{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T11:44:22Z","timestamp":1782992662895,"version":"3.54.5"},"reference-count":58,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UKRI MRC","award":["MR\/M01360X\/1"],"award-info":[{"award-number":["MR\/M01360X\/1"]}]},{"name":"UKRI MRC","award":["MR\/N010469\/1"],"award-info":[{"award-number":["MR\/N010469\/1"]}]},{"name":"UKRI MRC","award":["MR\/R025576\/1"],"award-info":[{"award-number":["MR\/R025576\/1"]}]},{"name":"UKRI MRC","award":["MR\/R020973\/1"],"award-info":[{"award-number":["MR\/R020973\/1"]}]},{"name":"UKRI MRC","award":["MR\/X005895\/1"],"award-info":[{"award-number":["MR\/X005895\/1"]}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["EP\/Y018842\/1"],"award-info":[{"award-number":["EP\/Y018842\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004681","name":"HEC-NRPU","doi-asserted-by":"publisher","award":["99436"],"award-info":[{"award-number":["99436"]}],"id":[{"id":"10.13039\/501100004681","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Multidrug-resistant (MDR) Klebsiella pneumoniae represents a major clinical and public health challenge worldwide, particularly in regions with limited genomic surveillance. This study investigated the clinical, phenotypic, and genomic characteristics of clinical K. pneumoniae isolates recovered from a tertiary-care hospital in Peshawar, Pakistan. A total of 2400 non-duplicate clinical specimens were processed, and antimicrobial susceptibility testing was performed according to CLSI guidelines. Whole-genome sequencing (WGS) was conducted on a purposively selected subset of 18 isolates representing diverse resistance and phenotypic profiles. Genomic analyses included multilocus sequence typing, resistome and virulome profiling, identification of resistance-associated chromosomal mutations, plasmid replicon typing, and phylogenomic comparison with publicly available international genomes. K. pneumoniae was identified in 256\/2400 (10.7%) specimens, predominantly from urine samples. MDR and extensively drug-resistant (XDR) phenotypes were detected in 83.2% and 13.3% of isolates, respectively. WGS revealed substantial genomic heterogeneity, with ST147 identified as the most frequent lineage among sequenced isolates. Extended-spectrum \u03b2-lactamase genes, particularly blaCTX-M-15, together with carbapenemase genes including blaOXA-48-like and blaNDM-5, were identified in multiple isolates alongside resistance-associated chromosomal alterations in gyrA, parC, ompK36, mgrB, pmrB, and ramR. Yersiniabactin-associated loci were detected in all sequenced isolates, whereas canonical hypervirulence-associated determinants (rmpA, iuc, iro) were absent. These findings highlight the complex genomic landscape of MDR K. pneumoniae in Pakistan and underscore the need for continued genomic surveillance and antimicrobial stewardship.<\/jats:p>","DOI":"10.3390\/microorganisms14071462","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T10:04:44Z","timestamp":1782986684000},"page":"1462","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Clinical and Genomic Characterization of High-Risk Multidrug-Resistant Klebsiella pneumoniae Lineages in Pakistan"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3681-8077","authenticated-orcid":false,"given":"Aakash Ahmad","family":"Khattak","sequence":"first","affiliation":[{"name":"Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadiq","family":"Azam","sequence":"additional","affiliation":[{"name":"Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noor","family":"Rehman","sequence":"additional","affiliation":[{"name":"Department of Pathology, Khyber Teaching Hospital, Peshawar 25120, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Asghar","sequence":"additional","affiliation":[{"name":"Department of Pathology, Khyber Teaching Hospital, Peshawar 25120, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiman","family":"Waheed","sequence":"additional","affiliation":[{"name":"Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody E.","family":"Phelan","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Campino","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taj Ali","family":"Khan","sequence":"additional","affiliation":[{"name":"Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-9265","authenticated-orcid":false,"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"},{"name":"Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Ndlovu, T., Kgosietsile, L., Motshwarakgole, P., and Ndlovu, S.I. 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