NYMC Faculty Publications

A Multicentre Study Reveals Dysbiosis in the Microbial Co-Infection and Antimicrobial Resistance Gene Profile in the Nasopharynx of COVID-19 Patients

Authors

A Sayeed Mahmud, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Christine A. Seers, The Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
Aftab Ali Shaikh, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Tarannum Taznin, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Mohammad Samir Uzzaman, SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh.
Eshrar Osman, SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh.
Md Ahashan Habib, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Shahina Akter, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Tanjina Akhtar Banu, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Md Murshed Sarkar, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Barna Goswami, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Iffat Jahan, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
Chioma M. Okeoma, Department of Pathology, Microbiology, and Immunology, New York Medical College, 40 Sunshine Cottage Rd, Valhalla, NY, 10595, USA.
Md Salim Khan, Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh. k2salim@yahoo.com.
Eric C. Reynolds, The Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia. e.reynolds@unimelb.edu.au.

Author Type(s)

Faculty

DOI

10.1038/s41598-023-30504-3

Journal Title

Scientific Reports

First Page

4122

Document Type

Article

Publication Date

3-13-2023

Department

Pathology, Microbiology and Immunology

Abstract

The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.

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