Whole Genome Sequencing Reveals Genetic Variability of Escherichia coli Across Dairy Farm Environments

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission.