Comparative Genomic Diversity of Escherichia coli Strains Isolated from Western Kenya

Introduction: Escherichia coli is a significant pathogen responsible for diarrheal and extraintestinal infections. Little information is available on the genomic diversity, virulence traits, and antimicrobial resistance (AMR) profiles of these pathogens circulating in East Africa, yet they have a major impact on public health. The study sought to assess the heterogeneity of E. coli strains circulating in Western Kenya Methods: Genomic surveillance of E.coli isolates was done by long-read Oxford Nanopore sequencing. Genomic diversity was characterized using multi-locus sequence typing (MLST), analysis of genes conferring resistance to antimicrobial agents, plasmids and virulence factors. Bacterial accessory binary gene phylogeny was generated with the isolates from Kisii and Kisumu Counties in Western Kenya, including the FASTA sequence files from Central, Northern Kenya and Central Uganda. Results: MLST identified the persistence of clonal lineages, E. coli D7, and detected globally important ExPEC clones such as ST648. Resistance determinants, such as aadA, blaTEM, dfrA, sul and qnrS11, were frequently harbored on plasmids, such as IncFIB/FII. Virulence profiling showed the presence of colonization (fimH), toxin (astA, stx) and iron utilization (fyuA, irp2, iutA) related genes. Phylogenetic analysis revealed regional clustering of isolates and potential transboundary transmission, with separate lineages in Central and Northern Kenya. Conclusion: The findings underscore the vast heterogeneity and AMR load of E. coli strains in Western Kenya. The results highlight the importance of ongoing genomic surveillance to monitor new clones, guide treatment approaches, and inform regional public health responses.