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Published on: September 22, 2023
Upper Respiratory Tract Resistome Exhibits SARS-CoV-2-associated Antimicrobial Resistance Patterns
Siddharth Singh Tomar1,2, Krishna Khairnar3,4
1Environmental Epidemiology and Pandemic Management (EE&PM), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.
Current Microbiology
|July 9, 2026
Summary
SARS-CoV-2 infection alters upper respiratory tract (URT) antimicrobial resistance (AMR) gene profiles. This study found increased AMR genes in SARS-CoV-2 positive individuals, suggesting a link between viral infection and resistance.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- SARS-CoV-2 infection's impact on the upper respiratory tract (URT) microbiome and antimicrobial resistance (AMR) is not fully understood.
- Investigating these changes is crucial for understanding potential secondary infections and treatment strategies.
Purpose of the Study:
- To analyze the alterations in the URT resistome associated with SARS-CoV-2 infection.
- To identify specific AMR genes and their potential link to opportunistic pathogens in COVID-19 patients.
Main Methods:
- Analysis of 95 URT swab samples (48 SARS-CoV-2 positive, 47 controls) from central India.
- Metagenomic DNA sequencing using Illumina NextSeq 550 and analysis via the CZ ID pipeline.
- Statistical analysis including diversity indices, beta-diversity, differential resistome analysis, and Bayesian regression.
Main Results:
- No significant differences in alpha diversity between SARS-CoV-2 positive and control groups.
- Distinct clustering in beta-diversity analysis, indicating altered resistome composition.
- 22 significantly altered AMR genes identified, with 21 enriched in the SARS-CoV-2 group, linked to pathogens like Klebsiella pneumoniae and Escherichia coli.
- SARS-CoV-2 infection was a significant predictor of increased AMR abundance.
Conclusions:
- SARS-CoV-2 infection is associated with significant alterations in the URT resistome.
- The findings highlight a potential link between viral infection and increased antimicrobial resistance, necessitating further research into the underlying mechanisms.
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