Dr. Clare Sloggett2,5, Mr. Samuel Carswell2,5, Mr. Vi Phu2,5, Ms. Jolene Farrell2, Mr. Mann Sheth2,5, Dr. Wytamma Wirth1, Dr. Ceyhun Güngör1,3,4, Ms. Tuyet Hoang1,3, Dr. Torsten Seemann1,2,3,5
1Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Australia, 2Department of Microbiology and Immunology, The University of Melbourne, Australia, 3AusTrakka Advisory Group, Australia, 4AusTrakka National Analysis Team, Australia, 5AusTrakka Development Team, Australia
Biography:
Dr. Clare Sloggett is the lead of AusTrakka platform development at the Peter Doherty Institute for Infection and Immunity. She began her research career with a PhD in computational physics before moving into genomics research at Melbourne Bioinformatics. She played a founding role in Australia's Genomics Virtual Laboratory project, establishing cloud-based Galaxy infrastructure as a core research service in Australia and a part of the international bioinformatics community. She now leads the development team designing, building and maintaining the AusTrakka platform, supporting secure data exchange and pathogen surveillance among public health laboratories in Australia and New Zealand.
Abstract:
AusTrakka is Australia’s platform for genomic pathogen surveillance, operationalised under the Communicable Diseases Genomics Network and funded by the Australian Government Department of Health and Aged Care. The SARS-CoV-2 pandemic highlighted the need for more rapid genomic data sharing and a unified approach to pathogen surveillance across states and territories. In response, AusTrakka was deployed in 2020 to coordinate genomic surveillance and provide regular genomics reports on the current trends and variants circulating across Australia and New Zealand. AusTrakka now hosts over 300,000 sample records and over 16TB of sequence data across a range of pathogens.
The AusTrakka development team has worked closely with end-users to respond to real-time needs in outbreak management, while planning for future requirements for public health surveillance. Key features implemented in the platform include: a data model covering both sequence data and epidemiological metadata, a permissions model to allow organisations to share selected data with the relevant people involved in an outbreak investigation, real-time validation feedback for data uploaders, visualisation features for interactive exploration of epidemiological metadata in the context of large-scale phylogenetic trees, and real-time plots and dashboards showing the current state of the data in the investigation.
AusTrakka also currently facilitates the national MRFF-funded AusPathoGen translational research program, which aims to develop best practices approaches for and evaluation of pathogen genomics implementation into public health.
We will share the design challenges and lessons we’ve encountered in building AusTrakka, and how this has informed our plans for the future.