Aerobic composting is used widely for animal manure recycling, and it may reduce the amount of antibiotic resistance genes (ARGs) that enter the environment. We sampled three types of animal (bovine, chicken, and pig) manure and the corresponding composts from 12 large-scale farms, and tested multiple ARGs and mobile genetic elements (MGEs) by high-throughput qPCR. A total of 109 ARGs were detected in the manure and compost samples, thereby demonstrating that both are important ARG reservoirs. The diversity and abundance of ARGs were significantly higher in chicken and pig manure than bovine manure, but industrial composting was more efficient at reducing the ARGs in chicken manure than pig and bovine manure. Composting universally reduced some ARGs, but inconsistently influenced other ARGs from different types of animal manures. Network analysis detected the widespread co-occurrence of ARGs and MGEs. floR, ermF, catB3, aac(6′)-lb(akaaacA4), and aadA were identified as suitable indicator genes for estimating the total abundance of ARGs. Our results suggest that different animal species had significant effects on the diversity, abundance, and persistence of ARGs, where the abundance of transposons, heavy metal concentration, total nitrogen level, and the dosage and duration of exposure to antibiotics may explain these differences.

有氧堆肥被广泛用于动物粪便的回收利用，它可以减少进入环境的抗生素抗性基因（ARG）的数量。我们从12个大型农场中采样了三种类型的动物（牛，鸡和猪）粪便和相应的堆肥，并通过高通量qPCR测试了多种ARG和移动遗传元件（MGE）。在粪便和堆肥样品中总共检测到109个ARG，从而证明这两者都是重要的ARG储库。鸡粪和猪粪中的ARGs的多样性和丰度均明显高于牛粪，但工业堆肥在降低鸡粪中的ARGs方面比猪粪和牛粪更有效。堆肥普遍减少了一些ARG，但不一致地影响了不同类型动物粪便中的其他ARG。floR，ermF，catB3，aac（6'）- lb（akaaacA4）和aadA被确定为合适的指示基因，用于估计ARG的总丰度。我们的结果表明，不同的动物物种对ARGs的多样性，丰度和持久性具有重大影响，其中转座子的丰度，重金属浓度，总氮水平以及接触抗生素的剂量和持续时间可以解释这些差异。