Explore recent research projects designed to answer clinical questions in infectious diseases using evolutionary biology, statistical genomics and machine learning approaches.

Research

Research Projects

Within-host evolution: theBARISTAverse

  • A deep dive into S. aureus evolution during bacteraemia and orthopaedic infections. In this prospective genomic study, we collect clinical samples and nasal swabs over a period of one year and perform deep sequencing to track the fate of bacterial subpopulations and their impact on clinical outcomes. ANZCTR registration here

  • Large-scale meta-analysis of within-host evolution, including 32 studies, > 5,000 genomes, > 1,000 independent colonisation/infection episodes

  • A clinical program to bring within-host evolution analysis to the bedside and support clinicians managing severe S. aureus infections. By sequencing and phenotyping baseline and persistent/recurrent isolates, we assess the mechanism of antibiotic treatment failure.

Bacterial GWAS of clinical outcomes

  • We assemble large collections of S. aureus bloodstream genomes and high-quality clinical data to perform bacterial GWAS of clinical outcomes such as treatment success and investigate new mechanisms of resistance to key anti-staphylococcal antibiotics

  • We perform phenogenomic investigations to “risk profile” endocarditis strains and explore the impact of bacterial factors on endocarditis severity (in collaboration with Dr Mathaios Papadimitriou, Lausanne University Hospital)

Research Collaborations

Australia

MGHA (Melbourne Genomics Health Alliance)
Established to contribute directly to future health practices and budgets, by determining where genomics has the most benefit to offer. Sharing lessonswith colleagues within the Australian Genomics Health Alliance (AGHA) and globally through the World Genomics Health Alliance.

Australian Hospitals

  • Royal Melbourne Hospital

  • Austin Hospital

  • Monash Hospital

  • Geelong Hospital

International

Trials

SNAP (Staphylococcus aureus Network Adaptive Platform)
Based in Melbourne, the SNAP Trials aims to improve treatment outcomes for patients with Staphylococcus aureus bloodstream infections. The study includes sites from Australia, New Zealand, Singapore, Canada, Israel, South Africa, Europe, the UK,

ROADMAP (RandOmised Arthroplasty infection worlDwide Multidomain Adaptive Platform trial)
ROADMAP Trial is an innovative trial to evaluate a range of interventions with the aim of improving outcomes for patients with prosthetic joint infections. The investigators are drawn from both infectious disease and orthopaedic surgery disciplines from Australia, New Zealand, Canada and the United Kingdom.

International Hospitals

  • Lausanne University Hospital (Switzerland)
    Dr Matthaios Papadimitriou Olivgeris

  • Basel University Hospital (Switzerland)
    Prof Nina Khanna, Dr Richard Kuehl)

International Universities

  • Duke University (US)
    Prof Vance Fowler, Dr Josh Parsons

  • Rutgers University (US)
    Dr Tania Wong

  • Oxford Big Data Institute (UK)
    Prof Daniel Wilson, Dr Bernadette Young