Genomic epidemiology of multidrug-resistant Klebsiella pneumoniae reveals lineage-specific resistance patterns with limited virulence determinants
Abstract
The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae undermines treatment efficacy, while limited genomic epidemiological data constrain understanding of local transmission dynamics. We therefore aimed to investigate the genomic epidemiology and the antimicrobial resistance landscape of K. pneumoniae in tertiary-care settings in Peshawar, Pakistan. A total of 497 clinical samples (urine, blood, sputum, pus, wound swabs, sterile body fluids) were collected from 01 August 2024 to 31 July 2025. K. pneumoniae was identified using the API 20E kit, followed by antimicrobial susceptibility testing (AST), with colistin and tigecycline susceptibility determined by broth microdilution. Whole-genome sequencing (WGS) was carried out on 43 MDR and XDR isolates to resolve clonal diversity, resistome composition, virulence-associated loci, and phylogenetic relationships. Among 497 samples, 152 K. pneumoniae isolates were identified, exhibiting widespread resistance to β-lactams, cephalosporins, fluoroquinolones, aminoglycosides, and carbapenems, while colistin and tigecycline retained substantial in vitro activity. Overall, 37% and 24% of isolates were classified as MDR and XDR, respectively. Forty-three MDR/XDR isolates were subjected to WGS, of which 34 high-quality K. pneumoniae genomes passed quality control and species verification for downstream analysis. Genomic analysis identified 18 sequence types, with ST147 (7/34, 20.6%), ST37 (4/34, 11.8%), ST2629 (3/34, 8.8%), ST39 (3/34, 8.8%), and ST870 (2/34, 5.9%) representing the predominant lineages. The dominant high-risk clones, particularly ST147, ST11, ST231, and ST42-3LV, harbored multiple antimicrobial resistance determinants, including blaCTX-M-15 (20/34) or blaCTX-M-14 (2/34), blaKPC-2 (2/34), blaOXA-48 (1/34), blaOXA-181 (1/34), blaNDM-5 (1/34), aminoglycoside-modifying enzymes, fluoroquinolone resistance determinants, porin disruptions (ompK35/ompK36; 9/34), and colistin resistance–associated mutations in pmrB in 4 isolates. ST147 was the predominant lineage and was consistently associated with the KL64 capsule type and O1/O2-associated O-loci. Virulence profiling demonstrated a predominantly low-virulence population, with 19/34 (55.9%) isolates carrying yersiniabactin as the only detected virulence determinant, whereas aerobactin, colibactin, and rmpA/rmpA2 were absent from all genomes. Collectively, these findings demonstrate that MDR K. pneumoniae circulating in Peshawar are dominated by internationally disseminated high-risk clones characterized by extensive antimicrobial resistance but limited virulence potential, underscoring the importance of genomic surveillance to strengthen infection prevention and antimicrobial stewardship.