School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR.
Water Res. 2022 Nov 1;226:119282. doi: 10.1016/j.watres.2022.119282.
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.
污水处理厂（WWTP）的废水排放可能会导致受纳水体中抗性基因库的富集。然而，由于缺乏稳健的抗生素抗性细菌（ARB）识别方法，抗性基因库在受纳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序列增强对 ARB 的识别能力，以区分本土 ARB 和 WWTP 携带的 ARB 在国内 WWTP 受纳水体中的积累。构建并评估了一个生物信息学框架（命名为 ARGpore2：https://github.com/sustc-xylab/ARGpore2），以促进纳米孔读数中抗生素抗性基因（ARGs）和 ARB 的识别。ARGpore2 对 ARGs 的识别精度和召回率与常用的 BLASTP 方法相当，而 ARB 的谱增加了一倍，比组装的 Illumina 数据集更多。总的来说，我们在受纳海水中鉴定了 33 个携带 65 种 ARG 亚型的 ARB 属，其浓度一般比清洁海水高 10 倍。值得注意的是，我们报告了由消毒处理后残留微生物复活引起的原发性抗性基因库入侵。这些 WWTP 携带的 ARB，包括几种动物/人类肠道病原体，对受纳水抗性基因库的贡献高达 85%。质粒和 class 1 整合子被认为是促进 ARGs 持续存在和传播的主要载体。此外，我们的工作表明，在复杂的环境条件下，广泛的载体识别对于确定多因素耦合抗性基因库激增的驱动力至关重要，从而为建立有效的 ARGs 缓解策略提供了优先顺序。
