Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of and in COVID-19 patients: a potential source of co-infection

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 (N...

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Veröffentlicht in:Molecular omics 2022-07, Vol.18 (6), p.49-55
Hauptverfasser: Prasad, Punit, Mahapatra, Soumendu, Mishra, Rasmita, Murmu, Krushna Chandra, Aggarwal, Shifu, Sethi, Manisha, Mohapatra, Priyanka, Ghosh, Arup, Yadav, Rina, Dodia, Hiren, Ansari, Shamima Azma, De, Saikat, Singh, Deepak, Suryawanshi, Amol, Dash, Rupesh, Senapati, Shantibhushan, Beuria, Tushar K, Chattopadhyay, Soma, Syed, Gulam Hussain, Swain, Rajeeb, Raghav, Sunil K, Parida, Ajay
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Zusammenfassung: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. Schematic representation of workflow to understand the nasal microbiome dysbiosis in COVID-19 patients. (Image created by Biorender.com).
ISSN:2515-4184
DOI:10.1039/d2mo00044j