FECES-TO-FARM: technologies and molecular tools for controlling the dissemination of antimicrobial resistance from humans to animals while recovering fertilizing nutrients

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As the number one global public health problem, the spread of antimicrobial resistance has profound impacts on human health, agriculture, the environment, and global trade. Animal production is a known amplification reservoir of mobile antimicrobial resistance genes (ARGs), with the food-supply chain likely being a major pathway to humans (FARM-to-FORK pathway). Recent data revealed that differences in ARGs profiles of human and animals correlated with differences in gut microbiomes. Thus, human-associated ARGs released to the environment may return to humans more readily than ARGs not previously associated with human microbiomes. The use of wastewater treatment residual biosolids as fertilizers creates a near direct link between municipal wastewaters and farms transferring human-associated ARGs (FECES-to-FARM pathway). Consequently, recycling nutrients using municipal biosolids may exacerbate the antimicrobial resistance crisis. ARG dynamics during methanogenic anaerobic digestion of biosolids (last treatment before disposal) remain poorly understood, precluding further developments to minimize ARG loads. Our Strategic Project will systematically assess new co-treatments that enhance digestion to determine the optimal ARG removal method. Focusing on reduction mechanisms, co-treatments will be selected either because they inactivate microbes and degrade antimicrobials (i.e., physicochemical treatments) or because they change microbial communities (e.g., extreme pH pre-fermentation). Fluoroquinolones (main antimicrobials in biosolids) will be quantified to evaluate their influence on ARG dynamics, and to provide regulators with novel community-defined lowest observed effect concentrations (LOECs) for setting removal targets. In parallel, our collaboration with the Canadian Antimicrobial Resistance Surveillance will identify ARGs that are more abundant in wastewater than in animal excrement to use as FECES-to-FARM monitoring targets. These key data will support governmental efforts to develop policies against the resistance crisis. Supporting companies will gain value-added knowledge to improve their equipments and their readiness for new market constraints.