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Real-time Surveillance of Salmonella Outbreaks


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

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





This PhD scholarship is funded by a competitive research grant. The project aims to introduce, for the first time, real time evolutionary analysis of pathogens so that outbreaks affecting 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.

To demonstrate this technique with real-world datasets, the student will analyse the genomes of Salmonella species that are the cause of the most severe foodborne gastroenteritis in Australia. The student will work closely with researchers at the Centre for Infectious Diseases and Microbiology-Public Health and NSW Health Pathology Enteric Reference Laboratory at Westmead, to achieve this aim. They will also further analyse sequencing data to improve understanding of bacterial disease structure in the Australian context and correlate relationships elucidated by genome sequencing with epidemiological, genotypical and phenotypical data.

Expected outcomes include new knowledge of statistical algorithms for evolutionary analysis, relevant to biological disciplines beyond infectious diseases; knowledge to support the management of diseases that reduce food production and enhanced capacity for infectious disease analysis.

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


  • Knowledge of microbial genomics and molecular evolution
  • Experience with Linux-based computing and/or biological sequence data analysis


  • Experience with at least one general-purpose programming (or command) language (e.g. Bash, R, Python, Perl, etc.)

Applications closed

31 April 2020.

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Other information

The student will be primarily based at Westmead Hospital, Sydney, and will work closely with experts in bio-surveillance and outbreak detection.