Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa

From BugSigDB
Needs review
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


Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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
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
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

Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Iram jamshed

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 ControlLinks
Acinetobacter
Micrococcus
Moraxella
Pseudomonas
Rothia

Revision editor(s): Claregrieve1, Iram jamshed

Experiment 2


Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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

Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Anoxybacillus
Acinetobacter
Pseudomonas
Pseudomonas aeruginosa

Revision editor(s): Claregrieve1

Experiment 3


Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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

Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Anoxybacillus
Pseudomonas aeruginosa

Revision editor(s): Claregrieve1

Signature 2

Needs review

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Burkholderia cepacia

Revision editor(s): Claregrieve1