Assessment of viable Enterobacteriaceae and Enterococcus spp. across the agro-ecosystem of an antibiotic-free swine farm.

Agricultural practices, specifically the use of antibiotics and other biocides, have repercussions on human, animal, and plant health. The aim of this study was to evaluate the levels of Enterobacteriaceae and Enterococcus, as antibiotic-resistant marker bacteria, in various matrices across the agro-ecosystem of an antibiotic-free swine farm in Quebec (Canada), namely pig feed, feces, manure, agricultural soil, water and sediment from a crossing stream, and soil from nearby forests. Samples were collected in fall 2022, spring and fall 2023, and spring 2024. All samples were subjected to counts of total, cefotaxime-, and ciprofloxacin-resistant Enterobacteriaceae as well as total and vancomycin-resistant Enterococcus spp. The frequency of total and cefotaxime-resistant Enterobacteriaceae along with the vancomycin-resistant Enterococcus decreased with age in pig feces, from weaning to the end of the fattening period. High proportions of the Enterobacteriaceae recovered from feces and environmental samples were resistant to cefotaxime. Application of manure on fields contributed a significant input of Enterococcus, but those resistant to vancomycin were under the detection limit. This study shows the prevalence of antibiotic-resistant bacteria in a farm agro-ecosystem even without the administration of antibiotics to the animals and highlights the complexity of components influencing antimicrobial resistance in the environment.