Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Rimsha, 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
Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx
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
Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Intubated patients with critically severe COVID-19 infection
Group 0 sample size Number of subjects in the control (unexposed) group
54
Group 1 sample size Number of subjects in the case (exposed) group
50

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
BGISEQ-500 Sequencing

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
PERMANOVA
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

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Text

Description: Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients

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

NCBI Quality ControlLinks
Acinetobacter
Klebsiella
Roseateles sp.
Ralstonia
Sphingomonas

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Text

Description: Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients

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

NCBI Quality ControlLinks
Actinomyces
Haemophilus
Neisseria
Prevotella
Streptococcus
Veillonella

Revision editor(s): Claregrieve1