Is DNA sequencing the secret to achieving the best water quality?

Posted 10 April 2017
DNA sequencing
As we move towards health-based targets (HBT) for water quality, a new study suggests DNA sequencing could prove a cheaper, more targeted tool for monitoring microbiological safety than existing methods. 

The Australian Water Quality Centre (AWQC) – a business unit within SA Water – has been investigating the use of high-throughput next-generation DNA sequencing (NGS). 

The move was spurred by observations that water utilities, particularly smaller ones, would find it challenging under a HBT regime to effectively assess the risk from pathogens such as Cryptosporidium while keeping costs down. 

“Directly monitoring Cryptosporidium is quite expensive; it can be at least $700 per sample test,” said AWQC Team Leader – Source Water and Environment Research Dr Paul Monis.

“That's expensive for large utilities, but at least they've got a large customer base and economy-of-scale to make it worthwhile. But for a smaller utility, that testing might not be feasible.”

He said that although high-throughput NGS was more expensive than E. coli testing, it was cheaper and – most importantly – more targeted than traditional Cryptosporidium testing.

“Other alternative faecal source tracking methods are a probability thing – there are some bacteria that are more common in humans than dogs and cattle,” Monis said.

“Other alternative faecal source tracking methods are a probability thing – there are some bacteria that are more common in humans than dogs and cattle,” Monis said.

“But NGS tells us exactly where the DNA is from. We can customise it to target groups of animals – like all vertebrates – or even groups of bacteria.

“It offers a powerful screening tool. Instead of having to specifically look for E. coli or a particular pathogen, utilities can collect a water sample and cost-effectively get a profile of what sort of animals have been contaminating the water.”

The trial showed great potential, but further work is underway to broaden the application of this technique.

“Quality control criteria need to be developed for assessing sample extracts prior to NGS, for verifying the performance of each NGS run, and for removing sequences present due to cross-contamination,” the resultant report stated. 

“Further work is also required to develop a curated database and to verify the accuracy of species identification.”

Monis will be discussing the development of DNA technology and its uses for water quality assessment at the upcoming Ozwater’17 conference in Sydney. To learn more and to register, click here