Bovine Clinical E. coli Mastitis in Italian Dairy Herds Is Not Associated with a Specific Pathotype

Background: Escherichia coli is a cause of severe clinical bovine mastitis; however, it is not yet fully understood what makes mastitis-associated bacteria different from commensal strains at the genetic level. The goal of this study was to compare the genomic features, sequence types, virulence, and antibiotic resistance profiles of E. coli isolated from healthy cows and cows with clinical mastitis in Northern Italy. Methods: Between 2023 and 2024, 46 E. coli isolates, 23 from healthy animals and 23 from mastitis cases were recovered. Standard phenotypic approaches and Oxford Nanopore sequencing were used to investigate the genomic landscape of the strains. Results: Phylogroups A and B1 were the most common in both groups. MLST showed several types, with ST10 (19.6%), ST58 (13.0%), and ST69 (8.7%) being the most common. There was no lineage that was uniquely able to describe the isolates as Mammary Pathogenic Escherichia coli (MPEC); indeed, the ST distribution and phylogeny were the same in both groups. A total of 47.8% of isolates had antimicrobial resistance determinants, with β-lactamases (21.7%) and tetA (15.2%) being the most common. No significant differences in resistance rates were observed between mastitis and healthy isolates. Pangenome investigation found a large pool of accessory genes, but no genomic signature that distinguished mastitis from commensal isolates across the MPEC. Conclusions: Bovine E. coli isolated from milk of both healthy and mastitic cows share sequence types, resistance rates, and accessory genome content, supporting the absence of a unique MPEC pathotype and highlighting the ecological versatility of these bacteria.