A framework to assess the terrestrial risk of antibiotic resistance from antibiotics in slurry or manure amended soils

Antibiotic resistance (ABR) or the silent pandemic is a major global health and economic issue, threatening both modern healthcare and food production. There is increasing concern that the presence of antibiotics in the environment may select for the emergence and spread of antibiotic resistance. Currently environmental regulatory guidelines fail to address ABR risks, and while there is ongoing work to address this within aquatic environments, terrestrial systems have been somewhat overlooked - perhaps in part due to a focus on wastewater treatment plant effluent as the main source of antibiotics within the environment. Within agriculture there is an increasing push to move away from chemical-based fertilisers and towards the use of organic soil amendments such as slurry, manure or sludge, to improve soil health. However, these organic soil amendments have been shown to contain antibiotics and other pharmaceuticals alongside antibiotic resistant bacteria, posing a potential risk to the environment, livestock and humans through the proliferation and spread of ABR. It is therefore important that a risk framework is developed in relation to ABR and organic soil amendment use. Using current knowledge on the fate of antibiotics within soil and mathematical models, this manuscript presents a novel framework for assessing the terrestrial risk of antibiotic resistance through the use of farmyard manure as fertiliser. Low concentration of antibiotics within the environment are known to select for antibiotic resistance (ABR), a global health and economic threat. This manuscript presents a framework to assess the ABR risk in soils where slurry or manure is applied.