Molecular typing and genetic diversity of multidrug-resistant Klebsiella pneumoniae isolated from Erbil City, Kurdistan Region, Iraq

Abstract

Background and objective: Klebsiella pneumoniae, a Gram-negative encapsulated bacterium, is one of the most significant etiological agents of healthcare- or community-acquired infections worldwide. This study set out to explore the phylogenetic relationships and genetic diversity of multidrug-resistant K. pneumoniae using 16S rRNA sequencing and Multilocus Sequence Typing (MLST). Methods: A total of 298 urine samples were analyzed from patients with symptoms of urinary tract infection. Standard biochemical tests were used for isolate identification. Resistant isolates were further analyzed by molecular diagnosis through 16S rRNA gene sequencing and Multilocus Sequence Typing (MLST), in accordance with international standards. Results: Out of 298 urine specimens, 49 K. pneumoniae isolates were confirmed (isolation rate: 16.4%). Resistance was high: 49% to amoxicillin/clavulanic acid, 38.8% to cefazolin, 34.7% to ceftriaxone, and 12.2% to ertapenem and 16.3% to both imipenem and meropenem among the carbapenems. Multidrug resistance was detected in 65.3% of isolates (32/49), and 18.4% were extensively drug-resistant. MLST testing of 13 MDR strains identified 13 different sequence types, the most dominant (15%) being ST147, followed by ST405 and ST268 (10% each). Both the 16S rRNA sequence analysis and MLST typing showed genetic variation among the resistant isolates, with multiple alleles differing across the seven loci, indicating substantial genetic diversity in the studied isolates. Conclusion: UTIs associated with antimicrobial-resistant K. pneumoniae pose a primary problem in this region. Genetic diversity was found within resistant isolates using molecular typing. Study limitations include the small sample size for MLST (n=13) and the absence of whole genome sequencing, which limit the epidemiological conclusions that can be drawn. Future studies with larger populations and more advanced sequencing methods (such as WGS) are needed for more comprehensive surveillance and a fuller understanding of resistance mechanisms and transmission patterns.