Advancing genomics for waterborne pathogen surveillance in Australia

Waterborne pathogens, particularly Cryptosporidium, pose a growing public-health risk in Australia and globally. Cryptosporidiosis notifications have increased markedly in recent years across multiple countries, driven by greater recreational water exposure, human mobility and climate variability. Climate change, including rising temperatures and extreme weather events, is expected to intensify transmission. Emerging drug resistance in some parasitic pathogens underscores the need for high-resolution surveillance. Despite its status as a nationally notifiable disease, cryptosporidiosis surveillance in Australia relies largely on conventional diagnostic methods that lack sufficient resolution for outbreak detection and source attribution. This Viewpoint examines the rationale for a national genomics-informatics platform integrating whole-genome sequencing, bioinformatics and analytics to modernise surveillance. Drawing on international experience, we outline how genomics can support outbreak tracking and transmission mapping. While bacterial and viral pathogen surveillance has advanced under national genomic initiatives, eukaryotic pathogens remain underrepresented. The proposed platform would leverage existing infrastructure to strengthen responses.