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
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.
Recommended Citation
Mahmud, A. S., Seers, C. A., Shaikh, A. A., Taznin, T., Uzzaman, M. S., Osman, E., Habib, M. A., Akter, S., Banu, T. A., Sarkar, M. M., Goswami, B., Jahan, I., Okeoma, C. M., Khan, M. S., & Reynolds, E. C. (2023). A Multicentre Study Reveals Dysbiosis in the Microbial Co-Infection and Antimicrobial Resistance Gene Profile in the Nasopharynx of COVID-19 Patients. Scientific Reports, 13 (1), 4122. https://doi.org/10.1038/s41598-023-30504-3
