Antibiotic resistance gene transfer characteristic and risk evaluation: The entire process from swine manure to biogas slurry and then to soil

The extensive use of antibiotics in livestock farming has led to the accumulation of antibiotic resistance genes (ARGs) in Livestock manure (LM), posing significant risks to ecological and human health. This study utilized metagenomic sequencing technology to systematically evaluate the dissemination characteristics and risks of ARGs across the “swine manure (SM) - biogas slurry (BS) - soil (BS residue as organic fertilizer application)” continuum. ARGs were abundant in SM and they were assigned to 21 antibiotics classes. The mesophilic continuous stirred-tank reactor (CSTR) reduced the total abundance of ARGs by 29.33 %, primarily by longer the hydraulic retention time (HRT) to suppress mobile genetic elements (MGEs). However, the BS retained 62.89 % of the ARGs from SM, and its application to tea plantation soil introduced 176 new ARG subtypes. With increasing application rates of BS, the abundance of ARGs and MGEs in the soil steadily increased. MGEs, particularly IS3, intI1, and IS6, were closely associated with the proliferation of ARGs, highlighting horizontal gene transfer (HGT) as a key driver. Pathogenic hosts carrying ARGs increased by 80.48 % in the soil treated with BS, exacerbating health risks. This study provides a basis for evaluating and controlling ARG contamination in livestock manure in the agricultural field. • The mesophilic CSTR anaerobic digestion reduced the abundance of ARGs by 29.33 %. • Biogas slurry retained 62.89 % of the ARGs, and introduced 176 ARG subtypes to soil. • Pathogenic hosts carrying ARGs added by 80.48 % in soil treated with biogas slurry. • MGE mediated HGT(e.g., IS3, intI1, IS6) is a key contributor to ARG proliferation. • Reduce ARGs in “swine manure-biogas slurry-soil” to control ARGs spread is needed.