Australian Pathogen Genomics Program

The Australian Pathogen Genomics (AusPathogen) Program is a large scale integrated public health pathogen genomics research program, that will demonstrate the utility, cost-effectiveness, and capacity for translation of genomics into public health nationally. The program will deploy the national genomic platform (AusTrakka), for consistent analysis and reporting, and will collaborate with health departments and public health laboratories to implement national genomics-based responses to major infectious diseases, focusing on respiratory and vaccine preventable diseases, foodborne diseases, sexually transmitted infections and antimicrobial resistance.

Our Studies

Salmonella enterica is a nationally notifiable disease, resulting in an annual median of 36 outbreaks nationally and an incidence of infection rate of 185 infections per 100,000 population per year.

A national surveillance system for Shigella species will allow for earlier detection of extensively drug resistant (XDR) isolate clusters, assist in understanding transmission and incursion dynamics, and identify major lineages that are XDR towards therapy drugs.

Australia is committed to eliminating Mycobacterium tuberculosis.

Working toward a national, One Health Escherichia coli genomic surveillance network to provide insights that can inform interventions that improve human, animal and environmental health.

Invasive group A Streptococcal disease (iGAS) became nationally notifiable in Australia in July 2021.

Invasive pneumococcal disease (IPD) has been nationally notifiable since 2001

Candida auris is an emerging fungal infection that has been identified in over 40 countries since it was first identified in Japan in 2009.

Staphylococcus aureus bloodstream (SAB) infections are highly prevalent in Australia with ~5,000 infections/year, require hospitalisation for treatment, can be deadly and the disease can be exacerbated by antibiotic resistance.

Enterococcus serves as a critical example of a One Health pathogen due to its ability to inhabit the gastrointestinal tracts of humans and animals and persist in environmental reservoirs including soil, fresh water and marine water.

Pathogen genomics has proved a critical tool in Australia’s response to the COVID-19 pandemic.