Genomic insights into antimicrobial resistance in ocular pathogens from India

Ocular infections have a substantial impact on global visual health. Despite their association with severe vision impairment, very few studies have systematically monitored antimicrobial resistance (AMR) over time using whole genome sequencing approaches. In the current study, we assembled 291 high-fidelity bacterial genomes isolated from patients attending a tertiary eye care centre in India, using long-read sequencing. Pseudomonas aeruginosa (n = 62) and Staphylococcus aureus (n = 60) were the most common pathogens in the cohort, with more than 45% of isolates exhibiting multidrug resistance and more than 15% classified as extensively drug-resistant. Genotype–phenotype analyses and multilocus sequence typing revealed a previously unreported mecA-negative methicillin-resistant Staphylococcus aureus strain, ST9578, resistant to vancomycin and teicoplanin. Potential AMR mechanisms, like a mutation in the 23S rRNA gene associated with linezolid resistance and a KorB-like protein-encoding gene associated with fluoroquinolone resistance, were identified using comparative genomics. This is the first large-scale genomic surveillance effort focused on ocular pathogens in the Indian subcontinent and the potential AMR mechanisms and sequence types identified underscore the need for larger such studies in low-and-middle-income countries. Genomic surveillance identifies emerging XDR strains and putative AMR mechanisms in isolates from ocular infections in India.