Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater.

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 ß-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.

A case study in participatory science with mutual capacity building between university and tribal researchers to investigate drinking water quality in rural Maine.

BACKGROUND: Participatory science or citizen science is increasingly being recognized for providing benefits to scientists and community members alike. However, most participatory science projects include community researchers only in the sample collection phase of the research project. Here we describe how a rural tribal community and urban university utilized participatory science methods to engage community researchers across an entire research study, creating numerous opportunities for mutual capacity building. OBJECTIVES: Researchers from MIT and the Sipayik Environmental Department, a tribal government department, partnered to co-launch a participatory science project to analyze municipal and private well drinking water quality in households in three Maine communities. The objective was to provide households with information about metals, primarily lead and arsenic, in their drinking water, and to improve public education, community partnerships, and local scientific capacity. METHODS: MIT and Sipayik researchers engaged local communities through public community meetings, mailed flyers sent to residents, and meetings with local stakeholders. MIT and community researchers worked together to design and implement the study to quantify metals in community drinking water samples, as well as hold capacity-building trainings. Individual drinking water results were communicated to households, and generalized results were discussed at community meetings in the report-back phase. RESULTS: The study attained a 29% household participation rate in the region. The researchers completed the analysis and report-back on 652 water samples. Isolated incidences of lead and geologically-attributable arsenic exceeding EPA standards were found. Individual report-backs of the results enabled local participatory scientists to make their own informed public health decisions. The study produced methodologies for navigating potential ethical issues, working with diverse communities, and collaborating over challenging geographical distances. DISCUSSION: This project developed methodologies to build long-term relationships with local scientists and to engage community members and enhance the environmental literacy of rural communities. Both MIT and Sipayik researchers learned from each other throughout the project; Sipayik researchers built technical capacity while MIT researchers gained local and cultural understanding. Community outreach methods were most effective when sent directly to residents as mailed flyers or through Sipayik researchers' outreach.