New diagnostic strategies for antibiotic-resistant infections

This project aims to address two major challenges in contemporary infectious diseases: Antimicrobial resistance (AMR) and the need for better diagnostics in bloodstream infections and sepsis. Approximately 10% of all hospital admissions will become colonised or infected with AMR pathogens. Healthcare-associated bloodstream infections lead to death in 10-15% of cases, with higher mortality risk, increased healthcare-related costs and prolonged admission if caused by AMR pathogens. There is an urgent need to evaluate new diagnostic technologies for AMR-related infections. The potential for rapid and information-rich diagnostics provided by whole genome sequencing offers great promise. Yet, scientific advances in the application of these tools have yet to make much impact on clinical management and outcomes in patients. This project aims to provide high-quality evidence to define the optimal use of these novel diagnostic strategies and provide a pathway for clinical translation.

Specific aims include:

1. Optimise and implement a metagenomics-based diagnostic approach to patients with life-threatening infections using a variety of techniques (shotgun metagenomics, pathogen enrichment and host depletion, culture-amplification) and sequencing technologies (e.g. Illumina, Oxford Nanopore)
2. Use machine learning to accurately model and predict antimicrobial susceptibility phenotypes from whole genome sequencing data using existing biobanks of well-curated isolates derived from clinical trials (e.g. MERINO-1, MERINO-2, GameChanger) and AMR surveillance projects (e.g. Qld Genomics)
3. Undertake clinical evaluations and small-scale pilot trials to define the impact on clinical outcomes.  Opportunities to explore the development of these workflows in rural/remote and low-income settings are also potentially available.

The project would be well-suited to clinicians with an interest in infectious disease or microbiology.  Equally, we welcome interest from biomedical scientists interested in the clinical translation of genomics.  Some background in clinical medicine, microbiology or genomics would be highly desirable, but motivated applicants with backgrounds in other related disciplines are welcome to apply.

UQCCR is located on the Royal Brisbane and Women’s Hospital site at Herston in Brisbane, Australia. The University of Queensland has a significant presence in the Herston Precinct, where we work closely with our hospital and health service colleagues to improve the health of our communities. The applicant would be working within the MERINO clinical trials group, a multi-disciplinary team with expertise in clinical medicine, microbiology, clinical trials, epidemiology, statistics and bioinformatics. The applicant would have access to world-class laboratory facilities at UQCCR, with on-site capacity for Illumina and nanopore sequencing. We also have excellent facilities for all aspects of clinical microbiology research (MALDI-TOF, PCR, broth microdilution susceptibility testing, etc) and work closely with other microbiology and genomics groups across the UQ network. The team has close links with the Herston Infectious Disease Institute (HeIDI), as well as the Royal Brisbane and Women's Hospital and the microbiology department at Pathology Queensland. We also collaborated closely with the ADVANCE-ID network in Singapore, led by Prof David Paterson, and have an international network developed through the influential MERINO clinical trials program. The applicant would have access to large biobanks of well-characterised antibiotic-resistant pathogens derived from these international trials and other hospital surveillance projects.

This is an Fellowship support scheme scholarship project that aligns with a recently awarded Australian Government grant.

The scholarship includes:

• living stipend of $36,400 per annum tax free (2025 rate), indexed annually
• your tuition fees covered
• single overseas student health cover (OSHC).

Learn more about the Fellowship support scheme 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 genomics, clinical microbiology and bioinformatics would be of benefit to someone working on this project.

You will demonstrate academic achievement in the field(s) of microbiology, infectious disease or bioinformatics and the potential for scholastic success.

A background or knowledge of genomic data analysis is highly desirable.

This project requires candidates to commence no later than Research Quarter 1, 2026. To allow time for your application to be processed, we recommend applying no later than 30 September, 2025 30 June, 2025.

You can start in an earlier research quarter. See application dates.

Before you apply

1. Check your eligibility for the Doctor of Philosophy (PhD).
2. Prepare your documentation.
3. Contact Dr Patrick Harris (p.harris@uq.edu.au) to discuss your interest and suitability.

When you apply

You apply for this scholarship when you submit an application for a PhD. You don’t need to submit a separate scholarship application.

In your application ensure that under the ‘Scholarships and collaborative study’ section you select:

• My higher degree is not collaborative
• I am applying for, or have been awarded a scholarship or sponsorship
• UQ Earmarked Scholarship type.

Apply now