Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44–97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

牲畜粪便中的抗性基因导致的环境污染已成为一个严重的问题，需要解决。但是，很少有研究集中在同时处理牲畜粪便和尿液中去除抗性基因。这项研究调查了在异位发酵系统（EFS）进行猪粪高温发酵过程中抗生素抗性基因（ARGs），金属抗性基因（MRGs）和1类整倍体整合酶基因（intI1）的命运。一种有效治疗粪便和尿液的新型系统。EFS中MRGs和四环素抗性基因的丰度降低34.44–97.71％。重金属的补充显着增加了intI1的丰度，铜的增强效果比锌的增强效果更加突出。在高铜水平（A2）下观察到最高的抗性基因和intI1丰度，表明铜可以增加抗性基因通过整形体的传播。网络分析显示ARGs，MRGs和intI1同时存在，并且这些基因可能共享相同的宿主细菌。冗余分析表明，细菌群落解释了ARGs的大部分变异，环境因素通过调节细菌群落组成对ARGs的丰度产生影响。减少的鞘氨醇单胞菌，昏迷，不动杆菌，乳杆菌，巴尔通体，根瘤菌和拟杆菌属是造成耐药性降低的主要原因。这些结果表明，EFS可以减少家畜粪便和尿液的同时加工中的抗性基因。