Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 178 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 4003 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 20 SARS 18 patient 14 China 13 H1N1 12 respiratory 11 infection 10 virus 10 PCR 10 COVID-19 8 ICU 7 study 7 influenza 6 covid-19 5 case 5 RSV 5 MERS 5 Hong 4 severe 4 child 4 H7N9 3 viral 3 sample 3 disease 3 Taiwan 3 Saudi 3 RNA 3 Kong 3 ILI 3 IFN 3 HIV 3 Arabia 3 ARDS 2 risk 2 pneumonia 2 pandemic 2 nosocomial 2 model 2 leptospirosis 2 household 2 figure 2 datum 2 cap 2 arm 2 adenovirus 2 acute 2 Wuhan 2 Staphylococcus 2 Sri 2 Singapore 2 PICU Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 5365 % 5101 patient 4616 study 4236 infection 3339 case 3020 virus 2609 influenza 2219 disease 1821 datum 1652 analysis 1647 child 1555 sample 1345 result 1333 year 1330 time 1321 rate 1309 day 1289 group 1207 pneumonia 1170 risk 1101 pathogen 1064 test 1043 p 1036 age 1002 outbreak 992 hospital 974 detection 954 number 936 control 924 factor 897 level 885 symptom 872 transmission 855 fever 819 treatment 805 author 789 population 762 model 753 pandemic 720 health 706 cell 693 care 691 assay 660 epidemic 656 adult 653 period 653 illness 639 laboratory 633 incidence 633 diagnosis Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1103 SARS 835 PCR 833 China 678 H1N1 525 COVID-19 512 A 442 RSV 418 Health 386 Fig 375 S. 375 ICU 358 Table 325 Hong 322 MERS 319 Kong 313 CoV 305 RT 290 al 289 M. 285 CoV-2 284 C 259 Hospital 251 HIV 247 RNA 246 CI 244 et 242 T 236 US 234 B 224 January 221 H7N9 219 Influenza 219 . 211 MRSA 204 University 199 Dis 188 USA 183 BMC 182 CT 176 Taiwan 169 National 169 ARDS 163 ILI 162 United 159 Wuhan 159 TB 156 CMV 153 II 151 H5N1 149 Germany Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2111 we 1068 it 620 they 314 i 181 he 135 them 69 she 59 us 41 you 37 themselves 28 itself 24 one 9 oneself 6 me 5 him 4 ours 4 netmhcpan4.0 4 igm/ 3 himself 2 s 2 herself 2 ermb 1 thyself 1 hme 1 her 1 hbov 1 flic 1 ed/ Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 24441 be 4115 have 2484 use 1429 associate 1402 include 1207 report 1164 show 933 base 895 identify 848 detect 841 compare 813 do 719 perform 685 increase 681 find 676 infect 676 confirm 646 follow 557 provide 548 cause 517 test 507 collect 497 consider 469 occur 448 relate 447 observe 446 describe 440 obtain 436 develop 421 indicate 415 hospitalize 410 conduct 405 require 392 receive 388 present 386 remain 375 suggest 364 determine 361 assess 359 define 347 evaluate 345 accord 338 reduce 328 estimate 323 take 321 give 318 analyze 309 acquire 301 make 287 know Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 3035 respiratory 2424 not 1832 high 1605 clinical 1583 - 1334 other 1304 severe 1220 more 1166 also 1154 low 1140 acute 1091 viral 1036 positive 1020 human 865 only 857 most 837 however 798 first 742 such 738 different 735 significant 602 non 598 well 559 significantly 548 bacterial 543 infectious 542 negative 508 early 486 available 484 common 474 old 468 specific 462 medical 441 respectively 434 further 415 less 412 as 410 additional 404 likely 385 similar 373 large 372 previous 372 new 362 therefore 349 public 341 important 327 possible 326 real 325 potential 322 multiple Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 217 most 131 least 130 high 104 Most 63 good 49 large 30 low 21 great 14 early 10 close 9 late 8 long 5 small 5 old 5 near 4 common 4 bad 3 strong 3 few 3 -t 2 big 1 young 1 wide 1 strict 1 southernmost 1 sick 1 short 1 rich 1 nonsevere 1 new 1 mild 1 hight 1 eld 1 cord-334746-anqvdi2k 1 cord-282898-hsqvkm2i 1 Least 1 HBcAb 1 -C5 Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 640 most 174 least 10 well 1 worst 1 lowest 1 groel Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 21 doi.org 20 www.biomedcentral.com 3 www.ncbi.nlm.nih.gov 3 www 3 blast.ncbi.nlm.nih.gov 2 www.clinicaltrialsregister.eu 2 www.cbs.dtu.dk 2 github.com 2 dhsprogram.com 1 www.who.int 1 www.tutiempo.net 1 www.rstudio.com 1 www.randomizer.org 1 www.r-project.org 1 www.oie.int 1 www.ncbi.nlm.nih 1 www.megasoftware.net 1 www.megasoftware 1 www.innatedb.ca 1 www.informatik.uni-ulm.de 1 www.hradecisiontools.org.uk 1 www.gleamviz.org 1 www.genestone.com.cn:8080 1 www.gematics 1 www.eunid.eu 1 www.eunid 1 www.embl.org 1 www.cdc.gov 1 www.cbs 1 www.r-project.org 1 wwsw.nhc.gov.cn 1 welcome.oda.sas.com 1 unifrac.colorado.edu 1 sysbio.unl.edu 1 shire.science.uq.edu.au 1 rdp.cme.msu 1 pyro.cme.msu.edu 1 pubmlst.org 1 platform.gisaid.org 1 pfam.sanger.ac.uk 1 ictvonline.org 1 hadvwg.gmu.edu 1 figshare.com 1 eztaxon-e.ezbiocloud.net 1 doi 1 blast Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 20 http://doi.org/10 3 http://www 2 http://dhsprogram.com 2 http://blast.ncbi.nlm.nih.gov/Blast.cgi 1 http://www.who.int/csr/don/archive/disease/mers-cov/en/ 1 http://www.tutiempo.net/en/Climate/Shantou/2011/ 1 http://www.rstudio.com/} 1 http://www.randomizer.org/ 1 http://www.r-project.org/ 1 http://www.oie.int/ 1 http://www.ncbi.nlm.nih.gov/SNP/ 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.ncbi.nlm.nih.gov 1 http://www.ncbi.nlm.nih 1 http://www.megasoftware.net/ 1 http://www.megasoftware 1 http://www.innatedb.ca/ 1 http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/mra/app/index.php?plugin=form 1 http://www.hradecisiontools.org.uk/research/ 1 http://www.gleamviz.org/simulator/ 1 http://www.genestone.com.cn:8080/microbial/index.jsp 1 http://www.gematics 1 http://www.eunid.eu 1 http://www.eunid 1 http://www.embl.org/ 1 http://www.clinicaltrialsregister.eu/ctr-search/trial/2014-001863-11/results 1 http://www.clinicaltrialsregister.eu/ctr-search/ 1 http://www.cdc.gov/flu/pandemic-resources/1918-pandemic-h1n1.html 1 http://www.cbs.dtu.dk/services/NetNGlyc/ 1 http://www.cbs.dtu.dk/services/NetMHCpan/ 1 http://www.cbs 1 http://www.biomedcentral.com/content/supplementary/1471-2334-9-51-S1.doc] 1 http://www.biomedcentral.com/content/backmatter/ 1 http://www.biomedcentral.com/1471-2334/9/9/prepub 1 http://www.biomedcentral.com/1471-2334/9/51/prepub 1 http://www.biomedcentral.com/1471-2334/9/115/pre 1 http://www.biomedcentral.com/1471-2334/8/86/prepub 1 http://www.biomedcentral.com/1471-2334/8/29/prepub 1 http://www.biomedcentral.com/1471-2334/8/23/prepub 1 http://www.biomedcentral.com/1471-2334/8/117/pre 1 http://www.biomedcentral.com/1471-2334/7/50/prepub 1 http://www.biomedcentral.com/1471-2334/7/35/prepub 1 http://www.biomedcentral.com/1471-2334/7/18/prepub 1 http://www.biomedcentral.com/1471-2334/6/82/prepub 1 http://www.biomedcentral.com/1471-2334/6/40/prepub 1 http://www.biomedcentral.com/1471-2334/6/20/prepub 1 http://www.biomedcentral.com/1471-2334/6/147/pre 1 http://www.biomedcentral.com/1471-2334/6/130/pre 1 http://www.biomedcentral.com/1471-2334/6/109/pre 1 http://www.biomedcentral.com/1471-2334/5/26/prepub Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 zhou3218@yahoo.com 1 veronika.v.vorobieva@gmail.com 1 sunxiaodong_scdc@163.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 35 study are available 17 study did not 10 samples were positive 10 study has several 10 study was not 9 % were positive 8 case report date 8 data are available 8 samples were not 7 data were not 7 patients did not 7 patients had positive 7 patients were more 6 data were available 6 infection is common 6 patients were male 6 patients were positive 6 rate was significantly 6 samples were also 6 study are not 5 % were male 5 cases were children 5 group were significantly 5 infection is not 5 patients tested positive 5 patients was significantly 5 patients were not 5 patients were significantly 5 pneumonia were more 5 results are available 5 results are consistent 5 results were not 5 sample was positive 5 samples were further 5 viruses were more 4 % were less 4 case report form 4 cases were male 4 groups was not 4 infections were more 4 infections were not 4 patients had fever 4 patients had more 4 patients were children 4 pneumonia is not 4 pneumonia is still 4 pneumonia was present 4 rate was high 4 rates were similar 4 results were available Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 6 study are not publicly 4 groups was not statistically 1 % do not generally 1 case did not significantly 1 cases is not equal 1 cases were no awareness 1 cases were no longer 1 cases were not epidemiologically 1 children are not well 1 children having no direct 1 control does not fully 1 controls were not significantly 1 data are not very 1 data were not always 1 data were not available 1 data were not normally 1 data were not sufficient 1 detection is not random 1 disease do not accurately 1 disease were not due 1 diseases was not significantly 1 group has no significantly 1 group was not significantly 1 groups showed no significant 1 hospital were not available 1 hospitals were not completely 1 infection is not always 1 infection is not clearly 1 infection is not fully 1 infection is not long 1 infection is not uncommon 1 infection was not present 1 infections are not likely 1 infections have not yet 1 infections is not obvious 1 infections were not available 1 influenza was not significantly 1 numbers were not high 1 outbreak is not as 1 outbreaks had not only 1 outbreaks was not available 1 pathogen does not necessarily 1 pathogens are not widely 1 pathogens did not always 1 patient had no specific 1 patients are not available 1 patients are not infectious 1 patients had no history 1 patients infected not only 1 patients is not necessary A rudimentary bibliography -------------------------- id = cord-326632-botshfa1 author = Abolfotouh, Mostafa A. title = Perception and attitude of healthcare workers in Saudi Arabia with regard to Covid-19 pandemic and potential associated predictors date = 2020-09-29 keywords = Arabia; Saudi; covid-19 summary = METHODS: In a cross-sectional study, HCWs at three tertiary hospitals in Saudi Arabia were surveyed via email with an anonymous link, by a concern scale about Covid-19 pandemic during 15–30 April, 2020. Predictors of high concern scores were; HCWs of Saudi nationality (p < 0.001), younger age (p = 0.003), undergraduate education (p = 0.044), living with others (p = 0.003) working in the western region (p = 0.003) and direct contact with patients (p = 0.018). In multiple regression analysis ( Table 4) , predictors of high concern scores were; HCWs of younger age (p = 0.003), Saudi nationality (p < 0.001), undergraduate education (p = 0.044), and those working in the western region (p = 0.003), living with others (p = 0.003) and in direct contact with patients (p = 0.018). doi = 10.1186/s12879-020-05443-3 id = cord-345046-str19r9a author = Al Ghamdi, Mohammed title = Treatment outcomes for patients with Middle Eastern Respiratory Syndrome Coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia date = 2016-04-21 keywords = East; MERS; Middle summary = doi = 10.1186/s12879-016-1492-4 id = cord-320928-flsaa1wx author = Aldohyan, Meshal title = The perceived effectiveness of MERS-CoV educational programs and knowledge transfer among primary healthcare workers: a cross-sectional survey date = 2019-03-21 keywords = Arabia; MERS; Saudi; knowledge summary = This study evaluated the perceived effectiveness of MERS-CoV educational programs and knowledge transfer among primary care HCWs at a hospital in Saudi Arabia that witnessed the largest outbreak of confirmed MERS-CoV cases in this country. CONCLUSIONS: A negative perception of the effectiveness of MERS-CoV knowledge transfer was associated with poorer knowledge and was more prevalent among male HCWs, physicians/pharmacists and less experienced HCWs. Hospitals should always refer to efficient knowledge sharing and educational strategies that render beneficial outcomes to patients, HCWs, and the public community. Therefore, there was an emerging need to evaluate the perceived effectiveness of MERS-CoV educational programs and knowledge transfer from the HCW''s perspective, in a setting that witnessed the largest outbreak of confirmed MERS-CoV cases in Saudi Arabia. This explains why HCWs with less work experience (< 5 years) had significantly more negative perceptions of knowledge transfer and the perceived effectiveness of MERS-CoV educational programs. doi = 10.1186/s12879-019-3898-2 id = cord-292828-29jbf9ik author = Alsaleh, Asma N title = Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date = 2014-01-09 keywords = ERV3; PCR; respiratory; virus summary = title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. doi = 10.1186/1471-2334-14-15 id = cord-283450-w6scpc65 author = Amariei, Raluca title = The United States and Canada as a coupled epidemiological system: An example from hepatitis A date = 2008-02-28 keywords = Canada; canadian summary = doi = 10.1186/1471-2334-8-23 id = cord-031710-1xl2isee author = Andrei, Stefan title = Successful treatment of pulmonary haemorrhage and acute respiratory distress syndrome caused by fulminant Stenotrophomonas maltophilia respiratory infection in a patient with acute lymphoblastic leukaemia – case report date = 2020-09-10 keywords = ICU; Stenotrophomonas; patient summary = title: Successful treatment of pulmonary haemorrhage and acute respiratory distress syndrome caused by fulminant Stenotrophomonas maltophilia respiratory infection in a patient with acute lymphoblastic leukaemia – case report CASE PRESENTATION: We present the rare case of successful outcome in a 61-year-old female who developed alveolar haemorrhage and acute respiratory distress syndrome 8 days after a chemotherapy session for her acute lymphoblastic leukaemia, in the context of secondary bone marrow aplasia. We report the case of successfully treated severe Stenotrophomonas maltophilia respiratory infection complicated with pulmonary haemorrhage in a chemotherapyinduced pancytopenia patient diagnosed with acute lymphoblastic leukaemia. To our knowledge, this is the first reported case of pulmonary haemorrhage and ARDS caused by a fulminant Stenotrophomonas maltophilia respiratory infection in Eastern Europe, and it seems to be a rare case of positive outcome in a patient with haematological malignancy. doi = 10.1186/s12879-020-05378-9 id = cord-287367-1sdt9zz8 author = Andrews, Denise title = Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use date = 2017-10-10 keywords = POC; arm; patient; study summary = doi = 10.1186/s12879-017-2784-z id = cord-261251-ylvqxpba author = Ansuini, Valentina title = Debate around infection-dependent hemophagocytic syndrome in paediatrics date = 2013-01-16 keywords = Barr; EBV; HPS summary = BACKGROUND: Hemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. In the case of severe EBV-related HPS, the introduction of immuno-chemotherapy and, if necessary, allogenic stem cell transplantation has radically changed the history and prognosis of the disease: in such cases, the optimal treatment strategy can be centred on immunosuppressive medications that inhibit overactive T and NK cell responses (i.e. corticosteroids, cyclosporine A, intravenous immunoglobulin, anti-thymocyte globulins, etoposide, rituximab, and plasma or blood exchange transfusions) [38, 39] . Clinicopathological study of severe chronic active Epstein-Barr virus infection that developed in association with lymphoproliferative disorder and/or hemophagocytic syndrome Quantitative analysis of cell-free Epstein-Barr virus genome copy number in patients with EBV-associated hemophagocytic lymphohistiocytosis Penicilliosis-associated hemophagocytic syndrome in a human immunodeficiency virus-infected child: the first case report in children doi = 10.1186/1471-2334-13-15 id = cord-354827-ipg1vwmv author = Baker, Stephen title = Searching for the elusive typhoid diagnostic date = 2010-03-05 keywords = Salmonella; Typhi; typhoid summary = Typhoid (enteric) fever is still a common disease in many developing countries but current diagnostic tests are inadequate. Enteric fever is an all encompassing term for the disease caused by several serovars of Salmonella enterica including (S.) Typhi and (S.)Paratyphi A. An additional caveat for an effective and appropriate diagnostic test is the cross section of organisms that can cause a disease syndrome that is, clinically, indistinguishable from typhoid fever. Transcriptional analysis of RNA extracted from the blood of typhoid patients could be performed to identify specific genes, pathways, interactions or transcriptional regulatory hubs that are activated in the host during infection. Quantitative detection of Salmonella enterica serovar Typhi from blood of suspected typhoid fever patients by real-time PCR Enzyme-linked immunosorbent assay for detection of Salmonella typhi Vi antigen in urine from typhoid patients Rapid diagnosis of typhoid fever by enzyme-linked immunosorbent assay detection of Salmonella serotype typhi antigens in urine doi = 10.1186/1471-2334-10-45 id = cord-001725-pw7coi3v author = Ballus, Josep title = Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes date = 2015-07-30 keywords = ICU; SSI; surgical summary = title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes We therefore aimed to assess the incidence, epidemiology and microbiology of SSI and its association with outcomes in patients with severe peritonitis in the intensive care unit (ICU). Physicians may consider antibiotic-resistant pathogens, gram-positive cocci and fungi when choosing empiric antibiotic treatment for SSI, although more studies are needed to confirm our results due to the inherent limitations of the microbiological sampling with swabs performed in our research. This study therefore aimed to describe the incidence, epidemiology, microbiology and outcomes of SSI in patients admitted with secondary or tertiary peritonitis to the ICU of a tertiary referral hospital. This study provides data on the incidence and microbiology of SSIs for a large cohort of critically ill patients admitted with secondary or tertiary peritonitis to a surgical ICU. doi = 10.1186/s12879-015-1050-5 id = cord-354690-ywb9krdp author = Barr, Margo title = Pandemic influenza in Australia: Using telephone surveys to measure perceptions of threat and willingness to comply date = 2008-09-15 keywords = influenza; pandemic; willing summary = doi = 10.1186/1471-2334-8-117 id = cord-276015-id15u3br author = Beran, Jiří title = Inosine pranobex is safe and effective for the treatment of subjects with confirmed acute respiratory viral infections: analysis and subgroup analysis from a Phase 4, randomised, placebo-controlled, double-blind study date = 2016-11-07 keywords = influenza; pranobex; study; subject summary = doi = 10.1186/s12879-016-1965-5 id = cord-344770-aoi42xq4 author = Bialasiewicz, Seweryn title = Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing date = 2014-05-19 keywords = PCR; PIV4; QLD-01 summary = doi = 10.1186/1471-2334-14-275 id = cord-011601-1u1rlwzp author = Biribawa, Claire title = Measles outbreak amplified in a pediatric ward: Lyantonde District, Uganda, August 2017 date = 2020-06-05 keywords = District; Lyantonde; Uganda summary = doi = 10.1186/s12879-020-05120-5 id = cord-281916-v6u5mr2i author = Bonnin, Paul title = Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date = 2016-08-09 keywords = respiratory; sample; viral summary = METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. If a rich cell collection appears to be an important prerequisite for the quality of respiratory viral diagnosis, there is currently no information on a possible cellularity threshold that would validate the result of the viral molecular detection. These 800 aliquots were selected in the laboratory samples bank according to their results in virological diagnosis: 400 Positive and 400 Negative for molecular detection of respiratory panel using the RespiFinder ® Smart_22_Fast technique (Pathofinder, Maastricht, Netherlands). The main objectives of this work have been to study the cellularity of these clinical respiratory specimens, to propose a possible definition of what is commonly called "cellular richness," and to measure the impact of this marker on the molecular viral diagnosis. (2014) performed a molecular cell quantification using real time PCR in order to validate viral detection on nasal swabs. doi = 10.1186/s12879-016-1730-9 id = cord-048489-ajafw966 author = Bozza, Fernando A title = Multiplex cytokine profile from dengue patients: MIP-1beta and IFN-gamma as predictive factors for severity date = 2008-06-25 keywords = IFN; cytokine; dengue; patient summary = doi = 10.1186/1471-2334-8-86 id = cord-000332-u3f89kvg author = Broeck, Wouter Van den title = The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale date = 2011-02-02 keywords = GLEaMviz; model; simulation; user summary = doi = 10.1186/1471-2334-11-37 id = cord-004395-erqmbi2b author = Bugembe, Daniel Lule title = Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort date = 2020-02-22 keywords = HIV-1; HLA summary = METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. Using experimental epitope mapping data generated from 757 peptides tested on cells of 6 early HIV-1 infected individuals at paired time points, we show that NetMHCpan4.0 can be useful for markedly reducing pooled peptide experiments as demonstrated by the 95% experimental and computational concordance. Experimental data of peptides previously mapped for HIV-1 epitope recognition of 6 individuals for a separate study (Table 1) at 2 time points each was used for comparison with the computationally predicted binders. In this analysis we showed that the computational method NetMHCpan4.0 predicted 95% of previously experimentally mapped HIV-1 epitopes in 6 HIV-1 infected individuals expressing a total of 22 different HLA class I alleles. doi = 10.1186/s12879-020-4876-4 id = cord-321235-h3w8827o author = Cabrera Alvargonzalez, Jorge Julio title = Pooling for SARS-CoV-2 control in care institutions date = 2020-10-12 keywords = Care; Homes; SARS summary = doi = 10.1186/s12879-020-05446-0 id = cord-315866-6vcts4w3 author = Chan, KC Allen title = Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study date = 2005-04-09 keywords = ARDS; SARS summary = title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Therefore, in this study, we investigated the association of the ACE insertion/deletion (I/D) polymorphism of the 287 bp Alu repeat to the susceptibility to SARS and the development of adult respiratory distress syndrome (ARDS) with a larger population. The genotypic distributions and allelic frequencies of ACE I/D polymorphism in the SARS patients and control subjects are shown in table 2. doi = 10.1186/1471-2334-5-26 id = cord-009210-qhul89z2 author = Chen, Jie title = Diagnosis of severe scrub typhus infection by next-generation sequencing:a case report date = 2020-04-07 keywords = Fig; Orientia; typhus summary = doi = 10.1186/s12879-020-04991-y id = cord-318984-8m9ygzn5 author = Chen, Yin-Yin title = Surveillance on secular trends of incidence and mortality for device–associated infection in the intensive care unit setting at a tertiary medical center in Taiwan, 2000–2008: A retrospective observational study date = 2012-09-10 keywords = DAI; ICU; infection summary = We examined the rates of DAI by antimicrobial-resistant pathogens, and 30–day and in–hospital mortality in the intensive care unit (ICU). Decreased susceptibility of both gram-positive and gram-negative microbes to antibiotics has been well described in several surveillance studies over the past decade, and increases in the rate of bloodstream infection caused by multi-drug resistant (MDR) gramnegative bacteria have been reported to be 16-fold [5, [8] [9] [10] [11] . In this study, prospective surveillance was conducted to determine the DAI rate and prevalence of antibiotic-resistant isolates at an adult medical-surgical ICU (MS ICU). Our aim was to analyze the secular trend of incidence for different types of DAIs, determine the common pathogens involved, and determine the rates of antimicrobial resistance and overall 30-day and in-hospital mortality during the period 2000-2008. The involved patient demographic information, the dates and sites of infection, device-utilization (DU) ratio, pathogens, antimicrobial susceptibilities, invasive procedures, and overall 30-day mortality and in-hospital crude mortality were recorded. doi = 10.1186/1471-2334-12-209 id = cord-330607-zn4urrxc author = Chi, Qiong title = Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date = 2020-09-18 keywords = COVID-19; SARS summary = METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. doi = 10.1186/s12879-020-05383-y id = cord-324638-gwd8qin6 author = Chiu, Rossa WK title = Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date = 2006-02-09 keywords = RNA; SARS summary = We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. doi = 10.1186/1471-2334-6-20 id = cord-345854-f0dq94j1 author = Chong, Wai Po title = The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date = 2006-05-04 keywords = IFN; SARS summary = doi = 10.1186/1471-2334-6-82 id = cord-004488-r50atew9 author = Chong, Zhuo Lin title = Diagnostic accuracy and utility of three dengue diagnostic tests for the diagnosis of acute dengue infection in Malaysia date = 2020-03-12 keywords = Dengue; NS1; RDT summary = This study evaluated the accuracy and utility of ViroTrack Dengue Acute a new biosensors-based dengue NS1 RDT, SD Bioline Dengue Duo NS1/IgM/IgG combo a commercially available RDT, and SD Dengue NS1 Ag enzyme-linked immunosorbent assay (ELISA), for the diagnosis of acute dengue infection. In this evaluation study, we aimed to estimate the diagnostic accuracy and utility of a newly developed biosensors-based dengue NS1 assay, and one each of commercially available NS1 ELISA and NS1/IgM/IgG RDT. The true positive (TP), false negative (FN), false positive (FP), and true negative (TN) of each index test and various combinations of the components of combo test as compared to the reference standard were used to calculate various diagnostic accuracy parameters and their 95% confidence intervals (95%CI) using standard formulas [24, 25] Subgroup analyses by exposure (serotype, day of illness or DOI, dengue infection status) and outcome (lab-confirmed vs presumptive dengue) were also performed to compare sensitivity estimates. doi = 10.1186/s12879-020-4911-5 id = cord-262646-64ldtrjf author = Chuang, Pei-Hung title = A dynamic estimation of the daily cumulative cases during infectious disease surveillance: application to dengue fever date = 2010-05-27 keywords = Taiwan; case summary = This study proposes a dynamic statistical model to estimate the daily number of new cases and the daily cumulative number of infected cases, which was then applied to historic dengue fever data. Our results show that when an infectious disease required a time-consuming process for diagnosis, such as the dengue fever using the previously mentioned protocol, the actual daily number of infected cases and cumulative positive cases are potentially underestimated. The Figure 3 and Table 1 for cumulative cases showed that a gamma distribution is a more appropriate assumption for the onset-todiagnosis time when estimating the probability of being a positive case using the dengue fever example; nonetheless, the difference between the gamma and the nonparametric method is again only slight except towards the end stage of the epidemic after January 1. This study has proposed a statistical method that more accurately estimates the real-time daily new cases and daily cumulative number of infected cases using a dengue fever epidemic as an example. doi = 10.1186/1471-2334-10-136 id = cord-276857-i948aq4b author = Chung, Grace TY title = A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date = 2005-10-18 keywords = SARS summary = We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [8, 12] . In this study, we demonstrate the feasibility of the adoption of allelic discrimination assays based on the use of fluorogenic oligonucleotide probes for the genotyping of SARS-CoV isolates. Our study has clearly demonstrated the feasibility of using allelic discrimination assays as a method for genetic characterization of SARS-CoV genotypes in patients. Genotype of SARS-CoV culture isolates from 30 patients determined by Taqman Allelic Discrimination assays Petric M, Skowronski DM doi = 10.1186/1471-2334-5-87 id = cord-048467-1dus0u4m author = Civaner, Murat title = Can "presumed consent" justify the duty to treat infectious diseases? An analysis date = 2008-03-06 keywords = HIV; SLR; profession; risk summary = doi = 10.1186/1471-2334-8-29 id = cord-288972-dc6xbxha author = Cowling, Benjamin J title = Entry screening to delay local transmission of 2009 pandemic influenza A (H1N1) date = 2010-03-30 keywords = H1N1; entry summary = BACKGROUND: After the WHO issued the global alert for 2009 pandemic influenza A (H1N1), many national health agencies began to screen travelers on entry in airports, ports and border crossings to try to delay local transmission. METHODS: We reviewed entry screening policies adopted by different nations and ascertained dates of official report of the first laboratory-confirmed imported H1N1 case and the first laboratory-confirmed untraceable or ''local'' H1N1 case. To explore potential delays in local H1N1 transmission associated with entry screening, we ascertained dates of official report of the first laboratory-confirmed imported H1N1 case and the first laboratory-confirmed untraceable or ''local'' H1N1 case (i.e. a case not otherwise epidemiologically linked with international travel, contact with an imported case or their secondary infectees) and the interval between these two events. Additional file 1: Use of entry screening* and interval between confirmation of first imported pandemic influenza A (H1N1) case and confirmation of first untraceable local case doi = 10.1186/1471-2334-10-82 id = cord-316245-n6tmn4ph author = Cui, Binglin title = Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date = 2015-03-13 keywords = HRV; PIV3; virus summary = METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). doi = 10.1186/s12879-015-0863-6 id = cord-299750-zkrlm3ds author = Cui, Wei title = Factors associated with death in hospitalized pneumonia patients with 2009 H1N1 influenza in Shenyang, China date = 2010-05-31 keywords = China; H1N1; patient summary = We describe the clinical characteristics and factors associated with the death of patients who were hospitalized with 2009 H1N1 influenza pneumonia in Shenyang, China, from November to December 2009. Therefore, this report summarizes the clinical manifestations, clinical outcomes and the risk factors associated with death in hospitalized pneumonia patients associated with 2009 H1N1 influenza infections in Shenyang, China, during November to December 2009. They used a standardized form that included demographic data, seasonal influenza vaccination history for the previous year, smoking status, underlying medical conditions, clinical signs and symptoms, selected laboratory tests including C reactive protein (CRP), white blood cell classification and count, lactic dehydrogenase (LDH), creatine kinase (CK), glutamic-oxaloacetic transaminase (AST), glutamic alanine aminotransferase (ALT), albumin (Alb), CD4, CD8 and CD3 T cell counts, blood gas analyses, blood or sputum cultures, radiographic findings, intervals between symptom onset and initiation of oseltamivir therapy, treatment course and length of stay. doi = 10.1186/1471-2334-10-145 id = cord-000441-5rm1za8z author = Curtale, Filippo title = Description of two measles outbreaks in the Lazio Region, Italy (2006-2007). Importance of pockets of low vaccine coverage in sustaining the infection date = 2010-03-11 keywords = Italy; Roma; Sinti summary = Pockets of low vaccine coverage individuals (Roma/Sinti communities, high school students) facilitated the reintroduction of serotypes not endemic in Italy and facilitated the measles infection to spread. Two cases among the Italian ethnic population, who developed symptoms on 19 and 20 July, reported contact with Roma/Sinti patients with measles in a hospital waiting area, on 4 and 10 July They confirmed that pockets of low vaccination coverage exist in some areas of the Lazio region, particularly among Roma/Sinti communities and adolescents Thanks to relatively high immunisation rates amongst new born children (90,7%) [10] and the work done by the local health authorities, conducting contact investigation of cases'', vaccination of susceptible school and household contacts, and implementing isolation measures, the outbreaks did not affect the whole region and, in the city of Rome, was mainly limited to a few peripheral districts (Figure 2 ). doi = 10.1186/1471-2334-10-62 id = cord-308655-zntwwqod author = Dabisch-Ruthe, Mareike title = Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay date = 2012-07-24 keywords = PCR; RVP; SMART-22 summary = title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. This study presents the first comparison of the analytical sensitivity of three novel multiplex PCR methods, the RespiFinder-19 assay, RespiFinder-SMART(Single tube Multiplex Amplification in Real-Time)-22 assay (both PathoFinder, Maastricht, Netherlands) and the xTAG Respiratory Virus Panel Fast Assay (Abbott Molecular, Wiesbaden, Germany), with quantified virus control material. Previous studies with clinical samples showed that the sensitivity and specificity of the RVP assay was 78.8% and 99.6%, respectively, compared to real-time PCR-methods, that are currently declared as the gold standard [21] . doi = 10.1186/1471-2334-12-163 id = cord-291393-iht5zndl author = De Angelis, Giulia title = Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features date = 2020-10-19 keywords = COVID-19; SARS summary = doi = 10.1186/s12879-020-05504-7 id = cord-271813-nroflfmc author = Deng, Wang title = Positive results for patients with COVID-19 discharged form hospital in Chongqing, China date = 2020-06-19 keywords = COVID-19; SARS summary = METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Among them, 61 patients had positive results of SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (RT-PCR) test, which provided the important information and clinical evidence for the improved management of patients recovered from COVID-19. The study revealed the clinical features of recovered patients with the recurrence of positive results of SARS-CoV-2.Multi-site screening including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. doi = 10.1186/s12879-020-05151-y id = cord-288372-48wao8a0 author = Dia, Ndongo title = Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date = 2014-04-08 keywords = ILI; Senegal; virus summary = doi = 10.1186/1471-2334-14-189 id = cord-001512-u3u2k8hj author = Ding, Hua title = A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China date = 2014-12-31 keywords = H7N9; Index; January; case summary = doi = 10.1186/s12879-014-0698-6 id = cord-300230-a3jk6w90 author = Ding, Ji-Guang title = Retrospective analysis of nosocomial infections in the intensive care unit of a tertiary hospital in China during 2003 and 2007 date = 2009-07-25 keywords = ICU; infection; nosocomial summary = RESULTS: Among 1980 patients admitted over the period of time, the overall patient nosocomial infection rate was 26.8% or 51.0 per 1000 patient days., Lower respiratory tract infections (LRTI) accounted for most of the infections (68.4%), followed by urinary tract infections (UTI, 15.9%), bloodstream (BSI, 5.9%), and gastrointestinal tract (GI, 2.5%) infections. In conclusion, there was a high and relatively stable rate of nosocomial infections in the ICU of a tertiary hospital in China through year 2003-2007, with some differences in the distribution of the infection sites, and pathogen and antibiotic susceptibility profiles from those reported in the Western countries. In conclusion, there was a high and relatively stable rate of nosocomial infections in the ICU of a tertiary hospital in China through year 2003-2007, with some differences in the distribution of the infection sites, and pathogen and antibiotic susceptibility profiles from those reported in the Western countries. doi = 10.1186/1471-2334-9-115 id = cord-025163-iyh0d6mj author = Ding, Lin title = Early diagnosis and appropriate respiratory support for Mycoplasma pneumoniae pneumonia associated acute respiratory distress syndrome in young and adult patients: a case series from two centers date = 2020-05-24 keywords = ARDS; pneumoniae summary = doi = 10.1186/s12879-020-05085-5 id = cord-274123-wgigtgl9 author = Dube, Felix S. title = Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa date = 2016-10-24 keywords = PTB; child summary = title: Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa We have recently shown [5] that specific pathogens (including Bordetella pertussis, influenza virus, respiratory syncyntial virus [RSV], adenovirus, parainfluenzavirus, bocavirus) are detected significantly more frequently from the nasopharynx (NP) of children with pneumonia than age-matched controls, and so are likely to play an important role in pneumonia aetiology. This is the first comprehensive detailed study of the diversity of respiratory microbes detected in children presenting with suspected PTB in a TB endemic setting and showed that multiple potential pathogens are present in th nasopharynx of such children. In conclusion, this study describes the detection of multiple respiratory microbes in the nasopharynx of children hospitalised with suspected PTB. pneumoniae, hMPV, coronavirus O43, influenza C virus, rhinovirus and cytomegalovirus formed the dominant microbial profile in children with PTB but this failed to reach statistical significance on testing of each individual microbe. doi = 10.1186/s12879-016-1934-z id = cord-261756-4lybl57r author = Dubert, Marie title = Late viral or bacterial respiratory infections in lung transplanted patients: impact on respiratory function date = 2020-02-24 keywords = BOS; infection; respiratory summary = METHODS: Patients, who survived 6 months or more following lung transplantation that took place between 2009 and 2014, were classified into three groups: a viral infection group (VIG) (without any respiratory bacteria), a bacterial infection group (BIG) (with or without any respiratory viruses), and a control group (CG) (no documented infection). In order to include patients at a steady state, we studied only the late respiratory infections, i.e. to censure the first 6 months after the lung transplantation, a period during which postoperative complications are frequent and usually intertwined. Concerning AR, the impact of late respiratory viral and/ or bacterial infections on the graft function was significantly different with three times more AR within 6 months for both the VIG and BIG compared to the CG. doi = 10.1186/s12879-020-4877-3 id = cord-004198-h8ch3x14 author = Ebuy, Hiluf title = HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study date = 2020-01-21 keywords = Ethiopia; HIV; PMTCT summary = title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study While world health organization recommends HIV exposed infants to be tested between 4 to 6 weeks of age, in developing countries like Ethiopia, access to timely infant testing is still very limited. The study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing HIV positivity among infants born to HIV positive mothers in public hospitals of Mekelle, Ethiopia. Timely infant testing, counselling on feeding options and adherence should be intensified, and prevention of mother-to-child transmission program in rural settings need to be strengthened. Thus, the present study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing overall HIV positivity and HIV positivity at 18 months among infants born to HIV positive mothers in public hospitals of Mekelle city, North Ethiopia. doi = 10.1186/s12879-020-4790-9 id = cord-004110-xc8vv9x8 author = Eslahi, Aida Vafae title = Prevalence of Toxocara and Toxascaris infection among human and animals in Iran with meta-analysis approach date = 2020-01-07 keywords = Iran; Toxascaris; Toxocara; prevalence summary = Herein, a meta-analysis was contrived to assess the prevalence of Toxocara/Toxascaris in carnivore and human hosts in different regions of Iran from April 1969 to June 2019. CONCLUSION: Our meta-analysis results illustrate a considerable prevalence rate of Toxocara/Toxascaris, particularly in cats and dogs of northern parts of Iran. A combination of the following search terms were employed in our literature searches as follows: ("Toxocariasis" OR "Toxocara infection" OR "Toxocara canis" OR "Toxocara cati" OR "Toxascaris leonina") AND ("Carnivora" OR "Human") AND ("Prevalence" OR "Epidemiology") AND ("Iran"). in various carnivores and human populations in Iran; (D) Studies that detected Toxocara infection using at least one of the parasitological, serological and molecular methods; (e) exact total sample size, positive samples and the respective prevalence rates were available. The weighted prevalence of Toxocara/ Toxascaris in Iran dogs by study method Additional file 5: Figure S5 . doi = 10.1186/s12879-020-4759-8 id = cord-342250-x5bzrpcu author = Faires, Meredith C title = The use of the temporal scan statistic to detect methicillin-resistant Staphylococcus aureus clusters in a community hospital date = 2014-07-08 keywords = MRSA; Staphylococcus; cluster; hospital summary = The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters, validate clusters using molecular techniques and hospital records, and determine significant differences in the rate of MRSA cases using regression models. The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters in a community hospital and to validate significant clusters using molecular techniques and hospital records concerning known MRSA outbreaks; and to determine if there were significant differences in the rate of MRSA infection and colonization cases by month, season, and year using regression models. Data pertaining to known MRSA outbreaks that occurred during the study period (e.g., start and end date, ward location, and number of patients involved) were collected from the hospital''s Infection Prevention and Control (IPC) department. doi = 10.1186/1471-2334-14-375 id = cord-334746-anqvdi2k author = Fischer, Doris title = Overcrowding in a neonatal intermediate care unit: impact on the incidence of multidrug-resistant gram-negative organisms date = 2019-04-29 keywords = MDRGN; NIMCU; PRAE summary = BACKGROUND: Overcrowding, reduced nurse to patient ratio, limited distance between incubators and absence of microbiological surveillance have been shown to promote spread of multidrug-resistant gram-negative organisms (MDRGN) in patients with birthweight < 1500 g. Care of MDRGN colonized patient was provided by staff wearing gloves and gowns according to the current recommendations by the Commission for Hospital Hygiene and Infection Prevention of the Robert Koch Institute, Berlin, Germany (KRINKO) [29] . In this study, we implemented the available recommendations concerning neonatal MDRGN transmission into the daily life settings on NIMCU in the scenario of a short-term and high risk overcrowding period. We therefore assume our management consisting of active surveillance, staff training as well as adherence to infection control demands has proven to be a successful procedure to escort through overcrowding period and prevent the spread of multidrug-resistant organisms in hospital setting. doi = 10.1186/s12879-019-3981-8 id = cord-252304-lwiulri7 author = Fragnoud, Romain title = Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue date = 2015-11-14 keywords = pf4; protein summary = doi = 10.1186/s12879-015-1271-7 id = cord-033833-woref5g8 author = Fragoso-Saavedra, Sergio title = A parallel-group, multicenter randomized, double-blinded, placebo-controlled, phase 2/3, clinical trial to test the efficacy of pyridostigmine bromide at low doses to reduce mortality or invasive mechanical ventilation in adults with severe SARS-CoV-2 infection: the Pyridostigmine In Severe COvid-19 (PISCO) trial protocol date = 2020-10-16 keywords = Pyridostigmine; covid-19; severe summary = title: A parallel-group, multicenter randomized, double-blinded, placebo-controlled, phase 2/3, clinical trial to test the efficacy of pyridostigmine bromide at low doses to reduce mortality or invasive mechanical ventilation in adults with severe SARS-CoV-2 infection: the Pyridostigmine In Severe COvid-19 (PISCO) trial protocol METHODS: A parallel-group, multicenter, randomized, double-blinded, placebo-controlled, phase 2/3 clinical trial to test the efficacy of pyridostigmine bromide 60 mg/day P.O. to reduce the need for invasive mechanical ventilation and mortality in hospitalized patients with severe COVID-19. Exclusion criteria include one or more of the following: allergy to pyridostigmine; pregnancy or breastfeeding status; concomitant autoimmune disease; diagnosed immunodeficiencies (including HIV infection); need for mechanical ventilation, admission to the ICU, or meeting criteria for septic shock before providing signed, informed consent; inability to receive orally or enterally administered drugs; use of immunosuppressants or immune-modulators (including chemotherapy and corticosteroids) in the preceding 28-day period unless recommended by the treatment medical team as part of the therapeutic approach for SARS-CoV-2 infection; and participation in clinical trials of any kind in the previous 28 days. doi = 10.1186/s12879-020-05485-7 id = cord-003425-c5jdp5jv author = Fu, Yangxi title = Human adenovirus type 7 infection causes a more severe disease than type 3 date = 2019-01-09 keywords = HAdV-3; adenovirus; cell; infection summary = doi = 10.1186/s12879-018-3651-2 id = cord-356349-ey5vnddu author = Fusco, Francesco M title = Infection control management of patients with suspected highly infectious diseases in emergency departments: data from a survey in 41 facilities in 14 European countries date = 2012-01-28 keywords = EDs; MADs; patient summary = METHODS: The EuroNHID (European Network for Highly Infectious Diseases) project collected data from 41 EDs and MADs in 14 European countries, located in the same facility as a national/regional referral centre for HIDs, using specifically developed checklists, during on-site visits from February to November 2009. CONCLUSIONS: Preparedness level for the safe and appropriate management of HIDs is partially adequate in the surveyed EDs and MADs. Emergency Departments (EDs) and Medical Admission Departments (MADs) are high-risk areas for disease transmission in hospitals, since they are often overcrowded, and potentially infectious patients and susceptible individuals may wait in close proximity for several hours. The Figure 1 shows the level of adequacy of infection control in the surveyed EDs and MADs. The project explored the availability of triage staff specifically trained for the early recognition of suspected HID patients, or alternatively the existence of other procedures for the early identification of these patients, such as a syndromic approach. doi = 10.1186/1471-2334-12-27 id = cord-350949-ystkjdwk author = Gao, Yi-jie title = Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date = 2020-08-03 keywords = COVID-19; SARS summary = The meta-analysis showed the following results: the incidence of severe case or death was 12, 95% CI: 0.03-0.20, I 2 = 0%, P = 0.006; the incidence of fever was 51, 95% CI: 0.35-0.67, I 2 = 89%, P < 0.00001; the incidence of cough was 31, 95% CI: 0.23-0.39, I 2 = 38%, P < 0.00001; the incidence of lymphopenia was 49, 95% CI: 0.29-0.70, I 2 = 83%, P < 0.00001; the incidence of positive CT findings was 71, 95% CI: 0.49-0.93, I 2 = 90%, P < 0.00001; the incidence of coexisting disorders was 33, 95% CI: 0.21-0.44, I 2 = 70%, P < 0.00001; the incidence of preterm labor was 23, 95% CI: 0.14-0.32, I 2 = 21%, P < 0.00001; the incidence of caesarean section was 65, 95% CI: 0.42-0.87, I 2 = 90%, P < 0.00001; the incidence of fetal distress was 29, 95% CI: 0.08-0.49, I 2 = 68%, P = 0.007; the incidence of neonatal asphyxia or neonatal death or stillbirth was 9, 95% CI: − 0.03-0.21, I 2 = 0%, P = 0.14; the incidence of neonatal infection was 12, 95% CI: − 0.01-0.26, I 2 = 0%, P = 0.06; and SARS-CoV-2 testing of breast milk was only mentioned in the study by Chen H (2020.2.12), and the incidence was 0, which cannot be calculated by metaanalysis. doi = 10.1186/s12879-020-05274-2 id = cord-267090-jc1k3fki author = Gardner, Emma G. title = A case-crossover analysis of the impact of weather on primary cases of Middle East respiratory syndrome date = 2019-02-04 keywords = Arabia; MERS; Saudi summary = METHODS: A case-crossover design was used to identify associations between primary MERS cases and preceding weather conditions within the 2-week incubation period in Saudi Arabia using univariable conditional logistic regression. Data from meteorological stations closest to the largest city in each province were used to calculate the daily mean, minimum, and maximum temperature ((ο)C), relative humidity (%), wind speed (m/s), and visibility (m). Middle East respiratory syndrome coronavirus (MERS--CoV) is an emerging zoonotic agent that was first isolated in 2012 from a patient hospitalized in Saudi Arabia [1] , and has since infected over 2200 people with a 36% case fatality ratio [2] . By comparing weather conditions immediately before MERS cases to weather conditions at other times, this study aimed to identify environmental factors that are associated with primary human MERS in Saudi Arabia. The risk of primary human cases of MERS was associated with a decrease in temperature and humidity, and an increase in ground visibility. doi = 10.1186/s12879-019-3729-5 id = cord-001746-pbahviaz author = Garg, Shikha title = Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008 date = 2015-08-26 keywords = AOR; influenza; pneumonia summary = doi = 10.1186/s12879-015-1004-y id = cord-318057-xagh68jc author = Gunson, Rory N title = During the summer 2009 outbreak of "swine flu" in Scotland what respiratory pathogens were diagnosed as H1N1/2009? date = 2011-07-13 keywords = April; h1n1/2009 summary = All were from patients clinically diagnosed as having H1N1/2009 (based on accepted criteria) and all were given a full respiratory screen using real time reverse transcriptase polymerase chain reaction (rtRT-PCR) assays. During April-July 2009 all respiratory samples submitted from patients with a clinical diagnosis of H1N1/2009 (as stated on the specimen request form), were initially tested using a universal influenza A real time rtRT-PCR assay and a H1N1/2009 specific real time rtRT-PCR assay [7] . To determine which respiratory pathogens had been misdiagnosed as H1N1/2009, we examined the results of 3247 samples which had been given a full respiratory screen during the period April-July 2009. Examination of the detection rate over the four-month period shows that respiratory pathogens were detected in 27.9% of all samples submitted (95% confidence interval, 26.3-29.5%) ( Table 4 ). doi = 10.1186/1471-2334-11-192 id = cord-032382-5tp9i9vh author = Hackert, Volker H. title = Signs and symptoms do not predict, but may help rule out acute Q fever in favour of other respiratory tract infections, and reduce antibiotics overuse in primary care date = 2020-09-21 keywords = acute; fever; symptom summary = CONCLUSION: Whereas signs and symptoms of disease do not appear to predict acute Q fever, they may help rule it out in favour of other respiratory conditions, prompting a delayed or non-prescribing approach instead of early empiric doxycycline in primary care patients with non-severe presentations. Specifically, we assessed whether signs and symptoms could accurately identify acute Q fever in suspect cases prior to laboratory confirmation, or help rule out the diagnosis in favour of other respiratory infections where, depending on national guidelines, treatment with amoxicillin as a first-line antibiotic or a delayed or non-prescribing approach would be considered more appropriate. We performed a retrospective case-control study assessing the association of acute Q fever case status with signs and symptoms of disease in a sample of questionnaire respondents from the cohort of all individuals tested for acute Q fever by GP''s or hospital-based medical specialists in the period from March 2009 through April 2010 (n = 1218). doi = 10.1186/s12879-020-05400-0 id = cord-000996-ef5d81cg author = Han, Seung Beom title = Clinical characteristics and antimicrobial susceptibilities of viridans streptococcal bacteremia during febrile neutropenia in patients with hematologic malignancies: a comparison between adults and children date = 2013-06-17 keywords = VSB; adult; child summary = BACKGROUND: This study was performed to compare the clinical characteristics and antibiotic susceptibilities of viridans streptococcal bacteremia (VSB) between febrile neutropenic adults and children with hematologic malignancies. We performed this retrospective study to compare clinical characteristics including the occurrence of severe complications and antibiotic susceptibilities of viridans streptococci between febrile neutropenic adults and children with hematologic malignancies, and to propose appropriate antibacterial treatment strategies for adults and children. Data gathered on patients'' demographics and clinical characteristics consisted of gender, underlying disease with remission status, type of therapy preceding febrile neutropenia, number of days from the beginning of respective therapies to the diagnosis of VSB, use of antibacterial prophylaxis, and occurrence of oral mucositis, respiratory symptoms, gastrointestinal symptoms, severe complications and polymicrobial infection by other bacteria or fungi. In this study, there were no definite differences in clinical and laboratory characteristics, mortality, or occurrence of severe complications between febrile neutropenic adults and children with VSB, despite a significant difference in antibiotic susceptibility to cefepime between the two groups. doi = 10.1186/1471-2334-13-273 id = cord-004643-uu4uipfy author = Hasan, Mohammad Rubayet title = Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report date = 2020-03-20 keywords = CMV; HLH; patient summary = Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. Ganciclovir resistance was confirmed by the presence of the A594V mutation in UL97 [6] What was unique in our patient compared to other reported CMV-associated HLH cases was the overwhelming infection with MDROs. On hospital admission, the patient was found to be colonized with multiple MDROs including VRE, and carbapenamase-producing Enterobacteriaceae, which may have been acquired during his previous hospital course in India. doi = 10.1186/s12879-020-04966-z id = cord-003803-1t4xyayf author = He, Hangyong title = Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review date = 2019-07-29 keywords = H7N9 summary = title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review Human infected with avian influenza A H7N9 virus were first confirmed on March 30th, 2013 in China [1, 2] , with high incidence of severe respiratory failure, high intensive care unit (ICU) admission and mortality. However, refractory severe respiratory failure caused by OP secondary to avian influenza H7N9 virus infection was first reported in this case. In these cases reported, OP onset mostly at the second to third week in the course of influenza, and occurred after the releasing of primary virus infection; And the OP is complicated with respiratory failure, and no evidence of other pathogen was found; And the main findings on HRCT for this kind of OP were GGO and consolidation. doi = 10.1186/s12879-019-4306-7 id = cord-003397-fvrd128w author = Herath, H. M. L. Y. title = Spotted fever rickettsioses causing myocarditis and ARDS: a case from Sri Lanka date = 2018-12-29 keywords = ARDS; Lanka; Sri summary = title: Spotted fever rickettsioses causing myocarditis and ARDS: a case from Sri Lanka We describe a patient with rapidly progressing ARDS and myocarditis secondary to spotted fever caused by Rickettsia conorii. He was confirmed to have spotted fever rickettsial infection with rising titre of indirect immunofluorescence antibodies to Ricketssia conorii and made a complete recovery with appropriate antibiotic therapy and supportive care. Emergence of spotted fever group of rickettsial infections in the hilly central province of Sri Lanka was first observed in early nineties [1] . The following case report highlights myocarditis and acute respiratory distress syndrome (ARDS) as complications in a severely ill patient with spotted fever group of rickettsioses where timely diagnosis and intervention saved the life. This case demonstrates a rather rare presentation of spotted fever rickettsial infection where patient deteriorated within short time leading to shock and ARDS. Cutaneous manifestations of spotted fever rickettsial infections in the Central Province of Sri Lanka: a descriptive study doi = 10.1186/s12879-018-3631-6 id = cord-012954-3x3rkor5 author = Honkpehedji, Yabo Josiane title = Prospective, observational study to assess the performance of CAA measurement as a diagnostic tool for the detection of Schistosoma haematobium infections in pregnant women and their child in Lambaréné, Gabon: study protocol of the freeBILy clinical trial in Gabon date = 2020-09-29 keywords = CAA; PZQ; Schistosoma; UCP summary = doi = 10.1186/s12879-020-05445-1 id = cord-000534-ztc5holk author = Hsieh, Ying-Hen title = Transmissibility and temporal changes of 2009 pH1N1 pandemic during summer and fall/winter waves date = 2011-12-02 keywords = H1N1; Taiwan summary = BACKGROUND: In order to compare the transmissibility of the 2009 pH1N1 pandemic during successive waves of infections in summer and fall/winter in the Northern Hemisphere, and to assess the temporal changes during the course of the outbreak in relation to the intervention measures implemented, we analyze the epidemiological patterns of the epidemic in Taiwan during July 2009-March 2010. METHODS: We utilize the multi-phase Richards model to fit the weekly cumulative pH1N1 epidemiological data (numbers of confirmed cases and hospitalizations) as well as the daily number of classes suspended under a unique "325" partial school closing policy in Taiwan, in order to pinpoint the turning points of the summer and fall/winter waves, and to estimate the reproduction numbers R for each wave. The estimates for effective reproduction number R obtained from the confirmed case and hospitalization data are in good agreement, with R in the range of 1.04-1.27 for the first summer wave during July-September, and 1.01-1.05 for the second wave in fall/winter, using the generation time estimated by [26] for the spring outbreak in Mexico. doi = 10.1186/1471-2334-11-332 id = cord-002828-ml6mgyf3 author = Huang, Linna title = Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration date = 2018-01-08 keywords = ECMO; H7N9; IPPV summary = title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Keywords: Extracorporeal membrane oxygenation (ECMO), Avian influenza A (H7N9), Acute respiratory distress syndrome (ARDS), Complications, Mortality Background Avian influenza A (H7N9) viral pneumonia can manifest with varying degrees of dyspnea and is associated with a mortality of~30% [1] . ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9)-induced severe ARDS. doi = 10.1186/s12879-017-2903-x id = cord-287931-cxqzac4a author = Huang, Weiwei title = An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date = 2013-09-20 keywords = China; EOPM; PCR; RNA summary = RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] . doi = 10.1186/1471-2334-13-437 id = cord-271105-eyigl0wz author = Ionidis, Georgios title = Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date = 2016-02-11 keywords = DVV; Guideline; RKI; virus summary = Under the Guideline of Deutsche Vereinigung zur Bekämpfung der Viruskrankeiten e.V. and the Robert Koch-Institute (DVV/RKI Guideline) [22] , disinfectants achieving at least 4 log 10 titer reduction factor (RF of 4) against vaccinia virus and bovine viral diarrhea virus (BVDV) are active against all enveloped viruses (limited spectrum virucidal) [23, 24] . The different formulations of the new hand rub based on ethanol, citric acid and urea were screened undiluted (80.0 % due to the addition of test virus suspension and interfering substance) against PV, AdV and polyomavirus SV40 as non-enveloped test viruses of the Guideline of DVV/RKI in the presence of FCS with a fixed exposure time of 60 s. Consequently, the formulation with the sufficient virucidal activity containing 69.39 % w/w ethanol, 3.69 % w/w 2-propanol, 2.0 % urea and 2.0 % citric acid was tested against several non-enveloped (MNV, AdV, PV, polyomavirus SV40) and enveloped viruses (BVDV, vaccinia virus strain Elstree) in the presence or absence of FCS according to Guideline of DVV/RK or in clean conditions according to EN 14476. doi = 10.1186/s12879-016-1410-9 id = cord-029423-o24dthlk author = Iwuji, Collins C. title = A phase IV randomised, open-label pilot study to evaluate switching from protease-inhibitor based regimen to Bictegravir/Emtricitabine/Tenofovir Alafenamide single tablet regimen in Integrase inhibitor-naïve, virologically suppressed HIV-1 infected adults harbouring drug resistance mutations (PIBIK study): study protocol for a randomised trial date = 2020-07-20 keywords = HIV; HIV-1; TAF; study summary = doi = 10.1186/s12879-020-05240-y id = cord-003533-8m0vyxq8 author = Jayathilaka, P. G. N. S. title = An outbreak of leptospirosis with predominant cardiac involvement: a case series date = 2019-03-18 keywords = day; leptospirosis; patient summary = We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. In this case series, we describe a series of male patients with severe leptospirosis with cardiac involvement, presented to a single medical ward during a period of one month. By day eleven of illness he was completely recovered clinically and full blood count, liver function tests, renal function tests and ECG were normal. Patient was discharged from the ward on day 7 of illness with complete recovery and normal full blood count, renal and liver function tests. Despite adequate fluid resuscitation patient developed shock with low urine output on the same day of admission. doi = 10.1186/s12879-019-3905-7 id = cord-321549-r7bmtloy author = Jendrny, Paula title = Scent dog identification of samples from COVID-19 patients – a pilot study date = 2020-07-23 keywords = SARS; dog; sample summary = METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. As dogs can be trained quickly, the aim of the present study was to test the concept of using dogs reliably and in real-time to discriminate between samples of SARS-CoV-2 infected patients and non-infected controls. The individuals were only tested for SARS-CoV-2 virus and therefore one cannot exclude that a former infection, especially with another human coronavirus like HCoV-OC43 resulted in false positive indications of the dogs and that cross detection occurred. Detection dogs were able to discriminate respiratory secretions of infected SARS-CoV-2 individuals from those of healthy controls with high rates of sensitivity and specificity. doi = 10.1186/s12879-020-05281-3 id = cord-002853-vj8t28hn author = Joffe, Michael title = Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient date = 2018-01-27 keywords = adenovirus; patient summary = BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. We report here a case of adenovirus pneumonitis which led to a fatal disseminated adenovirus infection in an adult patient with chronic lymphocytic leukaemia (CLL) on chemotherapy. This patient''s chemotherapy regimen included fludarabine which has severe lymphopaenia as a recognised adverse effect, and which has been present in treatment regimens where various other viral reactivations have occurred, including hepatitis B [10] [11] [12] , BK virus [13] , herpes simplex and Epstein-Barr viruses [14] , cytomegalovirus [15] , as well as adenovirus [16] . doi = 10.1186/s12879-018-2962-7 id = cord-003526-ykisq8nz author = Kallel, Hatem title = Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis date = 2019-03-15 keywords = Guiana; french summary = title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome" (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS. We report here a human case of acute Maripa virus related pulmonary syndrome managed in the ICU of French Guiana with a clear evidence of associated capillary leak syndrome responsible for the severity of the disease. Two patients with severe capillary leak syndrome caused by a Puumala hantavirus infection were successfully treated with a bradykinin receptor antagonist [11, 12] . Hantavirus pulmonary syndrome caused by Maripa virus in French Guiana doi = 10.1186/s12879-019-3887-5 id = cord-000963-pwz6rde0 author = Kalugalage, Thilini title = Low serum total nitrite and nitrate levels in severe leptospirosis date = 2013-05-06 keywords = MAT; leptospirosis summary = We previously demonstrated through a preliminary study that serum nitrite levels are elevated in patients with acute leptospirosis compared to healthy controls [20] . The aim of this study was to determine the relationship between NO x (i.e., total nitrite and nitrate) levels in the blood (as a marker of iNOS activity) and disease severity in leptospirosis. The objectives of our study were to a) determine serum NO x (nitrate and nitrite) levels in patients with confirmed leptospirosis, b) compare serum NO x levels in leptospirosis patients with mild and severe disease, healthy controls and non-leptospirosis fever patients (NLFs), and c) seek a correlation between serum NO x levels and disease severity after correcting for impaired renal clearance. Patients with severe leptospirosis were defined as those presenting with acute fever and clinical symptoms compatible with leptospirosis (confirmed serologically by a positive MAT result) with two or more of the following criteria: jaundice (bilirubin> 51.3 μmol/l), oliguria (urine output < 400 ml/day), serum creatinine> 133 μmol/l or blood urea > 25.5 mmol/l [14] , or the presence of acute organ dysfunction. doi = 10.1186/1471-2334-13-206 id = cord-297494-6yxmaihl author = Katsurada, Naoko title = The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date = 2017-12-06 keywords = patient; pneumonia; virus summary = However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). We conducted this prospective multicentre study to determine the distribution of viruses associated with pneumonia in adults and to establish their virus-specific effects on pneumonia mortality stratified by age group and comorbidity status. To the best of our knowledge, this study is the first to systematically investigate virus-specific effects on pneumonia mortality by age group and comorbidity status among adults. In our study, multiple viruses were identified in 5.1% of virus-associated pneumonia and were associated with higher mortality than single viral infection in patients with chronic respiratory disease and other comorbidities. Systematic reviews have shown that multiple viral infections in patients with respiratory disease are not associated with disease severity [27, 28] ; however, the majority of previous studies included young children but not adults. doi = 10.1186/s12879-017-2858-y id = cord-001050-lq9tp20z author = Khanafer, Nagham title = Severe leukopenia in Staphylococcus aureus-necrotizing, community-acquired pneumonia: risk factors and impact on survival date = 2013-08-01 keywords = Staphylococcus; severe summary = title: Severe leukopenia in Staphylococcus aureus-necrotizing, community-acquired pneumonia: risk factors and impact on survival BACKGROUND: Necrotizing pneumonia attributed to Panton-Valentine leukocidin-positive Staphylococcus aureus has mainly been reported in otherwise healthy children and young adults, with a high mortality rate. The objectives of this study were to define the characteristics of patients with severe leukopenia at 48-h hospitalization and to update our data regarding mortality predicting factors in a larger population than we had previously described. Multivariate analysis indicated that the factors associated with severe leukopenia were influenza-like illness (adjusted odds ratio (aOR) 4.45, 95% CI (95% confidence interval) 1.67-11.88, P=0.003), airway bleeding (aOR 4.53, 95% CI 1.85-11.13, P=0.001) and age over 30 years (aOR 2.69, 95% CI 1.08-6.68, P=0.033). Severe community-acquired pneumonia caused by Panton-Valentine leukocidin-positive Staphylococcus aureus: first reported case in the United Kingdom Factors predicting mortality in necrotizing community-acquired pneumonia caused by Staphylococcus aureus containing Panton-Valentine leukocidin doi = 10.1186/1471-2334-13-359 id = cord-351126-d6lfktf9 author = Kofman, Aaron D. title = A young adult with COVID-19 and multisystem inflammatory syndrome in children (MIS-C)-like illness: a case report date = 2020-09-29 keywords = MIS summary = doi = 10.1186/s12879-020-05439-z id = cord-297024-90qq0xsw author = Kramer, Axel title = How long do nosocomial pathogens persist on inanimate surfaces? A systematic review date = 2006-08-16 keywords = Acinetobacter; nosocomial; surface summary = doi = 10.1186/1471-2334-6-130 id = cord-274749-ji91qq9q author = Lagare, Adamou title = Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger date = 2015-11-14 keywords = Niger; respiratory; viral summary = The viruses most frequently detected in children with ARIs include respiratory syncytial virus (RSV), influenza virus (INF) types A and B, adenovirus (AV), parainfluenza virus (PIV), human metapneumovirus (HMPV) and rhinovirus (RV) [3] [4] [5] ; however, the clinical presentations of respiratory tract infections are similar, making it difficult to distinguish between etiologic agents without a laboratory diagnosis [6] . We aimed to document the prevalence of selected viral and bacterial infections among children <5 years of age hospitalized with severe acute respiratory illness (SARI) at selected hospitals in Niger from January 2010 through December 2012. We report the detection rate of selected viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger. This study reports the detection rate of viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger. doi = 10.1186/s12879-015-1251-y id = cord-307307-b5yl88mh author = Lau, Joseph TF title = Avoidance behaviors and negative psychological responses in the general population in the initial stage of the H1N1 pandemic in Hong Kong date = 2010-05-28 keywords = H1N1; Hong; Kong summary = This study investigated whether the general population in Hong Kong avoided visiting different places (going out, visiting crowded places and visiting hospitals) and assessed some negative psychological responses to H1N1, including whether people were much worried about contracting H1N1 and their level of emotional distress (panicking, depression or emotional disturbance) due to H1N1. Factors in association with the outcome variables on avoidance behaviors and negative psychological responses were investigated, including variables such as socio-demographic characteristics, confirmed knowledge and unconfirmed beliefs about modes of H1N1 transmission, evaluation towards governmental preparedness/ performance, perceived availability of treatment, and risk perception (perceived severity and susceptibility related to H1N1). Females, older respondents, those with >= 1 unconfirmed beliefs about modes of H1N1 transmission, those who knew that H1N1 could be transmitted ''via droplets'', ''bodily contact with infected person'' or ''touching contaminated objects'', those who were very worried that either they or their family members would contract H1N1, those expressing emotional distress (in panic or feeling very depressed or being highly emotionally disturbed due to H1N1) were more likely than others to avoid visiting crowded places (multivariate OR = 1.42 to 3.90, p < .05; Table 4 ). doi = 10.1186/1471-2334-10-139 id = cord-338054-n2r4pzan author = Lau, Joseph TF title = Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date = 2007-03-15 keywords = Hong; SARS summary = Respondents were asked how likely they would be to adopt the following preventive behaviors if a local human-to-human H5N1 outbreak (defined as "if 2-3 new human-to-human transmission of H5N1 cases were to be reported in Hong Kong") were to occur: face mask use in public venues, increased frequency of handwashing, avoidance of eating poultry, declaration of influenzalike illness (ILI) symptoms at border health checkpoints, the seeking of medical consultation immediately with the onset of a fever, face mask use in public venues when having ILI symptoms and compliance with any quarantine policies. Respondents were asked about perceptions related to human-to-human H5N1 transmission, including perceived modes of transmission (whether human-to-human transmission of the H5N1 virus could occur via respiratory droplets, bodily contact, contaminated objects, eating well-cooked poultry), perceived susceptibility to H5N1 in different groups of people (self, family members, children, adults, older people, health care workers, food handlers, food vendors and the general public), perceived chance of having a major outbreak in Hong Kong in the next 12 months and perceived efficacy of various prevention measures (quarantine of infected people, face mask use in public venues, frequent handwashing, home disinfection, mass extermination of poultry). doi = 10.1186/1471-2334-7-18 id = cord-035280-z0bbz19b author = Lee, Seung Hun title = First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report date = 2020-11-11 keywords = Anaplasma; Korea; PCR summary = doi = 10.1186/s12879-020-05522-5 id = cord-329256-7njgmdd1 author = Leecaster, Molly title = Modeling the variations in pediatric respiratory syncytial virus seasonal epidemics date = 2011-04-21 keywords = RSV; epidemic; model summary = doi = 10.1186/1471-2334-11-105 id = cord-004394-0h2wvv40 author = Li, Fengqin title = Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature date = 2020-02-22 keywords = Enterococcus; VRE summary = title: Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature CONCLUSIONS: Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations. In this case report, we aimed to present a uremic patient with VRE-fm pneumonia, possibly related to epileptic seizures, being treated successfully with linezolid. Previous case reports of enterococcal pneumonia were based on clinical findings and infiltrate on chest X ray or CT in combination with the isolation of enterococci in cultures from a transtracheal aspirate, protected brush (PS), bronchoalveolar lavage (BAL), sputum or lung tissue. Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations. doi = 10.1186/s12879-020-4892-4 id = cord-282533-w6kl74c8 author = Li, Jin title = Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date = 2018-10-11 keywords = respiratory summary = doi = 10.1186/s12879-018-3429-6 id = cord-272240-s1gnwb2s author = Li, Tiegang title = Attitudes, practices and information needs regarding novel influenza A (H7N9) among employees of food production and operation in Guangzhou, Southern China: a cross-sectional study date = 2014-01-02 keywords = Guangzhou; H7N9 summary = Previous studies have demonstrated the positive correlation between a willingness to adhere to the recommendations around infection control practices and perceived infectiousness and severity of the disease [8] [9] [10] , perceptions about the effectiveness of control measures [11] , and trust in the information being provided by national and international public health authorities [12] . Because a considerable number of H7N9 patients engaged in food-related work before symptom onset (including chef, food transporter, poultry seller and slaughter), we conducted face-to-face interviews on attitudes, practices and information needs among employees of food production and operation in Guangzhou, with an effort to assess the preparedness and response of the public, and to facilitate the development of effective prevention strategies against H7N9 infection. In a previous study designed to assess the implications of public understanding of avian influenza, researchers found that the majority of participants did not believe a pandemic would occur, and believed that dealing with the disease was the responsibility of the government [14] . doi = 10.1186/1471-2334-14-4 id = cord-003085-7krf1yxz author = Li, Xi title = Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date = 2018-06-28 keywords = CMV; ICU summary = doi = 10.1186/s12879-018-3195-5 id = cord-272207-jtvf257r author = Liao, Qiuyan title = Anxiety, worry and cognitive risk estimate in relation to protective behaviors during the 2009 influenza A/H1N1 pandemic in Hong Kong: ten cross-sectional surveys date = 2014-03-27 keywords = H1N1; Hong; Kong summary = This study was aimed to compare the strength of associations between different cognitive and affective measures of risk and self-reported protective behaviors in a series of ten cross-sectional surveys conducted throughout the first wave of influenza A/H1N1 pandemic. RESULTS: Excepting state anxiety, other affective measures including "anticipated worry", "experienced worry" and "current worry" specific to A/H1N1 risk were consistently and strongly associated with adoption of protective behaviors across different survey periods. This finding is consistent with those from other studies conducted during both SARS [6] and pandemic A/H1N1 [10, 24] , suggesting that affective components contribute significantly to adoption of protective behaviors in response to the threat during epidemics over and above simpler cognitive risk estimates. This study found that the proportions of missing data for purer cognitive risk perception measures, particularly perceived absolute/relative susceptibility to A/H1N1 were greater than for affect-loaded measures, suggesting that respondents may face greater Figure 3 Associations between psychological responses and disinfecting household frequently during A/H1N1 pandemic. doi = 10.1186/1471-2334-14-169 id = cord-287546-0x294f8t author = Lin, Feng title = An optimal control theory approach to non-pharmaceutical interventions date = 2010-02-19 keywords = NPI; control; figure; policy summary = doi = 10.1186/1471-2334-10-32 id = cord-288720-bd86zswo author = Lin, Sheng title = Epidemiological and clinical characteristics of 161 discharged cases with coronavirus disease 2019 in Shanghai, China date = 2020-10-20 keywords = Shanghai; covid-19 summary = doi = 10.1186/s12879-020-05493-7 id = cord-336663-fawcn6em author = Liu, Chunyan title = Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date = 2015-10-01 keywords = hadv; infection summary = Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. However, because most clinical laboratories do not type the isolates, there is little published information about epidemiologic and clinical features of HAdV infections by type in children with ALRTIs. To identify HAdV types and species in children with ALRTIs in Beijing area and to characterize clinical features and laboratory findings of hospitalized HAdVinfected cases, respiratory specimens were collected from hospital-admitted pediatric patients with ALRTIs and typed HAdV positive samples using PCR and sequencing. This may also suggest that schoolage children are exposed to the most common endemic types of HAdV early in life, thereby establishing a protective immunity resulting only in mild clinical symptoms, such that upper respiratory tract infection does not require care in an emergency department or hospital in this age group. doi = 10.1186/s12879-015-1126-2 id = cord-269772-4zrmsw2f author = Liu, Ming-Der title = Changing risk awareness and personal protection measures for low to high pathogenic avian influenza in live-poultry markets in Taiwan, 2007 to 2012 date = 2015-06-24 keywords = H5N2; HPAI; LPAI; Taiwan summary = Thus, understanding all possible factors associated with risk awareness, attitudes, and practice of prevention measures (RAP), as well as differences in risk perception of outbreaks due to LPAI versus HPAI viruses between the live-poultry market workers (LPMWs) and community residents (CRs) are all important for providing further education and implementing public health policies on preventing AI infection. Therefore, the data of the reported "acceptance of avian influenza vaccine between live-poultry market workers and community residents" were thus compared only after the 2nd survey in Table 4 respondents with higher risk perception (concerning human AI infections in Taiwan) before HPAI outbreaks had not only more awareness about the AI outbreaks in mainland China affecting Taiwan, but also better attitudes toward meeting domestic needs (endorsing the government''s new policy on AI, and supporting a ban on slaughtering live poultry in markets). doi = 10.1186/s12879-015-0987-8 id = cord-321848-qys8r6jo author = Liu, Nan title = An atypical winter outbreak of hand, foot, and mouth disease associated with human enterovirus 71, 2010 date = 2014-03-04 keywords = China; EV71; HFMD summary = BACKGROUND: To analyze the epidemiological characteristics and pathogenic molecular characteristics of an hand, foot, and mouth disease (HFMD) outbreak caused by enterovirus 71 in Linyi City, Shandong Province, China during November 30 to December 28, 2010. Complete sequence analyses of enterovirus 71 strains from fatal and non-fatal cases of the hand, foot and mouth disease outbreak in Identification of enterovirus 71 isolates from an outbreak of hand, foot and mouth disease (HFMD) with fatal cases of encephalomyelitis in Malaysia Outbreak of central nervous system disease associated with hand, foot, and mouth disease in Japan during the summer of 2000: detection and molecular epidemiology of enterovirus 71 An outbreak of hand, foot, and mouth disease associated with subgenotype C4 of human enterovirus 71 in Shandong China An atypical winter outbreak of hand, foot, and mouth disease associated with human enterovirus 71 doi = 10.1186/1471-2334-14-123 id = cord-000451-te75jsd3 author = Liu, Qiyong title = Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model date = 2011-08-15 keywords = ARIMA; China; HFRS summary = title: Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model In this study, we applied a stochastic autoregressive integrated moving average (ARIMA) model with the objective of monitoring and short-term forecasting HFRS incidence in China. This study aimed to develop a univariate time series model for the HFRS incidence; specifically, a stochastic ARIMA model, for short-term forecasting of HFRS incidence (per 100,000 population) in China. Thus, the fitted ARIMA(0,3,1) model can be used to predict the next three years'' HFRS incidence in China. To the best of our knowledge, this is the first study to apply ARIMA model to fit the HFRS incidence in China with as many as 34 observations at year level. A time series model in incidence forecasting of hemorrhagic fever with renal syndrome Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model doi = 10.1186/1471-2334-11-218 id = cord-274763-i6e3g3te author = Liu, Wen-Kuan title = Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region date = 2018-07-16 keywords = hbov1; infection; respiratory summary = title: Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region BACKGROUND: Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. METHODS: Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. We collected meteorological data for Guangzhou, including monthly mean temperature, mean relative humidity, rainfall, mean wind speed, mean air pressure, mean vapor pressure and sunshine duration for a 7-year period, to explore the correlation between meteorological conditions and prevalence of HBoV1. Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China doi = 10.1186/s12879-018-3225-3 id = cord-275211-1b56a6zc author = Liu, Wen-Kuan title = Epidemiology and clinical presentation of the four human parainfluenza virus types date = 2013-01-23 keywords = HPIV; HPIV-1 summary = To analyse epidemiologic and clinical characteristics of the four types of human parainfluenza viruses (HPIVs), patients with acute respiratory tract illness (ARTI) were studied in Guangzhou, southern China. CONCLUSIONS: HPIV infection led to a wide spectrum of symptoms, and similar clinical manifestations were found in the patients with four different types of HPIVs. The study suggested pathogenic activity of HPIV in gastrointestinal illness. The HPIV-1, HPIV-2 and HPIV-3 are second only to respiratory syncytial virus (RSV) as a cause of hospitalizations (2%-17%) for acute respiratory infection among children aged younger than 5 years in the United States [1, [8] [9] [10] . The aims of this study were to explore the epidemiologic features and clinical manifestations of HPIVs and other common respiratory pathogens in children and adults with acute respiratory tract illness (ARTI) in Guangzhou, southern China, and to uncover clues that might help to establish clinical distinctions between different HPIV types. doi = 10.1186/1471-2334-13-28 id = cord-313529-xm76ae08 author = Liu, Wen-Kuan title = Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China date = 2011-12-14 keywords = HBoV; human; patient summary = title: Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Our study is the first to analyze the characteristics of HBoV-positive samples from ARTI patients with a wide age distribution from Guangzhou, southern China. HBoV DNA positive samples were tested for 16 other potential pathogens, including influenza A virus, influenza B virus, parainfluenza virus (1, 2, 3, 4), respiratory syncytial virus, adenovirus, enterovirus, human metapneumovirus, human coronavirus (229E, OC43, NL63, HKU1), Mycoplasma pneumoniae, and Chlamydia pneumoniae by Taqman real-time PCR, in accordance with the manufacturer''s protocol (Guangzhou HuYanSuo Medical Technology Co., Ltd). Our study successfully analyzed the characteristics of HBoV-positive samples from ARTI-infected patients with a wide age distribution from Guangzhou, southern China for the first reported time. Phylogenetic analysis suggested that HBoV-GU338055 from an elderly patient is in a single lineage with other HBoVs. Osterhaus ADME: A newly discovered human pneumovirus isolated from young children with respiratory tract disease doi = 10.1186/1471-2334-11-345 id = cord-292609-e99y0l5a author = Liu, Ye title = Ferret badger rabies origin and its revisited importance as potential source of rabies transmission in Southeast China date = 2010-08-06 keywords = China; rabies summary = doi = 10.1186/1471-2334-10-234 id = cord-025155-ow3r3469 author = Lokida, Dewi title = Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results date = 2020-05-24 keywords = Indonesia; Rickettsia; infection summary = title: Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results METHODS: Acute and convalescent blood from 975 hospitalized non-dengue patients was tested for Rickettsia IgM and IgG by ELISA. For the 103/975 (10.6%) non-dengue patients diagnosed with acute rickettsial infection, presenting symptoms included nausea (72%), headache (69%), vomiting (43%), lethargy (33%), anorexia (32%), arthralgia (30%), myalgia (28%), chills (28%), epigastric pain (28%), and rash (17%). Clinicians should include rickettsioses in their differential diagnosis of fever to guide empiric management; laboratories should support evaluation for rickettsial etiologies; and public policy should be implemented to reduce burden of disease. To characterize the epidemiology of rickettsioses in Indonesia, we performed Rickettsia diagnostic panels on blood from subjects in the Acute Fever Requiring Hospitalization (AFIRE) study [13] . Patients found to have rickettsial infection by reference laboratory testing were identified from INA-RESPOND''s [14] AFIRE observational cohort study conducted in Indonesia from 2013 to 2016. doi = 10.1186/s12879-020-05057-9 id = cord-320808-taj5swwc author = Lu, Guilan title = An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55 date = 2020-07-23 keywords = ARI; B55; Beijing; China summary = doi = 10.1186/s12879-020-05258-2 id = cord-258611-uzzs8w1j author = Ma, Xuezheng title = No MERS-CoV but positive influenza viruses in returning Hajj pilgrims, China, 2013–2015 date = 2017-11-10 keywords = Hajj; MERS summary = BACKGROUND: There is global health concern that the mass movement of pilgrims to and from Mecca annually could contribute to the international spread of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). DISCUSSION AND CONCLUSION: The MERS-CoV and respiratory viruses detection results at points of entry in China from 2013 to 2015 indicated that there were no MERS-CoV infection but a 5.7% positive influenza viruses in returning Chinese pilgrims. As of November 2015, there had been 1618 laboratoryconfirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection reported to the World Health Organization, and at least 579 cases had died [1, 2] . Two hypotheses were tested: (1) There is a significant difference in the positive and negative rates of influenza virus detection between Hajj pilgrims with symptoms and those without. In this study, we did not detect any cases of MERS-CoV infection but respiratory virus infections including influenza A and B, hMPV, hRSV, and human coronavirus were detected among Hajj pilgrims returning to China. doi = 10.1186/s12879-017-2791-0 id = cord-004397-ypli7wtu author = Ma, Zhan-Ying title = Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection date = 2020-02-22 keywords = BALF; OPS; respiratory summary = title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. In the present study, we used the suspension microarray, a multipathogen detection platform, to simultaneously detect viral and bacterial respiratory pathogens in matched OPS and BALF specimens from pediatric patients for comparison of the sensitivities between the two sample types. To compare the OPS and paired BALF for pathogens detection in young children with RTI, we tested the two sample types using suspension microarray. In the present study, we used suspension array to simultaneously detect multiple viral and bacterial pathogens in paired BALF and OPS specimens from symptomatic patients hospitalized with respiratory illness. We used suspension-array to compare BALF and paired OPS specimens for detecting multiple pathogens in children hospitalized with respiratory illness. doi = 10.1186/s12879-020-4900-8 id = cord-000001-ug7v899j author = Madani, Tariq A title = Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia date = 2001-07-04 keywords = patient summary = title: Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia OBJECTIVE: This retrospective chart review describes the epidemiology and clinical features of 40 patients with culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. CONCLUSION: our results were similar to published data except for the finding that infections were more common in infants and preschool children and that the mortality rate of pneumonia in patients with comorbidities was high. Mycoplasma pneumoniae is a common cause of upper and lower respiratory tract infections. pneumoniae infections in Saudi Arabia is scarce, [8, 9, 10] we wished to study the epidemiology and clinical features of cultureproven infections caused by this organism at this hospital. pneumoniae culture were obtained from patients with upper or lower respiratory tract infections seen as inpatients or in the outpatient or emergency departments. Role of Mycoplasma pneumoniae in acute respiratory-tract infections in Saudi paediatric patients doi = 10.1186/1471-2334-1-6 id = cord-003856-05u4t67u author = Mao, Ying title = A descriptive analysis of the Spatio-temporal distribution of intestinal infectious diseases in China date = 2019-09-02 keywords = China; HFMD; Hepatitis; disease summary = In China, eight IIDs are listed as notifiable infectious diseases, including cholera, poliomyelitis, dysentery, typhoid and paratyphoid (TAP), viral Hepatitis A, viral Hepatitis E, hand-foot-mouth disease (HFMD) and other infectious diarrhoeal diseases (OIDDs). Plots and maps were constructed to visualize the spatio-temporal distribution of IIDs. RESULTS: Regarding temporal analysis, the incidence of HFMD and Hepatitis E showed a distinct increasing trend, while the incidence of TAP, dysentery, and Hepatitis A presented decreasing trends over the last decade. CONCLUSIONS: Based on our temporal and spatial analysis of IIDs, we identified the high-risk periods and clusters of regions for the diseases. Eight IIDs are listed in the law, including cholera, poliomyelitis, dysentery, typhoid and paratyphoid (TAP), viral Hepatitis A, viral Hepatitis E, hand-foot-mouth disease (HFMD) and other infectious intestinal diseases (OIIDs). Figure 1 shows the results of the decomposition analysis for all IIDs. Regarding the seasonal variation, the incidence rates of HFMD and dysentery were high in summer. doi = 10.1186/s12879-019-4400-x id = cord-349238-qfvm883x author = Maponga, Brian A title = Risk factors for contracting watery diarrhoea in Kadoma City, Zimbabwe, 2011: a case control study date = 2013-12-02 keywords = City; Kadoma; case summary = doi = 10.1186/1471-2334-13-567 id = cord-282898-hsqvkm2i author = Matsuda, Kentaro title = Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka, Japan date = 2013-12-16 keywords = A2063; Mycoplasma summary = title: Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka, Japan Serum IFN-gamma, IL-6 and IP-10 levels were significantly higher in patients infected by the macrolide-resistance genotypes than in those infected by the no-mutation strains (comparison of A2063G vs. pneumoniae isolated from clinical samples antimicrobial agent when compared with the patients infected not only by macrolide-sensitive strains (p = 0.001) but also by A2063T transversion strains (p = 0.02). Characteristics of macrolide-resistant Mycoplasma pneumoniae strains isolated from patients and induced with erythromycin in vitro High prevalence of macrolide resistance in Mycoplasma pneumoniae isolates from adult and adolescent patients with respiratory tract infection in China Nationwide surveillance of macrolide-resistant Mycoplasma pneumoniae infection in pediatric patients Characterization and molecular analysis of macrolide-resistant Mycoplasma pneumoniae clinical isolates obtained in Japan A comparative clinical study of macrolide-sensitive and macrolide-resistant Mycoplasma pneumoniae infections in pediatric patients Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka doi = 10.1186/1471-2334-13-591 id = cord-334424-z7ygy25e author = McCaw, James M title = Household transmission of respiratory viruses – assessment of viral, individual and household characteristics in a population study of healthy Australian adults date = 2012-12-11 keywords = ILI; household; influenza summary = Table 1 summarizes the descriptive statistics (and logistic model results) associated with presence or absence of transmission in the household for the 177 household ILI events in which the participant was the primary case. In correspondence with the logistic regression model for transmission, we include presence of children in the In a secondary analysis, we considered the influence of prior vaccination on the reported number of secondary household cases among participants testing positive for influenza compared with all other participants. This study, notable in its consideration of a broad range of respiratory pathogens in addition to influenza, demonstrates that household transmission of ILI is most strongly associated with host and demographic factors: female sex and the presence of children within the household (Tables 1 and 2) . doi = 10.1186/1471-2334-12-345 id = cord-256094-f85xc5uu author = Milinovich, Gabriel J title = Using internet search queries for infectious disease surveillance: screening diseases for suitability date = 2014-12-31 keywords = Google; Trends; disease summary = This study aims to systematically investigate the potential for developing surveillance and early warning systems using internet search data, for a wide range of infectious diseases. This study, however, did not aim to develop actionable surveillance systems, produce predictive models of infectious disease based on internet-based data or to identify the best search terms for use in these models. Briefly, the time series analysed were monthly case numbers for the 64 infectious diseases monitored by the Australian Government''s National Notifiable Disease Surveillance System (NNDSS) and Google Trends monthly search metrics for related internet search terms. To our knowledge, assessments of the use of internet-based surveillance have only been performed for five of the 17 diseases that were demonstrated to have a significant association with internet search terms (influenza [4] , dengue [9, 27] , chickenpox [11, 12] , hepatitis B [14] and cryptosporidiosis [13] the authors of the final study were, however, not able to detect signals from internet search queries). doi = 10.1186/s12879-014-0690-1 id = cord-313054-w90eitw9 author = Mobaraki, Kazhal title = Current epidemiological status of Middle East respiratory syndrome coronavirus in the world from 1.1.2017 to 17.1.2018: a cross-sectional study date = 2019-04-27 keywords = East; MERS summary = RESULTS: A total of 229 MERS-CoV cases, including 70 deaths (30.5%), were recorded in the disease outbreak news on world health organization website over the study period. Middle East respiratory syndrome coronavirus (MERS-CoV) infection is considered to cause a new viral epidemic [1] , and was first reported in a patient who died from a severe respiratory illness in a hospital in Jeddah, Saudi Arabia, in June 2012 [2, 3] . The occurrence of a large number of MERS-CoV cases and their associated deaths in the world indicate that this disease must be considered as a severe threat to public health [13] because millions of pilgrims from 184 countries converge in Saudi Arabia each year to perform Hajj and Umrah ceremony. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study doi = 10.1186/s12879-019-3987-2 id = cord-342210-r8vxz5vu author = Mukherjee, Pranab K. title = Randomized, double-blind, placebo-controlled clinical trial to assess the safety and effectiveness of a novel dual-action oral topical formulation against upper respiratory infections date = 2017-01-14 keywords = arm; group; placebo; study summary = We conducted a randomized, double-blinded, placebo-controlled pilot clinical trial to evaluate the safety and efficacy of ARMS-I™ (currently marketed as Halo™) in the prevention of URIs. METHODS: ARMS-I is patented novel formulation for the prevention and treatment of influenza, comprising a broad-spectrum antimicrobial agent (cetylpyridinium chloride, CPC) and components (glycerin and xanthan gum) that form a barrier on the host mucosa, thus preventing viral contact and invasion. The primary objectives were to establish whether ARMS-I decreased the frequency, severity or duration of URIs. Secondary objectives were to evaluate safety, tolerability, rate of virus detection, acceptability and adherence; effect on URI-associated absenteeism and medical visits; and effect of prior influenza vaccination on study outcomes. In the current study, we evaluated the safety and effectiveness of ARMS-I, a novel intra-oral formulation in the prevention of URIs in a randomized, double-blind, placebo-controlled proof-of-concept clinical trial in healthy adults. doi = 10.1186/s12879-016-2177-8 id = cord-297029-b38sm4y9 author = Murillo-Zamora, Efrén title = Male gender and kidney illness are associated with an increased risk of severe laboratory-confirmed coronavirus disease date = 2020-09-16 keywords = covid-19 summary = Demographic characteristics (sex, age), tobacco use (current), personal history of chronic communicable disease (HIV infection, no/yes) and noncommunicable disease (no/yes: obesity [body mass index of 30 or higher], arterial hypertension, type 2 diabetes mellitus, asthma, chronic kidney disease, immunosuppression, chronic obstructive pulmonary disease, or cardiovascular illness) were collected from the surveillance system. In the multiple regression analysis (Table 2) , male gender (RR = 1.13, 95% CI 1.06-1.20) and older patients ([reference: 15-29 years old] 30-44, RR = 1.02, 95% CI 0.94-1.11; 45-59, RR = 1.26, 95% CI 1.15-1.38; 60 years or older, RR = 1.44, 95% CI 1.29-1.60), subjects to thoracic pain (RR = 1.16, 95% CI 1.10-1.24) or chronic kidney disease (RR = 1.31, 95% CI 1.04-1.64) were also more likely to present severe COVID-19. doi = 10.1186/s12879-020-05408-6 id = cord-312522-mymgnf8z author = Nelson, Megan M. title = Rapid molecular detection of macrolide resistance date = 2019-02-12 keywords = RPA; dna; resistance summary = METHODS: We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. In this study, we developed and tested a novel RPA assay for the detection of the Macrolide Efflux A, or mef(A) gene, an efflux pump rendering host bacteria resistant to 14-and 15-membered macrolide antibiotics (including erythromycin A and azithromycin) [33, 34] . Our RPA assay uncovered an unexpected occurrence of the mef(A) gene within commensal Streptococcus salivarius strain, and subsequent laboratory testing confirmed that this strain has genuine antimicrobial resistance. To assess assay sensitivity we ran a serial dilution of DNA derived from mef(A)-positive Streptococcus pyogenes serotype M6 strain MGAS10394 [39] and found that confident detection was around 2000 genome copies (Fig. 1b) . doi = 10.1186/s12879-019-3762-4 id = cord-341347-nzptmdbe author = Neske, Florian title = High prevalence of antibodies against polyomavirus WU, polyomavirus KI, and human bocavirus in German blood donors date = 2010-07-20 keywords = IFA; VP1; sf9 summary = doi = 10.1186/1471-2334-10-215 id = cord-283190-fc05u8mx author = Neupane, Dinesh title = Knowledge, attitudes and practices related to avian influenza among poultry workers in Nepal: a cross sectional study date = 2012-03-30 keywords = Nepal; poultry summary = In early 2006 the Government of Nepal established the Avian Influenza Control Project (AICP) and endorsed a Joint Health and Agriculture National Avian Influenza and Influenza Pandemic Preparedness and Response Plan (NAIIPPRP) [4, 9] which placed particular emphasis on precautionary behaviours of poultry workers as well as the knowledge and attitudes which drive such practices. The objectives of the present study were 1) to identify levels of knowledge about preventive behaviours as well as actual preventive behaviours with regard to avian influenza in Nepalese poultry workers, 2) to investigate factors associated with knowing about and practising preventive behaviours against AI, among them sociodemographic characteristics, media use (health information from TV and newspapers), and experience of fear. Afterwards study participants were asked to indicate how often they were using the following preventive measures when dealing with poultry: washing hands with soap and water, donning gloves, face masks, boots/boots covers, putting on protective body garments, and washing and disinfecting utensils and surfaces (five-step-answering format from "always" to "never"). doi = 10.1186/1471-2334-12-76 id = cord-312544-vip4jtlv author = Ng, Lisa FP title = Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date = 2006-03-02 keywords = H5N1; RNA summary = METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. In this study, we describe the development of a nucleic acid detection test that is rapid, specific and sensitive, thus allowing greatly improved detection of the H5N1 avian influenza A virus. To establish the specificity of the assays for H5N1 subtype detection, we then tested the primers on several known strains of influenza A viruses derived from avian sources (H3N8, H5N3, H7N3 and H9N2). A total of 145 field samples comprising of known and suspect cases from chickens, ducks and muscovies isolated from Vietnam and Malaysia during the 2004 to 2005 outbreak were tested for H5N1 RNA (Table Detection of H5N1 avian influenza A virus by one-step RT-PCR 2). doi = 10.1186/1471-2334-6-40 id = cord-260550-ld9eieik author = Ng, Man Wai title = The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date = 2007-06-01 keywords = RANTES; SARS summary = title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese In this study, we investigated the single nucleotide polymorphisms (SNPs) of inflammatory chemokine genes, i.e. RANTES, IP-10 and monokine induced by gamma interferon gene (Mig) in two Chinese cohorts from Hong Kong and Beijing and found that the RANTES -28 G allele was associated with disease susceptibility and severity of SARS. Among them, 20 patients were classified as severe group, which were identified by their admissions to intensive care units or deaths from SARS (mean ± SD age = 39.45 ± 12.8, 11 male and 9 female). After correction by Bonferroni method, the significant P value should be less than 0.007 This study showed that RANTES -28 G allele was a risk factor that associated with severe clinical outcomes in both Hong Kong and Beijing Chinese SARS patients. doi = 10.1186/1471-2334-7-50 id = cord-003466-599x0euj author = Nickol, Michaela E. title = A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date = 2019-02-06 keywords = H1N1; influenza; pandemic; virus summary = MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . doi = 10.1186/s12879-019-3750-8 id = cord-296868-fn4gzsw1 author = Nishiura, Hiroshi title = Fever screening during the influenza (H1N1-2009) pandemic at Narita International Airport, Japan date = 2011-05-03 keywords = Airport; H1N1 summary = The first contained confirmed influenza cases (n = 16) whose diagnosis took place at the airport during the early stages of the pandemic, and the second contained a selected and suspected fraction of passengers (self-reported or detected by an infrared thermoscanner; n = 1,049) screened from September 2009 to January 2010. The first dataset contained the limited number of confirmed cases infected with H1N1-2009 or other influenza viruses whose diagnosis took place at the airport during the very early stages of the 2009 pandemic, and the second dataset contained non-randomly sampled passengers, comprising a selected and suspected fraction of passengers (selfreported or detected by an infrared thermoscanner) arriving at Narita International Airport from September 2009 to January 2010 ( Figure 1 ). doi = 10.1186/1471-2334-11-111 id = cord-000349-k0p166fr author = Olive, David title = Severe pneumococcal pneumonia: impact of new quinolones on prognosis date = 2011-03-15 keywords = ICU; cap summary = BACKGROUND: Most guidelines have been proposing, for more than 15 years, a β-lactam combined with either a quinolone or a macrolide as empirical, first-line therapy of severe community acquired pneumonia (CAP) requiring ICU admission. METHODS: Retrospective study of consecutive patients admitted in a 16-bed general intensive care unit (ICU), between January 1996 and January 2009, for severe (Pneumonia Severity Index > or = 4) community-acquired pneumonia due to non penicillin-resistant Streptococcus pneumoniae and treated with a β-lactam combined with a fluoroquinolone. CONCLUSION: Our results suggest that, when combined to a β-lactam, levofloxacin is associated with lower mortality than ofloxacin or ciprofloxacin in severe pneumococcal community-acquired pneumonia. Firstly, we retrospectively collected all consecutive patients aged > 18 years who were admitted into our ICU (16-bed medical and surgical intensive care unit in a 450-bed general hospital) between January 1996 and January 2009 for severe community-acquired pneumonia (CAP) and who received a definite diagnosis of pneumococcal pneumonia. doi = 10.1186/1471-2334-11-66 id = cord-302393-hrz3bypr author = Omrani, Ali S. title = The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date = 2020-10-19 keywords = COVID-19; ICU; SARS summary = Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. In this study, we describe 60-day outcomes of a nationwide COVID-19 cohort from Qatar, and explore patient characteristics associated with the need for admission to an intensive care unit (ICU). In the multivariable logistic regression, we found that older age, male sex, co-existing diabetes or chronic kidney disease, and higher BMI were all independently associated with increased risk of need for ICU admission ( Table 2) . doi = 10.1186/s12879-020-05511-8 id = cord-290432-4dli5emd author = O’Grady, Kerry-Ann F. title = Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date = 2017-04-04 keywords = child; indigenous; virus summary = We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Thus, in 164 urban-based Indigenous children presenting to an urban primary health care service, we described the prevalence of upper airway respiratory viruses and bacteria. We analysed data from a cohort of urban Aboriginal and Torres Strait Islander children aged less than 5 years collected at time of enrolment into a prospective study of ARIwC. In a study of upper airway viruses and bacteria in Central Australian Aboriginal children hospitalised for pneumonia [8] , a population with high rates of hospitalised lower ARI [15] and nasal colonisation [16] , the [8] . doi = 10.1186/s12879-017-2349-1 id = cord-328501-mbwgi56x author = Pang, Junxiong title = Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date = 2015-07-25 keywords = FRI; Singapore; respiratory summary = doi = 10.1186/s12879-015-1024-7 id = cord-303196-ltmu3ncu author = Pfitscher, L. C. title = Severe maternal morbidity due to respiratory disease and impact of 2009 H1N1 influenza A pandemic in Brazil: results from a national multicenter cross-sectional study date = 2016-05-21 keywords = H1N1; SMO; maternal; severe summary = title: Severe maternal morbidity due to respiratory disease and impact of 2009 H1N1 influenza A pandemic in Brazil: results from a national multicenter cross-sectional study BACKGROUND: The aim of this study was to assess the burden of respiratory disease, considering the influenza A pandemic season (H1N1pdm09), within the Brazilian Network for Surveillance of Severe Maternal Morbidity, and factors associated with worse maternal outcome. In each group, PLTC (less severe cases) and Severe Maternal Outcome (SMO: MNM + MD) cases were compared to evaluate the factors potentially associated with more severe disease, including delay in obstetric care, also using the Prevalence Ratios plus their respective 95 % CI adjusted for the design effect of cluster sampling. Our study presents the burden of severe respiratory diseases among cases of severe maternal morbidity and results of the 2009 H1N1 influenza pandemic, considering 27 referral maternity hospitals in Brazil. doi = 10.1186/s12879-016-1525-z id = cord-001470-hn288o97 author = Pivette, Mathilde title = Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review date = 2014-11-18 keywords = datum; drug; sale summary = CONCLUSIONS: Drug sales data analyses appear to be a useful tool for surveillance of gastrointestinal and respiratory disease, and OTC drugs have the potential for early outbreak detection. Published articles were searched for on electronic databases (Pubmed, Embase, Scopus, LILACS, African Index Medicus, Cochrane Library), using combinations of the following key words: ("surveillance" OR outbreak detection OR warning system) AND (overthe-counter OR "prescription drugs" OR pharmacy OR (pharmaceutical OR drug OR medication) sales). Articles excluded based on fulltext review (no drug sales data, no infectious disease, no outbreak detection) N= 85 Figure 1 Flow chart of study selection process in a systematic review of drug sales data analysis for syndromic surveillance of infectious diseases. Nineteen of the 27 studies were descriptive retrospective studies assessing the strength of the correlation between drug sales and reference surveillance data of the corresponding disease or evaluating outbreak-detection performance [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] . doi = 10.1186/s12879-014-0604-2 id = cord-000268-480d3yfv author = Porfyridis, Ilias title = Diagnostic value of triggering receptor expressed on myeloid cells-1 and C-reactive protein for patients with lung infiltrates: an observational study date = 2010-09-29 keywords = CRP; TREM-1; patient; pulmonary summary = title: Diagnostic value of triggering receptor expressed on myeloid cells-1 and C-reactive protein for patients with lung infiltrates: an observational study The aim of the present study was to define whether expression of TREM-1 on cell membranes of neutrophils (nTREM-1), of monocytes (mTREM-1) and serum sTREM-1 may help in the diagnosis of acute bacterial infections for patients admitted with a new pulmonary infiltrate or pleural effusion. In conclusion, the presented results indicate that serum sTREM-1 and expression of TREM-1 on neutrophils and monocytes may serve as markers of CAP in patients with pulmonary infiltrates. Increased levels of soluble triggering receptor expressed on myeloid cells-1 in patients with acute pancreatitis Prognosis of community acquired pneumonia(CAP): value of triggering receptor expressed on myeloid cells-1 (TREM-1) and other mediators of the inflammatory response Diagnostic implications of soluble triggering receptor expressed on myeloid cells-1 in BAL fluid of patients with pulmonary infiltrates in the ICU doi = 10.1186/1471-2334-10-286 id = cord-355309-nr8fwc8q author = Porten, Klaudia title = A super-spreading ewe infects hundreds with Q fever at a farmers'' market in Germany date = 2006-10-06 keywords = Soest; case summary = To investigate risk factors for infection we conducted a case control study (cases were Q fever patients, controls were randomly selected Soest citizens) and a cohort study among vendors at the market. To determine the outbreak size we therefore asked local public health departments in Germany to ascertain a possible link to the farmers'' market in Soest for all patients notified with Q-fever. To obtain an independent, second estimate of the proportion of hospitalizations among symptomatic patients beyond that reported through the statutory surveillance system we calculated the proportion of hospitalized patients among those persons fulfilling the clinical case definition (as used in the vendors'' study (s.b.)) identified through random sampling of the Soest population (within CCS2 (s.b.)) as well as in two cohorts (vendors'' study and the 9 sailor friends (see below)). doi = 10.1186/1471-2334-6-147 id = cord-003372-cpl7zf7f author = Provoost, Judith title = A retrospective study of factors associated with treatment decision for nontuberculous mycobacterial lung disease in adults without altered systemic immunity date = 2018-12-14 keywords = NTM; disease; treatment summary = METHODS: This retrospective, single center study (2013–2016, 45 months) addressed the criteria supporting treatment decision among adults with NTM lung disease without systemic immunodeficiency at our institution, with the assigned goal to harmonize the practice. Patients'' characteristics at diagnosis were collected in order to perform analysis on 146 selected variables: demographics; history of predisposing factors; underlying pulmonary diseases; comorbidities; pulmonary function testing; respiratory bacterial or mycological co-infection(s), which definition was similar to NTM criteria, namely positive culture isolation of the same species from at least two separate expectorated sputum samples or a positive culture result from at least one bronchial wash or lavage; immunologic status; nutritional status; clinical features; microbiologic assessment through identification of NTM species on positive NTM cultures and sample culture conversions; radiologic features on high-resolution CT-scans (fibrocavitary disease or nodular/bronchiectasis disease); prior treatment for NTM lung disease, treatment combination and duration; outcome. doi = 10.1186/s12879-018-3559-x id = cord-003460-legakasx author = Qiu, Junke title = APACHE-II score for anti-tuberculosis tolerance in critically ill patients: a retrospective study date = 2019-02-04 keywords = APACHE; tuberculosis summary = doi = 10.1186/s12879-019-3751-7 id = cord-286843-8qh1pblc author = Quah, Jessica title = Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date = 2018-09-04 keywords = cap; patient; severe; viral summary = Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Postulated prohibitive factors against the routine performance of viral diagnostics tests in patients with severe CAP may include a lack of clear clinical guidelines, perceived low cost-effectiveness and the paucity of effective anti-viral therapies for respiratory viruses other than influenza. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. performed a prospective observational study on physician practices in the use of respiratory virus diagnostics demonstrating that despite clinical guideline recommendations on testing of respiratory viruses during influenza season, less than half of patients admitted to the intensive care unit with pneumonia were tested for viral pathogens [14] . doi = 10.1186/s12879-018-3366-4 id = cord-302833-6kntd89t author = Radonovich, Lewis J. title = The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel date = 2016-06-02 keywords = N95; infection; respiratory; study summary = doi = 10.1186/s12879-016-1494-2 id = cord-253171-l56qcbat author = Rao, Huaxiang title = Using the Kulldorff’s scan statistical analysis to detect spatio-temporal clusters of tuberculosis in Qinghai Province, China, 2009–2016 date = 2017-08-21 keywords = China; Qinghai summary = title: Using the Kulldorff''s scan statistical analysis to detect spatio-temporal clusters of tuberculosis in Qinghai Province, China, 2009–2016 The Kulldorff''s retrospective space-time scan statistics, calculated by using the discrete Poisson probability model, was used to identify the temporal, spatial, and spatio-temporal clusters of TB at the county level in Qinghai. In this study, our aim was to use the Kulldorff''s scan statistical analysis to explore the spatial, temporal, and space-time dynamics of TB at the county level in Qinghai. Our study analyzed the spatial, temporal, and space-time clusters of TB incidents at the county level in Qinghai, from 2009 to 2016, using the Kulldorff''s retrospective scan statistic methods. The spatial and temporal clusters were statistically significant every year, and the spacetime scanning result indicated eight high-risk areas for TB incidents which were predominantly located in the southwest Qinghai. doi = 10.1186/s12879-017-2643-y id = cord-337028-8fh4pe3i author = Reyes, Leticia title = Different inflammatory responses are associated with Ureaplasma parvum-induced UTI and urolith formation date = 2009-01-26 keywords = CFU; UTI; animal summary = doi = 10.1186/1471-2334-9-9 id = cord-000457-e50a0suk author = Rhim, Jung-Woo title = Epidemiological and clinical characteristics of childhood pandemic 2009 H1N1 virus infection: an observational cohort study date = 2011-08-24 keywords = H1N1; infection; patient summary = METHODS: We evaluated the epidemiologic characteristics of all the subjects infected with the 2009 H1N1 influenza A virus (2,971 patients, ≤ 15 years of age), and the clinical and laboratory findings of the inpatients (217 patients, 80 had pneumonia) between 1 September 2009 and 31 January 2010 in a single hospital throughout the epidemic. In addition, during the study period we observed a dramatic effect of early treatment with corticosteroids and oseltamivir for patients with severe pneumonia including rapidly progressive pneumonia [9, 10] . We retrospectively evaluated all patients with 2009 H1N1 virus infection during the pandemic (2,971 patients) for epidemiologic characteristics, and for clinical characteristics, we reviewed the medical records and chest radiographic findings of 217 children admitted to The Catholic University of Korea, Daejeon St Mary''s Hospital between 1 September 2009 and 31 January 2010. In pandemic 2009 H1N1 virus infections, children of all ages were evenly affected, and males were predominant in pneumonia patients. doi = 10.1186/1471-2334-11-225 id = cord-336975-28mtmw2z author = Sadeghi, Christine D title = Twelve years'' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date = 2011-02-07 keywords = DFA; PCR summary = PCR-based studies have suggested the important role of respiratory picornaviruses (rhinovirus and enterovirus) as a leading cause of lower respiratory tract infections in children [5] , in particular wheezing illnesses such as bronchiolitis [6, 7] , wheezy bronchitis [8] and asthma exacerbations [9] , but also pneumonia [2] . In addition, PCR has allowed for the detection of new respiratory viruses, such as hMPV [10] , which has been implicated in upper and lower respiratory tract infections in children [11] [12] [13] . A significant proportion of asymptomatic children test positive by PCR to respiratory viruses [14] [15] [16] , and picornavirus RNA can be detected by PCR up to 5 weeks after an acute infection [17] . In order to determine the value of DFA in conducting epidemiological studies on respiratory viruses now that assays for respiratory picornaviruses and hMPV are available, we retrospectively analysed the results of 12 years of DFA screening of viral pathogens in hospitalized children with respiratory disease. doi = 10.1186/1471-2334-11-41 id = cord-322202-n6qe38bh author = Saiki-Macedo, Stephanie title = Identfication of viral and bacterial etiologic agents of the pertussis-like syndrome in children under 5 years old hospitalized date = 2019-01-21 keywords = ADV; pertussis summary = In a previous study we conducted on children under 1-year-old with a probable diagnosis of Pertussis from 5 Peruvian hospitals, we reported a prevalence of 39.54% pertussis cases [14] . The main objective of this study was to detect the presence of 8 respiratory viruses (Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza-1, Parainfluenza-2 and Parainfluenza-3) and atypical bacteria (Mycoplasma pneumoniae, Chlamydia pneumonia), via Polymerase Chain Reaction in samples from Peruvian children under 5 years-old previously analyzed for B. Demonstrating the high prevalence of these atypical bacteria among Peruvian children with ARIs. Our results from this current study also make noteworthy that clinical manifestations by Mycoplasma pneumoniae and Flu-B, ADV, or B. Surprisingly, in this study, we have observed 58% of coinfections in our samples, again being the viral-bacterial association the most frequent and the most commonly detected coinfection involving Bordetella pertussis-ADV and Mycoplasma pneumoniae-ADV with frequencies of 12.2 and 6.5%, respectively. doi = 10.1186/s12879-019-3671-6 id = cord-274438-tgslabi2 author = Schnee, Sarah Valerie title = Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children date = 2017-12-13 keywords = Alere; PCR; RSV summary = title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). Mann-Whitney-U-test was applied to compare C T values in samples with true positive versus false negative Alere i RSV result. In comparison to the RT-PCR reference standard, the Alere i RSV test result was true positive in 213 and true negative in 278 samples, respectively. The Alere i RSV performed well in the point-of-care setting, and sensitive test results were obtained across all pediatric age groups within 13 min. Evaluation of Alere i RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection Host and viral factors affecting clinical performance of a rapid diagnostic test for respiratory Syncytial virus in hospitalized children doi = 10.1186/s12879-017-2855-1 id = cord-004471-1r714dmm author = Seo, Jun-Won title = Scalp eschar and neck lymphadenopathy after tick bite (SENLAT) caused by Bartonella henselae in Korea: a case report date = 2020-03-12 keywords = Bartonella; SENLAT summary = title: Scalp eschar and neck lymphadenopathy after tick bite (SENLAT) caused by Bartonella henselae in Korea: a case report BACKGROUND: Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae and is characterized by enlarged lymph nodes following a tick bite. Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae (e.g. Rickettsia slovaca, Rickettsia raoultii) and is characterized by enlarged lymph nodes following a tick bite. hensealse was < 1:20 at both first visit and Fig. 1 A photograph of the eschar on the scalp and right cervical area of a 58-year-old male patient with a confirmed diagnosis of Bartonella henselae, and a cytology report from fine needle aspiration of an enlarged cervical lymph node. henselae from pus aspirates and lymph node biopsy specimens of patients with cat scratch disease have been reported [21] , and very low levels of sensitivity in serologic and PCR tests have been found against B. doi = 10.1186/s12879-020-4940-0 id = cord-314826-usfvulc2 author = Sharifipour, Ehsan title = Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU date = 2020-09-01 keywords = COVID-19; ICU; patient summary = In total, all patients were found positive for bacterial infections, including seventeen Acinetobacter baumannii (90%) and two Staphylococcus aureus (10%) strains. Although COVID-19 associated deaths have mainly occurred in the elderly with serious underlying diseases [3] , nosocomial pneumonia (NP) in intensive care units remains a major risk factor for the patients and the health of patients, especially when intubated, may deteriorate in the presence of lower respiratory tract infections. Some studies have shown that viral agents such as influenza viruses can be associated with secondary bacterial pneumonia that might occur throughout hospitalization and lead to the death of individuals with or without preexisting respiratory diseases [8] . Therefore, our aim was to evaluate secondary bacterial infections and their antibiotic resistance in COVID-19 positive patients admitted to ICUs in Qom, the first city in Iran to report COVID-19 disease [14] . However, further work is required to investigate whether there are increased mortality rates associated with patients co-infected with COVID-19 and antibiotic-resistant bacteria. doi = 10.1186/s12879-020-05374-z id = cord-008584-4eylgtbc author = Singh, David E. title = Evaluating the impact of the weather conditions on the influenza propagation date = 2020-04-05 keywords = SISSS; datum; influenza summary = doi = 10.1186/s12879-020-04977-w id = cord-278508-h145cxlp author = Streng, Andrea title = Continued high incidence of children with severe influenza A(H1N1)pdm09 admitted to paediatric intensive care units in Germany during the first three post-pandemic influenza seasons, 2010/11–2012/13 date = 2015-12-18 keywords = Germany; PICU; influenza summary = doi = 10.1186/s12879-015-1293-1 id = cord-319504-jb455t9p author = Suess, Thorsten title = The role of facemasks and hand hygiene in the prevention of influenza transmission in households: results from a cluster randomised trial; Berlin, Germany, 2009-2011 date = 2012-01-26 keywords = household; intervention; study summary = BACKGROUND: Previous controlled studies on the effect of non-pharmaceutical interventions (NPI) namely the use of facemasks and intensified hand hygiene in preventing household transmission of influenza have not produced definitive results. When analysing only households where intervention was implemented within 36 h after symptom onset of the index case, secondary infection in the pooled M and MH groups was significantly lower compared to the control group (adjusted odds ratio 0.16, 95% CI, 0.03-0.92). Since 2006, the World Health Organisation (WHO) and other organisations have highlighted the need for controlled trials to assist in formulating recommendations on the use of non-pharmaceutical interventions (NPI)such as facemasks or hand hygiene measures -as options to prevent influenza transmission, particularly in households [1, 2] . In intention-to-treat analysis, none of the four household based trials was able to show significant reductions in secondary attack rates (SAR) when comparing intervention to control groups. doi = 10.1186/1471-2334-12-26 id = cord-000562-ocp6yodg author = Swaan, Corien M title = Timeliness of contact tracing among flight passengers for influenza A/H1N1 2009 date = 2011-12-28 keywords = H1N1; contact summary = This study evaluates the timeliness of flight-contact tracing (CT) as performed following national and international CT requests addressed to the Center of Infectious Disease Control (CIb/RIVM), and implemented by the Municipal Health Services of Schiphol Airport. In this study, we assess the time delay in contact tracing of flight passengers for influenza A/H1N1 2009 as performed in the Netherlands during the initial phase of the pandemic. For each contact investigation performed in the period April 29th until June 22nd 2009, the following data were collected: flight arrival date, first day of illness of index patient, date of laboratory diagnosis, date of contact tracing request and the date passenger lists were obtained and contact details were completed (''contacts details identified''). Our study among 17 contact investigations showed an average total delay of 3,9 days between flight arrival and identification of contacts by passenger list, which is too late for effective PEP, and late for alerting on first symptoms of disease. doi = 10.1186/1471-2334-11-355 id = cord-294062-3esrg1jw author = Tam, Clarence C. title = Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study date = 2018-09-14 keywords = acute; non; respiratory; sample summary = doi = 10.1186/s12879-018-3358-4 id = cord-321704-jozrgcq3 author = Tan, Xin Quan title = Respiratory viral pathogens among Singapore military servicemen 2009 – 2012: epidemiology and clinical characteristics date = 2014-04-15 keywords = FRI; ILI; Singapore summary = doi = 10.1186/1471-2334-14-204 id = cord-348802-3f8kmw31 author = Tang, Jialiang title = Diversity of upper respiratory tract infections and prevalence of Streptococcus pneumoniae colonization among patients with fever and flu-like symptoms date = 2019-01-07 keywords = China; URTI summary = title: Diversity of upper respiratory tract infections and prevalence of Streptococcus pneumoniae colonization among patients with fever and flu-like symptoms METHODS: We performed qualitative real-time PCR tests to detect common upper respiratory tract pathogens including 9 viruses and 3 bacteria in 1221 nasopharyngeal swabs from patients with fever and influenza-like symptoms in a Chinese city. Common upper respiratory tract pathogens other than Flu, such as human rhinovirus (hRV), respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenovirus (ADV), human metapneumovirus (hMPV) and bacterial pathogens that are difficult to culture including Mycoplasma penumoniae, Chlamydophila pneumoniae and Bordetella pertussis are generally not tested in China, except for a few high-ranking academic medical centers (facts based on personal observations and communication with colleagues in China). pneumoniae colonization and its relationship with the pathogens causing URTIs may help solve the controversy over using antibiotic prophylaxis to prevent possible secondary lower respiratory tract infections (LRTIs) caused by S. doi = 10.1186/s12879-018-3662-z id = cord-311382-ioemd0ij author = Tellier, Raymond title = Recognition of aerosol transmission of infectious agents: a commentary date = 2019-01-31 keywords = Ebola; airborne; transmission; virus summary = For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] . doi = 10.1186/s12879-019-3707-y id = cord-285976-l7voruz7 author = Tewara, Marlvin Anemey title = Small-area spatial statistical analysis of malaria clusters and hotspots in Cameroon;2000–2015 date = 2018-12-07 keywords = Cameroon; DHS; malaria; spatial summary = doi = 10.1186/s12879-018-3534-6 id = cord-325635-don9qjpz author = Turner, Paul title = Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date = 2013-09-16 keywords = RSV; respiratory; virus summary = Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected. doi = 10.1186/1471-2334-13-434 id = cord-009606-xz23twqx author = Vorobieva S. Jensen, V. title = Epidemiological and molecular characterization of Streptococcus pneumoniae carriage strains in pre-school children in Arkhangelsk, northern European Russia, prior to the introduction of conjugate pneumococcal vaccines date = 2020-04-15 keywords = Arkhangelsk; Russia; child; serotype; streptococcus summary = doi = 10.1186/s12879-020-04998-5 id = cord-298002-jvnwivrg author = Wang, Jian title = COVID-19 confirmed patients with negative antibodies results date = 2020-09-22 keywords = PCR summary = CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. During the outbreak of coronavirus 2019 (COVID-19) [1] [2] [3] , a small proportion of confirmed COVID-19 patients fail to produce IgM or IgG antibodies against SARS-CoV-2 even 40 days or longer periods of time after onset of their initial symptoms. From January 30 to March 15, 310 of COVID-19 patients who were positive for SARS-CoV-2 real time reverse-transcription PCR (RT-PCR) testing and received IgM and IgG detection at Wuhan Union Hospital (Wuhan, China) were enrolled. In this study, two patients with confirmed COVID-19 failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. doi = 10.1186/s12879-020-05419-3 id = cord-327961-ysatxwph author = Wang, Le title = Risk factors of 90-day rehospitalization following discharge of pediatric patients hospitalized with mycoplasma Pneumoniae pneumonia date = 2019-11-12 keywords = MPP; patient; readmission summary = BACKGROUND: Among pediatric patients hospitalized for Mycoplasma pneumoniae pneumonia (MPP), the risk factors for 90-day readmission after discharge is undefined. CONCLUSIONS: Readmission after MPP are common and is related to patients'' age, body temperature and influenza A coinfection during initial hospital stay, indicating potential targets could be noticed to reduce the rehospitalization after pediatric MPP. A promising approach to resolve this problem is to narrow down study sample according to the pathogenic or clinical features, such as Mycoplasma pneumoniae pneumonia (MPP), which accounts for up to 40% pediatric CAP [12] , and its diagnosis is based on etiology and clinical evidence, thereby elevating the power to detect readmission risk factors associated with the current acute infections. Our aims were to (1) describe the incidence and type of readmission after MPP discharge, (2) investigate the differences between patients with and without readmission at the initial hospital stay, (3) examine the risk factors for 90-day pneumonia-related rehospitalization. doi = 10.1186/s12879-019-4616-9 id = cord-346669-7n75m669 author = Wang, Shixin title = Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date = 2008-02-29 keywords = SARS; TNF summary = doi = 10.1186/1471-2334-8-27 id = cord-304718-w469n0o8 author = Wang, Yan title = Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection date = 2009-05-01 keywords = MASP2; MBL; SARS summary = One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. A few case-control studies have reported an association between SARS susceptibility and human leucocyte antigen (HLA) and MBL [8] [9] [10] [11] . With regard to SARS-CoV infection, the codon 54 variant of the MBL gene has been shown to be associated with infection susceptibility but not with disease severity [11] . As the downstream protein of MBL, variants of the MASP2 gene may be associated with SARS-CoV infection. Genomic DNA from 30 individuals with SARS was chosen for analysis of MASP2 gene polymorphisms. doi = 10.1186/1471-2334-9-51 id = cord-333745-nwnt2tde author = Wang, Yi title = Clinical characteristics and laboratory indicator analysis of 67 COVID-19 pneumonia patients in Suzhou, China date = 2020-10-12 keywords = Group; covid-19 summary = RESULTS: The study found that fibrinogen (FIB) was increased in 45 (65.2%) patients, and when FIB reached a critical value of 4.805 g/L, the sensitivity and specificity、DA, helping to distinguish general and severe cases, were 100 and 14%、92.9%, respectively, which were significantly better than those for lymphocyte count and myoglobin. In a comparison of patients in Group A with patients in Group B, the lymphocyte count absolute value (L), myoglobin (MB) and fibrinogen of COVID-19 pneumonia patients in Group A were significantly higher than those in Group B, with statistically significant differences (P ≤ 0.001) ( Table 4 ). Laboratory data showed that the WBC, N%, and CRP in Group B COVID-19 pneumonia patients were significantly higher than those of Group A patients, and the differences were statistically significant (P < 0.05). doi = 10.1186/s12879-020-05468-8 id = cord-012875-joz31gie author = Weber, Katharina L. title = Simulating transmission of ESKAPE pathogens plus C. difficile in relevant clinical scenarios date = 2020-06-12 keywords = CFU; ESKAPE+C; skin; vitro summary = doi = 10.1186/s12879-020-05121-4 id = cord-030134-drw6nqge author = Weerasooriya, Nilusha title = Staphylococcal endocarditis in a quadricuspid aortic valve following uncomplicated dengue infection: a case report date = 2020-08-06 keywords = QAV; Sri summary = title: Staphylococcal endocarditis in a quadricuspid aortic valve following uncomplicated dengue infection: a case report Increased incidence of concurrent bacteremia in patients with dengue infection is a recognized complication. Quadricuspid aortic valve (QAV) is a rare congenital anomaly and few cases of infective endocarditis have been reported in QAV. CASE PRESENTATION: A 32-year-old Sri Lankan male presented to the National Hospital of Sri Lanka with recurrence of fever and acute left hemiplegia following an uncomplicated recovery of dengue fever. A few case series have recognized an increased incidence of concurrent bacteremia in patients with dengue infection [1, 2] . We report a patient presenting with endocarditis of previously undiagnosed QAV, soon after recovering from dengue fever. This patient''s recovery from dengue fever was complicated with MRSA endocarditis of aortic valve with septic embolization to the brain and spleen. There are two reported cases of linezolid induced rhabdomyolysis [5, 8] . doi = 10.1186/s12879-020-05315-w id = cord-284393-s9qp9a4e author = Wei, Yiping title = Clinical characteristics of 276 hospitalized patients with coronavirus disease 2019 in Zengdu District, Hubei Province: a single-center descriptive study date = 2020-07-29 keywords = Wuhan; Zengdu; covid-19 summary = title: Clinical characteristics of 276 hospitalized patients with coronavirus disease 2019 in Zengdu District, Hubei Province: a single-center descriptive study BACKGROUND: We aimed to report the epidemiological and clinical characteristics of hospitalized patients with coronavirus disease-19 (COVID-19) in Zengdu District, Hubei Province, China. Our study on 276 inpatients in Zengdu Hhospital confirms that COVID-19 patients in the areas surrounding the core COVID-19 outbreak region showed mainly mild and moderate illness with fever and lymphocytopenia as the main clinical features. Moreover, compared to studies in which only seriously ill COVID-19 patients were admitted, our admission criteria better reflect the disease characteristics in the area around the outbreak point, so as to provide a decision-making reference for hospitals in the residential area to decide which patients should stay at home for observation and which high-risk patients should be hospitalized in a timely manner. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1186/s12879-020-05252-8 id = cord-306175-p5rtp31m author = Weissbrich, Benedikt title = Frequent detection of bocavirus DNA in German children with respiratory tract infections date = 2006-07-11 keywords = DNA; PCR summary = METHODS: We tested 835 nasopharyngeal aspirates (NPA) obtained between 2002 and 2005 from pediatric in-patients with acute respiratory tract diseases at the University of Würzburg, Germany, for the presence of hBoV DNA. The samples tested for hBoV infection consisted of stored nasopharyngeal aspirates (NPA) that were sent by the University of Würzburg Children''s hospital for screening of respiratory viruses from January 2002 to September 2005. In 34 (39.1 %) of the hBoV positive infants and children, coinfections with other respiratory viruses were present, most frequently with RSV (n = 14) followed by influenza A (n = 9). Clinical data were available for 63 of the 87 hBoV positive NPAs. The patients suffered from upper and/or lower respiratory tract diseases (Table 4) . We found hBoV DNA in 10.3 % of NPA samples obtained from infants and children with respiratory tract diseases during the years 2002 to 2005 in the region of northern Bavaria in Germany. doi = 10.1186/1471-2334-6-109 id = cord-277010-2iecsho0 author = Wen, Xiaohong title = Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date = 2019-01-08 keywords = China; virus summary = title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. doi = 10.1186/s12879-018-3668-6 id = cord-272194-h7xnr389 author = Wiegers, Hanke M. G. title = Bacterial co-infection of the respiratory tract in ventilated children with bronchiolitis; a retrospective cohort study date = 2019-11-06 keywords = PICU; infection summary = doi = 10.1186/s12879-019-4468-3 id = cord-301393-d1duepnb author = Wolfensberger, Aline title = Implementation and evaluation of a care bundle for prevention of non-ventilator-associated hospital-acquired pneumonia (nvHAP) – a mixed-methods study protocol for a hybrid type 2 effectiveness-implementation trial date = 2020-08-17 keywords = bundle; implementation; nvhap; study summary = title: Implementation and evaluation of a care bundle for prevention of non-ventilator-associated hospital-acquired pneumonia (nvHAP) – a mixed-methods study protocol for a hybrid type 2 effectiveness-implementation trial A longitudinal, qualitative study and formative evaluation based on interviews, focus groups, and observations identifies supporting or hindering factors for implementation success in participating departments dynamically over time. DISCUSSION: This comprehensive hybrid mixed-methods study is designed to both, measure the effectiveness of a new nvHAP prevention bundle and multifaceted implementation strategy, while also providing insights into how and why it worked or failed. This comprehensive type 2 hybrid effectivenessimplementation study aims to assess the effectiveness and success factors of both, a new prevention bundle against nvHAP and a specifically designed departmentbased multifaceted implementation strategy in a medical and surgical patient population. doi = 10.1186/s12879-020-05271-5 id = cord-000280-zyaj90nh author = Wong, Samuel YS title = Willingness to accept H1N1 pandemic influenza vaccine: A cross-sectional study of Hong Kong community nurses date = 2010-10-29 keywords = H1N1; Hong summary = CONCLUSIONS: Similar to previous findings conducted in hospital healthcare workers and nurses, we confirmed that the willingness of community nurses to accept influenza A (H1N1) vaccination is low. In a study conducted of Hong Kong healthcare workers in hospitals, it was found that only 25% of nurses were willing to accept influenza A (H1N1) vaccination, compared with 47% of doctors and 29% of allied professionals [13] . Consistent with findings from previous surveys conducted in hospital healthcare workers and nurses [13, 17] , we have shown that the majority of nurses from community nursing services in Hong Kong were not willing to be vaccinated against H1N1 influenza when the vaccine becomes available. Consistent with previous findings which were conducted in healthcare workers and nurses [13, 17] , we confirm that the acceptance rate of pandemic influenza vaccination is low amongst community nurses. doi = 10.1186/1471-2334-10-316 id = cord-318340-hptjqmrl author = Xiang, Nijuan title = Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases date = 2019-09-03 keywords = China; PUE; case summary = We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. If a case is reported to the PUE system, the local center for disease control and prevention (CDC) will conduct a field investigation, collect respiratory specimens and send them to a national influenza surveillance network laboratory for testing of avian influenza viruses and, if associated with clusters of respiratory disease or relevant travel history, testing of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). For patients with illnesses meeting the PUE case definition, the surveillance officer used a standard questionnaire to collect information from the hospital information system related to demographics and, if available, epidemiological risk factors, including exposures to poultry, patients with similar symptoms, and travel history. doi = 10.1186/s12879-019-4345-0 id = cord-298899-lkrmg5qr author = Xie, Yewei title = Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date = 2020-08-31 keywords = COVID-19; China; SARS; Wuhan; clinical summary = To fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, CT results, and risk factors of the COVID-19. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study doi = 10.1186/s12879-020-05371-2 id = cord-324880-s1oqkqef author = Xu, Lili title = A fatal case associated with respiratory syncytial virus infection in a young child date = 2018-05-11 keywords = RSV; infection; patient summary = RSV-related encephalitis with acute encephalopathic symptoms such as seizure, severe sequelae and even death following RSV infection in children without underlying disease has sporadically been reported [5] . In this report, we present the case of a 2-year-old girl who was not born prematurely and had no underlying disease whose sudden death may have been related to an RSV infection identified by conventional methods and metagenomic analyses. Viral antigen detection based on both an immunofluorescence assay and the Luminex xTAG respiratory viral panel assay was positive for RSV in the patient''s nasopharyngeal aspirates (which were collected on 14 Nov, the 5th day of disease onset and the 2nd day of admission) and negative for adenovirus, influenza A and B viruses, parainfluenza virus 1-4, human metapneumovirus, enteroviruses and rhinoviruses, human coronavirus HKU1, 229E, NL63 and OC43, and human bocavirus. reported that influenza virus RNA was detected in the CSF of 71.4% (5/7) of patients who developed influenza-associated acute encephalopathy/encephalitis [17] . doi = 10.1186/s12879-018-3123-8 id = cord-349905-jniqriu6 author = Xu, Xinyin title = Should we remain hopeful? The key 8 weeks: spatiotemporal epidemic characteristics of COVID-19 in Sichuan Province and its comparative analysis with other provinces in China and global epidemic trends date = 2020-11-05 keywords = China; Province; Sichuan summary = METHODS: The number of confirmed cases, daily growth, incidence and length of time from the first reported case to the end of the local cases (i.e., non-overseas imported cases) were compared by spatial (geographical) and temporal classification and visualization of the development and changes of the epidemic situation by layers through maps. The time of the first confirmed case report in the 21 cities of Sichuan Province mainly came one week after the Wuhan lockdown (January 24-January 31) [17] . In the next four weeks after the Wuhan lockdown, 90% of the cities nationwide were affected, and the number of cases increased by a factor Fig. 3 Time distribution of the number of confirmed cases and counties with the first diagnosed cases in Sichuan Province (mainland cases). Data from various countries were from the WHO COVID-19 Daily Report published since January 21, 7, which also contained the confirmed information of the different provinces in China before the date of March 15. doi = 10.1186/s12879-020-05494-6 id = cord-293858-dk4snw9r author = Yang, Lin title = Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date = 2019-02-14 keywords = Hong; Kong; SARS summary = doi = 10.1186/s12879-019-3735-7 id = cord-300116-r93w4jm3 author = Yi, Hana title = Profiling bacterial community in upper respiratory tracts date = 2014-11-13 keywords = Moraxella; figure; respiratory summary = doi = 10.1186/s12879-014-0583-3 id = cord-341818-mm3d4jkh author = Ying, Mingliang title = COVID-19 with acute cholecystitis: a case report date = 2020-06-22 keywords = COVID-19 summary = CASE PRESENTATION: A case of 68-year-old female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that was finally diagnosed as acute cholecystitis. Ultrasound-guided percutaneous transhepatic gallbladder drainage (PTGD) was performed, and the real-time fluorescence polymerase chain reaction (RT-PCR) COVID-19 nucleic acid assay of the bile was found to be negative. Here, we report a confirmed case of a female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that finally diagnosed as acute cholecystitis. At first, the patient did not show any abdominal symptoms except diarrhea; however, she developed constant pain in the right upper quadrant of her abdomen and Murphy''s sign after 10 days of hospitalization, and her body temperature was elevated to 38.3°C (100.9°F). doi = 10.1186/s12879-020-05164-7 id = cord-324942-zfvzxlj7 author = Yu, Jianxing title = Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012–2015 date = 2018-02-08 keywords = China; RSV summary = doi = 10.1186/s12879-018-2982-3 id = cord-000619-3bakci02 author = Zhang, Peng-jun title = Clinical features and risk factors for severe and critical pregnant women with 2009 pandemic H1N1 influenza infection in China date = 2012-02-01 keywords = H1N1; NIV summary = title: Clinical features and risk factors for severe and critical pregnant women with 2009 pandemic H1N1 influenza infection in China Data on risk factors associated with death of pregnant women and neonates with pH1N1 infections are limited outside of developed countries. METHODS: Retrospective observational study in 394 severe or critical pregnant women admitted to a hospital with pH1N1 influenza from Sep. 1, 2009 to Dec. 31, 2009. Preterm delivery was a risk factor for neonatal death among pregnant women with pH1N1 influenza infection. However, information is limited concerning the risk factors for maternal and neonatal death when pregnancy is complicated by severe or critical illness related to 2009 pH1N1 influenza. In this report, we described the characteristics of pH1N1 influenza in pregnant women and the risk factors for maternal and neonatal death. The clinical data reported herein is consistent with previous studies that demonstrate that pregnant women with influenza are at an increased risk of serious illness and death. doi = 10.1186/1471-2334-12-29 id = cord-296375-gf0mgz5x author = Zhang, Xi title = Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date = 2020-10-30 keywords = COVID-19; SARS summary = CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. Therefore, in this study, by collecting the daily numbers of newly confirmed COVID-19 and SARS cases during the two epidemics, we aimed to determine the spatial behavior and temporal features of the COVID-19 spread in mainland China and compared them with respective features from the SARS epidemic using spatiotemporal analysis. Incident cases infected by COVID-19 were extracted from the daily briefings on novel coronavirus cases from January 20 to March 4, 2020, provided on the official website of the National Health Commission of the People''s Republic of China [5] . Incident cases of SARS were extracted from daily situation reports for mainland China from April 21 to August 3, 2003 , which were posted by China.org.cn (in Chinese) and were also provided by the National Health Commission. doi = 10.1186/s12879-020-05537-y id = cord-001922-zfpg6dgj author = Zhang, Xu-Sheng title = Construction of the influenza A virus transmission tree in a college-based population: co-transmission and interactions between influenza A viruses date = 2016-01-29 keywords = H1N1; H3N2 summary = The method uses knowledge of which subtype each case is infected with (and whether they were co-infected), contact information and symptom onset date of each case in the influenza outbreak. RESULTS: Analysis of the constructed transmission tree shows that the simultaneous presence of the two influenza viruses increases the infectivity and the transmissibility of A/H1N1 virus but whether it changes the infectivity of A/H3N2 is unclear. In this short report we extend this inference method to construct the transmission tree that includes two influenza A viruses and their co-infection. The likely reason for this difference lies in the fact that pandemic A/H1N1 is a novel virus while A/ H3N2 is an endemic seasonal virus in the study region [12] so some pre-existing immunity against A/H3N2 Fig. 2 Constructed transmission tree of influenza A virus: a The relative frequency of the generation intervals; b The average case reproduction number R t as it varies with time. doi = 10.1186/s12879-016-1373-x id = cord-004316-mnqn1t3q author = Zhao, Xia title = Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study date = 2020-02-10 keywords = HAI; elderly summary = title: Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study BACKGROUND: We analyzed the results of a 3-year surveillance study on the epidemiological and clinical characteristics of healthcare associated-infections (HAIs) in elderly inpatients in a large tertiary hospital in China. Here we describe and analyze the results of a 3-year real-time surveillance study on the incidence of HAIs and the epidemiological and clinical characteristics of elderly inpatients in a large tertiary hospital in China. The incidence of ventilator-associated pneumonia (VAP) in elderly patients was lower than in non-elderly patients, catheter-associated urinary tract infections (CAUTIs) were significantly more common in elderly patients, and central line-associated bloodstream infection (CLABSI) rates were similar in both groups (Tables 2 and 3 ). doi = 10.1186/s12879-020-4840-3 id = cord-328040-5qd05e4r author = Zhao, Xin-Ying title = Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date = 2020-04-29 keywords = COVID-19; SARS; patient summary = title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study Since December 2019, several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were first reported the virus has caused an outbreak in a short time by human-to-human transmission throughout China, especially in Hubei Province. A considerable proportion of COVID-19 patients develop severe pneumonia, pulmonary edema, acute respiratory distress syndrome, and even multiple organ failure within a short time. Patients suspected of having COVID-19 were admitted and quarantined, and throat swab samples were collected and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative polymerase chain reaction assay (qPCR). Clinical data [age, previous chronic disease, epidemiological history, symptoms, vital signs, computed tomography (CT) images, virus load, laboratory tests, complications, and treatment process] of the 91 patients involved in this study were collected. doi = 10.1186/s12879-020-05010-w id = cord-316493-wszoi6p2 author = Zhou, Weimin title = First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood date = 2013-09-16 keywords = IFA; SARS summary = BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. To expand the epidemiological knowledge of four non-SARS-related endemic HCoVs in China, we expressed S proteins in a eukaryotic system and established an IFA for the detection of IgG or IgM antibodies against these four viruses. Our results showed that the S-based IFA enabled specific detection of IgG or IgM to four individual HCoVs. Using IFA, we investigated the natural seroprevalence of four non-SARS-related HCoVs in blood samples from a general population that comprised a variety of age groups. doi = 10.1186/1471-2334-13-433 id = cord-328620-d2jrn1ip author = van Gageldonk-Lafeber, Arianne B title = Risk factors for acute respiratory tract infections in general practitioner patients in The Netherlands: a case-control study date = 2007-04-27 keywords = ARTI; risk summary = doi = 10.1186/1471-2334-7-35 id = cord-312222-aw5849rc author = Österdahl, Marc F. title = Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR) date = 2020-10-20 keywords = LAMP; PCR summary = METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. Since then, a number [13] of other groups have published high-quality studies demonstrating that RT-LAMP has the potential to replace RT-PCR as a means for detecting SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) within RNA extracted from nose -throat swabs and endotracheal secretions/bronchoalveolar lavage fluid [5, 14, 15] . doi = 10.1186/s12879-020-05484-8 id = cord-028945-p3hhd5ed author = Şahar, Esra Atalay title = Development of a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V and determination of its protective efficacy against acute toxoplasmosis date = 2020-07-10 keywords = IFN; ISA; MHC; Montanide summary = doi = 10.1186/s12879-020-05220-2