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, Laura Rix, Max Lacour
- Collaborators: Gary Schenk, Marc Morris, 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)
Hyperactive endogenous retroviruses and their impact on the koala genome
Koala populations are in steep decline with the ubiquitous koala retrovirus (KoRV) strongly linked with disease. KoRV and other less studied endogenous retrovirus (ERVs) are extremely active within the genome of koalas to a level never observed in any other vertebrate genome.
This study will map ERV integration sites within koalas from across their geographic range and use long-read genomics approaches to understand the link between KoRV and other ERVs, the impact on koala caused by dramatic genomic rewiring, and the mechanisms of genomic immunity which supress ERV activity and mitigate disease. Findings will provide insights into the ongoing arms race between virus and host and inform conservation of an iconic species.
- Project team: Michaela Blyton
- Collaborators: Keith Chappell (CI), Jake O’Donnell, William Theurkauf (University of Massachusetts)
KoRV surveillance of NSW sentinel koala populations
Part of the NSW Government’s Koala Strategy, the koala sentinel monitoring program is a multi-year monitoring program assessing koala populations for disease, genetic diversity, and ecology at 6 key populations. The aim is to establish demographic trends and determine the factors underlying them.
As part of this program, we are screening the koalas for their koala retrovirus (KoRV) subtypes and plasma viral loads. This information will be used to track how KoRV load and subtypes change within animals over time and to assess the geographic extent of particular subtypes unique to NSW.
- Project team: Michaela Blyton (CI), Max Lacour, Julian Zaugg
- Collaborators: Keith Chappell