Beyond Pasteur; Controlling fowl cholera in today’s layer industry

Fowl cholera (FC), caused by Pasteurella multocida, has re-emerged as a significant threat to Australian layer industry.

Current preventive measures rely heavily on killed vaccines prepared from isolates taken directly from the affected farm (‘autogenous vaccines’). Despite these interventions, persistent outbreaks occur in layer flocks which indicates critical gaps in current control strategies and increases antibiotic treatment rates.

You will be a part of an industry funded project to perform a cross-sectional study of commercial free-range layer farms to assess vaccination routines, disease prevalence, and possible environmental reservoir for P. multocida. 

Samples from clinically affected birds will be cultured to isolate P. multocida. You will then characterise and compare outbreak and vaccine strains through whole genome sequencing.

Studies have shown that for the autogenous fowl cholera vaccine to be effective, the lipopolysaccharide (LPS) outer structure of the vaccine strain should be the same as the outbreak strain.

You will investigate how bacterial growth conditions affect the LPS outer structure through testing different culture media and harvesting bacteria at different stages of growth. The LPS structure will be evaluated through electrospray ionization mass spectrometry (ESI-MS) for detailed glycan analysis and RNA sequencing to examine gene expression changes.

This project is a collaboration between the University of Queensland (QAAFI) and a leading Australian animal health consultancy and is part of the new Australian Eggs-funded research program on fowl cholera in free-range layers.

You will join a multidisciplinary team in veterinary microbiology, genomics and bioinformatics, Glycan analysis and will have access to field isolates and vaccine strains through our industry partners.

Laboratory work will take place in PC2 laboratory facilities at EcoSciences Precinct and includes bacterial culture, molecular typing and whole-genome sequencing on Oxford Nanopore and Illumina platforms. 

You will use our established bioinformatics pipelines for genome assembly and LPS typing and sub-typing, with access to UQ high-performance computing. Training will be provided in each of these areas.

This project is supported by the Research project scholarship.

Learn more about the Research project scholarship.

Your application will be assessed on a competitive basis.

We take into account your:

• previous academic record
• publication record
• honours and awards
• employment history.

A working knowledge of microbiology, animal science, biotechnology, or veterinary medicine would be of benefit to someone working on this project.

You will demonstrate academic achievement in the fields of veterinary bacteriology and/or bacterial genomics and the potential for scholastic success.

A background or knowledge of veterinary medicine or microbiology is highly desirable.

Eligibility

Only domestic applicants are eligible for this project.

You must submit an expression of interest (EOI) by 27 December, 2026 27 December, 2026.

Before you apply

1. Check your eligibility for the Doctor of Philosophy (PhD).
2. Prepare your documentation.
3. If you have any questions about whether the project is suitable for your research interests, contact Dr Lida Omaleki (l.omaleki@uq.edu.au).

When you apply

To apply, submit an expression of interest (EOI) for the program. You don't need to apply separately for the project or scholarship. How to submit an EOI

In your EOI, complete the ‘Scholarship/Sponsorship’ section with the following details:

1. Are you applying for an advertised project: 'Yes'
2. Project: 'Research project scholarship'
3. Scholarship Code Listed in the Advertisement: CHOLERA-OMALEKI
4. Link to Scholarship Advertisement: https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/beyond-pasteur-controlling-fowl-cholera-todays-layer-industry

Submit an EOI