One health analysis of antimicrobial resistance in Escherichia coli from humans, animals, and the environment.

SUMMARY: Antimicrobial resistance (AMR) poses a critical public health threat, with evidence suggesting the transfer of resistance genes between humans, animals, and the environment. This study investigates the distribution of AMR genes, plasmid types, and the population structure of Escherichia coli isolates from humans, livestock, fish, and the environment in Tanzania, with a subset of data from Kenya, using a One Health approach. A total of 174 Whole-genome sequencing (WGS) data were analyzed to identify AMR genes and evaluate their population structure. The findings reveal widespread dissemination of AMR genes across all sources. Aminoglycoside resistance genes and β-lactam resistance genes were prevalent across all environments. Quinolone resistance mutations were detected in isolates from humans, livestock, fish, and the environment. Tetracycline resistance genes were found in humans, livestock, and fish. Plasmid types IncFIA, IncI1, and IncFII exhibited extensive cross-source sharing, with strong connectivity between human and livestock. Principal Component Analysis (PCA) revealed that E. coli isolates from Kenya formed a tight, distinct cluster, while other isolates were more dispersed. These findings emphasize the interconnected nature of AMR across human, animal, and environmental sectors and underscore the need for integrated surveillance under a One Health framework to monitor and control the spread of clinically significant AMR genes.

AVAILABILITY AND IMPLEMENTATION: The genomic datasets analyzed in this study are available from public repositories. Bioinformatics analyses were conducted using established pipelines and standard tools for AMR gene detection, plasmid typing, and population structure analysis.