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Real-time Phylogenetics for Food-borne Outbreak Surveillance


$27,596 (2019 rate, indexed) per annum, plus an additional $10,000 top-up.

3 years, with the possibility of a 1 session extension.





Recent events have underlined the critical importance of rapid outbreak response and control to human health, food production and the broader economy. In addition to viral threats, bacterial pathogens such as Xanthomonas and Salmonella drastically affect the yields of important food and fibre crops, reduce the productivity of food animals, and can be highly detrimental to both food safety and human health. Correctly identifying sources of infection is essential to the maintenance of a safe food supply and the protection Australia’s food sources from exotic disease incursions.

This project aims to introduce, for the first time, a system that allows the real time evolutionary analysis of agricultural pathogens so that outbreaks affecting crops and the food supply can be managed precisely and rapidly. An interdisciplinary team will implement a large-scale data analytics framework in user-friendly software that integrates Australian infectious disease genomics data with global data. Underpinning this work are new theory and algorithms that apply Sequential Monte Carlo to update phylogenetic analyses continuously as new data arrives.

The successful applicant will demonstrate this technique with real-world datasets. They will analyse the genomes of significant Xanthomonas species that are threats to fruit, vegetable, grain and fibre crops and bacterial diseases important to production animal health. The student will work closely with molecular epidemiologists and bacteriologists at the NSW Department of Primary Industries to achieve this aim. They will also apply molecular epidemiology to further analyse sequencing data, aim to improve the understanding of Xanthomonas strains and types.

Who is eligible?

This scholarship is open to Australian Permanent Residents and New Zealand Citizens. 

Applicants must hold either:

  • Honours with First Class or Second Class Div 2; or
  • MSc with a research thesis of at least 6 months; or
  • An international equivalent degree. 

Selection process


  • Basic experience in microbiology and molecular biology
  • Experience with Linux-based computing and/or biological sequence data analysis 

Applications closed

Closed 31 August 2020.

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Other information

The student will be primarily based at Elizabeth Macarthur Agricultural Institute, the NSW Department of Primary Industries Centre of Excellence for Plant and Animal Health, and will work closely with experts in Biosecurity and Food Safety. This scholarship offers valuable experience for students looking for careers in government research.