Pathogenomics
We aim to use next-generation DNA sequencing to better understand how medically important Bacteria cause disease, become resistant to antibiotics and disseminate globally.
See the projects that we're working on, below.
The impact of bacteriophage on severity of Pseudomonas infections in paediatric cystic fibrosis patients
Pseudomonas aeruginosa infections in cystic fibrosis (CF) patients are a key chronic infection that progressively leads to organ damage and lung failure. Recent evidence suggests that certain viruses infecting Pseudomonas aeruginosa can make infections more severe, however the epidemiology and clinical outcomes, particularly in paediatric CF patients, where targeted interventions can make the most difference, are still not well understood. This project combines clinical data with bacterial and viral genomics to search for and characterise such viruses in Australian paediatric CF patients, and investigates if these viruses correlate with poorer clinical outcomes.
- Project team: Seweryn Bialasiewicz (CI), Philip Hugenholtz (CI), Julian Zaugg, Rylee Deehan
- Collaborators: Claire Wainwright (CI), Tim Kidd
Antimicrobial drug resistance monitoring in the food system
Antimicrobial drug resistance is a growing threat to humans and animals. The presence of such antimicrobial drug resistance can't always be correlated with direct antibiotic use. This Queensland Alliance for One Health Sciences-led project, in collaboration with our centre, is using modern molecular approaches including metagenomic sequencing to track and identify the potential sources of antimicrobial drug resistance to help inform improvements to farm practices.
- Project team: Seweryn Bialasiewicz (CI), Julian Zaugg, Rylee Deehan
- Collaborators: Ricardo Soares Magalhaes, Justine Gibson, Charlotte Tinsley, Tatiana Ibertti
Dual-function ribonucleases: unexpected agents of antibiotic resistance
Intensive use of antibiotics over the past 70 years has resulted in widespread antibiotic resistance in microorganisms. This project aims to characterise the evolution of metallo-β-lactamase (MBL) 1 activity in ribonucleases, which is a novel and unexpected source of resistance to front-line drugs of last resort.
- Project team: Phil Hugenholtz (CI), Rochelle Soo, Marc Morris, Laura Rix
- Collaborators: Gary Schenk, Mikael Boden, Chris Schofield (University of Oxford)
Using genomics to track drug-resistant Bacteria in healthcare settings
The emergence of multidrug-resistant Bacteria in healthcare settings poses a significant burden to patients and healthcare providers. Whole-genome sequencing (WGS) enables high-resolution typing and transmissions reconstruction, facilitating more accurate and targeted infection prevention and control. This project aims to use WGS to investigate the spread of drug-resistant Bacteria in healthcare settings and develop web-based visualisation and analytical platforms for real-time infection control and surveillance.
- Project team: Scott Beatson (CI)
- Collaborators: Brian Forde, Budi Permana, Patrick Harris, David Paterson
Determining potential selection patterns in pathogenic Escherichia coli using comparative genomics
Infections caused by multidrug-resistant Bacteria are increasing worldwide. Understanding the evolutionary history of predominant and emerging lineages is crucial to monitor antibiotic resistance and evolutionary mechanisms within a population over time. Whole-genome sequencing allows for the completion of novel genomes, characterisation of mobile genetic elements and the identification of single nucleotide polymorphisms (SNPs), which may have contributed to the success of a lineage. This project aims to investigate the clonal dissemination of antibiotic-resistant Bacteria.
- Project team: Scott Beatson (CI)
- Collaborators: Brian Forde, Thomas Connor (Cardiff University), James Connolly (Newcastle University), Rhys White (Institute of Environmental Science and Research)
Do environmental stressors increase retrovirus activity and exacerbate disease in koalas?
All NSW and Queensland koalas have a retrovirus that is known to cause cancer and likely suppresses the koala’s immune system, increasing their chances of getting chlamydia. Environmental factors such as habitat degradation and climate change can lead to chronic stress. We suggest that such chronic stress impairs a koala’s ability to control the retrovirus and fight off disease.
This project will study the links between environmental stress, the retrovirus and resulting disease. In the first aim, we will survey koalas in areas that have different levels of human activity (captive colonies, suburban environments, rural areas and national parks). Stress levels in the koalas will be assessed by measuring levels of stress hormones in the faeces and this will be compared with the level of retrovirus circulating in the blood. We will also assess overt symptoms of disease and chlamydia infection in these koalas. In the second aim, captive and wild koalas will be tracked for two years to understand how seasonal variation and potentially extreme weather (e.g. heatwaves) events affect stress levels and retrovirus activity. We will also measure stress levels and retrovirus activity in koalas admitted into care with chlamydial infection and track how these change over the course of rehabilitation and release into the wild.
This research program will provide direct data on how human changes to the landscape, heatwaves and disease affect koalas’ chronic stress levels and retrovirus activity. It will establish how chronic stress affects the koala’s ability to control the retrovirus, providing general predictions of how koala population health is impacted by environmental stressors.
- Project team: Michaela Blyton (CI)
- Collaborators: Keith Chappell, Jake O’Donnell, Tamara Keeley, Steve Johnson, Lyndal Hulse, Michael Pyne (Currumbin Wildlife Hospital), Cheyne Flanagan, Astrid Van Aggelen and Shali Fischer (Port Macquarie Koala Hospital), Don Hudson (Port Stephens Koala Hospital)