BSc (Otago) Microbiology, MSc (Otago) Microbiology, PhD (Queensland) Genetics, MSc (Manchester) Bioinformatics.
Associate Professor
3365 4863

Group Leader / NHMRC Career Development Fellow


I specialize 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.

Brief Research Description: 
Bacterial Pathogenomics
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)). 

Example projects:

  • 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).


Funded Projects: 

Queensland Genomics Health Alliance Demonstration Project 2017-2018 ($600,000) 

Whole genome sequencing to track, treat and prevent nosocomial infections (David Paterson, Patrick Harris, Graeme Nimmo, Anthony Allworth, Krispin Hadjkowicz, Jeffrey Lipman, Geoffrey Playford, David Looke, Jason Roberts, Mark Schembri, Scott Beatson, David Whiley, Mark Walker, Sanmarie Schlebusch)

NHMRC Project Grant 2018-2021 ($727,000)

GNT1146820: Integrated bacterial genomics and virulence analysis of uropathogenic Streptococcus agalactiae (Glen Ulett, Scott Beatson)

ARC Discovery Project Grant 2017-2019 ($626,000)

DP170103962: Epigenetic regulation in bacteria (Scott Beatson, Mark Schembri)

NHMRC Career Development Fellowship 2015-2018 ($455,000)

GNT1090456: Bacterial Pathogenomics: whole-genome sequencing to investigate infection transmission, pathogenesis and antibiotic resistance (Scott Beatson)

NHMRC Project Grant 2014-2017 ($793,056).

GNT1067455: Functional and genomic analysis of the globally disseminated multidrug resistant Escherichia coli ST131 clone (Mark Schembri, Scott Beatson)

ARC Linkage project grant 2014-2017 ($758,000).

LP130100736: Superbugs and veterinary drugs: are multidrug zoonotic pathogens residing in Australia (Darren Trott, Mark Schembri, Jacqueline Norris, Justine Gibson, Scott Beatson, Stephen Page, Allen Andrew, Joanne Platell, David Jordan, Nicky Buller)

ARC Linkage project grant 2014-2017 ($317,000).

LP130100242: A reverse vaccinology approach to vaccination of fish against highly variable pathogens (Andrew Barnes, Scott Beatson, Mark Walker, Les Gabor)

NHMRC Project Grant 2012-2014 ($622,350).

GNT1033799: Evolution and pathogenicity of NDM-1 positive Escherichia coli (Mark Schembri, Tim Walsh, Scott Beatson)

ARC Linkage project grant 2011-2013 ($333,000).

LP120100282: Smarter fermentations through starter culture genomics (Mark Turner, Scott Beatson, Ian Godwin, Ian Powell)

NHMRC Project Grant 2011-2013 ($555,000).

GNT1012076: Escherichia coli ST131: an emerging pathogen (Mark Schembri, Scott Beatson)

ARC Discovery Project Grant and Australian Research Fellowship ($503,686).

DP0881347: The evolution of bacterial pathogenesis: a genomic approach (Scott Beatson)


I coordinate BINF7001 (Advanced Genome Informatics), a Masters in Bioinformatics core course designed to provide hands-on training in command-line genomics using dedicated high-performance computing resources. 

I have taught a variety of courses at undergraduate and postgraduate level in microbiology, bioinformatics and genomics (including BIOL1020, SCIE2100, MICR3003, BINF6000). I taught and coordinated BIOL3004 (Genomics and Bioinformatics) between 2007 and 2017. 

Significant Professional Activities and Awards: 

Professional Awards:

2016: Australian Society for Microbiology Frank Fenner Award

2015: Australian National Health and Medical Research Council Career Development Fellowship (Level 2) 

2008: ARC Australian Research Fellowship.

2006: Australian National Health and Medical Research Council Howard Florey Centenary Fellowship.

2003: Medical Research Council (UK) Special Fellowship in Bioinformatics.

2001: Royal Commission for the Exhibition of 1851 Fellowship.

Professional Activities:

2018: Chair, Data Enhanced and user Enhanced Genomics Virtual Laboratory (DeVL) project governance group.

2017-now: Editorial board Scientific Reports 

2015-now: Associate editor BMC Genomics

2012-2015: Associate editor Microbiology Open

2012-2013: Bacpath 2013 local organizing committee member.

2008-2011: Lorne Genomes conference organizing committee.

2009-2011: Australian Society for Microbiology Queensland Branch ex-officio member.

Other Information

Current Group Members:

Brian Forde Postdoctoral Research Fellow

Lida Omaleki Postdoctoral Research Fellow (Pat Blackhall lab)

Leah Roberts PhD candidate (co-advisor Mark Schembri)

Areej Alsheikh PhD (submitted July 2018)

Melinda Ashcroft PhD (submitted June 2018)

Cameron Buckley PhD candidate (co-advisor David Whiley)

David Wakeham PhD candidate (associate advisor; principle advisor Justine Gibson)

Budi Permana PhD candidate

Rhys White PhD candidate

Caitlin Falconer MBioinf project student

Kirt Hanks PhD candidate

Previous Group Members:

Nhu Nyugen PhD (2018) (associate advisor; principal advisor Mark Schembri)

Nouri Ben Zakour Postdoctoral Fellow - now at Westmead Hospital/USyd

Mitchell Stanton-Cook BioIT specialist - Engineering Manager, Mastercard Australia

Nabil Alikhan (PhD awarded 2015) - now in Achtman group (University of Warwick, UK)

Mitchell Sullivan (PhD awarded 2015) - now in van Bakel group (Ichan School of Medicine, Mt Sinai, NYC)

Bryan Wee (PhD awarded 2015) - now in Stinchenko group (Westmead Hospital, Sydney)

Nathan Bachmann PhD (awarded 2014) - now in Woolhouse group (University of Edinburgh, UK); previously in Fitzgerald group (Roslin, UK)

Nicola Petty Postdoctoral Fellow - now at University of Technology Sydney

Jan Szubert Postdoctoral Fellow - now at European Patent Office, The Hague, Netherlands

Selected Publications: