Implementation, integration, analysis and genomic informed responses

Research, develop and implement effective national genomics-based responses to infectious diseases and antimicrobial resistance (AMR).

Implementation, integration, analysis and genomic informed responses
Project 1

Foodborne Diseases

Australia has one of the highest rates of reported foodborne diseases globally, with salmonellosis alone costing $147 million each year¹. Foodborne diseases are the result of consuming food contaminated with bacteria, viruses, parasites or chemical substances such as heavy metals, and can occur during any step of the food production, delivery and consumption chain². Internationally, genomics for foodborne diseases has been shown to reduce the burden and size of outbreaks. Here, we will investigate and optimise genomics for national surveillance and response to foodborne diseases using two exemplars:

  • Listeria
  • Salmonella Typhimurium (STM)

¹ World Health Organization

² World Health Organization

Project 2

Respiratory and Vaccine-Preventable Diseases (VPDs)

Vaccines are one of the most cost-effective public health interventions against communicable diseases. Genomics-based investigations can shed new light on the transmission of VPDs and inform targeted vaccination efforts. This project will involve conducting multi-centre studies of exemplar vaccine-preventable diseases to identify the added value of genomics-based investigations, optimise the reporting and communication of results, and evaluate the impact on national response to infectious diseases. The following pathogens will be studied:

  • Tuberculosis (TB)
  • Influenza
  • Invasive bacterial VPDs (IB-VPDs)
  • Measles
Project 3

Sexually Transmitted Infections (STIs)

STIs, especially Neisseria gonorrhoeae, have increased sharply in Australia over the past decade, increasing pressure on health services and resulting in escalating morbidity. Antimicrobial resistance in STIs is a critical threat to public health globally and will be investigated as part of this program. This programs aims to use genomics to better understand how and when these pathogens are spreading, to better understand resistance and inform and measure public health responses at the national level.

• N. gonorrhoeae

• Sexually transmitted shigellosis (Here, we will undertake the first national genomic epidemiological study of shigellosis in Australia, and determine the factors driving the emergence of AMR Shigella infections.)

Project 4

AMR and emerging pathogens (biothreat agents)

AMR occurs when microorganisms such as bacteria, viruses, fungi and parasites change over time and become resistant to antimicrobial medicines such as antibiotics, resulting in the increased risk of disease spread, severe illness and death¹. Working closely with health departments, this program aims to sequence all CARAlert pathogens to define the accuracy of AMR prediction compared to phenotypic data, to investigate potential transmission networks using genomics and AusTrakka. This program will also look to further investigate approaches for further improving the use of genomics in emerging pathogens including pathogens that pose a biosecurity risk.


• Emerging pathogens and biosecurity 

¹ Ford L, Haywood P, Kirk MD, Lancsar E, Williamson DA, Glass K. Cost of Salmonella Infections in Australia