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Mahmud ASM, Seers CA, Shaikh AA, Taznin T, Uzzaman MS, Osman E, Habib MA, Akter S, Banu TA, Sarkar MMH, Goswami B, Jahan I, Okeoma CM, Khan MS, Reynolds EC. A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients. Sci Rep 2023; 13:4122. [PMID: 36914691 PMCID: PMC10009844 DOI: 10.1038/s41598-023-30504-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
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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Affiliation(s)
- A Sayeed M 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
| | | | - 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 Hasan 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.
| | - Eric C Reynolds
- The Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Ukuhor HO. The interrelationships between antimicrobial resistance, COVID-19, past, and future pandemics. J Infect Public Health 2021; 14:53-60. [PMID: 33341485 PMCID: PMC7831651 DOI: 10.1016/j.jiph.2020.10.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/21/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 was first reported in Wuhan, China in December 2019 and is associated with high levels of morbidity and mortality. Various types of bacterial and fungal infections occur in patients with COVID-19 with some resistant to antimicrobials that are associated with significantly worse outcomes and deaths. Besides, antimicrobial-resistant (AMR) co-infections are responsible for clinically significant mortality in past pandemics. There is evidence to suggest that factors such as the proliferation of adulterated antimicrobials in some developing countries, international travels, issues with healthcare financing, use/misuse by humans, and in agricultural production and climate change are determinants of AMR at various levels of society. These complex interrelated determinants intersect with AMR in current and past pandemics and could amplify the potential of a future antimicrobial resistance pandemic. Therefore, global concerted interventions targeted at all levels of society to reduce the use/misuse of antimicrobials and disrupt these multifaceted, interrelated, and interdependent factors are urgently needed. This paper leverages prior research to describe complex major determinants of antimicrobial resistance and provides fresh insights into possible intervention strategies to tackle antimicrobial resistance including in the current and future pandemics.
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Affiliation(s)
- Hyacinth O Ukuhor
- Saudi Electronic University, Department of Public Health, P. O. Box 93499, Riyadh 11673, Saudi Arabia.
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