Upper Respiratory Tract Resistome Exhibits SARS-CoV-2-associated Antimicrobial Resistance Patterns

SARS-CoV-2 infection can influence the antimicrobial resistance (AMR) profiles of the upper respiratory tract (URT), although the extent and nature of these alterations remain insufficiently understood. In this study, we analysed 95 URT swab samples, including 48 SARS-CoV-2-positive cases and 47 RT-PCR-negative controls, collected from five districts of central India. Metagenomic DNA sequencing was performed on the Illumina NextSeq 550 platform, and the data were analysed using the Chan Zuckerberg Initiative (CZ ID) pipeline. Alpha diversity indices (Chao1, Shannon, and Simpson) did not differ significantly (p = 0.264, 0.985, and 0.902, respectively). Beta-diversity analysis revealed distinct clustering of SARS-CoV-2 and control resistomes. Differential resistome analysis identified 22 significantly altered AMR genes, of which 21 were enriched in the SARS-CoV-2 group. Pathogen-of-origin analysis linked several AMR genes to opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. Bayesian regression analysis identified SARS-CoV-2 infection as a significant factor associated with increased AMR abundance (β = 1.549, HDI [1.409, 1.691]), whereas age and location were not significantly associated. Results demonstrate an association between SARS-CoV-2 infection and alterations in the URT resistome, warranting further investigation into the mechanisms linking viral infection and antimicrobial resistance.