National Microbial Genomics Framework 2019 – 2022

Page last updated: 06 April 2021

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Implementation plan for the National Microbial Genomics Framework 2021–2022

The Framework

On 23 April 2019, the National Microbial Genomics Framework 2019-2022 (Framework) was endorsed by the Australian Health Protection Principal Committee (AHPPC). The Framework is the first national strategic document for microbial genomics in Australia. It provides a nationally consistent and strategic view for integrating microbial genomics in the Australian public health system, and for identifying microbial genomics policy issues and challenges.

It was developed by the Office of Health Protection within the Department of Health, in close collaboration with a joint Public Health Laboratory Network (PHLN) - Communicable Diseases Network Australia (CDNA) Project Reference Group on Microbial Genomics, which was established to guide development of the Framework. Both PHLN and CDNA are standing committees of the Australian Health Protection Principal Committee (AHPPC).

The Framework includes a set of strategic priorities which cover standardising the national approach, technology and data governance, integration into public health, equitable access, workforce and financing. The Framework places a strong focus on issues that will benefit from collaboration across all jurisdictions and between public health laboratories and public health units specifically and is consistent with, and complementary to, the National Health Genomics Policy Framework.

It aims to harness the public health benefits of microbial genomics, genomics knowledge and technology in the national public health system in a consistent, effective and efficient way in order to improve public health outcomes.


The Framework sets out how the Australian Government and the states and territories will work collaboratively to integrate microbial genomics approaches into the health system over time. While the Framework outlines agreed national policy approaches and high-level priorities for microbial genomics, it does not identify all the specific actions needed to take the framework forward.

As such, the development of an associated implementation plan is currently underway. It is being developed by the Office of Health Protection, in close collaboration with the Communicable Diseases Genomics Network, an Expert Reference Panel under the Public Health Laboratory Network (PHLN) which consists of laboratory representation from all jurisdictions as well as public health unit representation where needed.

The purpose of the implementation plan will be to identify actions, responsibilities, time frames, priorities and resourcing requirements for the integration of microbial genomics into the Australian public health system.


The development of the Framework was informed by national, state and territory consultation, notably, with AHPPC, PHLN, CDNA and CDGN.


The timeframe of the Framework is three years, with a review anticipated in 2022 to inform the next iteration. This Framework is not intended to address all issues related to microbial genomics. Instead, it has been designed to be adaptable to the rapidly advancing and accessible technologies and to draw attention to particular issues for initial consideration. It indicates where further work is needed and recognises that subsequent reviews of the Framework are expected to identify other emerging issues and policy challenges.

Strategic Priorities, Principles and Enablers

Five Strategic Priorities are identified in the Framework for Implementation:

  1. Strategic Priority 1 – Standardised National Approach
  2. Strategic Priority 2 – Technology and Data Governance
  3. Strategic Priority 3 – Integration into Public Health
  4. Strategic Priority 4 – Access and Workforce
  5. Strategic Priority 5 – Financing

The following six principles underpin the Strategic Priorities of the Framework:

  1. National — developed jointly by Australian and state and territory governments
  2. High-level, strategic framework — identification of themes, principles and considerations for embedding consistency and national coordination as enablers for more efficient, equitable and effective utilisation of microbial genomics.
  3. System-focused — an understanding of what the system can deliver and consideration of how a change within one system domain will impact, interact with and change the other domains and affect the system as a whole.
  4. Evidence-informed public policy — ensuring that the best available research and information is used to guide decisions at all stages of policy processes.
  5. Flexible to keep up with scientific advances — adaptable to the evolving nature of microbial genomics technology, latest scientific findings, advances and potential shifts in microbial genomics policy issues and challenges.
  6. Identify priority areas — prioritising the microbial genomics policy issues and challenges that need to be addressed and identifies directions for change / opportunities for action and areas that require further work.

To help guide decision and policy makers in successfully implementing the Framework, three key enablers have been identified:

  • collaborative governance and leadership;
  • stakeholder engagement; and
  • national and international partnerships.


Oversight for the Framework is provided by a time-limited joint PHLN-CDNA Microbial Genomics Project Reference Group (PRG), which was established to guide development of the Framework and associated Implementation Plan. Both PHLN and CDNA are standing committees of AHPPC. The PRG is chaired by the Commonwealth and comprises nominated representatives from state and territory public health laboratories and public health units.

Oversight by the PRG provides opportunities for open dialogue between public health laboratories and public health units to share their expertise, explore complex challenges and provides opportunities to align efforts in the implementation of microbial genomics in the public health system. This is important in the successful implementation of the Framework, which will require strong collaborative relationships between national, state and territory governments, public health laboratories and units, researchers and other health professionals.

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