Australian centre for genomic epidemiological microbiology

  Contact : +61 2 4640 6333


LAND: New technologies fight pests and disease in livestock and crops

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

Ausgem research is working to improve the health and prosperity of the farming sector in NSW, with implications for agriculture nationally and around the globe. Projects already underway are using the latest DNA sequencing technology to be able to develop new vaccines, devise more effective treatments and enable faster diagnosis. The work will potentially reduce the use of antibiotics on our farms as well as protect valuable crops and livestock from emerging diseases.


Protecting cattle against international parasite

Ausgem is leading work towards the development of a vaccine for the emerging parasitic disease Bovine anemia and Theileriosis orientalis group (BATOG).

First detected on the NSW mid-north coast in 2006, BATOG already costs the NSW cattle industry an estimated $20 million each year and that cost is expected to increase substantially. In Japan, where it is well established, the annual cost is $100 million.

The Ikeda variant of Theileria, which is spread by common ticks and infects and kills the red blood cells of cattle, is related to the same microscopic parasite that causes malaria in humans. In affected cattle, it causes anaemia, weakness, abortions, reduced milk production and death.

An effective vaccine for endemic pig pneumonia

The widespread chronic dry cough and slow growth caused by swine pneumonia, a worldwide problem for the pork industry, could soon be eliminated thanks to Ausgem research.

Vaccines that exist for the Mycoplasma hyopneumoniae bacteria that cause pneumonia in pigs, reduce symptoms, but do not prevent infection, so farmers still need to rely on the extended use of antibiotics in many commercial herds for prevention and treatment of disease.

However, Ausgem analysis of the broken proteins produced by Mycoplasma hyopneumoniae has pointed towards previously unexplored avenues for the development of a more effective vaccine. These will be tested in an animal trial in 2018.

By reducing the need for use of preventative antibiotics in pig herds and improving the health of herds across NSW, the work is likely to substantially improve the bottom line for the state’s $260 million-plus pork industry.


Ausgem is working to develop more effective vaccines for swine pneumonia.

In its work towards a vaccine, Ausgem researchers have sequenced 16 Ikeda genomes and created a system to be able to analyse the genetic diversity of the theileriosis parasites. This information will inform treatment development and, ultimately, lead to a BATOG vaccine.

The transmission of disease between animals and humans

It’s estimated that 6 out of 10 known human infections began in animals and three-quarters of all new human diseases are zoonotic, meaning they can cross over between animals and humans.

Scientists with Ausgem are now investigating the link between E.coli  bacteria, which are responsible for most human urinary tract infections (UTIs), sepsis and meningitus, extra-intestinal pathogenic Escherichla coli, and pigs and chickens. Genomic surveillance by Ausgem – that includes full genome sequences for more than 1000 E. coli – has already identified strong similarities between the E. coli isolated from people treated in hospital for sepsis and the E. coli found within pork and poultry.


It suggests that, rather than UTIs always being infections picked up from the bacteria in people’s faeces, as commonly thought, people may also acquire the infection through their food.

With 60% of women expected to experience a UTI infection at least once in their life, annual global treatments costs reach billions of dollars. The Ausgem discoveries are helping to shed more light on why infection rates may be so high and could lead to new techniques to prevent the infection crossing from farm animals to humans.

Rapid diagnosis and more effective disease treatment for fruit and vegetable crops

Genomic analysis and identification of the common bacterial plant infection Xanthomonas will enable earlier diagnosis that facilitates more effective management of this potentially devastating disease.

Varieties of the Xanthomonas bacteria afflict more than 400 plant types and are responsible for citrus canker, black rot in cabbage, bacterial blight of hazelnuts, bacterial leaf spot of pumpkins and squash, black spot on mangoes and black chaff in wheat.

The Xanthomonas collection held by NSW DPI’s Plant Pathology and Mycology Herbarium is a valuable resource to allow accurate identification of the genomic diversity of these pathogens. This information is being used to develop quick turnaround diagnostics, a project funded though the Plant Biosecurity CRC with additional support from Ausgem.

Genomic sequencing of the NSW DPI’s entire Xanthomonas collection (1000 samples) has already been completed and the team has developed a diagnostic assay for Xanthomonas citri subsp citri.


Ausgem is working towards early diagnosis of bacterial infections that cause citrus canker.

In keeping with a One Health approach, Ausgem’s research recognises that the health of people is connected to the health of animals and the environment.