E. coli strains from artisanal foods. Escherichia coli from Italian artisanal food productions of animal origin

Italian cheese and salami artisanal productions were investigated to assess the presence, phylogeny and genomic traits (antimicrobial resistance, virulence and mobilome) of E. coli along 6 batches of each processing chain (raw materials, semi-finished and finished products, and environment). Among the 34 strains preliminarily identified (3% of prevalence), 33 were confirmed after WGS. Higher occurrence (91%) was highlighted in salami key processing stages from raw materials to final products, and associated environmental sites, whereas only 3 strains were identified from cheese (raw material and final products). The accumulation of high SNPs differences within small clusters of strains encompassing same batches or processing stages, combined with high serotype and phylogroups diversity, suggested the occurrence of different contamination phenomena among the facility. 8 isolates harboured plasmid-mediated resistance genes, of which one cheese strain carried a IncQ1 multi-drug resistant plasmid to macrolide [mph(B)], sulfonamide (sul1, sul2), trimethoprim (dfrA1) and aminoglycoside [aph(3'')-Ib and aph(6)-Id]. Besides a diverse pool of virulence-associated genes in the class of adhesion, colonization, iron uptake, and toxins, putative ColV-positive iron uptake systems sit, iro or iuc (8 salami and 2 cheese), plasmid-encoded hemolysin operon hlyABCD (1 salami) and potential atypical enteropathogenic E. coli (a-EPEC) (3 salami environment) were reported. Overall, our findings underscore the importance of routine surveillance towards the artisanal food chain to prevent the dissemination of AMR and virulence.