About AusPathoGen

The Australian Pathogen Genomics Program (AusPathoGen) is funded by the Medical Research Future Fund as part of the Genomics Health Futures Mission (GHFM) Flagships - Pathogen Genomics grant opportunity to address the rise in infectious diseases and antimicrobial resistance (AMR) in Australia.

Responding to areas of need

AusPathoGen, facilitated by the Communicable Diseases Genomics Network (CDGN), will build upon the successes achieved during the COVID-19 pandemic response, which demonstrated the value of pathogen genomics in detecting outbreaks in near real-time, and will apply this model on a broader scale to manage other infectious pathogens within Australia.

Leveraging the momentum from 2020 and advances made within the field, AusPathoGen will implement and evaluate a nationally synchronised approach to public health pathogen genomics. Utilising AusTrakka, a real-time genomic analysis and reporting platform, the program will facilitate rapid and coordinated responses to four areas of national need:

National alignment

Directly aligned with the objectives of the National Microbial Genomics Framework 2019-2022, AusPathoGen aims to:

  • Optimise national genomics-based surveillance and investigation of infectious diseases through real-time pathogen genomics analysis and alert platform (AusTrakka)
  • Implement effective, national genomics-based responses to infectious diseases and AMR
  • Evaluate the utility and cost-effectiveness of genomics-based public health responses.

Underpinned by a clear governance and data management framework, AusPathoGen aims to transform public health surveillance and investigation and drive equitable access to pathogen genomics capacity to all jurisdictions in Australia.


The transition into using pathogen genomics for public health was pioneered by a group of multidisciplinary laboratory and academic experts, across public health, bioinformatics, genomic epidemiology, and medical microbiology.

Years of expertise and learnings from translational research, and well-established relationships with key national and international stakeholders, including government, industry and genomics leaders, have been essential to the establishment of AusPathoGen, as well as the development of a roadmap for national integration of pathogen genomics into public health.

Roadmap for National Intergration

As demand continues to increase for genomics investigations and surveillance of public health concerns, this roadmap will be built upon and adapted for each pathogen to establish capacity for sustainable, best-practice models for the successful deployment of pathogen genomics into public health.

Pathogen genomics
Grown out of translational research activities undertaken in the larger jurisdictions within Australia.
CDGN established
National data sharing agreement
Established between genomics public health laboratories in every state and territory.
Expert Reference Panel of the Public Health Laboratory Network (PHLN)
CDGN embedded within the Australian Government public health committee governance as an Expert Reference Panel under PHLN.
Concept to reality
The COVID-19 pandemic accelerated the need for national genomics surveillance and rapid genomic data sharing of SARS-CoV-2 for public health.
AHPPC endorsement
Australian Health Principal Protection Committee (AHPPC) endorse Framework for data sharing and analysis for SARS-CoV-2 using AusTrakka, formalising rapid COVID-19 genomic data sharing and real-time national surveillance.
AusTrakka workforce
Established a dedicated AusTrakka National Analysis Team (genomic epidemiologists and bioinformaticians) to support operation.
Rapid national reporting
Real-time uploading, analysis and reporting of SARS-CoV-2 sequences in AusTrakka.
National surveillance