In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.

深入研究不同环境的微生物组和移动抵抗组谱对于了解环境在抗微生物药物耐药性 (AMR) 中的作用至关重要，抗微生物药物耐药性是全球公共卫生的紧迫威胁之一。在这项研究中，我们展示了使用快速（且易于携带）的测序方法与用户友好的生物信息学工具 MinION（牛津纳米孔技术）相结合，用于评估微生物以及移动金属和抗生素耐药谱半农村废水。在从阿默斯特污水处理厂收集的样品中，共鉴定了 20 个独特的门、43 个类、227 个属和 469 个物种，包括初级和二级处理废水。阿尔法多样性指数表明，初级样品比次级样品更丰富，微生物多样性更高。本研究共检测到 1041 个 ARG、68 个 MRG 和 17 个 MGE。初级废水中的 AMR 基因种类多于次级废水，但在这两种情况下，多药、β-内酰胺和肽类 AMR 占主导地位。值得注意的是，OXA β-内酰胺酶，其中一些也是碳青霉烯酶，在二级样品中富集。对砷、铜、锌和钼的金属抗性基因是大多数样品中的显性 MRG。除了主要位于质粒衍​​生序列中的移动基因外，大部分抗性基因位于染色体衍生序列中。与转座酶相关的遗传元件是所有样品中最常见的 MGE。在大多数样品中检测到移动或 MGE/质粒相关的抗性基因，这些基因赋予对碳青霉烯类和粘菌素等最后抗微生物药物的抗性。令人担忧的是，这些潜在可转移基因中的一些被发现由临床相关宿主携带，包括气单胞菌目、梭菌目、肠杆菌目和假单胞菌目中的病原菌。该研究表明，MinION 可用作宏基因组学方法来评估初级和次级废水的微生物组、抵抗组和移动组谱。发现这些潜在可转移基因中的一些由临床相关宿主携带，包括气单胞菌目、梭菌目、肠杆菌目和假单胞菌目中的病原菌。该研究表明，MinION 可用作宏基因组学方法来评估初级和次级废水的微生物组、抵抗组和移动组谱。发现这些潜在可转移基因中的一些由临床相关宿主携带，包括气单胞菌目、梭菌目、肠杆菌目和假单胞菌目中的病原菌。该研究表明，MinION 可用作宏基因组学方法来评估初级和次级废水的微生物组、抵抗组和移动组谱。