Metagenomics and Whole Genome Sequencing to Understand Drinking Water Quality

Brent Gilpin, William Taylor, Iain Haysom, Kirstin Thom, Susan Lin, Paula Scholes, Beth Robson, Paula Scholes, Belinda Cridge and Megan Devane - Institute of Environmental Science & Research Limited

Regulatory responsibility in Aotearoa for drinking water has shifted from the Ministry of Health to Taumata Arowai whose expanded remit will encompass an estimated 75,000 drinking water supplies. Traditionally the only tool used by water suppliers for monitoring microbial contamination was testing for the indicator bacteria E. coli. Taumata Arowai is developing new drinking water quality standards and rules, with increased testing requirements in the source water, at the treatment plant and within the reticulation network. This includes adding another indicator bacteria - Total Coliforms. The key issue is that while detection of E. coli and Total Coliforms suggests there is a problem, it provides little guidance as to the source of that problem, or what to do about it. This has led to inaction by some water suppliers, and default boil water notices by others. Taumati Arowai is emphasising a “Find & Fix” approach, which while increased testing of more supplies will certainly find more issues, fixing those requires new science and new understanding.

Technological advances in DNA sequencing have now reached the point of maturity that they can be applied to better understanding and management of drinking water. Whole genome sequencing of isolates, and microbial community analysis using metagenomic approaches provide new tools for evaluating drinking water. There are two key applications:

1) Understanding source water (rivers, lakes and ground water aquifers) and contamination pathways. Metagenomic approaches provide opportunities to understand the sources affecting water supplies and the microbial community present including non-faecal pathogens such as Legionella.

2) Investigating the causes of detections of Total Coliforms and E. coli within a drinking water supply. Is the detection due to contamination events affecting the source water, treatment failure, network contamination (breaks in pipes or backflows, storage tank issues), network biofilm sloughing, or in fact sampler or laboratory errors?

This paper will explore these revolutionary technologies with examples of their actual or theoretical application to the 2016 Havelock North campylobacteriosis outbreak ill.