Genomic Insights into Possible Zoonotic, Anthroponotic, and Environmental Transmission of Escherichia coli in Ekiti and Ondo States, Nigeria

Background Escherichia coli can be pathogenic or non-pathogenic, depending on its genetic makeup, which characterises its virulence potential. The transmission dynamics of E. coli are complex due to its dual nature and its ability to be transmitted among humans, animals, and the environment in both directions. The objective of this study was to gain insight into the resistome, virulome, and mibiolome of E. coli from matched samples using the One-Health Approach in Ekiti and Ondo States, Nigeria. Methods Whole-genome sequencing (WGS) was used to characterise the genomic features of 8 E. coli isolates from humans (n = 3), animals (n = 2), and the environment (n = 3). Antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements (MGEs) were identified, followed by multi-locus sequence typing (MLST), core genome MLST, serotyping, phylogrouping, and local and global phylogenomic analysis. Results The 8 E. coli recovered in this study showed variation in the presence of ARGs, virulome, and mobilome, with total ARGs > 30 genes and virulome > 40 genes. There was an identical genetic makeup in three pairs (NGEK1 vs. NGEK1, NGEK13 vs. NGEK17, and NGEK21 vs. NGEK22A) recovered from humans, animals and environments. Some significant resistance genes (blaCTX-M-15, blaCMY-2, blaTEM-1B, blaOXA-1, blaOXA-181 and qnrS1) were found in the isolates. The MGEs analysis found two groups: plasmid-mediated and non-plasmid-mediated, with both carrying resistance (blaTEM, blaCTX-M-15, qnrS1, qnrB19, and blaOXA181) and virulence genes (hylE, hha, senB). The STs found in the study were ST 2, 38,181, 693, and 998. Clonality was observed among some E. coli isolates from the same household or farms, and these isolates were also phylogenetically associated with certain global E. coli isolates. Conclusion Our study emphasised that the E. coli isolates analysed possessed ARGs and virulence factors that drive pathogenicity and presented evidence for possible zoonotic and anthroponotic modes of transmission.