Antimicrobial resistance and virulence profiling of Klebsiella pneumoniae isolated from urinary tract infections in community and hospital settings in Pakistan

Urinary tract infections (UTIs) caused by multidrug-resistant (MDR) bacteria pose escalating challenges in resource-limited settings. This cross-sectional study addresses critical gaps in molecular surveillance by directly comparing antimicrobial resistance (AMR) genotypes, virulence factors, and resistance phenotypes of K. pneumoniae isolates from community (CA-UTI) and hospital-acquired (HA) UTI. in Pakistan. Bacterial identification was performed using standard microbiological techniques and MALDI-TOF MS. Antimicrobial susceptibility was assessed via the Kirby-Bauer disk diffusion and broth microdilution methods, following CLSI guidelines. PCR was employed to detect AMR genes and virulence factors. Of 2,700 urine samples analyzed, 721 (26.7%) tested positive for uropathogens, with K. pneumoniae accounting for 128 isolates (17.8%). HA-UTI isolates exhibited significantly higher resistance to amoxicillin-clavulanic acid (p = 0.0117) as well as cefotaxime and ceftriaxone (p = 0.0002). All isolates remained fully susceptible to colistin and tigecycline. Genotypic analysis revealed HA-UTI isolates carried higher frequencies of ESBL (blaCTXM-15: 23.1% vs. 13.5%) and carbapenemase genes (blaNDM: 9.9% vs. 2.7%), alongside tetracycline (tetB: 64.8% vs. 54.1%) and fluoroquinolone resistance determinants (qnrA: 37.4% vs. 29.7%). Virulence factors fimH (32.0%) and mrkD (26.6%) were common overall with no statistical difference between CA and HA UTI cases. The burden of AMR particularly in HA-UTI isolates coupled with carbapenemase production underscore the urgent need for hospital-specific infection control and stewardship programs prioritizing carbapenem-sparing regimens in Pakistan.