Prevalence and Genotypic Analyses of Clinical Multidrug-Resistant Klebsiella pneumoniae from Community Acquired Urinary Tract Infection in Calabar, Nigeria

Microorganisms are developing resistance to antibiotics faster due to misuse, threatening to make infections untreatable. Klebsiella pneumoniae, common in the gut is a major cause of dangerous antibiotic-resistant urinary tract infections. This study performed genomic characterization of multidrug-resistant K. pneumoniae from urine, focusing on identifying antimicrobial resistance genes, sequence types (ST), plasmid content, and virulence genes. A cross-sectional study was conducted involving 384 urine samples from symptomatic outpatients at General hospital Calabar, Nigeria. The bacterial isolates were identified using API system and antibiotics susceptibility test was evaluated using CLSI standards. Further analysis using next-generation sequencing was carried out on multidrug-resistant isolates. K. pneumoniae was most frequently isolated from individuals >60 years (64.10%). Gender-based distribution of 96 K. pneumoniae urine isolates in Calabar showed 64 (66.67%) female and 32 (33.33%) male cases. Multidrug-resistant K. pneumoniae ST (clones) predominantly ST11 and ST147 were identified, harboring comprehensive resistance profiles driven by tet(A) (tetracycline), fosA/6/3 (Fosfomycin), and diverse bla genes (SHV, TEM, CTX-M, OXA, NDM, KPC-2 for beta-lactams). All isolates carried Col44OI/ColRNAI plasmids and key virulence factors (fimH, iutA, fun, irp2, nlpl, terC, iucC). By illuminating the molecular determinants, mechanisms, virulome, and plasmid content of these MDR-strains, this study underscores the necessity of continuous beta-lactamase surveillance and rigorous antimicrobial stewardship to combat community-acquired K. pneumoniae resistance.