Ready to make your mark in antimicrobial resistance research (AMR)?
Looking for an opportunity that nurtures research excellence, real-world impact and professional development?
This SAAFE CRC PhD chance is for you!

In partnership with Solving Antimicrobial Resistance in Agribusiness, Food and the Environment Cooperative Research Centre (SAAFE CRC), The University of Queensland and the Scolexia Pty Ltd, this PhD aims to investigate persistent fowl cholera outbreaks in Australian layer farms by assessing disease prevalence, vaccination practices and environmental reservoirs, while characterising Pasteurella multocida strains and factors affecting vaccine effectiveness to inform improved disease control strategies.

Who are we seeking?

This opportunity is best suited to applicants with a background in microbiology, veterinary bacteriology, bacterial genomics, animal science, biotechnology or veterinary medicine, with demonstrated academic achievement and the potential for research success.

Candidates must have completed Honours or Masters level research and be able to enrol as a domestic student at The University of Queensland to be eligible for this position.

Sound like you? Read on!

Project summary

- Program - PhD

- Location - Dutton Park

- Research area - Agricultural, veterinary and food sciences

Project description

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.

Scholarship

This project is supported by the Research project scholarship.

This scholarship includes:

- living stipend of $45,000 per annum

- $21,000 professional development fund

- tuition fees covered.

Research environment

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.

Principal supervisor

Dr Lida Omaleki

Queensland Alliance for Agriculture and Food Innovation

View Dr Lida Omaleki's profile

How to apply

To be considered for this scholarship, please include the following documents in your application:

- Cover letter

- CV

- Academic transcript/s

- Evidence for meeting UQ's English language proficiency requirements eg TOEFL, IELTS

📌 SAAFE CRC PhD Opportunity ($45,000 per year) - AMR Research (Dutton Park)
🏢 SAAFE
📍 Dutton Park