Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/04/20
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J, Zhao J
Journal
Cell discovery
Year
2021
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, the microbial composition of the respiratory tract and other infected tissues as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Between 27 January and 26 February 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients in Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. We identified distinct signatures of microbial dysbiosis among severely ill COVID-19 patients on broad spectrum antimicrobial therapy. Co-detection of other human respiratory viruses (including human alphaherpesvirus 1, rhinovirus B, and human orthopneumovirus) was demonstrated in 30.8% (4/13) of the severely ill patients, but not in any of the mildly affected patients. Notably, the predominant respiratory microbial taxa of severely ill patients were Burkholderia cepacia complex (BCC), Staphylococcus epidermidis, or Mycoplasma spp. (including M. hominis and M. orale). The presence of the former two bacterial taxa was also confirmed by clinical cultures of respiratory specimens (expectorated sputum or nasal secretions) in 23.1% (3/13) of the severe cases. Finally, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes was demonstrated in one severely ill patient, which might accelerate his disease deterioration and death occurring one month after ICU admission. Our findings point to SARS-CoV-2-related microbial dysbiosis and various antibiotic-resistant respiratory microbes/pathogens in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking strategies are needed to prevent the spread of antimicrobial resistance, improve the treatment regimen and clinical outcomes of hospitalized, severely ill COVID-19 patients.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/07/02

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1, WikiWorks, Peace Sandy

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Mild COVID-19 patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
Severe COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
DNBSEQ-T7

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/07/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2c

Description: Differential abundance in microbial taxa between mild and severe COVID-19 patients

Abundance in Group 1: decreased abundance in Severe COVID-19 patients

NCBI Quality ControlLinks
Veillonella
Neisseria
Streptococcus
Prevotella

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/07/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2c

Description: Differential abundance in microbial taxa between mild and severe COVID-19 patients

Abundance in Group 1: increased abundance in Severe COVID-19 patients

NCBI Quality ControlLinks
Staphylococcus
Escherichia

Revision editor(s): Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/07/02

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
Group 0 sample size Number of subjects in the control (unexposed) group
7

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/07/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Figure S6b

Description: Differential abundance in microbial taxa between mild and severe COVID-19 patients

Abundance in Group 1: increased abundance in Severe COVID-19 patients

NCBI Quality ControlLinks
Parabacteroides

Revision editor(s): Claregrieve1