Résumé
Manure and slurry spreading can contribute to the environmental dissemination of antibiotic resistance genes (ARGs) and food-borne pathogens through contamination of soil, water, and crops, posing potential risks to human health. This pilot study tracked the dynamics of bacterial communities, Escherichia coli and ARGs and virulence genes usually associated with E. coli throughout the manure management process—from bovine faeces to field-edge manure - to investigate the potential risks to humans and animals and the critical points to monitor or manage. Sampling was conducted at an experimental dairy farm between November 2022 and April 2023. Sequencing of 16S rRNA genes revealed distinct bacterial diversity and composition between dairy cow and calf faeces, and across various effluents (slurry, straw, manure), indicating progressive shifts in bacterial communities during storage. E. coli levels decreased by approximately 1 log CFU/g between faeces and direct effluents (cow slurry, calf straw), and again between those and stored effluents (manure, covered slurry). On the contrary, the ARGs conferring resistance to tetracyclines, aminoglycosides, and streptomycin were more abundant in stored slurry and straw than in faeces, and several virulence markers associated with foodborne pathogens also persisted in slurry. Dynamical models adjusted to E. coli and ARG abundances indicated differences in bacterial growth rates between the matrices and key roles of effluent management interventions on the dynamics and overall levels of the bacteria. However, ARG increases were not systematically linked to antibiotic treatments, effluent management practices, or E. coli abundance, suggesting a possible horizontal transfer to other bacteria. An ongoing metagenomic analysis, incorporating DNA conformation, aims to associate ARGs and virulence genes with their genomic context. This pilot study highlights the potential for livestock effluents to amplify and disseminate ARGs and pathogenic traits in the environment, underscoring the need for refined management strategies.