Australian Pathogen Genomics Program: evaluation and cost-effectiveness of pathogen genomics

Scientist examines the result of a plaque assay
In Australia and globally, infectious disease and antimicrobial resistance (AMR) are associated with substantial morbidity and mortality, posing a significant threat to public health. Accurate detection and genetic characterisation of causative pathogens are critical for controlling disease outbreaks and detecting AMR. Genomic epidemiology combines whole-genome sequencing of pathogens with epidemiological data to identify disease outbreaks, sources of infection, and AMR.
While Australia has made considerable advances in pathogen genomics, there are opportunities for data standardisation and integration across public health areas. The experience of the COVID-19 pandemic highlights the benefits of pathogen genomics to rapidly identify pathogens of public health concern, reduce spread locally and globally, and minimise the economic burden.
Australian Pathogen Genomics Program logo
The Australian Pathogen Genomics Program (AusPathoGen) was approved as the Australian government’s flagship program to address the rise in infectious diseases and AMR in Australia. AusPathoGen aims to reduce the impact of infectious diseases on public health by improving pathogen characterisation and optimising responses through large-scale integration of pathogen genomics, epidemiological data and surveillance data at the population health level.
There are three main aims of the AusPathoGen Program. These are:
  1. Optimise national genomics-based surveillance and investigation of infectious diseases through a real-time pathogen genomics analysis and alert platform.
  2. Implement effective, national genomics-based responses to infectious diseases and AMR.
  3. Evaluate the utility and cost-effectiveness of genomics-based public health responses.
This study led by the Australian National University addresses aim three. For more information on the first two aims and the AusPathoGen Program:

Visit the official study website
The objectives and components of this study are:
  1. Assess the public health utility and implementation of pathogen genomics
    • Situation analysis of pathogen sequencing by jurisdiction
    • Expert elicitation – ranking the benefits of sequencing different pathogens for public health
    • Importance and usefulness of genomics in public health for data users
    • Exploration of ethical, legal, and social implications of pathogen genomics
  2. Measure incremental costs, effectiveness, and cost-effectiveness of implementing whole genome sequencing-based surveillance for selected key pathogens
    • Economic evaluation of genomics-based public health responses
  3. Public health translation - investigate and optimise end user acceptability and interpretation of results.


AusPathoGen is funded by a $10M Medical Research Future Fund (MRFF) Genomics Health Futures Mission Flagship Pathogen Genomics grant.


AusPathoGen works closely with government, national committee groups, public health units and public health laboratories across Australia to develop nationally consistent and standardised approaches to genomic data integration, analysis and reporting of priority public health pathogens in line with the National Microbial Genomics Framework 2019-2022. The system underpinning the AusPathoGen program, AusTrakka, is governed by the CDGN and embedded in the public health system, having been endorsed by the PHLN and the AHPPC in 2020 as Australia’s national genomics surveillance platform.


Full list of partners available here: