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): WikiWorks, Rimsha, Claregrieve1, 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
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 Control | Links |
|---|---|---|
| Acinetobacter | ||
| Klebsiella | ||
| Roseateles sp. | ||
| Ralstonia | ||
| Sphingomonas |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/11
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 Control | Links |
|---|---|---|
| Actinomyces | ||
| Haemophilus | ||
| Neisseria | ||
| Prevotella | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Claregrieve1
