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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.date2022-08-11T08:08:11.000
dc.date.accessioned2022-08-23T15:45:39Z
dc.date.available2022-08-23T15:45:39Z
dc.date.issued2022-02-28
dc.date.submitted2022-04-07
dc.identifier.citation<p>Bradley 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. medRxiv [Preprint]. 2022 Feb 28:2022.02.28.22271627. doi: 10.1101/2022.02.28.22271627. PMID: 35262096; PMCID: PMC8902889. <a href="https://doi.org/10.1101/2022.02.28.22271627" target="_blank" title="view preprint in medRxiv">Link to preprint on medRxiv</a>.</p>
dc.identifier.doi10.1101/2022.02.28.22271627
dc.identifier.pmid35262096
dc.identifier.urihttp://hdl.handle.net/20.500.14038/27579
dc.description<p>This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.</p>
dc.description.abstractThe clinical course of infection due to respiratory viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), the causative agent of Coronavirus Disease 2019 (COVID-19) is thought to be influenced by the community of organisms that colonizes the upper respiratory tract, the oropharyngeal microbiome. 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 enrolled patients, 74 were confirmed COVID-19+ and 50 had symptom duration of 14 days or less; 38 acute COVID-19+ patients (76%) went on to require respiratory support. Although no microbiome features were found to be significantly different between COVID-19+ and COVID-19-patients, when we conducted random forest classification modeling (RFC) to predict the need of respiratory support for the COVID-19+ patients our analysis identified a subset of organisms and metabolic pathways whose relative abundance, when combined with clinical factors (such as age and Body Mass Index), was highly predictive of the need for respiratory support (F1 score 0.857). Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis was then applied to the features identified as predicative of the need for respiratory support by the RFC. This analysis revealed reduced abundance of Prevotella salivae and metabolic pathways associated with lipopolysaccharide and mycolic acid biosynthesis to be the strongest predictors of patients requiring respiratory support. These findings suggest that composition of the oropharyngeal microbiome in COVID-19 may play a role in determining who will suffer from severe disease manifestations. Importance: The microbial community that colonizes the upper airway, the oropharyngeal microbiome, has the potential to affect how patients respond to respiratory viruses such as SARS-CoV2, the causative agent of COVID-19. In this study, we investigated the oropharyngeal microbiome of COVID-19 patients using high throughput DNA sequencing performed on oral swabs. We combined patient characteristics available at intake such as medical comorbidities and age, with measured abundance of bacterial species and metabolic pathways and then trained a machine learning model to determine what features are predicative of patients needing respiratory support in the form of supplemental oxygen or mechanical ventilation. We found that decreased abundance of some bacterial species and increased abundance of pathways associated bacterial products biosynthesis was highly predictive of needing respiratory support. This suggests that the oropharyngeal microbiome affects disease course in COVID-19 and could be targeted for diagnostic purposes to determine who may need oxygen, or therapeutic purposes such as probiotics to prevent severe COVID-19 disease manifestations.
dc.language.isoen_US
dc.relationNow published in Frontiers in Microbiology doi: 10.3389/fmicb.2022.1009440
dc.rightsThe copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectoropharyngeal microbiome
dc.subjectrespiratory viruses
dc.subjectCOVID-19
dc.subjectCOVID-19+
dc.subjectrespiratory support
dc.subjectBacteria
dc.subjectImmunology and Infectious Disease
dc.subjectInfectious Disease
dc.subjectMicrobiology
dc.subjectVirus Diseases
dc.titleOropharyngeal Microbiome Profiled at Admission is Predictive of the Need for Respiratory Support Among COVID-19 Patients [preprint]
dc.typePreprint
dc.source.journaltitlemedRxiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1387&amp;context=covid19&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/covid19/379
dc.identifier.contextkey28518642
refterms.dateFOA2022-08-23T15:45:40Z
html.description.abstract<p>The clinical course of infection due to respiratory viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), the causative agent of Coronavirus Disease 2019 (COVID-19) is thought to be influenced by the community of organisms that colonizes the upper respiratory tract, the oropharyngeal microbiome. 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 enrolled patients, 74 were confirmed COVID-19+ and 50 had symptom duration of 14 days or less; 38 acute COVID-19+ patients (76%) went on to require respiratory support. Although no microbiome features were found to be significantly different between COVID-19+ and COVID-19-patients, when we conducted random forest classification modeling (RFC) to predict the need of respiratory support for the COVID-19+ patients our analysis identified a subset of organisms and metabolic pathways whose relative abundance, when combined with clinical factors (such as age and Body Mass Index), was highly predictive of the need for respiratory support (F1 score 0.857). Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis was then applied to the features identified as predicative of the need for respiratory support by the RFC. This analysis revealed reduced abundance of Prevotella salivae and metabolic pathways associated with lipopolysaccharide and mycolic acid biosynthesis to be the strongest predictors of patients requiring respiratory support. These findings suggest that composition of the oropharyngeal microbiome in COVID-19 may play a role in determining who will suffer from severe disease manifestations. Importance: The microbial community that colonizes the upper airway, the oropharyngeal microbiome, has the potential to affect how patients respond to respiratory viruses such as SARS-CoV2, the causative agent of COVID-19. In this study, we investigated the oropharyngeal microbiome of COVID-19 patients using high throughput DNA sequencing performed on oral swabs. We combined patient characteristics available at intake such as medical comorbidities and age, with measured abundance of bacterial species and metabolic pathways and then trained a machine learning model to determine what features are predicative of patients needing respiratory support in the form of supplemental oxygen or mechanical ventilation. We found that decreased abundance of some bacterial species and increased abundance of pathways associated bacterial products biosynthesis was highly predictive of needing respiratory support. This suggests that the oropharyngeal microbiome affects disease course in COVID-19 and could be targeted for diagnostic purposes to determine who may need oxygen, or therapeutic purposes such as probiotics to prevent severe COVID-19 disease manifestations.</p>
dc.identifier.submissionpathcovid19/379
dc.contributor.departmentGraduate School of Biomedical Sciences
dc.contributor.departmentDepartment of Medicine
dc.contributor.departmentDepartment of Microbiology and Physiological Systems
dc.contributor.departmentProgram in Microbiome Dynamics
dc.contributor.departmentDepartment of Emergency Medicine


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The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Except where otherwise noted, this item's license is described as The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.