Genomic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in Jos, Plateau State

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as one of the most formidable healthcare-associated pathogens worldwide, yet genomic characterization of Nigerian CRKP isolates to understand resistance mechanisms, virulence attributes, and clonal relationships is lacking. This study performed whole-genome sequencing (WGS) on 30 CRKP clinical isolates recovered from blood cultures, urinary specimens, and wound swabs at Jos University Teaching Hospital (JUTH), Plateau State, North Central Nigeria. WGS was performed on the Illumina MiSeq platform. De novo genome assembly, multilocus sequence typing (MLST), resistome analysis using RGI-CARD, and virulome analysis using Kleborate were applied. Comparative genomics with global reference genomes identified phylogenetic relationships. Results revealed that ST258 was the predominant sequence type (56.7%), a globally disseminated carbapenem-resistant lineage. blaNDM-1 was the most common carbapenemase gene (63.3%), followed by blaOXA-48 (26.7%). Co-carriage of hypervirulence genes (rmpA2, iuc locus) was identified in 23.3 percent of isolates. Pangenome analysis showed 85.6 percent accessome variability, suggesting active horizontal gene transfer. Comparative phylogenomics placed 40 percent of Jos isolates within European and South Asian pandemic clades, implicating global transmission networks. These findings represent the first WGS-based characterization of CRKP from North Central Nigeria and provide foundational data for genomic AMR surveillance and infection control prioritization. Keywords: carbapenem-resistant Klebsiella, whole-genome sequencing, NDM, ST258, Jos.