Genomic characterization of antimicrobial resistance genes, mobile genetic elements, sequence types and serotypes of Escherichia coli derived from water buffalo in Italy

Objective The spread of antimicrobial resistance (AMR) in Escherichia coli is driven by the acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements in animal and environmental reservoirs. This study aimed to characterize the resistome, mobilome, and their associations in E. coli isolates from water buffaloes in southern Italy, evaluating their contribution to AMR dissemination. Methods Thirty E. coli isolates were collected from water buffaloes on 16 farms in the Campania region between 2016 and 2023. Whole-genome sequencing was performed, and assemblies were analyzed to determine sequence types, serotypes, virulence factors, mobile genetic elements, and ARGs using bioinformatic tools. Statistical analyses were applied to assess associations between resistance gene and isolation data. Results Genomic analysis identified 18 sequence types, with ST10, ST29, and ST58 most frequent. The mobilome included 155 plasmids, 1175 prophages, 29 integrons, and over 700 insertion sequences, reflecting high genomic plasticity. A total of 87 ARGs, conferring resistance to β-lactams, aminoglycosides, tetracyclines, and sulfonamides, were detected, and all isolates were multidrug-resistant. About 30% of resistance genes were linked to plasmids or integrons. Significant associations between specific ARGs and farm or sampling year suggest environmental and temporal influences. Conclusions E. coli from water buffaloes in Campania harbor a complex resistome and mobilome, supporting their role as reservoirs of AMR. The co-localization of multiple resistance genes on mobile elements highlights the risk of interspecies and zoonotic transmission, emphasizing the need for genomic surveillance within a One Health framework.