{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:56:16Z","timestamp":1792788976924,"version":"4.5.0"},"reference-count":47,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Health Research","id":[{"id":"https:\/\/ror.org\/00z72fs19","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"\n Background<\/jats:title>\n \n Klebsiella pneumoniae<\/jats:italic>\n 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)\n K. pneumoniae<\/jats:italic>\n from North India remain limited.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Ninety-six non-duplicate clinical\n K. pneumoniae<\/jats:italic>\n isolates collected from a tertiary-care hospital in North India during 2022\u20132024 underwent antimicrobial susceptibility testing and\n de novo<\/jats:italic>\n 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.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n 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\n bla<\/jats:italic>\n OXA-232<\/jats:sub>\n (75.6%; 68\/90), followed by\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n (14.4%; 13\/90) and\n bla<\/jats:italic>\n NDM-5<\/jats:sub>\n (8.9%; 8\/90). A total of 82 antimicrobial resistance genes spanning 16 antibiotic classes were identified, with\n fosA<\/jats:italic>\n (86\/90, 95.6%),\n oqxA<\/jats:italic>\n (85\/90, 94.4%),\n qnrS1<\/jats:italic>\n (75\/90, 83.3%), and\n bla<\/jats:italic>\n CTX-M-15<\/jats:sub>\n (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\n ompK35<\/jats:italic>\n ,\n ompK36<\/jats:italic>\n ,\n gyrA<\/jats:italic>\n ,\n parC<\/jats:italic>\n ,\n ramR<\/jats:italic>\n , and\n cirA<\/jats:italic>\n were identified. Virulence profiling revealed conserved genes for adherence, biofilm formation, secretion systems, and iron acquisition, whereas\n rmpA<\/jats:italic>\n and\n rmpA2<\/jats:italic>\n were absent. Phylogenomic analysis demonstrated clustering according to sequence type and capsular locus.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n This study provides a comprehensive genomic characterization of MDR\n K. pneumoniae<\/jats:italic>\n circulating in a North Indian tertiary care hospital. The predominance of the ST515 and KL62 lineage, together with high prevalence of\n bla<\/jats:italic>\n OXA-232<\/jats:sub>\n , with an extensive accessory genome and diverse resistance determinants, highlights the value of WGS for genomic surveillance of carbapenem-resistant\n K. pneumoniae<\/jats:italic>\n and for informing infection prevention and antimicrobial stewardship.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1831365","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T05:44:17Z","timestamp":1790228657000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive genomic characterization of multidrug-resistant Klebsiella pneumoniae from North India"],"prefix":"10.3389","volume":"17","author":[{"given":"Nargis Kaur","family":"Bali","sequence":"first","affiliation":[{"name":"Sher-i-Kashmir Institute of Medical Sciences","place":["Srinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aktarul Islam","family":"Siddique","sequence":"additional","affiliation":[{"name":"Regional Medical Research Centre (ICMR)","place":["Dibrugarh, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umaya","family":"Majid","sequence":"additional","affiliation":[{"name":"Sher-i-Kashmir Institute of Medical Sciences","place":["Srinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dona","family":"Mathew","sequence":"additional","affiliation":[{"name":"Sher-i-Kashmir Institute of Medical Sciences","place":["Srinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susheem","family":"Ramakrishnan","sequence":"additional","affiliation":[{"name":"Sher-i-Kashmir Institute of Medical Sciences","place":["Srinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biswajyoti","family":"Borkakoty","sequence":"additional","affiliation":[{"name":"Regional Medical Research Centre (ICMR)","place":["Dibrugarh, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"ofaf164","DOI":"10.1093\/OFID\/OFAF164","article-title":"Whole genome sequencing analysis of Klebsiella pneumoniae isolates from health care\u2013associated bacteremia of urinary origin in Spain: findings from the multicenter ITUBRAS-2 cohort study","volume":"12","author":"Becerra-Aparicio","year":"2025","journal-title":"Open Forum Infect. 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