Antimicrobial Resistance Inputs in Agriculture Settings: Insights for a One Health Approach

Biosolids and reclaimed water are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive food production system. This work aimed at assessing Antibiotic-Resistant Bacteria (ARBs) and Antibiotic Resistance Genes (ARGs) inputs in agriculture settings under circular economy practices. Resistome of 25 biosolid and 14 irrigation water samples under field conditions was characterized using shotgun metagenomic sequencing, followed by identification of antibiotic-resistant phenotypes of cultured samples and isolation of live ARBs followed by characterization through whole-genome sequencing The most prevalent resistance determinants in biosolid samples conferred resistance to daptomycin, followed by mupirocin, fusidic acid and bacitracin. In water samples, the ARG profile was similar to that of biosolids, but with lower bacitracin resistance and higher polymyxin resistance determinants. Notably, beta-lactamases of all Amber classes were more abundant in water samples than in biosolids. We observed that metagenomic findings had correspondence with live bacteria isolated from the samples expressing the same antimicrobials’ resistance. ARGs have recently been recognized as emerging hazards in urban wastewater, the source of reclaimed water for agriculture. Despite the treatment process, our data demonstrate that, in both biosolids and reclaimed water, the resistome persists and spreads to the resident microbial communities. This creates a reservoir of functional ARGs, potentially able to disrupt microbial ecosystems of agriculture soils and possibly reach animal and human subjects via feed and food chain.