{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T20:29:10Z","timestamp":1789504150540,"version":"build-2803163510"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,11,15]],"date-time":"2018-11-15T00:00:00Z","timestamp":1542240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["1U01P000497-01)"],"award-info":[{"award-number":["1U01P000497-01)"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,30]]},"DOI":"10.1093\/cid\/ciy821","type":"journal-article","created":{"date-parts":[[2018,10,4]],"date-time":"2018-10-04T20:10:42Z","timestamp":1538683842000},"page":"1993-2002","source":"Crossref","is-referenced-by-count":43,"title":["The Effect of Influenza Virus on the Human Oropharyngeal Microbiome"],"prefix":"10.1093","volume":"68","author":[{"given":"Elisa","family":"Ramos-Sevillano","sequence":"first","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William G","family":"Wade","sequence":"additional","affiliation":[{"name":"King\u2019s College London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Mann","sequence":"additional","affiliation":[{"name":"hVIVO Services Limited, Queen Mary BioEnterprises Innovation Centre, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Gilbert","sequence":"additional","affiliation":[{"name":"hVIVO Services Limited, Queen Mary BioEnterprises Innovation Centre, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Lambkin-Williams","sequence":"additional","affiliation":[{"name":"hVIVO Services Limited, Queen Mary BioEnterprises Innovation Centre, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben","family":"Killingley","sequence":"additional","affiliation":[{"name":"Department of Infection and Acute Medicine, University College London Hospital, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan S","family":"Nguyen-Van-Tam","sequence":"additional","affiliation":[{"name":"Faculty of Medicine & Health Sciences, University of Nottingham, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph M","family":"Tang","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,11,15]]},"reference":[{"key":"2019053001011011600_CIT0001","first-page":"327","article-title":"Secondary bacterial infections in influenza virus infection pathogenesis","volume":"385","author":"Smith","year":"2014","journal-title":"Curr Top Microbiol Immunol"},{"key":"2019053001011011600_CIT0002","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1086\/511989","article-title":"The 1918 influenza pandemic: insights for the 21st century","volume":"195","author":"Morens","year":"2007","journal-title":"J Infect Dis"},{"key":"2019053001011011600_CIT0003","doi-asserted-by":"crossref","first-page":"16416","DOI":"10.1073\/pnas.1111179108","article-title":"Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak","volume":"108","author":"Sheng","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019053001011011600_CIT0004","doi-asserted-by":"crossref","first-page":"1498","DOI":"10.1086\/652446","article-title":"Fatalities associated with the 2009 H1N1 influenza A virus in New York city","volume":"50","author":"Lee","year":"2010","journal-title":"Clin Infect Dis"},{"key":"2019053001011011600_CIT0005","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0140-6736(00)78541-2","article-title":"A virus obtained from influenza patients","volume":"2","author":"Smith","year":"1933","journal-title":"Lancet"},{"key":"2019053001011011600_CIT0006","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1128\/CMR.00058-05","article-title":"Insights into the interaction between influenza virus and pneumococcus","volume":"19","author":"McCullers","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"2019053001011011600_CIT0007","doi-asserted-by":"crossref","first-page":"e8705","DOI":"10.1371\/journal.pone.0008705","article-title":"Community-acquired pneumonia due to pandemic A(H1N1)2009 influenzavirus and methicillin resistant Staphylococcus aureus co-infection","volume":"5","author":"Murray","year":"2010","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0008","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/0140-6736(91)91112-8","article-title":"Influenza A and meningococcal disease","volume":"338","author":"Cartwright","year":"1991","journal-title":"Lancet"},{"key":"2019053001011011600_CIT0009","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/S0966-842X(00)88892-7","article-title":"Viral potentiation of bacterial superinfection of the respiratory tract","volume":"3","author":"Bakaletz","year":"1995","journal-title":"Trends Microbiol"},{"key":"2019053001011011600_CIT0010","doi-asserted-by":"crossref","first-page":"S121","DOI":"10.1097\/INF.0b013e3181b6d7ec","article-title":"Microbial interactions in the respiratory tract","volume":"28","author":"Murphy","year":"2009","journal-title":"Pediatr Infect Dis J"},{"key":"2019053001011011600_CIT0011","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrmicro3231","article-title":"The co-pathogenesis of influenza viruses with bacteria in the lung","volume":"12","author":"McCullers","year":"2014","journal-title":"Nat Rev Microbiol"},{"key":"2019053001011011600_CIT0012","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1086\/430954","article-title":"Influenza virus neuraminidase contributes to secondary bacterial pneumonia","volume":"192","author":"Peltola","year":"2005","journal-title":"J Infect Dis"},{"key":"2019053001011011600_CIT0013","doi-asserted-by":"crossref","first-page":"7161","DOI":"10.1128\/IAI.70.12.7161-7164.2002","article-title":"Neuraminidase expressed by Streptococcus pneumoniae desialylates the lipopolysaccharide of Neisseria meningitidis and Haemophilus influenzae: a paradigm for interbacterial competition among pathogens of the human respiratory tract","volume":"70","author":"Shakhnovich","year":"2002","journal-title":"Infect Immun"},{"key":"2019053001011011600_CIT0014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molimm.2014.12.010","article-title":"Desialylation of airway epithelial cells during influenza virus infection enhances pneumococcal adhesion via galectin binding","volume":"65","author":"Nita-Lazar","year":"2015","journal-title":"Mol Immunol"},{"key":"2019053001011011600_CIT0015","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1111\/j.1462-5822.2012.01838.x","article-title":"Galectin-3 binds Neisseria meningitidis and increases interaction with phagocytic cells","volume":"14","author":"Quattroni","year":"2012","journal-title":"Cell Microbiol"},{"key":"2019053001011011600_CIT0016","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.chom.2014.06.005","article-title":"Influenza promotes pneumococcal growth during coinfection by providing host sialylated substrates as a nutrient source","volume":"16","author":"Siegel","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2019053001011011600_CIT0017","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/nrmicro2832","article-title":"Microbial interactions: from networks to models","volume":"10","author":"Faust","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"2019053001011011600_CIT0018","doi-asserted-by":"crossref","first-page":"e15216","DOI":"10.1371\/journal.pone.0015216","article-title":"Disordered microbial communities in the upper respiratory tract of cigarette smokers","volume":"5","author":"Charlson","year":"2010","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0019","doi-asserted-by":"crossref","first-page":"201","DOI":"10.3201\/eid2002.131220","article-title":"Seven-valent pneumococcal conjugate vaccine and nasopharyngeal microbiota in healthy children","volume":"20","author":"Biesbroek","year":"2014","journal-title":"Emerg Infect Dis"},{"key":"2019053001011011600_CIT0020","doi-asserted-by":"crossref","first-page":"e9836","DOI":"10.1371\/journal.pone.0009836","article-title":"Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome","volume":"5","author":"Jakobsson","year":"2010","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0021","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1164\/rccm.201111-2030ED","article-title":"From microbe to microbiota: considering microbial community composition in infections and airway diseases","volume":"185","author":"Huang","year":"2012","journal-title":"Am J Respir Crit Care Med"},{"key":"2019053001011011600_CIT0022","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/ismej.2015.99","article-title":"Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients","volume":"10","author":"de Steenhuijsen Piters","year":"2016","journal-title":"ISME J"},{"key":"2019053001011011600_CIT0023","doi-asserted-by":"crossref","first-page":"5809","DOI":"10.1073\/pnas.1120577109","article-title":"Decade-long bacterial community dynamics in cystic fibrosis airways","volume":"109","author":"Zhao","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019053001011011600_CIT0024","doi-asserted-by":"crossref","first-page":"2813","DOI":"10.1128\/JCM.00035-14","article-title":"Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease","volume":"52","author":"Huang","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2019053001011011600_CIT0025","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1186\/s12879-014-0583-3","article-title":"Profiling bacterial community in upper respiratory tracts","volume":"14","author":"Yi","year":"2014","journal-title":"BMC Infect Dis"},{"key":"2019053001011011600_CIT0026","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/2049-2618-2-22","article-title":"Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge","volume":"2","author":"Allen","year":"2014","journal-title":"Microbiome"},{"key":"2019053001011011600_CIT0027","doi-asserted-by":"crossref","first-page":"e71227","DOI":"10.1371\/journal.pone.0071227","article-title":"Bacterial community development in experimental gingivitis","volume":"8","author":"Kistler","year":"2013","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0028","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2019053001011011600_CIT0029","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"2019053001011011600_CIT0030","first-page":"265","article-title":"Nonparametric-estimation of the number of classes in a population","volume":"11","author":"Chao","year":"1984","journal-title":"Scand J Stat"},{"key":"2019053001011011600_CIT0031","first-page":"121","article-title":"Estimating the number of species with CatchAll","author":"Bunge","year":"2011","journal-title":"Pac Symp Biocomput"},{"key":"2019053001011011600_CIT0032","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/163688a0","article-title":"Measurement of diversity","volume":"163","author":"Simpson","year":"1949","journal-title":"Nature"},{"key":"2019053001011011600_CIT0033","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst Tech J"},{"key":"2019053001011011600_CIT0034","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/biomet\/40.3-4.237","article-title":"The population frequencies of species and the estimation of population parameters","volume":"40","author":"Good","year":"1953","journal-title":"Biometrika"},{"key":"2019053001011011600_CIT0035","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1080\/STA-200066418","article-title":"A similarity measure based on species proportions","volume":"34","author":"Yue","year":"2005","journal-title":"Commun Stat Theory Methods"},{"key":"2019053001011011600_CIT0036","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1111\/j.1574-6976.2008.00111.x","article-title":"Species divergence and the measurement of microbial diversity","volume":"32","author":"Lozupone","year":"2008","journal-title":"FEMS Microbiol Rev"},{"key":"2019053001011011600_CIT0037","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1128\/JCM.03529-13","article-title":"Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene","volume":"52","author":"Bennett","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2019053001011011600_CIT0038","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1128\/JCM.02498-06","article-title":"Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA","volume":"45","author":"Carvalho","year":"2007","journal-title":"J Clin Microbiol"},{"key":"2019053001011011600_CIT0039","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/genetics\/131.2.479","article-title":"Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data","volume":"131","author":"Excoffier","year":"1992","journal-title":"Genetics"},{"key":"2019053001011011600_CIT0040","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/genetics\/126.1.249","article-title":"Detecting isolation by distance using phylogenies of genes","volume":"126","author":"Slatkin","year":"1990","journal-title":"Genetics"},{"key":"2019053001011011600_CIT0041","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol"},{"key":"2019053001011011600_CIT0042","doi-asserted-by":"crossref","first-page":"e69559","DOI":"10.1371\/journal.pone.0069559","article-title":"Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza","volume":"8","author":"Chaban","year":"2013","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0043","doi-asserted-by":"crossref","first-page":"e9413","DOI":"10.1371\/journal.pone.0009413","article-title":"The influence of IS1301 in the capsule biosynthesis locus on meningococcal carriage and disease","volume":"5","author":"Kugelberg","year":"2010","journal-title":"PLoS One"},{"key":"2019053001011011600_CIT0044","doi-asserted-by":"crossref","first-page":"11411","DOI":"10.1038\/s41598-018-29793-w","article-title":"Nasal microbiota clusters associate with inflammatory response, viral load, and symptom severity in experimental rhinovirus challenge","volume":"8","author":"Lehtinen","year":"2018","journal-title":"Sci Rep"}],"container-title":["Clinical Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/cid\/article-pdf\/68\/12\/1993\/28739318\/ciy821.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,3]],"date-time":"2022-09-03T09:12:55Z","timestamp":1662196375000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/cid\/article\/68\/12\/1993\/5184302"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,15]]},"references-count":44,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2018,11,15]]},"published-print":{"date-parts":[[2019,5,30]]}},"URL":"https:\/\/doi.org\/10.1093\/cid\/ciy821","relation":{},"ISSN":["1058-4838","1537-6591"],"issn-type":[{"value":"1058-4838","type":"print"},{"value":"1537-6591","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,6,15]]},"published":{"date-parts":[[2018,11,15]]}}}