Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong.
Microbiome. 2019 Mar 21;7(1):44. doi: 10.1186/s40168-019-0663-0.
Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.
In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification.
Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.
污水处理厂（WWTP）被认为是抗生素耐药基因（ARGs）水平基因转移（HGT）的热点。尽管我们了解 WWTP 中 ARGs 的组成和分布，但 ARGs 的遗传位置、宿主和命运在很大程度上仍不清楚。
在这项研究中，我们结合了 Oxford Nanopore 和 Illumina 宏基因组测序，全面揭示了三个 WWTP 的进水、活性污泥和出水的耐药组背景，并同时跟踪 ARGs 的宿主。结果表明，WWTP 所有部位检测到的大多数 ARGs 都由质粒携带。转座子和整合子在质粒上的出现频率也高于 ARG 携带染色体。值得注意的是，检测到了携带五种类型 ARGs 的整合子和共轭元件（ICEs），它们可能在促进 ARG 转移方面发挥重要作用，特别是对四环素和大环内酯-林可酰胺-链阳性菌素（MLS）。质粒（29 种亚型）和 ICEs（4 种亚型）携带的广谱 ARGs 在 WWTP 中持续存在。宿主追踪显示出流出物中存在多种抗生素耐药细菌，这表明它们具有向接受环境传播的高潜力。重要的是，表型-基因型分析证实了共轭质粒在 WWTP 中促进多药耐药菌的生存和持久性方面的重要作用。最后，Nanopore 和 Illumina 测序平台对主要 ARGs 类型的定量结果的一致性表明了 Nanopore 测序在耐药组定量方面的可行性。
总的来说，这些发现大大扩展了我们对 WWTP 耐药组的现有知识，并有助于建立一个基线分析框架来研究环境中的 ARGs。
