Characterization and antimicrobial resistance of commensal and pathogenic Escherichia coli from pigs in Sardinia (Italy)

Abstract

This study investigated commensal and pathogenic E. coli isolated 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. Carcass surface, mesenteric lymph nodes and colon content samples were sampled at the five slaughterhouses (S1-S5), in total 38 samples from 152 animals were collected. At the slaughterhouses, environmental samples were also collected from food-contact surfaces and non-food-contact surfaces (36 samples overall). E. coli was detected in all farms, 97 % of pigs, and all slaughterhouses. Whole genome sequencing and antimicrobial susceptibility testing were performed on 95 isolates, revealing 13.7 % pathogenic isolates, including ExPEC, ETEC, STEC-ETEC hybrids, and UPEC. A total of 40 sequence types (STs) were identified, with ST10 being the most common. High-risk clones (ST88, ST101, ST410, and ST648) were also detected. Over half of the isolates (52.6 %) carried at least one AMR gene, with 43 % harboring multiple AMR genes, particularly tet (37.9 %) and blaTEM (32.6 %). Phenotypic resistance was observed for tetracycline, ampicillin, and sulfamethoxazole-trimethoprim. This study reveals extensive AMR in commensal and environmental E. coli, underscoring their role as resistance gene reservoirs. The presence of AMR genes without direct antimicrobial exposure suggests complex transmission dynamics. Findings support the significance of AMR surveillance also for commensal E. coli, and the importance of combining phenotypical and sequencing methods to assess antimicrobial removal effects in pig farms.