A mixed method, realist evaluation approach will be adopted to assess the importance and usefulness of genomics in public health for users of the data, including health departments and Australian Government agencies. The evaluation will be conducted in three phases:

1. Development of initial program theory (IPT)
2. Testing of IPT using empirical data; and
3. Refinement of IPT

Focus groups and key informant interviews with key stakeholders and end-users of the system will be used to develop, test and refine a national IPT. These data will also identify contextual factors and key areas for capacity-building, training and knowledge translation throughout the initiative and will inform the design of the workshops in project three.

In addition to contextual factors we will measure key public health outcomes of surveillance to test the IPT including:

• Timeliness of WGS data generation;
• Timeliness of public health response to WGS;
• Surveillance data trends;
• Interoperability with national surveillance and other platforms;
• Infrastructure usability; and
• Platform use and comprehension

End user satisfaction will also be tested, together with a detailed cost effectiveness analysis.

This program builds on existing cost-effectiveness studies to assess incremental costs, effectiveness and cost effectiveness of implementing WGS-based surveillance for the selected exemplar pathogens—Salmonella, CPE and TB compared to current approaches for surveillance.

Costing will consider both health care system and societal perspectives and will include assessment of direct and indirect costs of illness. For each pathogen, this program will estimate the additional health burden and costs of antibiotic resistant infections compared to infection with sensitive strains.

Our aim is to compare the incremental cost and effectiveness of WGS compared to current methods of testing and typing, and so assess the incremental cost effectiveness of WGS as the core tool for surveillance of these pathogens.

The use and utility of pathogen genomics varies by pathogen and context.  As part of a realist evaluation which seeks to understand how pathogen genomics works, for whom and under what circumstances, this project will inform the factors that contribute to pathogen genomics utility and support selection of priority pathogens for sequencing for public health surveillance.

This project will elicit opinions of genomic scientists and public health specialists to identify perceived benefits of whole genome sequencing different pathogens at the local and national level to assist with disease control efforts.

As with many new technologies, there is a risk that the benefits of public health pathogen genomics are inequitably distributed.  This may be due to unintended consequences such as the stigmatisation of affected communities, or through the neglect of diseases that primarily affect marginalised populations.  Additionally, legal implications of pathogen genomics are becoming increasingly salient.  

This research project aims to explore the ethical, legal and social implications of pathogen genomics to highlight emerging issues and develop a response set of guidelines.

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Building on work by CDGN, this program will evaluate the capacity for incorporating genomics into the public health system through a series of consultations and workshops with jurisdictional health departments and laboratory partners.

These consultations will identify how to best combine pathogen genomics with epidemiological data, enabling analysis and reporting at both jurisdictional and national levels. Working with key end-users to generate meaningful reports that can be interpreted and used by all, and at the laboratory level, this program will investigate the ideal approach for reporting genomics-based results at the jurisdictional level.Additionally, the program will develop and test methods (including on-line tools and test) for training and accreditation of end-users.

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