Antimicrobial resistance (AMR), particularly against critically important antimicrobials (CIA), has been recognised as one of the world’s most pressing public health problems. The presence of AMR determinants in different environments is of concern and likely contributes to AMR maintenance and diffusion.
Illumina whole genome sequencing and a range of bioinformatic tools were employed to investigate 300 Escherichia coli isolated from 12 sources (dairy, beef, wild boar, rabbit, poultry, swine, companion animal, vegetable, fishery, mollusc, wild animal and human) in Italy. We evaluated phylogenetic diversity, presence of antimicrobial resistance genes (ARGs), virulence-associated genes (VAGs), disinfectant resistance genes and their association with mobile genetic elements (MGEs).
Poultry and rabbit meat were the most worrisome sources, showing an extremely high number of both ARGs and VAGs. Also 3 genes, usually associated with mobile genetic elements and coding for quaternary ammonium compound resistance, were identified. The presence of both ExPEC and IPEC VAGs in these strains indicated the potential presence of hybrid pathogens.
Mobile colistin resistance gene mcr1 was identified in rabbit meat and intestine samples in association with IS6 family elements. STs commonly associated with human infections were identified among poultry strains.
Dairy strains carried the most extended spectrum beta lactamases (ESBL) genes. Companion animals, living in close contact with humans, harboured the highest number of VAGs among the collection. Interestingly, wild animals and wild boar showed a wide variety and a relatively high rate of different virulence determinants, suggesting their hypothetical role as a reservoir of VAGs.
Different environments (food chain, food-producing and companion animals, wildlife) have been identified as possible reservoirs of ARGs and/or VAGs and, ultimately, of hypothetical pathogens for humans. Understanding the role of different sources in the maintenance and diffusion of AMR represents an essential step for preventive measure implementation and epidemiological evaluation.