Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment

Background Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge focusing on the spread dispersion of ARGs from in pig production units to thesystem, including the external environment. Results In the present study, we longitudinally followed two one swine farmsfarm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. Specifically, wWe identified 309 SGBs being shared able to spread frombetween the the animals gut microbiome, the internal and external farm environments to the soil surrounding the farms. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe. Conclusions Collectively, our results highlight the urgency to implement more effective countermeasures to limit the spread dispersion of ARGs from in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems. This work was carried out in the context of the “Controlling Microbiomes Circulations for Better Food Systems” (CIRCLES) project, which was funded by the European Union's Horizon 2020 research and innovation program under grant agreement no. 818290.