I specialise in bacterial pathogenomics: using whole-genome sequencing to investigate transmission, pathogenesis and antibiotic resistance in bacteria. Recent work from my group includes genomic investigations of hospital outbreaks and a phylogenomic analysis of the multidrug resistant Escherichia coli ST131 superbug.
I was awarded a PhD from UQ for my work in bacterial pathogenesis in 2002 and developed my career in bacterial genomics in the United Kingdom with fellowships from the Royal Commission for the Exhibition of 1851 (University of Oxford) and the UK Medical Research Council (University of Birmingham). Since returning to Australia I have held fellowships from both the NHMRC and ARC and have led a successful research group in the School of Chemistry and Molecular Biosciences at UQ since 2008. I am a member of the Australian Centre for Ecogenomics and the Australian Infectious Diseases Research Centre. In 2016 I received the Frank Fenner Award from the Australian Society for Microbiology in recognition of my contribution to microbiology research in Australia.
Research focus and collaborations
My group aims to better understand the evolution of clinically important bacterial pathogens through phylogenomics and comparative genomic analysis, and apply this knowledge in the clinical setting. Ongoing studies encompass Escherichia coli, Klebsiella, Pseudomonas aeruginosa, Staphylococci, Streptococci, Acinetobacter baumannii, and Legionella pneumophila, many of which are considered “superbugs” via their resistance to multiple antibiotics. With expertise in bioinformatics, evolution and a detailed understanding of bacterial pathogenesis and antibiotic resistance, we are driving the way that high-throughput and long-read genomic data is translated into precision medicine.
Major research themes include genomic approaches to characterise the emergence and spread of multidrug resistant superbugs at the global scale of pandemic clones (e.g. E. coli ST131) and at the local scale of health-care associated infections (e.g CPE and CRAB outbreaks). A major focus is the evolution and function of virulence factors that are widely conserved amongst pathogenic (e.g. fimbriae, pili and type III and type IV secretion systems and secreted effectors).
Virulence and antibiotic resistance genes are commonly transferred between bacterial cells by mobile genetic elements such as phage, plasmids, genomic islands and insertion sequences. Genomic (and metagenomic) study of mobile elements is difficult due to their repetitive nature. Meeting these challenges with novel bioinformatic approaches and high quality complete reference genome sequences is a priority of the group.
Software for comparative analysis of bacterial genome data have been developed by PhD students in our lab. These include the widely used BRIG (by Nabil Alikhan) and Easyfig (by Mitchell Sullivan) tools, which collectively have more than 1200 citations (GS 28/07/18). Recent software projects include an interactive web-based visualiser for communicating genomic and epidemiological data for Healthcare-associated infections (HAIviz (Budi Permana)).
- Developing software for Next-Gen bacterial genome and meta-genome assembly, annotation and analysis
- PacBio or Nanopore sequencing of multidrug resistant superbugs from hospital patients
- Genomic epidemiology: investigating outbreaks using genome sequencing
- Reverse vaccinology: identifying candidate bacterial vaccine candidates
- Investigating the role of bacteriophage in mobilizing virulence genes
- Genomic epidemiology, antibiotic resistance and virulence of E. coli and other Gram negative superbugs: Mark Schembri (UQ), David Paterson (UQ), Patrick Harris (UQ/PathQ), Andrew Henderson (UQ/PAH), Amy Jennison (QFFS), Jeff Lipman (UQ/RBH), Jason Roberts (UQ), Mat Upton (Manchester), Tim Walsh (Cardiff), James Ussher (Otago), Deborah Williamson (Doherty/MDU).
- Streptococcal pathogens: Mark Walker (UQ), Andrew Barnes (UQ), Glen Ulett (Griffith).
- Veterinary bacterial genomics (one health): Darren Trott (UAdelaide), Justine Gibson (UQ), Rowland Cobbold (UQ), Pat Blackhall (UQ).
- Phage genomics: Karen Weynberg (UQ), Phil Hugenholtz (UQ).
- Pseudomonas aerguinosa: Scott Bell (UQ/PCH), Claire Wainwright (UQ/LCCH), Tim Kidd (UQ).
- Legionella pneumophila: Elizabeth Hartland (Hudson/Monash), Phil Bond (UQ), Gene Tyson (UQ).
- Metagenomics and long-read sequencing: Phil Hugenholtz (UQ), Gene Tyson (UQ), Nicole Webster (UQ/AIMS), Kok Gan Chan (UMalaysia).
- Bacterial pathogenomics: Nick West (UQ), David Gally (Roslin/UEdinburgh), Andrew Roe (UGlasgow), Ian Henderson (UBirmingham), Kari Gobius (CSIRO).
More information can be found here.