The Australian Pathogen Genomics Program (AusPathoGen) brings together expertise from across academic and public health disciplines to investigate effective models that demonstrate equitable access to pathogen genomics capacity for public health surveillance of four areas of national need:

  • Foodborne diseases
  • Respiratory and vaccine-preventable diseases
  • Sexually transmitted infections
  • Antimicrobial resistance (AMR) and emerging pathogens (biothreat agents)

Pathogen-specific teams will undertake milestone activities under the guidance of the Steering Committee and national program partners.These teams will comprise of:

  • Academic Leads
    Responsible for pioneering the academic and strategic aims of the study in line with program aims and priorities.
  • CDGN Public Health Laboratories and Partner Clinical Laboratories
    Responsible for providing microbial genomics expertise and advice on program activities.
  • Postdoctoral Researchers and PhD students
    Responsible for developing the study design and research framework, and coordinating data and resources under the guidance of Academic Leads.
  • AusTrakka National Analysis Team representatives
    Responsible for translating research outputs into public health practice, and considering important factors such as public health and privacy legislation, governance for data sharing and analysis, and accreditation of pipelines.
  • Evaluation scientists
    Evaluation is a key component of this program, evaluation scientists will collect quantitative and qualitative data from pathogen-specific groups to inform their evaluation studies.  
  • Stakeholders
    Responsible for contributing towards discussions and guidance on program implementation on a broader level, and ensuring program activities aligns with national and international public health needs in the field of pathogen genomics and communicable diseases.

Our Studies

Working across all jurisdictions in Australia, AusPathoGen has established the following milestones for each infectious pathogen under investigation, to form the foundation for accessible and efficient national models for pathogen genomics implementation that solve public health problems.

AusPathoGen uses innovative methodologies to deliver key milestones, including:

  • Identifying processes for comparative analysis and responses to Australian pathogen genomic data compared to international agencies.
  • Novel data approaches to enhance data utilisation
  • Cross-sectoral data integration
  • Quality assurance programs


  • Establish multi-disciplinary project team
  • Define and develop translational research project and plan
  • Capture and share research findings
  • Translate research outcomes into national implementation frameworks
  • Integration into AusTrakka for real-time genomic surveillance

Salmonella enterica

Salmonella enterica is a nationally notifiable disease, resulting in an annual median of 36 outbreaks nationally and an incidence of infection rate of 185 infections per 100,000 population per year.

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Shigella species

A national surveillance system for Shigella species will allow for earlier detection of extensively drug resistant (XDR) isolate clusters, assist in understanding transmission and incursion dynamics, and identify major lineages that are XDR towards therapy drugs.

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Mycobacterium tuberculosis

Australia is committed to eliminating Mycobacterium tuberculosis.

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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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Invasive group A streptococcal disease

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

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Invasive pneumococcal disease

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

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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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Pathogen genomics has proved a critical tool in Australia’s response to the COVID-19 pandemic.

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