Hazard reduction and persistence of risk of antibiotic resistance during thermophilic composting of animal waste

Animal production contributes substantially to the dissemination of antibiotic resistance genes (ARGs) in the environment. Thermophilic composting is cost-effective for reducing hazards in animal wastes. However, ARGs can still persist in composts and the mechanism remains largely unclear. In the present study, metagenomics and real-time quantitative PCR were employed to assess the dynamics of ARGs, especially those of high risk to human health, their host species and pathogenicity of the bacterial community during thermophilic composting of chicken manure. The results showed that thermophilic composting was effective at reducing the majority of the spreading risk of antibiotic resistance by 1) eliminating more than half of allARGs that accounted for 80% of the total abundance, 2) reducing the number and abundance of high-risk ARGs significantly, and 3) removing the ARG hosts and the pathogenicity of the bacterial community substantially. The attenuation of ARGs was primarily driven by the bacterial community succession. However, the abundance of some ARGs, especially those associated with plasmids, rebounded during the cooling phase, likely caused by horizontal gene transfer. Our research reveals that minimising the horizontal transfer of plasmid-associated ARGs during the cooling phase of thermophilic composting is crucial for a more effective reduction of the hazards associated with the spread of antibiotic resistance.