Dr Nijoy John

Using his expertise in developing molecular diagnostics to profile diverse microbial communities, Dr Nijoy John is monitoring AMR in drinking, waste and recreational waters.

Q: You’re working on the ‘Comprehensive Monitoring of Antimicrobial Resistance in Australia’s Drinking, Waste and Recreation Water’ project, part of the SAAFE Monitoring Program. What does that involve?

Nijoy: The project focuses on identifying, mapping and tracking the distribution and transmission of AMR genes in water. We want to enhance our understanding of AMR dynamics across water systems so we can support the development of effective monitoring and mitigation strategies.

Q: What will information on AMR genes tell you?

Nijoy: We know that there are AMR genes and antimicrobial-resistant organisms present in wastewater treatment plants, but we want to understand how those genes spread between organisms.

We also want to know how much of this AMR survives throughout the treatment chain, from the influent all the way to the effluent. Treated water can end up being used for irrigation purposes or be released back into the environment, so we want to know the AMR risk. I’ll test water samples from multiple points in the treatment chain and after different kinds of treatment, such as UV disinfection or chlorination.

By identifying where and how AMR genes persist and move through water systems, we can help water and public health industries to better understand and respond to AMR risks. We can inform evidence-based strategies for AMR monitoring and mitigation or develop standardised protocols that will allow for much more scalable and reproducible methods for AMR surveillance.

Ultimately, I hope my work will contribute to developing proactive risk-based approaches that help industry stakeholders to safeguard public and environmental health.

Q. How does this project make use of your expertise?

Nijoy: My PhD at the University of Melbourne focused on developing diagnostic platforms to monitor harmful algal blooms. Most of the techniques that I used in my PhD and post-doc research have been based on PCR [polymerase chain reaction] and next-generation sequencing techniques, and I’ll be applying the same sort of technologies to this project.

In the past, I've worked extensively across diverse aquatic environments in Australia – including freshwater, wastewater, and recycled water ecosystems – to understand microbial communities and develop tools for the water industry and for public health surveillance. That’s a good foundation for my research into AMR.

Q. What techniques will you use in this project?

Nijoy: I’ll be applying different technologies to water samples from about 30 sites including wastewater treatment plants, recreational waters and drinking water catchments.

This includes quantitative PCR and next-generation sequencing to detect key AMR marker genes. Most of the methods are already available, but I will have to optimise them for use in this context. An assay that works on clinical samples may not work as well on wastewater samples, for example.

I'm particularly excited to explore advanced techniques that I've never previously worked with. For example, we are looking at some relatively new methods like EPIC-PCR, which is used to link a gene (in this case, an AMR gene) to its host microbial organism, and Spatial omics, which allows us to match AMR genes with the cells encoding them and to determine if those cells are viable and can transmit infection. These methods will open up new dimensions in understanding AMR ecology.

Another benefit is that all the methods and technologies that I use here can be applied to other sectors as well. Even though my project focuses on water systems, the same approach can be applied to many other sectors within SAAFE, including agriculture and aquaculture.