Comprehensive genomic characterization of multidrug-resistant Klebsiella pneumoniae from North India

Abstract

Klebsiella pneumoniae is a major cause of healthcare-associated infections and an important contributor to the global burden of antimicrobial resistance. However, comprehensive genomic epidemiological data on multidrug-resistant (MDR) K. pneumoniae from North India remain limited. Ninety-six non-duplicate clinical K. pneumoniae isolates collected from a tertiary-care hospital in North India during 2022–2024 underwent antimicrobial susceptibility testing and de novo whole-genome sequencing (WGS). Following genomic quality assessment and targeted re-evaluation, 90 genomes were retained for genome-based analyses. MLST and pangenome analyses included 72 and 69 genomes, respectively, according to their respective inclusion criteria. Genome-based analyses included capsular typing, resistome and virulome profiling, plasmid replicon prediction, pangenome analysis, identification of resistance-associated chromosomal mutations, and phylogenomic reconstruction. Phenotypic analysis showed carbapenem resistance in 93/96 (96.9%) isolates. Genomic analysis identified 32 sequence types, with ST515 (37.5%; 27/72) as the predominant lineage, while KL62 (60.0%; 54/90) was the most common capsular locus. The predominant carbapenemase gene was bla OXA-232 (75.6%; 68/90), followed by bla NDM-1 (14.4%; 13/90) and bla NDM-5 (8.9%; 8/90). A total of 82 antimicrobial resistance genes spanning 16 antibiotic classes were identified, with fosA (86/90, 95.6%), oqxA (85/90, 94.4%), qnrS1 (75/90, 83.3%), and bla CTX-M-15 (69/90, 76.7%) being the most prevalent. Pangenome analysis of 69 genomes identified 13,720 gene families, indicating extensive accessory genome diversity. Resistance-associated mutations involving ompK35 , ompK36 , gyrA , parC , ramR , and cirA were identified. Virulence profiling revealed conserved genes for adherence, biofilm formation, secretion systems, and iron acquisition, whereas rmpA and rmpA2 were absent. Phylogenomic analysis demonstrated clustering according to sequence type and capsular locus. This study provides a comprehensive genomic characterization of MDR K. pneumoniae circulating in a North Indian tertiary care hospital. The predominance of the ST515 and KL62 lineage, together with high prevalence of bla OXA-232 , with an extensive accessory genome and diverse resistance determinants, highlights the value of WGS for genomic surveillance of carbapenem-resistant K. pneumoniae and for informing infection prevention and antimicrobial stewardship.