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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





Bacterial pathogens such as Xanthomonas and Salmonella can drastically affect the yields of important food and fibre crops, reduce the productivity of food animals, and be highly detrimental to both food safety and human health. Correctly identifying sources of bacterial infection is essential to the maintenance of a safe food supply and the protection Australia’s food sources from exotic disease incursions.

In recent years, the use of genomics has revolutionised source identification during outbreaks of pathogenic bacteria. Comparison of bacterial genomes with phylogenetics can provide high-quality evidence that two or more infections from different locations are linked by a common source. However, the analysis required for this is time-consuming and not user-friendly. Furthermore, the incorporation of new data often requires a complete reanalysis, which is highly undesirable in outbreak situations where samples are processed in small batches over an extended time-period.

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.

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 biological sequence data analysis

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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.