Whole-genome characterization of a colistin-resistant Klebsiella quasipneumoniae subsp. quasipneumoniae isolate from a urinary tract infection in Peshawar, Pakistan

Klebsiella quasipneumoniae is a Gram-negative, non-motile, capsulated, facultative anaerobic rod within the K. pneumoniae species complex (KpSC) and is increasingly recognized as an opportunistic pathogen associated with bloodstream infections, urinary tract infections (UTIs), and other clinically significant conditions. Because it shares many phenotypic characteristics with K. pneumoniae, accurate diagnosis remains challenging in routine clinical settings, particularly in low-resource laboratories lacking access to molecular identification tools. In this study, we characterized the antimicrobial resistance (AMR) profile of a K. quasipneumoniae subsp. quasipneumoniae isolate obtained from a UTI case in Peshawar, Pakistan. The isolate exhibited a multidrug resistant (MDR) phenotype, with resistance to β-lactams, carbapenems, fluoroquinolones, and colistin (MIC 4 µg/mL), while remaining susceptible to aminoglycosides (amikacin and gentamicin) and tigecycline (MIC 2 µg/mL). Whole-genome sequencing (WGS) identified chromosomally encoded AMR determinants, including blaOKP-A-8, oqxAB, and fosA6, with no identifiable plasmid replicons detected. Multiple nonsynonymous mutations were observed in mgrB, pmrA/B, phoP/Q, lpxM, ompK35/36, and gyrA/parC, which have been previously associated with resistance phenotypes; however, their functional contribution in this isolate was inferred from genomic data and not experimentally validated. Virulence-associated loci such as fim, ecp, entB, and fepC were present, consistent with a classical (non-hypervirulent) phenotype. Phylogenomic analysis positioned the isolate (Kq1223) on a distinct branch relative to publicly available genomes, but given that this study is based on a single isolate, no definitive conclusions regarding regional lineage or evolutionary patterns can be established. The allelic profile identified by multilocus sequence typing (MLST) has not been previously reported and may represent an unassigned sequence type pending formal database validation. The presence of chromosomally mediated MDR, including colistin resistance, highlights potential therapeutic challenges and underscores the importance of accurate species identification and expanded genomic surveillance of Klebsiella species in clinical microbiology, particularly in resource limited settings.