This project aims to further develop and implement AusTrakka, a national genomics surveillance platform already being utilised across states and territories for SARS-CoV-2. By working together with the pathogen specific teams this program aims to investigate key functional features of the platform that will make it useful and meaningful to informing public health response. Key features that will be analysed and evaluated include accessibility and acceptability, turn-around times to data analysis and presentation, simplicity of analysis interpretation, and capacity for rapid multi-jurisdictional outbreak detection.

As genomic sequencing is routinely established, genomic data will be submitted in realtime to AusTrakka for daily analyses to define genomic matches between bacterial isolates within and between jurisdictions, and internationally. Subsequent actions will be pathogen-specific, in line with current structures for disease groups.

Considerable debate exists regarding optimal bioinformatic methods for assessing genetic relatedness of public health pathogens, and how to best interpret and report these results. Additionally, there are no standardised national bioinformatic approaches for rapidly and accurately detecting antimicrobial resistant (AMR) genes from public health pathogens. This project will identify, test and define optimal bioinformatics analysis approaches and deploy tools for addressing key questions at a national level and implemented through AusTrakka.

Importantly, the program’s partnerships will facilitate working towards a consensus in the interpretation of pathogen genomic results to harmonise reporting across jurisdictions.

Development of national capacity to undertake rapid whole-genome sequencing (WGS) in Australia, including in remote regions, will improve public health responses. This project will pilot and evaluate models of national pathogen sequencing implementation, including comparison of different structural models of WGS-based workflows, for example through the establishment of referral networks or more streamlined in-field capacity. Key components of the evaluation of these approaches will include quality of data generated, turn-around times for data generation, cost of WGS per sample, and knowledge and expertise gaps that limit the capacity for national implementation.