How we work

Translation of pathogen genomics academic research into public health is at the core of the Australian Pathogen Genomics Program (AusPathoGen). The following enablers will influence the AusPathoGen approach to successful integration of pathogen genomics into public health.


Translational Research

Translational research activities will inform where pathogen genomics could be best utilised in clinical and public health responses to the four areas of national need - foodborne diseases, respiratory and vaccine-preventable diseases and sexually transmitted infections, and antimicrobial resistance (AMR) and emerging pathogens (biothreat agents). Led by a multidisciplinary team of academics, clinicians, and laboratory scientists, AusPathoGen will continually review and optimise studies to best inform approaches for solving public health problems using pathogen genomics.

Genomic Preparedness

The Communicable Diseases Genomics Network (CDGN) has been essential to public health preparedness in Australia and New Zealand since the network was established in 2015 by a group of passionate laboratory experts. CDGN includes representatives from public health laboratories across all jurisdictions in Australia and New Zealand. In 2019, CDGN was formalised as an Expert Reference Panel under the Australian Government Public Health Laboratory Network (PHLN) a standing committee under the Australian Health Protection Principal Committee (AHPPC). CDGN facilitates sharing of microbial genomics data and knowledge, including antimicrobial resistance pathogens and other pathogens of outbreak significance, in a collaborative and responsible manner to improve public health activities nationally. As the key facilitating partner of AusPathoGen, CDGN has established frameworks and relationships which will be leveraged to mutually achieve the program and networks aims of strengthening and broadening utility of public health pathogen genomics.

Governance and Agreements

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.

Technical Development, Implementation and Deployment

The AusTrakka system provides equitable access to computational capability between all states and territories supported by the AusTrakka National Analysis Team and platform. The AusTrakka platform enables real-time uploading of genomic sequence data by public health laboratories, allowing jurisdictions to view their sequence data in the national context and identify ‘matches’ signifying potential transmission or emerging clusters.

AusPathoGen will apply learnings from the COVID-19 pandemic, in using innovative technologies, communication, and coordination, to inform the implementation of other pathogen genomics into public health on a national level. Together with CDGN, the AusTrakka team will work closely with the pathogen-specific teams to ensure translational research developments and outcomes can be implemented within a public health laboratory accredited environment and integrated into the AusTrakka system.

National Demand and International Context

Globally, the demand for pathogen genomics is increasing with countries working towards developing their own capacity or partnering with genomics-enabled laboratories to enhance surveillance activities and contribute to the global genomic context. AusPathoGen will share learning to the global genomics community and will contribute  to and implement international best-practices and standards.


The COVID-19 pandemic accelerated the use of pathogen genomics in public health when the urgent need arose for a nationally consistent and real-time approach for sharing and analysing SARS-CoV-2 genome sequences. Taking key learnings acquired by program partners and the CDGN during this response, AusPathoGen will adopt and build upon this pathogen genomics implementation model, whichwill be adapted to each pathogen and further optimised through translational activities by leading academic researchers involved in this program.  

AusPathoGen Studies

Candida auris

Candida auris is an emerging fungal infection that has been identified in over 40 countries since it was first identified in Japan in 2009.

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Invasive pneumococcal disease

Invasive pneumococcal disease (IPD) has been nationally notifiable since 2001

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Invasive group A streptococcal disease

Invasive group A Streptococcal disease (iGAS) became nationally notifiable in Australia in July 2021.

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Escherichia coli

Working toward a national, One Health Escherichia coli genomic surveillance network to provide insights that can inform interventions that improve human, animal and environmental health.

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Our Partners

The Australian Pathogen Genomics Program (AusPathoGen) is made possible through national and international partnerships that bring together expertise from across academic, industry, government, and publi chealth sectors, to solve public health problems using optimised pathogen genomics models.