This project will conduct systematic assessments of priority pathogens (Salmonella enteritidis, Shigella, Mycobacterium tuberculosis, Vibrio, invasive Group A Streptococcus, Mpox) to define available epidemiological data and requirements for integration of genomic data into public health systems. It will consult public health professionals to refine how genomics can best contribute to current surveillance of the pathogens, how the data most effectively should be reported, and design methodology to link laboratory genomic sequences with existing public health data sources in real-time. The research will run as a time limited pilot for each pathogen, of integrated analysis with a feedback loop from public health professionals using the data, to optimise functionality ahead of final implementation into routine public health use. 

Outcome:

‍Functional near real-time nationally integrated genomic surveillance pilots for six priority pathogens (Salmonella Enteritidis, Shigella species, Mycobacterium tuberculosis, Vibrio parahaemolyticus, invasive Group A Streptococcus, Mpox)

Determine the future for genomics-enabled surveillance in Australia

The project will conduct a mixed-methods evaluation to assess timeliness, interoperability, usability, and end-user satisfaction. The project will also conduct health economics analysis of cost-effectiveness of the pilot surveillance projects and use focus groups to determine prioritisation principles and implementation timelines across jurisdictions, including priorities for Aboriginal and Torres Strait Islander populations.

Outcome:‍

Evidence-based assessments of genomics utility of pilot surveillance projects for public health action including stakeholder-informed scoping of future priorities. Report findings will be shared with the Australian CDC to inform future planning and published publicly.

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