Using Next-Generation Metagenomic Tools for Microbial Characterisation of Drinking Water

M. Devane (1), W. Taylor(1), K. Russell(1), C. Roxburgh(2), H. Proffit (2), J. Williamson(3), L. Weaver(1), B. Gilpin(1)

1) Institute of Environmental Science and Research Ltd. (ESR)

2) 3 Waters, Waimakariri District Council

3) 3 Waters, Christchurch City Council

Current Drinking Water Quality Assurance Rules 2022 refer to Escherichia coli and total coliforms as the primary methods for microbiological monitoring of water quality within drinking water distribution systems, water leaving treatment plants and source waters. Secondary investigations into source water contamination currently use faecal source tracking tools to identify sources of contamination to aid mitigation efforts.

This paper describes innovative research by ESR that attempts to improve monitoring and surveillance for water resource management by implementing next-generation sequencing and metagenomic tools to characterise microbial contaminants. These tools allow us to investigate the entire bacterial community associated with a water sample rather than relying on single bacterial species (E. coli) as sentinels of contamination. Therefore, we can identify which microbes are present naturally (i.e., environmental), which are influenced by contamination events (e.g., flooding and rainfall), and how they are altered by treatment and processing. This approach creates a clearer picture of areas of concern in the drinking water supply, and when testing should be increased. Our innovative approach allows us to perform timely identification as well as longerterm studies of chronic pollution to mitigate contamination events and protect water resources.

This drinking water research is aspirational and builds on ESR’s well-established research background characterising faecal sources and microbial contaminants in surface waters such as rivers. However, in comparison to surface waters drinking water and groundwater provide more challenging environments due to typically lower levels of contaminants. These lower concentrations of bacterial and/or faecal contaminants still represent a health risk but require innovative sequencing techniques to identify microbes of interest. We have applied amplicon metagenomic sequencing to the drinking water samples to increase confidence in identification of environmental bacteria and potential pathogens and improve the sensitivity of detection.

We first presented the methodological concept of this work at WaterNZ, 2022. Since then, we have established partnerships with drinking water suppliers, and here we present case studies profiling real-world samples from sampling locations throughout the network supply, literally taking a source to tap approach. The case studies illustrate our research towards implementing cost-effective, rapid metagenomic approaches that identify bacterial populations and characterise contamination events.