of the fluoroquinolones studied are clinically effective against viral and parasitic infections, whereas higher doses administered topically were active against Candida spp. causing ophthalmological infections. Well-designed clinical studies should be performed to substantiate these findings.


id: cord-274567-xd37wxxf
author: Monpoeho, S.
date: 2002-07-13
txt: ./txt/cord-274567-xd37wxxf.txt
cache: ./cache/cord-274567-xd37wxxf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12172744/
doi: 10.1007/s10096-002-0766-5
summary:
  title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay

title:
  Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid

abstract:
  A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. In order to prevent false-negative results, a one-step multiplex RT-PCR was optimized. It contains two dual-labelled fluorogenic probes to quantify the 5′ noncoding region of enterovirus and detect an internal positive control. In the present study, 104 cerebrospinal fluid samples collected during an outbreak of enteroviral meningitis were analyzed using this method. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. The sensitivity of the RT-PCR was 96.8%, while that of cell culture was 34.9%. Genomic viral loads found ranged between 3.3 and 5.9 log(10) copies per milliliter of cerebrospinal fluid (mean, 4.8 log(10) copies/ml). This fluorogenic enterovirus RT-PCR allows large numbers of samples to be screened rapidly. Moreover, its sensitivity and reproducibility make it highly reliable. With these characteristics, the enterovirus RT-PCR can be a useful tool that may offer considerable benefit in the clinical management of patients with enteroviral infections.


id: cord-275561-9f1las3y
author: Wielders, C. C. H.
date: 2015-01-11
txt: ./txt/cord-275561-9f1las3y.txt
cache: ./cache/cord-275561-9f1las3y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25577174/
doi: 10.1007/s10096-014-2310-9
summary:
  title: Single nucleotide polymorphisms in immune response genes in acute Q fever cases with differences in self-reported symptoms Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 (rs1914408), and VDR (rs2228570) genes were determined in 85 patients from the 2007 Dutch acute Q fever outbreak, and a symptom score was calculated. burnetii antigens ≥1:64 (indirect immunofluorescence assay, IFA; Focus Diagnostics, Cypress, CA, USA)], based on available questionnaire data (self-reported symptoms), including no more than one person per household, and giving consent for the investigation of genetic differences. This study investigated the association of four SNPs in several immune response genes with susceptibility to and severity of self-reported symptoms in acute C. In conclusion, a significant difference was found for the IFNG rs1861493 SNP between persons with a mild or more severe presentation of acute Q fever, which was not confirmed in a second study population.

title:
  Single nucleotide polymorphisms in immune response genes in acute Q fever cases with differences in self-reported symptoms

abstract:
  Genes involved in human immune response are well recognized to influence the clinical course of infection. The association of host genetics with susceptibility to and severity of clinical symptoms in acute Q fever was investigated. Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 (rs1914408), and VDR (rs2228570) genes were determined in 85 patients from the 2007 Dutch acute Q fever outbreak, and a symptom score was calculated. IFNG rs1861493 showed a significant association with the symptom score; IFNG rs2430561 showed a similar trend. These SNPs were then used to reproduce results in a 2009 outbreak population (n = 123). The median symptom score differed significantly in both populations: 2 versus 7. The significant association of IFNG rs1861493 with symptom score in the first population was not reproduced in the second population. We hypothesize that individuals in the second outbreak were exposed to a higher Coxiella burnetii dose compared to the first, which overruled the protection conferred by the A-allele of IFNG rs1861493 in the first population.


id: cord-283399-iz4l9i0d
title: Human metapneumovirus in adults: a short case series
author: O’Gorman, C.
date: 2006-03-14
txt: ./txt/cord-283399-iz4l9i0d.txt
cache: ./cache/cord-283399-iz4l9i0d.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16534565/
doi: 10.1007/s10096-006-0116-0
summary:
  This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. In young children and elderly patients hMPV is most commonly associated with a clinical diagnosis of bronchiolitis or bronchitis, respectively, whereas in middle-aged adults, it may produce an influenza-like illness, which can be complicated by pneumonitis in the presence of immunocompromising factors [5] . This retrospective observational study reviewed all cases of hMPV detected in patients over 18 years of age, from the time the RT-PCR method was adopted in July 2003 through to January 2005.

abstract:
  This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. Among a cohort of 741 symptomatic patients tested since 2003, the virus was diagnosed in six adults using reverse transcriptase polymerase chain reaction. Of the six, two were from the community, two were hospital inpatients with chronic obstructive pulmonary disease and two were immunocompromised patients, both of whom required ventilation and later died. This report discusses the clinical features, epidemiology and diagnosis of hMPV, highlighting that this infection may be associated with death in high-risk adults. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame.


id: cord-285757-fiqx4tll
author: Mäkelä, M. J.
date: 1999
txt: ./txt/cord-285757-fiqx4tll.txt
cache: ./cache/cord-285757-fiqx4tll.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/10534191/
doi: 10.1007/s100960050370
summary:
  To study whether MxA protein expression is systemically upregulated during rhinovirus infection, blood specimens were collected from 40 patients with common cold and MxA expression in mononuclear cells analyzed by flow cytometry. In conclusion, expression of MxA in blood lymphocytes and an apparently systemic type I interferon response is not induced during rhinovirus infection or during most other cases of common cold in young adult patients. In the present study, the induction of a systemic IFN response as reflected by the expression of MxA protein in blood lymphocytes of patients with rhinovirus infection was examined. Our data suggests that type I IFN production in serum is not comparable to that seen in most other respiratory viral infections in vivo, since the rhinovirus-positive patients had only low or no expression of the MxA protein and no IFN-a/b was detectable in serum samples.

title:
  Lack of Induction by Rhinoviruses of Systemic Type I Interferon Production or Enhanced MxA Protein Expression During the Common Cold

abstract:
  To study whether MxA protein expression is systemically upregulated during rhinovirus infection, blood specimens were collected from 40 patients with common cold and MxA expression in mononuclear cells analyzed by flow cytometry. None of the patients with a confirmed rhinovirus infection (n=15) or with an infection of unknown etiology (n=20) had elevated expression of the MxA protein (median fluorescence intensity, 549 and 582, respectively) when compared to healthy controls (n=11, median 590). Patients with influenza infections had significantly elevated values (n=5, median 750), and interferon could be detected only in serum samples from influenza patients. In conclusion, expression of MxA in blood lymphocytes and an apparently systemic type I interferon response is not induced during rhinovirus infection or during most other cases of common cold in young adult patients.


id: cord-286749-si83t03j
author: Lu, Q.-B.
date: 2014-07-29
txt: ./txt/cord-286749-si83t03j.txt
cache: ./cache/cord-286749-si83t03j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25070494/
doi: 10.1007/s10096-014-2215-7
summary:
  title: Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection Human bocavirus (HBoV) is a novel parvovirus, often associated with respiratory tract diseases in children. This study was aimed to explore the epidemiology pattern and clinical characteristics of HBoV-1 infection in Chinese children, as well as the molecular evolutionary pattern, for HBoV-1, by performing a 4-year laboratory surveillance of ARTI cases. According to our results, the prevalence of HBoV-1 in pediatric ARTI patients is higher than those from other hospital-based studies [2, 6, 21, 22] , whereas it was lower than that previously detected in persistently wheezing children [16] . Human bocavirus in children: mono-detection, high viral load and viraemia are associated with respiratory tract infection Detection and clinical characteristics analysis of human bocavirus 1-3 in children for acute respiratory infection in Lanzhou area

title:
  Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection

abstract:
  Human bocavirus (HBoV) is a novel parvovirus, often associated with respiratory tract diseases in children. This study explored the epidemiological characteristics and molecular evolution of HBoV-1 in southeastern China. Nasopharyngeal aspirates were collected from children admitted to hospital with acute respiratory tract infections. HBoV-1 was detected using real-time reverse transcription polymerase chain reaction and further characterized by complete genome sequences analysis. Among the 3,022 recruited children, 386 (12.77 %) were HBoV-1-positive and 300 (77.72 %) had co-detection with other respiratory viruses. Seasonal prevalence peaked in summer. HBoV-1 presence was significantly associated with asthma attack [odds ratio = 1.74; 95 % confidence interval: 1.30, 2.31; p < 0.001]. Similar results were obtained when either single detection or co-detection of HBoV-1 was considered, demonstrating the minor impact of co-detection on the clinical characteristics or epidemic pattern. Phylogenetic analysis based on the complete genome sequences showed that all the HBoV-1 sequences clustered together and no branch was formed that was supported by bootstrap value ≥750. The overall evolutionary rate of the complete genome of HBoV-1 was estimated at 1.08 × 10(−4) nucleotide substitutions per site per year (s/s/y) [95 % highest probability density: (0.40–1.86) × 10(−4) s/s/y]. Selective pressure analysis showed that all the ω-values were less than 1, suggesting that HBoV-1 was under negative selective pressure. Site-by-site analysis identified the codon site 40 of the VP1 gene under positive selection. In conclusion, our study disclosed the epidemiological and genetic dynamics of HBoV-1 epidemics in southeastern China in the most recent 3 years, the information of which might help to further improve our understanding of HBoV-1 infection and guide better surveillance and control strategies in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10096-014-2215-7) contains supplementary material, which is available to authorized users.


id: cord-291052-nstfe15a
title: A novel approach to managing COVID-19 patients; results of lopinavir plus doxycycline cohort
author: Cag, Yasemin
date: 2020-08-27
txt: ./txt/cord-291052-nstfe15a.txt
cache: ./cache/cord-291052-nstfe15a.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32856202/
doi: 10.1007/s10096-020-04016-1
summary:
  This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. Second, moderate to severe cases were hospitalized and prescribed with a regimen of lopinavir plus doxycycline plus ceftriaxone for 5 days. We hospitalized moderate to severe cases and administered lopinavir combined with doxycycline and ceftriaxone to 343 patients, among whom 161 had positive PCR test results (161/343, 46.9%). We administered hydroxychloroquine to mild cases isolated at home, lopinavir plus doxycycline to hospitalized moderate to severe cases, and favipiravir in the salvage treatment. We concluded that home isolation of mild cases is an effective means to manage the burden of disease, while lopinavir plus doxycycline is an alternative to current treatment regimens for COVID-19.

abstract:
  This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. During the study period, 2043 patients with suspected COVID-19 were admitted to the emergency department. Molecular tests indicated that 475 of these patients tested positive for COVID-19. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. The overall case fatality rate was 4.2% (20/475).


id: cord-293710-f1tzt6jb
title: Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients
author: Karolyi, M.
date: 2020-09-23
txt: ./txt/cord-293710-f1tzt6jb.txt
cache: ./cache/cord-293710-f1tzt6jb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32965656/
doi: 10.1007/s10096-020-04044-x
summary:
  SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Studies showed reduced mortality in hospitalized COVID-19 patients treated vs not treated with anticoagulants in patients with a sepsis-induced-coagulopathy (SIC) score ≥ 4 or D-Dimer > 6 times upper limit of normal [4] . We describe a case series of four outpatients with proven SARS-CoV-2 infection who developed pulmonary embolism (PE) with a delay of 2-4 weeks after symptom onset with complete resolution of initial symptoms. The characteristics of outpatients who are suitable for anticoagulation have to be determined.In conclusion, new onset of dyspnea and tachycardia after initial resolution of COVID-19 symptoms ("disease trajectory characterised by two peaks") should raise suspicion of PE and a CT scan should be considered.

abstract:
  SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Our case series consists of four male otherwise healthy patients between 32 and 50 years of age. Initial symptoms completely resolved but they developed new onset of dyspnea and thoracic pain at days 14 to 26. CT scan revealed pulmonary embolism in all patients which led to hospitalization. Standard anticoagulation practice needs to be re-evaluated and may be considered for certain outpatients with COVID-19.


id: cord-294551-s3nsiano
title: Early diagnosis of SARS: lessons from the Toronto SARS outbreak
author: Muller, M. P.
date: 2006-04-04
txt: ./txt/cord-294551-s3nsiano.txt
cache: ./cache/cord-294551-s3nsiano.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16586072/
doi: 10.1007/s10096-006-0127-x
summary:
  To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Patients were classified as confirmed SARS if they had a compatible clinical illness (fever or nonproductive cough or dyspnea), an exposure to SARS (direct contact with a known SARS case or travel to a SARS-endemic area or time spent at an institution where SARS transmission was occurring, within 12 days of symptom onset), and a positive microbiological test (positive acute or convalescent serology, or positive PCR from clinical or pathological specimens). Findings associated with a confirmed diagnosis included direct exposure to a known case (OR, 2.34; 95%CI, 1.01-5.40), symptomatic fever as an initial symptom (OR, 5.07; 95%CI, 2.24-11.50), a documented temperature of 38.0°C on admission to hospital (OR, 2.6; 95%CI, 1.14-5.92), and the presence of a pulmonary infiltrate by the time of admission (OR, 2.46; 95%CI, 1.09-5.56).

abstract:
  The clinical presentation of SARS is nonspecific and diagnostic tests do not provide accurate results early in the disease course. Initial diagnosis remains reliant on clinical assessment. To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Findings were compared between patients with laboratory-confirmed SARS and those in whom SARS was excluded by laboratory or public health investigation. Of 364 cases, 273 (75%) had confirmed SARS, 30 (8%) were excluded, and 61 (17%) remained indeterminate. Among confirmed cases, exposure occurred in the healthcare environment (80%) or in the households of affected patients (17%); community or travel-related cases were rare (<3%). Fever occurred in 97% of patients by the time of admission. Respiratory findings including cough, dyspnea and pulmonary infiltrates evolved later and were present in only 59, 37 and 68% of patients, respectively, at admission. Direct exposure, fever on the first day of illness, and elevated temperature, pulmonary infiltrates, lymphopenia and thrombocytopenia at admission were associated with confirmed cases. Rhinorrhea, sore throat, and an elevated neutrophil count at admission were associated with excluded cases. In the absence of fever or significant exposure, SARS is unlikely. Other clinical, laboratory and radiographic findings further raise or lower the likelihood of SARS and provide a rational basis for estimating the likelihood of SARS and directing initial management.


id: cord-311207-qkkn0297
author: Pegoraro, Manuela
date: 2020-10-20
txt: ./txt/cord-311207-qkkn0297.txt
cache: ./cache/cord-311207-qkkn0297.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33078222/
doi: 10.1007/s10096-020-04040-1
summary:
  Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. In COVID-19 confirmed cases (symptomatic patient with SARS-CoV-2 positive molecular detection), date of symptoms onset was used to timing infection at the moment of specimens'' collection. Three stages were identified: early (0-7 days from symptoms onset), intermediate (8China), COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co., Ltd Huzhou, Zhejiang, China), and PRIMA Professional (PRIMA Lab SA, Balerbna, Switzerland) are lateral flow immunochromatographic assays. Sensitivities were assessed on confirmed COVID-19 cases, combining IgG and IgM/IgA positive results, while specificities were estimated on the group of healthy volunteer''s. Compared with the automated immunoassays, the ability of ICTs to detect anti-SARS-CoV-2 IgG was equivalent to that of CLIA-MAGLUMI and better than ELISA-Euroimmun, whose IgG positive rates ranged between 0 and 86% at 14 days after symptoms onset.

title:
  Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness

abstract:
  Results of three rapid immunochromatographic tests (ICTs) were compared with those obtained with two automated immunoassays for evaluation of their usefulness. One hundred fifty-nine patients and 67 healthy volunteers were included. Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. ICTs could have a role as screening approach due to their easy usability. Subjective interpretation, significant rate of uncertain results, uncertainty on viral antigens source are undoubtedly drawbacks.


id: cord-314311-xbpb9nfi
title: The epidemiology and clinical information about COVID-19
author: Ge, Huipeng
date: 2020-04-14
txt: ./txt/cord-314311-xbpb9nfi.txt
cache: ./cache/cord-314311-xbpb9nfi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32291542/
doi: 10.1007/s10096-020-03874-z
summary:
  In November 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong, China, and resulted in more than 8000 infections and 774 deaths in 37 countries. This review makes a comprehensive introduction about this disease, including the genome structure and receptor of SARS-CoV-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of COVID-19. The clinical manifestations of SARS-CoV-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. The COVID-19 patients around the world were diagnosed based on World Health Organization interim guidance [65] , and China updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in Chinese) according to epidemic situation and improved awareness of disease. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series

abstract:
  In December 2019, pneumonia of unknown cause occurred in Wuhan, Hubei Province, China. On 7 January 2020, a novel coronavirus, named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was identified in the throat swab sample of one patient. The World Health Organization (WHO) announced the epidemic disease caused by SARS-CoV-2 as coronavirus disease 2019 (COVID-19). Currently, COVID-19 has spread widely around the world, affecting more than seventy countries. China, with a huge burden of this disease, has taken strong measures to control the spread and improve the curative rate of COVID-19. In this review, we summarized the epidemiological characteristics, clinical features, diagnosis, treatment, and prognosis of COVID-19. A comprehensive understanding will help to control the disease.


id: cord-321284-0y69n1ea
author: El Kholy, A. A.
date: 2016-06-10
txt: ./txt/cord-321284-0y69n1ea.txt
cache: ./cache/cord-321284-0y69n1ea.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-016-2698-5
doi: 10.1007/s10096-016-2698-5
summary:
  title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses.

title:
  The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season

abstract:
  Respiratory tract infection is a major cause of hospitalization in children. Although most such infections are viral in origin, it is difficult to differentiate bacterial and viral infections, as the clinical symptoms are similar. Multiplex polymerase chain reaction (PCR) methods allow testing for multiple pathogens simultaneously and are, therefore, gaining interest. This prospective case-control study was conducted from October 2013 to February 2014. Nasopharyngeal (NP) and oropharyngeal (throat) swabs were obtained from children admitted with severe acute respiratory infection (SARI) at a tertiary hospital. A control group of 40 asymptomatic children was included. Testing for 16 viruses was done by real-time multiplex PCR. Multiplex PCR detected a viral pathogen in 159/177 (89.9 %) patients admitted with SARI. There was a high rate of co-infection (46.9 %). Dual detections were observed in 64 (36.2 %), triple detections in 17 (9.6 %), and quadruple detections in 2 (1.1 %) of 177 samples. Seventy-eight patients required intensive care unit (ICU) admission, of whom 28 (35.8 %) had co-infection with multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected among asymptomatic children. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected in asymptomatic children, resulting in challenges in clinical interpretation. Studies are required to provide quantitative conclusions that will facilitate clinical interpretation and application of the results in the clinical setting.


id: cord-321455-ooouqna7
author: Li, Tao
date: 2020-07-01
txt: ./txt/cord-321455-ooouqna7.txt
cache: ./cache/cord-321455-ooouqna7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-03967-9
doi: 10.1007/s10096-020-03967-9
summary:
  In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. In the process of continuous monitoring, the expression of CRE in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, and 7th days of admission, and showed an overall downward trend (Fig. 3a) . The expression of Ca 2+ in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, 7th and 10th days of admission, and showed an overall upward trend (Fig. 3d ).

title:
  Characteristics of laboratory indexes in COVID-19 patients with non-severe symptoms in Hefei City, China: diagnostic value in organ injuries

abstract:
  This study compared the laboratory indexes in 40 non-severe COVID-19 patients with those in 57 healthy controls. In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. SARS-CoV-2 infection can affect hematopoiesis, hemostasis, coagulation, fibrinolysis, bone metabolism, thyroid, parathyroid glands, the liver, and the reproductive system.


id: cord-323476-rb9n5wc0
author: Poole, Stephen
date: 2020-09-09
txt: ./txt/cord-323476-rb9n5wc0.txt
cache: ./cache/cord-323476-rb9n5wc0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-04031-2
doi: 10.1007/s10096-020-04031-2
summary:
  title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. The International Society of Antimicrobial Chemotherapy (ISAC)''s Rapid Diagnostics and Biomarkers Working Group conducted this international survey aiming to identify and highlight some key issues related to RDTs and their impacts in clinical practice and provide a number of key points to consider while adopting a RDT. Our survey highlights the availability of these tests in different resource settings, as well as the current models for governance, quality control and reporting.

title:
  How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC)

abstract:
  Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. In this study, we aim to assess the current patterns of use around the world, identify issues for successful implementation and suggest best practice advice on how to introduce new tests. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. It was circulated to ISAC members in December 2019. Results were collated according to the UN human development index (HDI). 81 responses were gathered from 31 different countries. 84% of institutions reported the availability of any test 24/7. In more developed countries, this was more for respiratory viruses, whereas in high and medium/low developed countries, it was for HIV and viral hepatitis. Only 37% of those carrying out rapid tests measured the impact. There is no ‘one-size fits all’ solution to RDTs: the requirements must be tailored to the healthcare setting in which they are deployed and there are many factors that should be considered prior to this. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-04031-2) contains supplementary material, which is available to authorized users.


id: cord-325238-2nhade3s
author: Seleem, Noura M.
date: 2020-04-23
txt: ./txt/cord-325238-2nhade3s.txt
cache: ./cache/cord-325238-2nhade3s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-03882-z
doi: 10.1007/s10096-020-03882-z
summary:
  The studied virulence factors include biofilm formation, twitching and swarming motilities, proteolytic enzyme production, and resistance to oxidative stress. The virulence factors were detected in absence and presence of 1 8 MIC of potential QSIs. Assay of biofilm formation, twitching motility, sensitivity to oxidative stress and protease, and gelatinase activity were performed for both P. Among the tested drugs, erythromycin, levamisole, propranolol, and chloroquine showed the highest inhibition of quorum sensing in CV026 as they produced a large clear zone around each well on a purple background (Fig. 1) ; hence, these four drugs were tested in the further experiments. The obtained results revealed that PAO1 biofilm (strong) was markedly inhibited in presence of 1/8 MIC of tested drugs (> 68%); the highest inhibition was observed with erythromycin (82.7%) as shown in Table 2 and Fig. 2a .

title:
  Drugs with new lease of life as quorum sensing inhibitors: for combating MDR Acinetobacter baumannii infections

abstract:
  The emergence of multidrug-resistant (MDR) strains is a major health problem worldwide. There is an urgent need for novel strategies to combat bacterial infections caused by MDR strains like Pseudomonas aeruginosa and Acinetobacter baumannii. Quorum sensing (QS) is a critical communication system in bacterial community controlling survival and virulence. The awareness of the importance of QS in bacterial infections has stimulated research to identify QS inhibitors (QSIs) to defeat microbes. In this study, four FDA-approved drugs (besides azithromycin as positive QSI) were tested for potential QS inhibition against clinical A. baumannii isolates and P. aeruginosa (PAO1) standard strain. The inhibitory effect of these drugs on virulence factors of both microbes has been investigated. The studied virulence factors include biofilm formation, twitching and swarming motilities, proteolytic enzyme production, and resistance to oxidative stress. The four tested drugs (erythromycin, levamisole, chloroquine, and propranolol) inhibited QS in Chromobacterium violaceum by 84, 72, 55.1, and 37.3%, respectively. They also significantly inhibited virulence factors in both PAO1 and A. baumannii at sub-inhibitory concentrations. These findings were confirmed by qRT-PCR and mice mortality test, where tested drugs highly repressed the expression of abaI gene and showed significantly improved mice survival rates. In addition, molecular docking studies against AbaI and AbaR proteins of QS system in A. baumannii revealed the potential inhibition of QS by tested drugs. Beside their known activities, the tested drugs could be given new life as QSIs to combat A. baumannii nosocomial infections (alone or in combination with antimicrobials). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03882-z) contains supplementary material, which is available to authorized users.


id: cord-335671-j3wrtsxj
author: Wagenvoort, J. H. T.
date: 2004-12-14
txt: ./txt/cord-335671-j3wrtsxj.txt
cache: ./cache/cord-335671-j3wrtsxj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15599644/
doi: 10.1007/s10096-004-1256-8
abstract: nan
summary:
  title: Similar environmental survival patterns of Streptococcus pyogenes strains of different epidemiologic backgrounds and clinical severity S. pyogenes strains 2, 6 and 8 were isolated from different patients during a hospital outbreak reported previously by Davies et al. It can be seen that from an initial measurement of approximately 10 8 cfu the strains died off rapidly, with the decline ranging from 4 to 7-log 10 cfu during the 14-day dry-out period to counts between 20 and 9,000 cfu. pyogenes strains tested-even our own outbreak strain that had demonstrated MRSAlike spread [4] -contrasts sharply with the prolonged survival of around a year reported previously for epidemic MRSA strains [7] . pyogenes strains in the hospital environment is shorter than the period of 3 months reported by Lidwell and Lowbury [8] , it should be noted that their study measured survival in dust.

title:
  Similar environmental survival patterns of Streptococcus pyogenes strains of different epidemiologic backgrounds and clinical severity


id: cord-336909-nnxa5ant
author: Guedez-López, Gladys Virginia
date: 2020-08-17
txt: ./txt/cord-336909-nnxa5ant.txt
cache: ./cache/cord-336909-nnxa5ant.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32808111/
doi: 10.1007/s10096-020-04010-7
summary:
  The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. RT-qPCR tests presented a high specificity with a low probability of false positive; however, sensitivity relies on different factors as specimen site, method of collection, viral load and time from the onset of symptoms [3, 7] . Detection rate of IgM, IgG and IgM/IgG antibodies against SARS-CoV-2 with the three ICT strip assays in positive and negative RT-PCR patients along three periods of time since the onset of symptoms is shown in Table 3 . Detection rates of total antibodies (IgM/IgG) obtained with Sienna® and Wondfo® by the two groups of patients along the three stages since the symptoms onset are collected in Table 4 . In this study, we have investigated the diagnostic value of detection of SARS-CoV-2 IgM and IgG antibodies in different stages of the disease, using three ICT strip assays, in comparison with RT-qPCR.

title:
  Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2

abstract:
  Lateral flow immunoassays (LFIA) for rapid detection of specific antibodies (IgM and IgG) against SARS-CoV-2 in different human specimens have been developed in response to the pandemic. The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. A total of 145 serum samples from 145 patients with clinical suspicion of COVID-19 were collected: all of the samples were tested with Sienna®, 117 with Wondfo® and 89 with Prometheus®. The overall results of sensitivity, specificity, positive predictive value and negative predictive value obtained were as follows: 64.4%, 75%, 85.5% and 47.8% with Sienna®; 45.2%, 81.8%, 80.5% and 47.4% with Wondfo® and 75.5%, 12.5%, 51.4% and 29.4% with Prometheus®. The accuracy of the test for Sienna®, Wondfo® and Prometheus® was 67.6%, 59% and 47.2%, with a prevalence of COVID-19 of 69.7%, 62.4% and 55.1% respectively. Sensitivity of the three tests (Sienna®, Wondfo® and Prometheus® respectively) along the three different stages was 36.6%, 18.8% and 68.6% in the early stage (first week); 81.3%, 74.1% and 90.9% in the intermediate stage (second week) and 100%, 83.3% and 100% in the late stage (third week). The results demonstrate that even though Prometheus® presented a high sensitivity, the specificity was notably lower than the other two tests. Sienna® showed the greatest contrast between sensitivity and specificity, achieving the best accuracy, followed by Wondfo®. The sensitivity of the three ICT assays was higher in late stages of the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-04010-7) contains supplementary material, which is available to authorized users.


id: cord-338070-y8zi8iz9
author: Liu, Wei
date: 2020-08-31
txt: ./txt/cord-338070-y8zi8iz9.txt
cache: ./cache/cord-338070-y8zi8iz9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-04020-5
doi: 10.1007/s10096-020-04020-5
summary:
  This study aimed to explore the effects of PARP-1 inhibitor olaparib on IAV-induced lung injury and the underlying mechanisms. To the expectations, mice in the olaparib group showed higher survival rate compared with that in the IAV group in a dose-dependent manner, indicating that olaparib could powerfully protect against influenza virus challenge in by H&E staining and the quantitative analysis of histological changes in the lung tissues (e) (n = 8 for each group). The detection of cytokine/chemokine in BALF samples at day 6 post-infection showed that IL-6, MCP-1, G-CSF, TNF-α, CXCL1, CXCL10, CCL3, and RANTES were remarkably increased in the IAV group compared with those in the control group, while olaparib treatment significantly reduced the abnormal increased levels of the above cytokine/chemokines, which was similar with the results obtained from lung tissue (Fig. 4a-h) . To explore the mechanisms underlying the protective effect of olaparib against IAV-induced injury to murine lungs, western blot was performed to detect the PARPs, the marker of apoptosis.

title:
  Pharmacological inhibition of poly (ADP-ribose) polymerase by olaparib ameliorates influenza-virus-induced pneumonia in mice

abstract:
  Treatments against influenza A viruses (IAV) have to be updated regularly due to antigenic drift and drug resistance. Poly (ADP-ribose) polymerases (PARPs) are considered effective therapeutic targets of acute lung inflammatory injury. This study aimed to explore the effects of PARP-1 inhibitor olaparib on IAV-induced lung injury and the underlying mechanisms. Male wild-type C57BL/6 mice were intranasally infected with IAV strain H1N1 to mimic pneumonia experimentally. Olaparib at different doses was intraperitoneally injected 2 days before and 5 consecutive days after virus stimulation. On day 6 post-infection, lung tissues as well as bronchoalveolar lavage fluid (BALF) were sampled for histological and biochemical analyses. Olaparib increased the survival rate of IAV mice dose-dependently. Olaparib remarkably reduced IAV mRNA expression, myeloperoxidase (MPO) level, and inflammatory cell infiltration in IAV lungs. Moreover, olaparib significantly reduced the level of interleukin (IL)-1β, tumor necrosis factor (TNF)-α, interferon (IFN)-γ, IL-6, and IL-4 and increased IL-10 in IAV lungs. Also, olaparib efficiently reduced IL-6, monocyte chemotactic protein (MCP)-1, granulocyte colony-stimulating factor (G-CSF), TNF-α, chemokine (C–X–C motif) ligand (CXCL)1, CXCL10, chemokine (C–C motif) ligand (CCL)3, and regulated on activation, normal T cell expressed and secreted (RANTES) release in IAV BALF. Olaparib decreased PARylated protein content and p65, IκBα phosphorylation in IAV lung tissues. This study successfully constructed the pneumonia murine model using IAV. Olaparib decreased IAV-induced mortality in mice, lung injury, and cytokine production possibly via modulation of PARP-1/NF-κB axis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-04020-5) contains supplementary material, which is available to authorized users.


id: cord-344017-qldawc8m
author: Edouard, S.
date: 2020-11-11
txt: ./txt/cord-344017-qldawc8m.txt
cache: ./cache/cord-344017-qldawc8m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33179133/
doi: 10.1007/s10096-020-04104-2
summary:
  Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. In this study, we are reporting our experience to develop an indirect immunofluorescent assay (IFA) for the detection of anti-SARS-CoV-2 antibodies that we implemented before any other serological test was available in France. ELISA To compare our IFA with commercial ELISA IgG, we randomly selected 70 sera with possible cross-reactivity (including 45 sera with possible nonspecific serological interference and 25 sera from patients diagnosed with common others human coronavirus), 30 sera collected before the pandemic and 100 sera from our cohort of SARS-CoV-2-infected patients among all the sera that we tested by IFA. Some other studies also reported an earlier serological response in severe compared to mild SARS-CoV-2 infection [5, 20, 25] that is consistent with the earlier seroconversion that we found in patients with poor clinical outcome (PClinO).

title:
  Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France

abstract:
  An indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. IFA presented substantial agreement (86%) with ELISA EUROIMMUN SARS-CoV-2 IgG kit (Cohen’s Kappa = 0.61). The presence of antibodies was then measured at 3% before a 5-day evolution up to 47% after more than 15 days of evolution. We observed that the rates of seropositivity as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that detection anti-SARS-CoV-2 antibodies is useful as a marker associated with COVID-19 severity. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10096-020-04104-2.


id: cord-346726-u7dhbmht
author: Keske, Şiran
date: 2018-01-13
txt: ./txt/cord-346726-u7dhbmht.txt
cache: ./cache/cord-346726-u7dhbmht.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29332209/
doi: 10.1007/s10096-017-3174-6
summary:
  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). It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice. In adults, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus (RSV), human coronavirus, and parainfluenza virus cause infections with considerable morbidity and mortality [1, 3] , and in infants, RSV is the most common reason for RTIs among hospitalized patients [4] . 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. 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.

title:
  The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs

abstract:
  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 1 January 2015 and 31 December 2016 in a 265-bed private hospital in Istanbul. At the end of 2015, we implemented antimicrobial stewardship including systematic use of MRT. Then, we compared our observations between the year 2015 and the year 2016. 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 17 viruses and three bacteria was used for diagnosis. In total, 1317 patients were included; 630 (48%) were inpatients and 569 (43%) were older than 16 years of age. At least one virus was detected in 747 (57%) patients. Rhinovirus/enterovirus, influenza virus, and adenovirus were the most commonly detected. Among hospitalized patients, in children, a significant decrease in antibiotic use (44.5% in 2015 and 28.8% in 2016, p = 0.009) was observed, but in adults, the decrease was not statistically significant (72% in 2015 and 63% in 2016, p = 0.36). The duration of antibiotic use after the detection of virus was significantly decreased in both children and adults (p < 0.001 and p = 0.007, 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.


id: cord-348840-s8wjg4ar
title: High-touch surfaces: microbial neighbours at hand
author: Cobrado, L.
date: 2017-06-25
txt: ./txt/cord-348840-s8wjg4ar.txt
cache: ./cache/cord-348840-s8wjg4ar.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-017-3042-4
doi: 10.1007/s10096-017-3042-4
summary:
  Microorganisms contaminating such high-touch surfaces include Gram-positive and Gram-negative bacteria, viruses, yeasts and parasites, with improved cleaning and disinfection effectively decreasing the rate of HAIs. Manual and automated surface cleaning strategies used in the control of infectious outbreaks are discussed and current trends concerning the prevention of contamination by the use of antimicrobial surfaces are taken into consideration in this manuscript. Additionally, evidence that hightouch surfaces (HTS) will work as an extra source of microbial pathogens accumulated over the years, e.g., several microorganisms can survive on medical equipment for hours to months, improved cleaning and disinfection of surfaces decrease the rate of HAI, and hospital environmental screening results and the study of clonal outbreaks, all have given support to the role of contaminated HTS in the transmission of pathogens between patients and healthcare personnel [4] . Microbial pathogens most frequently involved in the contamination of hospital environmental surfaces are (methicillinresistant) Staphylococcus aureus (MRSA), vancomycinresistant enterococci (VRE), Clostridium difficile, multidrug resistant Gramme-negative bacilli (such as Pseudomonas, Acinetobacter and Enterobacteriaceae), Norovirus, Coronavirus and Candida species [6] [7] [8] [9] [10] .

abstract:
  Despite considerable efforts, healthcare-associated infections (HAIs) continue to be globally responsible for serious morbidity, increased costs and prolonged length of stay. Among potentially preventable sources of microbial pathogens causing HAIs, patient care items and environmental surfaces frequently touched play an important role in the chain of transmission. Microorganisms contaminating such high-touch surfaces include Gram-positive and Gram-negative bacteria, viruses, yeasts and parasites, with improved cleaning and disinfection effectively decreasing the rate of HAIs. Manual and automated surface cleaning strategies used in the control of infectious outbreaks are discussed and current trends concerning the prevention of contamination by the use of antimicrobial surfaces are taken into consideration in this manuscript.


id: cord-349562-ivu632j2
author: Hernes, S. S.
date: 2010-09-18
txt: ./txt/cord-349562-ivu632j2.txt
cache: ./cache/cord-349562-ivu632j2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-010-1064-2
doi: 10.1007/s10096-010-1064-2
summary:
  The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Samples for the diagnosis of a respiratory viral infection can be obtained by swabbing the oropharynx, the nasal cavity, the nasopharynx or alternatively, by nasopharyngeal aspiration (NPA) or nasopharyngeal washings (NPW). The aim of this study was to compare the respective efficacies of rayon swabs and nylon flocked swabs in providing material for direct respiratory virus detection by real-time PCR in adults above 60 years of age. Using monoplex (RSV and human metapneumovirus) or multiplex (influenza A/B, adenovirus/internal control and parainfluenza virus 1-4) PCR methods, the specimens were examined for, in total, nine different respiratory viruses (Table 2) .

title:
  Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs

abstract:
  The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Samples were obtained from patients 60 years of age or above who were newly admitted to Sorlandet Hospital Arendal, Norway. The patients were interviewed for current symptoms of a respiratory tract infection. Using rayon swabs and nylon flocked swabs, comparable sets of mucosal samples were harvested from the nasopharynx and the oropharynx. The samples were analysed using real-time polymerase chain reaction (PCR) methods. A total of 223 patients (mean age 74.9 years, standard deviation [SD] 9.0 years) were swabbed and a virus was recovered from 11% of the symptomatic patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Also, regardless of the type of swab, a calculated 19 times higher viral load was found in the samples from the nasopharynx as compared to the oropharynx (95% CI 5.4–67.4, p < 0.001). When swabbing for respiratory viruses in elderly patients, nasopharyngeal rather than oropharyngeal samples should be obtained. Nylon flocked swabs appear to be more efficient than rayon swabs.


id: cord-350328-wu1ygt6w
title: SARS: responding to an unknown virus
author: Tambyah, P. A.
date: 2004-07-14
txt: ./txt/cord-350328-wu1ygt6w.txt
cache: ./cache/cord-350328-wu1ygt6w.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15252720/
doi: 10.1007/s10096-004-1175-8
summary:
  The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. The severe acute respiratory syndrome (SARS) is a newly recognized coronavirus infection that emerged in southern China [1] with subsequent global spread to 29 countries [2] [3] [4] [5] . The newly infected individuals traveled onward to their homes or next destinations in the USA, Canada, Singapore, Hong Kong and Ireland sparking off epidemics of varying degrees of severity in each of those countries, mainly in hospitals but also in their respective communities. A directive had gone out from the Hong Kong Department of Health on 21 February 2003 to maintain strict infection control with droplet precautions for all cases of "atypical" community-acquired pneumonia because of concerns that highly pathogenic avian influenza might be easily transmissible from person to person. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts

abstract:
  The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. In early 2003, through a single incident, it spread to Hong Kong, Singapore, Canada and Vietnam. For busy clinicians in large public hospitals, the response to the virus was initially based on ensuring a high level of protection for staff. However, as the epidemic progressed and more information became available about the virus, procedures were rationalized and the virus is currently under control worldwide. There are, however, numerous unanswered questions concerning super-spreading events, the modes of transmission of the virus and, perhaps most importantly, the rapid detection of the virus early in the course of disease. These issues need to be addressed in case the virus becomes more widespread in the near future.


id: cord-350807-qdq96723
author: Reckziegel, Maria
date: 2020-05-27
txt: ./txt/cord-350807-qdq96723.txt
cache: ./cache/cord-350807-qdq96723.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32462500/
doi: 10.1007/s10096-020-03878-9
summary:
  Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Furthermore, particularly transplant patients are at risk for reactivation of diverse herpesviruses (herpes simplex virus-1/-2, HSV-1/-2; varicella zoster virus, VZV; cytomegalovirus, CMV; human herpesvirus 6, HHV-6; Epstein-Barr virus, EBV) [12, 15, [17] [18] [19] [20] . In this monocentric study, genome equivalents of viruses and M.p. were frequently detected in immunocompromised (66.7%) and immunocompetent (69.2%) patients with respiratory symptoms (Table 1) . Same authors indicated a mean age of 1.8 years Table 2 Detection of multiple pathogens in the respiratory tract of the overall study population (a) as well as of immunocompromised (b) and immunocompetent (c) patients.

title:
  Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection

abstract:
  Respiratory tract infections (RTI) can take a serious course under immunosuppression. Data on the impact of the underlying pathogens are still controversial. Samples from the upper (n = 322) and lower RT (n = 169) were collected from 136 children and 355 adults; 225 among them have been immunocompromised patients. Exclusion criteria were presence of relevant cultivable microorganisms, C-reactive protein > 20 mg/dl, or procalcitonin > 2.0 ng/ml. Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Viral/bacterial genome equivalents were detected in more than two-thirds of specimens. Under immunosuppression, herpesviruses (EBV 30.9%/14.6%, p < 0.001; CMV 19.6%/7.9%, p < 0.001; HSV-1: 14.2%/7.1%, p = 0.012) were frequently observed, mainly through their reactivation in adults. Immunocompromised adults tended to present a higher RSV prevalence (6.4%/2.4%, p = 0.078). Immunocompetent patients were more frequently tested positive for IV (15.0%/5.8%, p = 0.001) and M.p. (6.4%/0.4%, p < 0.001), probably biased due to the influenza pandemic of 2009 and an M.p. epidemic in 2011. About 41.8% of samples were positive for a single pathogen, and among them EBV (19.9%) was most prevalent followed by HRV (18.2%) and IV (16.6%). HSV-2 and C.p. were not found. Marked seasonal effects were observed for HRV, IV, and RSV. Differences in pathogen prevalence were demonstrated between immunocompetent and immunocompromised patients. The exact contribution of some herpesviruses to the development of RTI remains unclear. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03878-9) contains supplementary material, which is available to authorized users.


id: cord-355450-v3eh1rtk
title: Influenza and respiratory syncytial virus infections in the oldest-old continent
author: Boattini, Matteo
date: 2020-06-27
txt: ./txt/cord-355450-v3eh1rtk.txt
cache: ./cache/cord-355450-v3eh1rtk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10096-020-03959-9
doi: 10.1007/s10096-020-03959-9
summary:
  Influenza and respiratory syncytial virus (RSV) infections are associated with high rate of morbidity, mortality, and an important burden on healthcare systems worldwide, especially among elderly patients [1] [2] [3] [4] [5] [6] . Especially in epidemiological research, oldest-old patients are considered to be a part of the wider age group of the elderly (≥ 65 years old), and there is limited published evidence about predictors of severity of illness and mortality in viral infections, such as caused by influenza and RSV. The aim of this study was to describe the clinical features of an oldest-old population admitted with influenza and/or RSV infections in three southern European hospitals over two consecutive winter seasons and identify predictors of pneumonia, non-invasive ventilation (NIV), and in-hospital death (IHD). Moreover, in our study, hospital-acquired influenza and/or RSV infections were not identified as predictors of pneumonia, use of NIV, and IHD for patients aged 65 years and older, moving away from evidence available so far [9, 10] .

abstract:
  SARS-CoV-2 dramatically revealed the sudden impact of respiratory viruses in our lives. Influenza and respiratory syncytial virus (RSV) infections are associated with high rates of morbidity, mortality, and an important burden on healthcare systems worldwide, especially in elderly patients. The aim of this study was to identify severity predictors in the oldest-old admitted with influenza and/or RSV infections. This is a multicenter, retrospective study of all oldest-old patients (≥ 85 years old) admitted for laboratory-confirmed influenza and/or RSV infection in three tertiary hospitals in Portugal, Italy, and Cyprus over two consecutive winter seasons. The outcomes included the following: pneumonia on infection presentation, use of non-invasive ventilation (NIV), and in-hospital death (IHD). The association with possible predictors, including clinical features and type of virus infection, was assessed using uni- and multivariable analyses. A total of 251 oldest-old patients were included in the study. Pneumonia was evident in 32.3% (n = 81). NIV was implemented in 8.8% (n = 22), and IHD occurred in 13.9% (n = 35). Multivariable analyses revealed that chronic obstructive pulmonary disease (COPD) or asthma was associated with pneumonia (OR 1.86; 95% CI 1.02–3.43; p = 0.045). COPD or asthma (OR 4.4; 95% CI 1.67–11.6; p = 0.003), RSV (OR 3.12; 95% CI 1.09–8.92; p = 0.023), and influenza B infections (OR 3.77; 95% CI 1.06–13.5; p = 0.041) were associated with NIV use, respectively, while chronic kidney disease was associated with IHD (OR 2.50; 95% CI 1.14–5.51; p = 0.023). Among the oldest-old, chronic organ failure, such as COPD or asthma, and CKD predicted pneumonia and IHD, respectively, beyond the importance of viral virulence itself. These findings could impact on public health policies, such as fostering influenza immunization campaigns, home-based care programs, and end-of-life care. Filling knowledge gaps is crucial to set priorities and advise on transition model of care that best fits the oldest-old.


