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Published today in the Lancet Microbe, AusPathoGen’s translational research model outlines how data sharing agreements, program governance and ethics protocols, amongst other factors, were key in the successful implementation of national genomic surveillance of priority public health pathogens in Australia.

While other countries have managed to implement whole genome sequencing for routine surveillance, as can be seen by the United Kingdom Health Security Agency’s (UKHSA) pathogen genomics strategy and the United States Food and Drug Administration’s GenomeTrakr Network, this paper represents the first documented method that can serve as a template or protocol for other countries to follow.

Pathogen genomics is a powerful tool for further understanding infectious diseases. By analysing the genetic makeup of pathogens, such as SARS-CoV-2 (the virus that causes COVID-19) or the foodborne pathogen Salmonella enterica, health authorities can track outbreaks, identify emerging threats and inform effective responses. This complements traditional epidemiological methods, providing a broader perspective on the situation and enabling better decision-making.

The University of Melbourne’s Dr Jessica Webb, Research Fellow in genomic epidemiology with AusPathoGen and a lead author of the paper said globally, the uptake of pathogen genomics was accelerated by the COVID-19 pandemic.

“However as we move forward it is important to consider models for the sustainable implementation of this technology,” she said.

AusPathoGen, established in 2021 with a $10 million grant from the Medical Research Future Fund (MRFF), has generated datasets of unprecedented coverage on a national scale and has been a key contributor to increasing the knowledge and understanding of pathogens of public health significance in the international space.

“We have collated the first and largest national collection of pathogen sequences over seven individual pathogens, underpinning the identification of previously undetected cross-jurisdictional clusters that span long time periods for Mycobacterium tuberculosis, Salmonella and Shigella thanks to whole genome sequencing and collaborative networks across academia and public health in Australia,” she said.

“This program has been powerful in unearthing novel trends in the transmission of extensively drug resistant (XDR) Shigella spp. in high-risk groups that are highly connected in Eastern Australia, giving health departments a better idea of how to address outbreaks of this disease.”

The understanding of cross-jurisdictional outbreaks is particularly relevant in the context of Australia, with the six states and two territories being independently responsible for public health activities. Following the response to the COVID-19 pandemic, AusPathoGen was able to build on the previous work of the Communicable Diseases Genomics Network (CDGN) in bringing together not only the public health laboratories (PHLs), but also the Commonwealth Government, public health units (PHUs), and research and academic institutes to focus their efforts on generating the best possible data.

The University of Melbourne’s Dr Patiyan Andersson, Genomic Epidemiologist and Research Fellow with AusPathoGen and co-lead author of the paper, emphasised the potential of the collaborative networks that now exist thanks to the program.

“We now have inter-connected teams of bioinformaticians, genomic epidemiologists, and epidemiologists across public health laboratories and public health departments with an established working relationship that will strengthen future national public health surveillance capabilities,” he said.

Queensland Health’s Associate Professor Amy Jennison, Chief Scientist of Public Health Microbiology, current CDGN Chair and member of the AusPathoGen Executive Group, reflected on Australia’s strong history of genomic research and the applications of the technology for the future.

“Key players in genomics from across the country were first brought together in 2015 to form the CDGN, which lead to Australia having an established community of practice in the genomics space prior to the pandemic,” she said.

“These long-standing relationships allowed us to effectively coordinate nationally to contribute to the COVID-19 response prior to the availability of vaccines and helped in the public health decision making to keep Australia largely disease-free.”

The University of Melbourne’s Professor Ben Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory at the Peter Doherty Institute for Infection and Immunity (Doherty Institute), Principal Investigator of AusPathoGen and senior author of the paper, commented on the importance of this enhanced surveillance for public health.

“Our approach across jurisdictions to implementing the AusPathoGen Program underscores the importance of a well-structured and collaborative framework for pathogen genomics programs. By establishing clear data sharing agreements, robust governance frameworks and ethics protocols, we've been able to generate invaluable insights and inform effective public health interventions,” he said.

“This paper systematically outlines the key factors to consider when implementing these processes and provides the opportunity for others to utilise the power of pathogen genomics in their own public health surveillance.”

Additional information:

1. This research was funded by Australian Government Department of Health and Aged Care’s Medical Research Future Fund (MRFF) - $10 million under the Genomic Health Futures Mission (https://www.health.gov.au/our-work/mrff-genomics-health-futures-mission)
2. Peer-review: https://www.sciencedirect.com/science/article/pii/S2666524724002301 (DOI: https://doi.org/10.1016/j.lanmic.2024.100969)
3. This media release was originally published on the AusPathoGen website (https://www.auspathogen.org.au/blog/harnessing-genomics-for-public-health-the-auspathogen-program)