Whole-Genome Analysis of Genomic Diversity and Antimicrobial Resistance Among Clinical Klebsiella pneumoniae Isolates from Farwaniya Hospital in Kuwait

Background: K. pneumoniae is a major opportunistic pathogen recognized by the World Health Organization as a critical-priority antimicrobial-resistant pathogen. This study characterized isolates for antibiotic resistance determinants, virulence-associated genes, mobile genetic elements, and population structure of the isolates, and evaluated the correlation between antimicrobial resistance genotype and phenotype. Methods: Ninety-five isolates were collected from different clinical specimens in August–December 2024 in Farwaniya Hospital, Kuwait. Fifty-six isolates were selected for whole-genome sequencing (WGS) using Oxford Nanopore Technology. Antimicrobial resistance genes, virulence-associated genes, plasmid replicons, insertion sequences, transposons, and sequence types were identified using different bioinformatics tools. Results: The 56 isolates comprised 47 multidrug-resistant and 9 non-multidrug-resistant isolates. β-lactam resistance genes were detected in all isolates, with blaSHV (96.4%), blaCTX-M-15 (75.0%), blaOXA (64.3%), and blaNDM-5 (30.4%) being the most prevalent. IncFIB(K) was the predominant plasmid replicon, whereas ISSen9, IS26, and IS903 were the most common insertion sequences. Twenty-eight virulence-associated genes were identified, with enterobactin-associated genes, fimbrial adhesion genes, and ompA detected in over 90% of the isolates. MLST identified 32 sequence types, including eight novel sequence types, with ST16 and ST147 predominating. High genotype–phenotype concordance was observed for cephalosporins (87.5%) and penicillins (85.7%). Conclusions: K. pneumoniae isolates exhibited extensive genomic diversity and multidrug resistance associated with multiple resistance determinants, mobile genetic elements, and high-risk lineages. These findings highlight the value of WGS for antimicrobial resistance surveillance and support continued genomic monitoring to support infection prevention and antimicrobial stewardship programs in Kuwait.