Comparative Genomics of Antibiotic Resistance in Escherichia coli Isolates from Human and Agricultural Sources in Kogi State

The emergence of antibiotic-resistant Escherichia coli as a One Health challenge involves complex resistance gene transfer between human clinical, animal, and environmental reservoirs. Comparative genomics enables tracking of resistance gene flow and phylogenetic relatedness across these sectors. This study applied whole genome sequencing (WGS) to conduct comparative genomics of antibiotic resistance in E. coli isolates from human clinical specimens, poultry, and irrigation water in Kogi State, North Central Nigeria. Forty human clinical isolates (20 urinary tract infection, 20 bloodstream infection), 40 poultry isolates, and 20 irrigation water isolates were collected from three local government areas. WGS was performed on the Illumina NextSeq platform. Genome assembly, annotation, resistance gene identification (using ResFinder), plasmid typing, and multi-locus sequence typing (MLST) were performed. Phylogenomic trees were constructed using core genome SNP analysis. Shared sequence types and identical resistance plasmids were identified between human clinical and poultry isolates, implicating zoonotic transmission. Extended-spectrum beta-lactamase (ESBL) genes (blaCTX-M-15) were prevalent across all source types. These findings reinforce the urgency of a One Health antimicrobial resistance surveillance programme for Kogi State. Keywords: E. coli, comparative genomics, antibiotic resistance, One Health, Kogi State