Tracking how AMR spreads through water environments

A key challenge in tackling antimicrobial resistance (AMR) is the lack of detailed information on how AMR moves through complex environmental systems. Little is known about the distribution, abundance and transmission of AMR in water environments such as rivers, wastewater networks, drinking water catchments and treatment plants.

A SAAFE project led by Professor Aaron Jex at WEHI is addressing this knowledge gap. Water Research Australia and industry partners including Melbourne Water are also involved.

“Melbourne Water is supporting the SAAFE CRC’s water monitoring project to ensure the water sector continues to deliver safe, reliable products while minimising environmental impact,” says Dr Nick Crosbie, acting Manager of Wastewater and Marine Research at Melbourne Water.

The goal of the project is to develop and deploy tools to identify, quantify and track AMR genes and organisms throughout the water cycle. Understanding how water treatment processes, post-treatment storage practices and environmental conditions affect the abundance and spread of AMR is essential for developing effective interventions.

“We want a better understanding of the risk of AMR transmission through the different phases of water treatment, as well as the impact of different upstream effects like major rainfall events or large cyanobacterial blooms,” says Prof. Jex.

Much of the project’s first phase has focused on establishing and validating the methods needed to undertake this work. The team has adapted and optimised existing technologies for sensitive, specific DNA detection and broad-spectrum surveillance of AMR.

Multiplex quantitative PCR is used to target common genes conferring AMR. “This method allows us to look very precisely and sensitively for a small number of things we already know about,” says Prof. Jex.

This approach can identify, for example, where in the treatment chain there could be an AMR hotspot. The team can then narrow down areas for deeper analysis using shotgun metagenomic sequencing, which provides information on all genetic material in a sample.

Working with technology partners, the team has also developed hybrid capture technology specifically for detecting AMR. The technology uses DNA fragments that are designed to interact with thousands of AMR gene markers. “This means we can focus our DNA sequencing on just the material we’re interested in, which will increase the sensitivity and reduce the cost,” says Prof. Jex.

The project team is now moving on to the next phase of the research: using these tools to monitor AMR in water samples. Melbourne Water is supplying data and samples from across the city’s waterways, drinking water catchments and wastewater systems. “This will ensure the research reflects real-world conditions,” says Dr Crosbie.

“Once we have a couple of seasons’ worth of monitoring data, we can start to make scientific observations and look at trends,” says Prof. Jex.

Through this collaboration, Melbourne Water is working toward practical outcomes: more cost-effective monitoring methods, stronger risk assessment models, and viable approaches to managing AMR within water systems. “These will support better decision-making across our operations and help the sector respond to emerging risks with confidence,” says Dr Crosbie.

But the project is expected to have wider benefits. The AMR monitoring data will be fed into other SAAFE research, such as the risk assessment projects led by Professor Nick Ashbolt. The optimised DNA detection methods could also be valuable to other groups that are extracting genetic material from environmental samples.