Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.

从废物中不充分去除抗生素和抗生素抗性基因 (ARG) 会增加在非临床环境中选择抗生素抗性的风险。虽然堆肥是减少 ARG 的有效方法，但大多数传统方法在处理高度污染的抗生素发酵废物时无效。在这里，我们探讨了超高温堆肥在去除泰乐菌素抗生素发酵残留物 (TFR) 和相关 ARG 和移动遗传元件（MGE；质粒、整合子和转座子）方面的功效和潜在机制。超高温堆肥去除了 95.0% 的 TFR、75.8% 的 ARG 和 98.5% 的 MGE，这种减少主要发生在长时间暴露在 60°C 以上的温度至少 6 天后。基于测序和培养依赖性实验，ARGs 和 MGEs 的减少与最初与 ARGs 和 MGEs 相关的细菌分类群数量的减少密切相关。此外，我们发现质粒基因丰度减少了 94.1%（ISCR1和IncQ-oriV）与堆肥过程中减少的 ARG 显着相关，这表明质粒是 ARG 的主要载体。我们使用直接培养验证了这一点，以表明在堆肥的早期阶段，ARG 更常见于质粒中。这些结果共同表明，超嗜热堆肥通过减少抗生素抗性质粒和相关宿主细菌的丰度，可有效地从抗生素发酵废物中去除 ARG 和相关抗性基因。