What question did this study set out to answer?

The aim is to characterize the genomic landscape and antimicrobial resistance of K. pneumoniae in clinical isolates from India.

June 6, 2026Open Access

Genomic characterization of multidrug-resistant Klebsiella pneumoniae clinical isolates from India

Key Points

The aim is to characterize the genomic landscape and antimicrobial resistance of K. pneumoniae in clinical isolates from India.
Analyzed two clinical isolates of K. pneumoniae (NG_299 and NG_300) from Pune using whole-genome sequencing and PCR-based methods.
Performed antimicrobial susceptibility testing to assess resistance determinants and virulence factors.
Conducted pan-genome resistome analysis in comparison with global isolate collections.
NG_299 exhibited 32 resistance determinants and was susceptible to amikacin, colistin, and trimethoprim/sulfamethoxazole; NG_300 had 52 resistance determinants and was only susceptible to colistin and trimethoprim/sulfamethoxazole.
Both isolates produced extended-spectrum β-lactamases and showed carbapenem resistance linked to metallo-β-lactamase activity.
Virulence factors associated with adhesion, biofilm formation, and iron acquisition were identified in both isolates.

Abstract

Klebsiella pneumoniae is an emerging global threat driven by rising antimicrobial resistance and the spread of hypervirulent lineages. To investigate its evolving genomic landscape in India, we characterized two clinical K. pneumoniae isolates, NG₂99 and NG₃00, obtained from a tertiary care hospital in Pune and analyzed them in the context of Indian and global isolate collections. Comprehensive phenotypic and genomic analyses were performed using antimicrobial susceptibility testing, Illumina NovaSeq whole-genome sequencing and PCR-based confirmation of resistance and virulence markers. Both isolates exhibited multidrug resistance, remaining susceptible to only a limited subset of tested antibiotics. NG₂99 (ST231) was susceptible to amikacin, colistin, and trimethoprim/sulfamethoxazole, whereas NG₃00 (ST20) was found to be susceptible only to colistin and trimethoprim/sulfamethoxazole. Genomic profiling revealed thirty-two resistance determinants in NG₂99 and fifty-two in NG₃00, both of which produce extended-spectrum β-lactamases. Carbapenem resistance was linked to metallo-β-lactamase activity and the presence of AmpC was confirmed by antimicrobial susceptibility testing and PCR in NG₃00. Pan-genome resistome analysis of global isolates identified conserved core genes (CRP, PhoP, rpoB) and a sparse occurrence of AMR genes (NDM, CTX-M, KPC, OXA, mcr) associated with horizontal gene transfer. Notably, NDM and CTX-M were present in both study isolates, with OXA variants detected in NG₂99. Distinct missense mutations within shared resistance genes highlighted independent evolutionary trajectories. Both isolates carried virulence factors associated with adhesion, biofilm formation, iron acquisition, and secretion systems, including siderophores. Plasmid analysis identified IncF replicons in both isolates and blaNDM-5 on an IncFII plasmid in NG₂99. These findings document the circulation of multidrug-resistant K. pneumoniae in Pune and underscore the urgent need for strengthened genomic surveillance.

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