The OUTBREAK history

Learn how the AMR knowledge engine was born

Inspired by a small news story…

Our newest weapon in the fight against antimicrobial resistance (AMR) was inspired by a small news story on a US university website.

In the story, weather-like visualisation techniques had been used to demonstrate geographical patterns of AMR. This sparked the thinking: could overlaying and integrating additional and diverse data sets lead to new knowledge about AMR? And could this help us develop a solution to the growing problem?

For decades, countries across the world have focussed on monitoring antibiotic prescribing practises in the medical and veterinary sectors, as well as detecting and reporting on key disease-causing bacteria and their AMR status.

More recently, however, whole genome DNA sequencing of bacteria has been used to support traditional approaches for tracking infectious disease spread and antibiotic resistance.

OUTBREAK was born from a group of researchers who explored and took this technique further. They understood that tracking drug-resistant genes using DNA sequencing could provide greater insights on the growth and spread of AMR when using a One Health approach (integrating data from humans, animals and the environment).

This team included several University of Technology Sydney (UTS) researchers: Professor Steven Djordjevic who, through AusGEM, a long-standing collaboration with the NSW Department of Primary Industries (NSW DPI) was already using genomics to monitor AMR prevalence in farms, abattoirs and hospitals; other AusGEM staff included Dr Branwen Morgan, who had been researching the idea of adding blockchain to track AMR in agriculture and food; Professor Aaron Darling, a computational biologist, and Dr Daniel Bogema, a bioinformatician. Associate Professor Erica Donner, an environmental scientist from the University of South Australia brought extensive knowledge of AMR in water and wastewater. They then drew together additional people across UTS and added skills such as in AI, health geography, pharmacy, law and health regulation.

Together, the team investigated how One Health genomics could inform risk assessments based on the likelihood of AMR infection. They devised an AMR track and trace visualisation system that could collect and analyse data from humans, animals, plants and the environment; that is, OUTBREAK.

As further discussions, investigations and connections evolved, so too did the project’s team. An existing, well-developed AMR program at the University of Wollongong added significant strength and clinical collaborations (Sonic IML and the Illawarra Shoalhaven Local Health District). As did the extensive expertise from CSIRO’s Data 61 and Health and Biosecurity teams who provide risk modelling, e-Health, One Health economics, and a track record in epidemic preparedness. This was rounded out by the University of Newcastle, the Quadram Institute (UK), the Sax Institute and several SMEs (MicroGEM, Microba, Sensing Value) with support from Oracle.

In February 2019, a UTS-led submission was made to the Department of Health’s Medical Research Future Fund Frontier Program. OUTBREAK was one of ten successful stage 1 applicants, leading to the appointment of key personnel and an expert advisory board.

This team has put together their proof of concept and will apply for stage 2 funding by Q4 2020.

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