Reducing antibiotic resistance genes, integrons, and pathogens in dairy manure by continuous thermophilic composting

•Thermophilic and mature phases of composting had important roles in reducing ARGs.•Sufficiently high temperature led to greater decreases in 5/10 ARGs and integrons.•Both bacterial succession and HGT play important roles in the variation of ARGs.•Variation in different ARGs involved diverse mechanisms.•CTC performed better at reducing ARGs, integrons, and HPB. This study explored the effects of composting using three temperature regimes, namely, insufficient thermophilic composting (ITC), normal thermophilic composting (NTC), and continuous thermophilic composting (CTC), on antibiotic resistance genes (ARGs), integrons, and human pathogenic bacteria (HPB), as well as the mechanisms involved. The NTC and CTC treatments led to greater decreases in 5/10 ARGs and two integrons than ITC, and the abundances of ARGs (tetC, tetG, and tetQ) and int1 only declined in the NTC and CTC treatments. The abundances of HPB decreased by 82.8%, 76.9%, and 96.9% under ITC, NTC, CTC, respectively. Redundancy analysis showed that both bacterial succession and horizontal gene transfer play important roles in the variation of ARGs, and the changes in different ARGs were due to diverse mechanisms. CTC performed significantly better at reducing ARGs, integrons, and HPB, thus it may be used to manage the public health risks of ARGs in animal manure.