Characterization of upper airway microbiome across severity of COVID-19 during hospitalization and treatment

Longitudinal studies on upper respiratory tract microbiome in coronavirus disease 2019 (COVID-19) without potential confounders such as antimicrobial therapy are limited. The objective of this study is to assess for longitudinal changes in the upper respiratory microbiome, its association with disea...

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Published in:	Frontiers in cellular and infection microbiology Vol. 13; p. 1205401
Main Authors:	Ling, Lowell, Lai, Christopher K C, Lui, Grace, Yeung, Apple Chung Man, Chan, Hiu Ching, Cheuk, Chung Hon Shawn, Cheung, Adonia Nicole, Chang, Lok Ching, Chiu, Lok Ching Sandra, Zhang, Jack Zhenhe, Wong, Wai-Tat, Hui, David S C, Wong, Chun Kwok, Chan, Paul K S, Chen, Zigui
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 04-07-2023
Subjects:	16S rRNA Adult Cellular and Infection Microbiology COVID-19 Hospitalization Humans intensive care unit Microbiota - genetics Nose RNA, Ribosomal, 16S - genetics SARS-CoV-2 upper airway microbiome COVID-19 upper airway microbiome 16S rRNA SARS-CoV-2 intensive care unit
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Summary:	Longitudinal studies on upper respiratory tract microbiome in coronavirus disease 2019 (COVID-19) without potential confounders such as antimicrobial therapy are limited. The objective of this study is to assess for longitudinal changes in the upper respiratory microbiome, its association with disease severity, and potential confounders in adult hospitalized patients with COVID-19. Serial nasopharyngeal and throat swabs (NPSTSs) were taken for 16S rRNA gene amplicon sequencing from adults hospitalized for COVID-19. Alpha and beta diversity was assessed between different groups. Principal coordinate analysis was used to assess beta diversity between groups. Linear discriminant analysis was used to identify discriminative bacterial taxa in NPSTS taken early during hospitalization on need for intensive care unit (ICU) admission. A total of 314 NPSTS samples from 197 subjects (asymptomatic = 14, mild/moderate = 106, and severe/critical = 51 patients with COVID-19; non-COVID-19 mechanically ventilated ICU patients = 11; and healthy volunteers = 15) were sequenced. Among all covariates, antibiotic treatment had the largest effect on upper airway microbiota. When samples taken after antibiotics were excluded, alpha diversity (Shannon, Simpson, richness, and evenness) was similar across severity of COVID-19, whereas beta diversity (weighted GUniFrac and Bray-Curtis distance) remained different. Thirteen bacterial genera from NPSTS taken within the first week of hospitalization were associated with a need for ICU admission (area under the receiver operating characteristic curve, 0.96; 95% CI, 0.91-0.99). Longitudinal analysis showed that the upper respiratory microbiota alpha and beta diversity was unchanged during hospitalization in the absence of antimicrobial therapy.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors have contributed equally to this work Reviewed by: Kelvin Li, University of Pittsburgh, United States; Wong Kon Ken, National University of Malaysia, Malaysia; Benjamin G. Wu, New York University, United States Edited by: Jianmin Chai, Foshan University, China
ISSN:	2235-2988 2235-2988
DOI:	10.3389/fcimb.2023.1205401