New research highlights the role of genomics in tracking waterborne disease

Two recent publications from the Centre for Pathogen Genomics (CPG), in collaboration with the University of Melbourne Veterinary School, are helping to reshape how waterborne diseases are detected and managed in Australia, highlighting both a growing public health challenge and the value of genomics in response.

Tracking a surge in infections

In a recent study led by Dr Marielle Babineau (CPG), in collaboration with Dr Anson Koehler and Professor Robin Gasser (University of Melbourne Veterinary School), researchers conducted the most comprehensive molecular analysis to date of Cryptosporidium and Giardia in southern Australia.

Analysing more than 2,300 samples from Victoria (2020–2024), the team identified substantial genetic diversity, including multiple previously unreported subtypes during a period that saw a major rise in cryptosporidiosis cases in 2024.

By combining genomic and epidemiological data, the study was able to:

• Link infections to recreational water outbreaks, particularly public swimming pools
• Identify previously undetected potential outbreak-related cases
• Highlight potential zoonotic transmission pathways

Read the full study: Large-scale molecular epidemiological survey of Giardia and Cryptosporidium in Victoria, Australia (2020–2024)

Strengthening national surveillance

A second publication, led by Dr Koehler and Professor Gasser and co-authored by Dr Babineau, outlines the need to integrate genomics into routine surveillance of waterborne pathogens.

Current approaches rely on conventional diagnostics, limiting the ability to detect outbreaks and trace sources. The authors propose a national genomics-enabled surveillance approach, building on existing infrastructure such as AusPathoGen and AusTrakka, to support real-time data sharing and more targeted public health responses.

Read the viewpoint: Advancing genomics for waterborne pathogen surveillance in Australia

Looking ahead

Together, these studies highlight how genomics can strengthen outbreak detection, improve understanding of transmission, and support more proactive public health responses, positioning Australia to better respond to emerging waterborne disease threats.