摘要
      污水处理厂（WWTP）的污水排放会导致受纳水体环境中的抗性富集。然而，由于普遍缺乏强有力的抗生素耐药性细菌（ARB）鉴定方法，耐药性在接受环境中积累的驱动机制尚不清楚。在这里，我们利用纳米孔长读数增强的ARBs识别，来区分本地ARBs和生活污水处理厂接收水体中污水处理厂携带的ARBs的积累。生物信息学框架（命名为ARGpore2:https://github.com/sustc-xylab/ARGpore2)构建并评估以促进抗生素抗性基因（ARGs）和ARGs在纳米孔读数中的鉴定。ARGpore2的ARGs鉴定显示出与通常采用的基于BLASTP的方法相当的精度和召回率，而ARBs的光谱是组装的Illumina数据集的两倍。我们在接收海水中总共鉴定出33个ARB属，携带65种ARG亚型，其浓度通常是清洁海水的10倍。值得注意的是，我们报告了一种由消毒处理后残留微生物的复活引起的主要耐药性入侵。这些由污水处理厂传播的ARB，包括几种动物/人类肠道病原体，在接受水耐药性中占85%。质粒和1类整合子被认为是促进ARGs持续存在和传播的主要载体。此外，我们的工作证明了广泛的载体识别在确定复杂环境条件下多因素耦合耐药性激增的驱动力方面的重要性，从而为制定有效的ARGs缓解策略的优先次序铺平了道路。
Abstract
Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.

https://www.sciencedirect.com/science/article/abs/pii/S0043135422012271