There is considerable interest and momentum in the application of large-scale routine pathogen genomic public health surveillance. The high-resolution characterisation provides a powerful means to identify high risk clones, monitor development of resistance to counter measures, or accurately describe transmission patterns, and in conjunction with epidemiological data inform public health action. The reality of finite resourcing, however, means that implementation decisions need to be based on empirical evidence.
Here we will present on findings from the first nationally comprehensive genomic studies of key public health priority pathogens. The work has been undertaken by the Australian Pathogen Genomics program (AusPathoGen), a four-year Medical Research Future Fund project ($10M, 2021-25), supported by the Australian Government Department of Health and Aged Care, bringing together over 60 stakeholder organisations across Australia and New Zealand. AusPathoGen aims to investigate approaches to integrate genomic surveillance for priority pathogens of public health concern. The program invested in democratisation of genomic sequencing capability, through establishment or strengthening in jurisdictions where it was lacking or emerging - enabling all jurisdictions to contribute data to the national picture.
Through stakeholder engagement AusPathoGen identified non-typhoidal Salmonella, Shigella spp, and Mycobacterium tuberculosis as the first priority pathogens to study. Snapshots, where all notified cases in all jurisdictions are attempted to be sequenced, form central parts of these projects, generating comprehensive and representative datasets. AusTrakka, Australia’s government-funded platform for genomic surveillance deployed during the COVID-19 pandemic, has been further developed and utilised for the data management of the projects, which will enable impacts beyond AusPathoGen.
The projects have generating truly representative views of transmission patterns and extent of outbreaks of these pathogens previously not seen at the national level. The data not only provide foundations underpinning policy decisions but also forming a crucial scientific reference resource for future studies of these pathogens nationally and internationally.