摘要
      养猪场的废水处理过程（WTP）受到抗生素抗性基因（ARGs）的严重污染，而移动遗传元件（MGE）在形成ARGs图谱中发挥着重要作用。在这里，我们首先使用宏基因组测序来跟踪中国东南部三个养猪场的ARG相关移动遗传元件（AAMGEs）的多样性和迁移，包括插入序列（IS）和质粒沿着WTP的变化。IS平均相对丰度从最初的猪粪便源到废水储存泻湖（WSL）上升，但在厌氧消化器（AD）的进水中下降，在出水中上升。相反，质粒在这个过程中被迅速消除。这些结果表明，AD减少了质粒拷贝，而IS丰度增加。我们发现，包括IS91、ISNCY、IS630和IS701在内的多种IS对多药耐药性的转移有很大贡献。此外，与其他ARG类相比，四环素抗性基因与更大的IS多样性共存，这可能是我们发现的四环素抗性基因丰度高的原因之一。由MGE介导的ARGs沿养猪场水处理厂的转移是ARGs在养猪场环境中持续存在的关键因素。总的来说，我们的发现证明了ISs和质粒在养猪场WTP沿线的不同命运，并表明AAMGE监测在控制猪粪便中的ARGs方面发挥着重要作用。
Abstract
The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722034106