Australian centre for genomic epidemiological microbiology

  Contact : +61 2 4640 6333


Research Programmes

Recent technology developments have enabled the genome sequencing of a range of pathogens providing many new insights into the host/pathogen relationship and the evolution of pathogens. Loosely termed genomic epidemiology, the scientific opportunities are considerable, but have yet to be effectively utilised both within Australia and globally. The approach may lead to the development of more targeted vaccines and diagnostics and information on new ways to manage outbreaks.

Ausgem Programmes

The Ausgem research projects include:

  • Identification of the basis of antibiotic resistance in key bacteria
  • Identification of the mechanism for transfer of antibiotic resistance between key bacteria and the development of approaches to mitigate this
  • Understanding the disease and mitigation strategies for pesti-virus infections of livestock
  • Further characterisation of the BTVs present in Australia and the implications for disease control
  • Better characterisation and management of pathogens affecting citrus plants
  • Characterisation of infections of oysters and the mitigation of their risks to both oyster and human health.

High throughput sequencing

Sequencing technologies & data acquisition & storage

Aim To generate sequence data on a range of pathogen genomes

Key areas These will include those infectious agents that cause diseases of high priority for human, livestock and plant health. Sequence activities may include whole or partial sequencing of the agents

Utilisation of sequence data for epidemiological study

Bioinformatics & epidemiology

Aim To utilise sequence date to better understand the infectious disease process

Key Areas These will include the host interaction with a pathogen, pathogen evolution and emergence and mechanisms of host switching

Development of innovative control & mitigation strategies based on genomic epidemiological data use

Disease mitigation

Aim To develop a range of control strategies based around a better understanding of the host, the pathogen and the host pathogen interaction. Proteomics has a critical role in the development of vaccines. Vaccines can help to alleviate reliance on antibiotics

Key Areas These will include intervention strategies that mitigate the generation of disease through the host pathogen interaction, insight into new generation vaccines that target specific pathogen strains or areas of the pathogen, alternative approaches to vector control based on vector manipulations, next generation diagnostics and new generation therapeutics based on utilization of pathogen or host genome information

Global Health Security

In particular the emergence and spread of epidemic-prone infectious diseases (EID), has become of major international concern, not least because of the significant economic impact of outbreaks

The term EID has become synonymous with new (newly recognised, previously unknown) infectious diseases (such as SARS which appeared suddenly and unexpectedly in 2003) or with known infections that are increasing in incidence, increasing geographically (such as the dengue viruses causing dengue fever and dengue haemorrhagic fever) or expanding their host range (such as H5N1 avian influenza). Evidence clearly indicates an increase in the risks from Infectious diseases to humans, to animals, to plants and to the environment. The vast majority of such diseases are trans-boundary in nature and require both national and international approaches for their effective management.

Table 1 Economic costs of recent animal disease outbreaks
Disease Economic impact
SARS (2003) Cost to East Asia in excess of US$40 billion.
Global cost approximately US$60 billion
Avian influenza Direct economic cost currently more than US$20 billion
Nipah (1999) Cost to Malaysia – estimated to be US$500 million
BSE Cost to the UK – estimated to be US$7.5 billion
Bluetongue virus France (2007): US$1.4 billion
Netherlands: US$85 million
Unites States: US$130 million annually
Foot-and-mouth Disease (2001) United Kingdom: US$35 billion
Equine influenza Australia (2007): A$1 billion

Protecting food production

The risks from pathogens found in our food have been known for many years and the early approaches dealt with managing these post farm-gate.  By applying detection processes, both for infectious agents as well as chemical contamination, linked to food production processes, these risks were seen to have been managed.  However the increasing impact of food borne pathogens such as Escherichia coli or Salmonella spp. along with the risk management challenges posed by BSE has led to whole of production chain approaches.

Combating antibiotic resistance

Increasingly important is the growing occurrence of antibiotic resistance in a range of different bacteria to a growing number of antibiotics. This is creating a major problem in diverse areas of human and animal health, as the availability of effective antibiotics diminishes. There are a number of underlying causes including misuse of antibiotic, their use as growth promoters in specialised livestock industries, in aquaculture and their widespread use in hospitals. Understanding the mechanisms of resistance development and the transfer of resistance factors across different bacteria genera is a major area of present research.