Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I
Journal
bioRxiv : the preprint server for biology
Year
2021
Much of the research conducted on SARS-CoV-2 and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients. Very few studies have investigated the impact of acute SARS-CoV-2 within the nasopharynx, the site of initial infection and viral replication. In this study we profiled changes in the nasal microbial communities as well as in host transcriptional profile during acute SARS-CoV-2 infection using 16S amplicon sequencing and RNA sequencing. These analyses were coupled to viral genome sequencing. Our microbiome analysis revealed that the nasal microbiome of COVID patients was unique and was marked by an expansion of bacterial pathogens. Some of these microbes (i.e. Acinetobacter ) were shared with COVID negative health care providers from the same medical center but absent in COVID negative outpatients seeking care at the same institutions suggesting acquisition of nosocomial respiratory pathogens. Specifically, we report a distinct increase in the prevalence and abundance of the pathogen Pseudomonas aeruginosa in COVID patients that correlated with viral RNA load. These data suggest that the inflammatory environment caused by SARS-CoV-2 infection and potentially exposure to the hospital environment leads to an expansion of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections. Additionally, we observed a robust host transcriptional response in the nasal epithelia of COVID patients, indicative of an antiviral innate immune repones and neuronal damage. Finally, analysis of viral genomes did not reveal an association between viral loads and viral sequences.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Subjects
- Location of subjects
- United States of America
- 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
- COVID-19 negative controls and healthcare workers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 positive patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients positive for SARS-CoV-2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 66
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: Figure 2a
Description: Differential microbial abundance between COVID-19 patients and non-COVID patients (COVID negative patients and healthcare workers)
Abundance in Group 1: increased abundance in COVID-19 positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Micrococcus | ||
| Moraxella | ||
| Pseudomonas | ||
| Rothia |
Revision editor(s): Claregrieve1, Iram jamshed
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 negative controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative patients
Abundance in Group 1: increased abundance in COVID-19 positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anoxybacillus | ||
| Acinetobacter | ||
| Pseudomonas | ||
| Pseudomonas aeruginosa |
Revision editor(s): Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 negative healthcare workers (controls)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers
Abundance in Group 1: increased abundance in COVID-19 positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anoxybacillus | ||
| Pseudomonas aeruginosa |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers
Abundance in Group 1: decreased abundance in COVID-19 positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderia cepacia |
Revision editor(s): Claregrieve1
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Viral load viral burden,viral titer,viral titre,Viral load,viral load
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- high Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with low cycle threshold value (>23.5)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Low Ct
Abundance in Group 1: increased abundance in low Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Neisseria | ||
| Pseudomonas | ||
| Pseudomonas aeruginosa |
Revision editor(s): Folakunmi
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mid Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0)
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct
Abundance in Group 1: increased abundance in mid Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Neisseria |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct
Abundance in Group 1: decreased abundance in mid Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Folakunmi
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mid Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with low cycle threshold value (>23.5)
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into Mid and Low Ct
Abundance in Group 1: increased abundance in low Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas aeruginosa |
Revision editor(s): Folakunmi
Experiment 7
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low and mid Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with high cycle threshold value (>34.6)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Low and Mid Ct
Abundance in Group 1: increased abundance in high Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Mid and Low Ct
Abundance in Group 1: decreased abundance in high Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Cutibacterium | ||
| Neisseria | ||
| Pseudomonas |
Revision editor(s): Folakunmi
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