Characterization and Antimicrobial Resistance of Commensal and Pathogenic <em>Escherichia coli </em>from Pigs in Sardinia (Italy)

This study investigated commensal and pathogenic E. coli from pigs at farms and slaughterhouses in Sardinia, focusing on genetic relatedness and antimicrobial resistance (AMR). Samples were collected from six fattening pig farms (A-F) and five slaughterhouses (S1-S5). In the farms, environmental fecal sampling from the fattening pigs’ pens was carried out and information regarding farm management and biosecurity measures were collected. Pigs that had been in the sampled pens were selected for sampling at the slaughterhouse. Mesenteric lymph nodes, colon content and carcass surface samples were collected at the five slaughterhouse (S1-S5), in a total of 38 samples form 152 animals. At the slaughterhouses, also environmental samples were collected from food-contact surfaces and non-food-contact surfaces (36 samples overall). E. coli was detected in all farms, 97% of pigs, and 100% of slaughterhouses. Whole genome sequencing and antimicrobial susceptibility testing were per-formed on 96 isolates, revealing 13.5% pathogenic isolates, including ExPEC, ETEC, STEC-ETEC hy-brids, and UPEC. A total of 40 sequence types (STs) were identified, with ST10 being the most com-mon. High-risk clones (ST88, ST101, ST410, and ST648) were also detected. Over half of the isolates (52.1%) carried at least one AMR gene, with 42.7% harboring multiple AMR genes, particularly tet (37.5%) and blaTEM (32.3%). High phenotypic resistance was observed for tetracycline, ampicillin, and sulfamethoxazole-trimethoprim. The study highlights the widespread presence of pathogenic E. coli in pigs, even in isolated environments, and emphasizes the need for continuous surveillance due to the significant AMR found in both pathogenic and non-pathogenic isolates.