Australian centre for genomic epidemiological microbiology

  Contact : +61 2 4640 6333


Focusing a DNA-scale lens on aquaculture disease and water contamination

University of Technology Sydney, Broadway, NSW 2007
NSW Department of Primary Industries, Menangle, NSW 2568

Water can be a critical environment for the transmission of disease and antimicrobial resistance – affecting both the aquaculture industry and nearby populations. Understanding how disease and drug resistance are transmitted in the aquatic environment, and what triggers an outbreak is vital for protecting Australia’s valuable aquaculture industry, preventing further spreading of antimicrobial resistance, and ensuring the health of people and products above and below the shoreline.


Applying science to help prevent Pacific oyster deaths

The almost $100 million-a-year Australian oyster industry has suffered a series of devastating infections and environmental stressors in recent years. In NSW, where the 70 million oysters harvested each year represent 30 per cent of the state’s total seafood produce, oyster-farming regions such as the Georges River and the Hawkesbury have been hit by expensive temporary estuary closures.

In an effort to better understand why these disease outbreaks happen and prevent or predict their occurrence, Ausgem researchers are using data analysis and DNA sequencing to examine the genomics of oyster pathogens and determine what the microbiomes of both healthy and diseased oysters look like. This information will then be linked to data on environmental factors affecting oysters to create a predictive tool. Among other achievements, the group has already sequenced dozens of microbe genomes taken from the site of an infection in the Port Stephens region.

This knowledge application will be transformative for the oyster industry by enabling them to more accurately predict disease outbreaks and take steps to prevent or mitigate the costly damage to the valuable molluscs.


Ausgem research is providing opportunities for NSW aquaculture to prevent disease and enhance production.

The Pacific Oyster dominates Australia’s commercial harvest but has been vulnerable to the Pacific Oyster Mortality Syndrome (POMS) since its appearance in 2008.

POMS is thought to be triggered by a combination of environmental and microbial factors, including the OsHV-1 virus. Ausgem scientists are using DNA sequencing to analyse OsHV-1 and other microbes associated with POMS in research that could enable both prevention and treatment.

International collaboration

In addition to applying a genomic lens to antimicrobial water contamination in Australia, Ausgem has been applying its expertise to assist researchers at the University of Warwick and the University of Exeter in the United Kingdom.

The UK researchers have been studying the prevalence of antibiotic resistant bacteria in water and sediment samples from the River Thames, initially focussing on sites in the vicinity of waste water treatment plants.

They have called on Ausgem’s genomics and bioinformatics expertise to help determine exactly which genetic elements that enable resistance to antibiotics are present in one of the world’s most famous waterways and how these are being distributed. The collaboration has now expanded to include hundreds of water samples from British beaches.


Contaminated water as a source of antibiotic resistance

Concern is growing that antibiotic resistance may be significantly spread indirectly via effluent from farms, hospitals and nursing homes in addition to the direct impacts from overuse of antibiotics.

New Ausgem research will monitor potential sources of water and land contamination to determine whether the waste is introducing antibiotic resistance genes and drug resistant bacteria into the community. One project is looking at the possibility of the common seagull, the silver gull, as a carrier of antibiotic resistance due to its foraging in rubbish dumps.

In 2018, Ausgem researchers will sample faeces from gulls from NSW’s largest breeding colony on Five Island Reserve, which is 500m off the coast of Wollongong and 12 kilometres from the city’s Whyte Gully rubbish tip where up to 6,000 gulls have been counted leaving the tip every hour. They will compare the antimicrobial-resistant bacteria found in the gull samples with the bacteria already isolated from bird scats obtained in the back waters of NSW marshlands. These will likely act as a control group.

In 2017, the Australian Commission on Safety and Quality in Healthcare found that carbapenemaseproducing bacteria, which are resistant to even the last-line antibiotics, are now endemic along the east coast of Australia. Ausgem researchers plan to track their presence in order to determine if the genes that convey carbapenem resistance are being passed between different bacterial communities. This information can then be used to inform clinical and environmental responses



A 2016 government survey of aged care homes found nearly ¼ of residents’ antibiotic prescriptions were for more than six months.