Primary research interest

Molecular pathogenomics

Lab website

Beatson lab

About me

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)). 

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

Collaborations

  • 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).

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

Teaching interests

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. 

Achievements and awards

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.

Appointments

  • 2018: Chair, Data Enhanced and user Enhanced Genomics Virtual Laboratory (DeVL) project governance group.
  • 2017-now: Editorial board, Scientific Reports 
  • Associate editor BMC Genomics
  • Associate editor Microbiology Open
  • 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.

Featured publications

Researcher biography

Scott Beatson is an Associate Professor and NHMRC Career Development Fellow at The University of Queensland (UQ). He specializes in bacterial pathogenomics: using whole-genome sequencing to investigate transmission, pathogenesis and antibiotic resistance in bacteria. Recent work from his group includes genomic analyses of pandrug resistant enterobacteriaceae and the multidrug resistant Escherichia coli ST131 pandemic clone. He was awarded a PhD from UQ for his work in bacterial pathogenesis in 2002 and developed his career in bacterial genomics in the United Kingdom with the support of 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 he has held fellowships from both the NHMRC and ARC and has led a successful research group in the School of Chemistry and Molecular Biosciences at UQ since 2008. He is also a member of the Australian Infectious Diseases Research Centre and the Australian Centre for Ecogenomics. In 2016 he received the Frank Fenner Award from the Australian Society for Microbiology in recognition of his contribution to microbiology research in Australia.