Skip to main content

Monitoring Program

The Monitoring Program focuses on developing tools and diagnostic programs to better detect, track and reduce the impacts of pathogens, pollutants and other AMR risks to Australia’s food and agribusiness industries.


Research supported through our Monitoring Program ranges from large surveillance programs tracking the distribution and spread of AMR genes and organisms, through to environmental pathways and supply chains to highly-sensitive, pathogen-specific detection within targeted sectors or facilities. This information will help us to identify the sources and drivers of AMR, assess AMR risks, and develop strategies and interventions to improve AMR management.

We are creating core resources – including best-practice guidelines, standard operating procedures (SOPs), decision matrices and other documentation and expertise – to support the development of standardised methods and approaches that can be shared and adopted nationally.

Research projects in the Monitoring Program are designed to benefit the food, agribusiness and environmental management industries in multiple ways. We are undertaking research to reduce food and animal loss through earlier disease detection, thereby improving yields; cut treatment costs by ensuring that new interventions are necessary and cost-effective; improve consumer confidence in the quality and sustainability of Australian produce and water resources, and improve environmental stewardship and the reduced transmission of AMR pathogens.

Program objectives

  • Establishing best-practice guidelines for AMR diagnostics
  • Enabling cost-effective AMR monitoring within food production and processing
  • Monitoring AMR in water, wastewater and environments
  • Obtaining actionable insights for AMR contaminants in circular economies
  • Determining if new treatment solutions are needed and are cost-effective

Program lead

Dr Aaron Jex is Associate Professor in Veterinary Parasitology at the University of Melbourne. He is a laboratory head in the Population Health and Immunology division at WEHI, where he leads an infectious diseases research laboratory. He has worked in the Victorian water industry for more than 15 years, focusing on development and use of molecular-diagnostics and systems biology for the improved surveillance of pathogenic and toxigenic aquatic micro-organisms. During the COVID-19 pandemic, Aaron played a key role in developing advanced technologies underpinning Victoria’s COVID wastewater monitoring program, including methods to track high-risk SARS-CoV-2 variants and whole-genome sequencing methods to assist community tracing.

Current projects

Comprehensive monitoring of antimicrobial resistance in Australia’s drinking, waste and recreational waters
Proponent: Water Research Australia (Water RA)
Lead research provider: WEHI
Timeframe: 4 years (Foundational Project)

Advancing diagnostics for monitoring and management of fungicide resistance in grapevine
Proponent: Wine Australia
Lead research provider: South Australian Research and Development Institute (SARDI)
Timeframe: 4 years

Improved management of apple scab to reduce pesticide usage and fungicide resistance in Australian orchards
Proponent: Western Australian Department of Primary Industries and Regional Development (WA DPIRD)
Lead research provider: Curtin University
Timeframe: 4 years