Indian journal of medical microbiology · 2026
Genomic insights into carbapenem- and colistin-resistant Klebsiella pneumoniae reveal co-occurrence of resistance and virulence determinants in India.
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Kansal Shubhangi, Kundu Jyoti, Sharma Vikas, Mamik Shubhneet Kaur, Soni Shivani, Angrup Archana, Biswal Manisha, Walia Kamini, Ray Pallab, Taneja Neelam
Аннотация
BACKGROUND: Carbapenem- and colistin-resistant Klebsiella pneumoniae poses a major challenge to critical care due to limited therapeutic options. Combined with hypervirulence, the infections caused by multi-drug-resistant isolates become exceptionally difficult to treat, often resulting in prolonged illness and higher mortality.
METHODS: We analysed 65 clinical isolates of carbapenem and colistin resistant K. pneumoniae using whole genome sequencing to characterize resistance, virulence, and associated mobile genetic elements that may facilitate horizontal gene transfer.
RESULTS: The isolates represented 17 sequence types, with ST147, ST231 and capsular loci KL64 and KL51 being the most prevalent. Pan-genome analysis revealed high genetic diversity with an open genome structure. Resistance genes were widely distributed where carbapenem resistance was primarily mediated by NDM-1 or OXA-232 in combination with mutations in OmpK35/36 porin. Colistin resistance was mostly associated with mutations in mgrB, pmrB, or crrB genes though 30% of phenotypically resistant isolates lacked known determinants, suggesting the presence of additional unknown mechanisms. Virulence factors included frequent detection of yersiniabactin with aerobactin (iucA) and hypermucoidy loci (rmpA) in subset of isolates.
CONCLUSION: The co-occurrence of resistance and virulence determinants in multiple genomes suggests that highly pathogenic and multidrug resistant K. pneumoniae strains are already circulating in India. The detection of multiple IncF and Col-type plasmids, known to facilitate the mobilization of antimicrobial and virulence genes, further highlights the potential for future convergence events. Collectively, this study provides a genomic snapshot and valuable baseline for India, emphasising the importance of continued surveillance to monitor and contain the emergence of high-risk convergent lineages.
METHODS: We analysed 65 clinical isolates of carbapenem and colistin resistant K. pneumoniae using whole genome sequencing to characterize resistance, virulence, and associated mobile genetic elements that may facilitate horizontal gene transfer.
RESULTS: The isolates represented 17 sequence types, with ST147, ST231 and capsular loci KL64 and KL51 being the most prevalent. Pan-genome analysis revealed high genetic diversity with an open genome structure. Resistance genes were widely distributed where carbapenem resistance was primarily mediated by NDM-1 or OXA-232 in combination with mutations in OmpK35/36 porin. Colistin resistance was mostly associated with mutations in mgrB, pmrB, or crrB genes though 30% of phenotypically resistant isolates lacked known determinants, suggesting the presence of additional unknown mechanisms. Virulence factors included frequent detection of yersiniabactin with aerobactin (iucA) and hypermucoidy loci (rmpA) in subset of isolates.
CONCLUSION: The co-occurrence of resistance and virulence determinants in multiple genomes suggests that highly pathogenic and multidrug resistant K. pneumoniae strains are already circulating in India. The detection of multiple IncF and Col-type plasmids, known to facilitate the mobilization of antimicrobial and virulence genes, further highlights the potential for future convergence events. Collectively, this study provides a genomic snapshot and valuable baseline for India, emphasising the importance of continued surveillance to monitor and contain the emergence of high-risk convergent lineages.
Предметные рубрики MeSH
ColistinKlebsiella pneumoniaeHumansCarbapenemsAnti-Bacterial AgentsVirulence FactorsIndiaKlebsiella InfectionsWhole Genome SequencingDrug Resistance, Multiple, BacterialGenome, BacterialVirulenceBacterial ProteinsMicrobial Sensitivity Testsbeta-LactamasesPorinsGenomicsGenetic VariationInterspersed Repetitive SequencesGene Transfer, Horizontal