Characterization of upper airway microbiome across severity of COVID-19 during hospitalization and treatment
Copyright © 2023 Ling, Lai, Lui, Yeung, Chan, Cheuk, Cheung, Chang, Chiu, Zhang, Wong, Hui, Wong, Chan and Chen..
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.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:13 |
|---|---|
| Enthalten in: |
Frontiers in cellular and infection microbiology - 13(2023) vom: 14., Seite 1205401 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Ling, Lowell [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
16S rRNA |
|---|
| Anmerkungen: |
Date Completed 21.07.2023 Date Revised 21.07.2023 published: Electronic-eCollection Citation Status MEDLINE |
|---|
| doi: |
10.3389/fcimb.2023.1205401 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM359700519 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM359700519 | ||
| 003 | DE-627 | ||
| 005 | 20231226081432.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.3389/fcimb.2023.1205401 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1198.xml |
| 035 | |a (DE-627)NLM359700519 | ||
| 035 | |a (NLM)37469595 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Ling, Lowell |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Characterization of upper airway microbiome across severity of COVID-19 during hospitalization and treatment |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 21.07.2023 | ||
| 500 | |a Date Revised 21.07.2023 | ||
| 500 | |a published: Electronic-eCollection | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 Ling, Lai, Lui, Yeung, Chan, Cheuk, Cheung, Chang, Chiu, Zhang, Wong, Hui, Wong, Chan and Chen. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a COVID-19 | |
| 650 | 4 | |a 16S rRNA | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a intensive care unit | |
| 650 | 4 | |a upper airway microbiome | |
| 650 | 7 | |a RNA, Ribosomal, 16S |2 NLM | |
| 700 | 1 | |a Lai, Christopher K C |e verfasserin |4 aut | |
| 700 | 1 | |a Lui, Grace |e verfasserin |4 aut | |
| 700 | 1 | |a Yeung, Apple Chung Man |e verfasserin |4 aut | |
| 700 | 1 | |a Chan, Hiu Ching |e verfasserin |4 aut | |
| 700 | 1 | |a Cheuk, Chung Hon Shawn |e verfasserin |4 aut | |
| 700 | 1 | |a Cheung, Adonia Nicole |e verfasserin |4 aut | |
| 700 | 1 | |a Chang, Lok Ching |e verfasserin |4 aut | |
| 700 | 1 | |a Chiu, Lok Ching Sandra |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Jack Zhenhe |e verfasserin |4 aut | |
| 700 | 1 | |a Wong, Wai-Tat |e verfasserin |4 aut | |
| 700 | 1 | |a Hui, David S C |e verfasserin |4 aut | |
| 700 | 1 | |a Wong, Chun Kwok |e verfasserin |4 aut | |
| 700 | 1 | |a Chan, Paul K S |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Zigui |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Frontiers in cellular and infection microbiology |d 2011 |g 13(2023) vom: 14., Seite 1205401 |w (DE-627)NLM220414289 |x 2235-2988 |7 nnns |
| 773 | 1 | 8 | |g volume:13 |g year:2023 |g day:14 |g pages:1205401 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.3389/fcimb.2023.1205401 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 13 |j 2023 |b 14 |h 1205401 | ||