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dc.contributor.authorBradley, Evan S
dc.contributor.authorZeamer, Abigail L
dc.contributor.authorBucci, Vanni
dc.contributor.authorCincotta, Lindsey
dc.contributor.authorSalive, Marie-Claire
dc.contributor.authorDutta, Protiva
dc.contributor.authorMutaawe, Shafik
dc.contributor.authorAnya, Otuwe
dc.contributor.authorTocci, Christopher
dc.contributor.authorMoormann, Ann M
dc.contributor.authorWard, Doyle V
dc.contributor.authorMcCormick, Beth A
dc.contributor.authorHaran, John P
dc.date.accessioned2022-12-09T20:04:47Z
dc.date.available2022-12-09T20:04:47Z
dc.date.issued2022-09-30
dc.identifier.citationBradley ES, Zeamer AL, Bucci V, Cincotta L, Salive MC, Dutta P, Mutaawe S, Anya O, Tocci C, Moormann A, Ward DV, McCormick BA, Haran JP. Oropharyngeal microbiome profiled at admission is predictive of the need for respiratory support among COVID-19 patients. Front Microbiol. 2022 Sep 30;13:1009440. doi: 10.3389/fmicb.2022.1009440. PMID: 36246273; PMCID: PMC9561819.en_US
dc.identifier.issn1664-302X
dc.identifier.doi10.3389/fmicb.2022.1009440en_US
dc.identifier.pmid36246273
dc.identifier.urihttp://hdl.handle.net/20.500.14038/51433
dc.description.abstractThe oropharyngeal microbiome, the collective genomes of the community of microorganisms that colonizes the upper respiratory tract, is thought to influence the clinical course of infection by respiratory viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Infectious Disease 2019 (COVID-19). In this study, we examined the oropharyngeal microbiome of suspected COVID-19 patients presenting to the Emergency Department and an inpatient COVID-19 unit with symptoms of acute COVID-19. Of 115 initially enrolled patients, 50 had positive molecular testing for COVID-19+ and had symptom duration of 14 days or less. These patients were analyzed further as progression of disease could most likely be attributed to acute COVID-19 and less likely a secondary process. Of these, 38 (76%) went on to require some form of supplemental oxygen support. To identify functional patterns associated with respiratory illness requiring respiratory support, we applied an interpretable random forest classification machine learning pipeline to shotgun metagenomic sequencing data and select clinical covariates. When combined with clinical factors, both species and metabolic pathways abundance-based models were found to be highly predictive of the need for respiratory support (F1-score 0.857 for microbes and 0.821 for functional pathways). To determine biologically meaningful and highly predictive signals in the microbiome, we applied the Stable and Interpretable RUle Set to the output of the models. This analysis revealed that low abundance of two commensal organisms, Prevotella salivae or Veillonella infantium (< 4.2 and 1.7% respectively), and a low abundance of a pathway associated with LPS biosynthesis (< 0.1%) were highly predictive of developing the need for acute respiratory support (82 and 91.4% respectively). These findings suggest that the composition of the oropharyngeal microbiome in COVID-19 patients may play a role in determining who will suffer from severe disease manifestations.en_US
dc.language.isoenen_US
dc.relationThis article is based on a previously available preprint in medRxiv, https://doi.org/10.1101/2022.02.28.22271627.en_US
dc.relation.ispartofFrontiers in Microbiologyen_US
dc.relation.urlhttps://doi.org/10.3389/fmicb.2022.1009440en_US
dc.rights© 2022 Bradley, Zeamer, Bucci, Cincotta, Salive, Dutta, Mutaawe, Anya, Tocci, Moormann, Ward, McCormick and Haran. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms; Attribution 4.0 Internationalen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectCOVID-19en_US
dc.subjectLPS biosynthesisen_US
dc.subjectPrevotellaen_US
dc.subjectSARS-CoV-2en_US
dc.subjectcommensal organismsen_US
dc.subjectoropharyngeal microbiomeen_US
dc.subjectrandom forest classificationen_US
dc.titleOropharyngeal microbiome profiled at admission is predictive of the need for respiratory support among COVID-19 patientsen_US
dc.typeJournal Articleen_US
dc.source.journaltitleFrontiers in microbiology
dc.source.volume13
dc.source.beginpage1009440
dc.source.endpage
dc.source.countrySwitzerland
dc.identifier.journalFrontiers in microbiology
refterms.dateFOA2022-12-09T20:04:48Z
dc.contributor.departmentEmergency Medicineen_US
dc.contributor.departmentMedicineen_US
dc.contributor.departmentMicrobiology and Physiological Systemsen_US
dc.contributor.departmentMorningside Graduate School of Biomedical Sciencesen_US


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© 2022 Bradley, Zeamer, Bucci, Cincotta, Salive, Dutta, Mutaawe, Anya, Tocci, Moormann, Ward, McCormick and Haran. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms; Attribution 4.0 International
Except where otherwise noted, this item's license is described as © 2022 Bradley, Zeamer, Bucci, Cincotta, Salive, Dutta, Mutaawe, Anya, Tocci, Moormann, Ward, McCormick and Haran. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms; Attribution 4.0 International