Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: a potential source of co-infection
- 4 May 2022
- journal article
- research article
- Published by Royal Society of Chemistry (RSC) in Molecular Omics
- Vol. 18 (6), 490-505
- https://doi.org/10.1039/d2mo00044j
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx, which may be involved in co-infection in COVID-19 patients. The 16S rRNA variable regions, V1–V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in the COVID-19 NP microbiome with an increase in the abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggests their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.Keywords
Funding Information
- Department of Biotechnology, Ministry of Science and Technology (BT/ILS/Flagship/2019, BT/RLF/Re-entry/25/2015)
- Science and Engineering Research Board (CRG/2018/002052)
This publication has 54 references indexed in Scilit:
- The nasal microbiome in asthmaJournal of Allergy and Clinical Immunology, 2018
- Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosisMicrobiome, 2018
- Homeostatic Immunity and the MicrobiotaImmunity, 2017
- Natural history ofMycobacterium aviumcomplex lung disease in untreated patients with stable courseEuropean Respiratory Journal, 2017
- SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq DataPLOS ONE, 2016
- The role of the local microbial ecosystem in respiratory health and diseasePhilosophical Transactions B, 2015
- Opportunistic Infections--Coming to the Limits of Immunosuppression?Cold Spring Harbor Perspectives in Medicine, 2013
- Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic AnalysisPLOS ONE, 2011
- Epidemiology of Extrapulmonary Tuberculosis in the United States, 1993–2006Clinical Infectious Diseases, 2009
- WGCNA: an R package for weighted correlation network analysisBMC Bioinformatics, 2008