Livestock manure is a valuable bioresource, but its management requires consideration of antimicrobial resistance (AMR) to support safe nutrient recycling. Organic and conventional dairy systems differ in antibiotic use and manure and herd management, potentially influencing environmental resistomes. However, cross-country evidence linking farming systems to antibiotic resistance genes (ARGs) and their associated risks remains limited. This study compared ARG profiles and potential ARG-associated health risks in manure and soil from organic and conventional dairy farms in the United Kingdom and Canada.
Paired organic and conventional dairy farms in both countries were investigated. Soil and manure samples were collected with replicates (156 samples in total). Shotgun sequencing and bioinformatic analyses were applied to characterise ARGs, MGEs, and bacterial communities.
Manure from organic farms exhibited higher ARG richness than manure from conventional farms in both countries (P < 0.05), whereas ARG abundance showed the opposite pattern. Farming system was significantly associated with ARG composition in both manure and soil (P < 0.001). Associations between ARGs, mobile genetic elements and bacterial communities were more complex in manure than in soil. Risk assessment indicated higher potential ARG-associated health risks in conventional systems, particularly in Canadian manure samples (P < 0.01).
These findings reveal contrasting patterns in ARG richness, abundance and potential risk across dairy farming systems, highlighting that ARG richness alone may not adequately indicate AMR-related hazards. The results support considering ARG abundance, potential mobility and host associations together when assessing manure-associated AMR. Cross-country evidence from this study can inform risk-based monitoring priorities for livestock manure management and the safe recycling of organic nutrients.