Genomic landscape of antimicrobial resistance in India: findings from a multi-species surveillance study

The paper reports whole-genome sequencing and antimicrobial susceptibility testing of 266 resistant bacterial isolates from Northern and Western India collected between 2022 and 2024 to map the genomic landscape of antimicrobial resistance (AMR) across diverse pathogens. It reveals notable discrepancies between genomic predictions of resistance and phenotypic results, with genomic tools often overpredicting resistance, and systematically characterizes the prevalence and distribution of resistance genes—including β-lactamases, colistin, methicillin and vancomycin resistance determinants—as well as their association with plasmids and mobile genetic elements. The study also examines sequence types and mobile element contexts, highlighting species-specific genomic patterns that inform how resistance spreads, and underscores the value and limitations of genomics for surveillance and the development of molecular diagnostics for AMR in low- and middle-income settings such as India.