Research

The Beatson group aims to better understand the molecular mechanisms of infectious disease and identify potential therapeutic and diagnostic targets by exploiting “Next-gen” genomic data. This will enable us to further understand how medically important bacteria cause disease, become resistant to antibiotics and disseminate globally. Our major focus is the role of mobile genetic elements in the evolution of virulence and antimicrobial resistance amongst pathogens such as Escherichia coli, Streptococcus pyogenes, and Pseudomonas aeruginosa. Our group develops new computational approaches for the rapid analysis of bacterial genome data from the latest sequencing technologies.

Current projects range from researching fundamental questions such as “how has Escherichia coli pathogenesis evolved?” and “how are genes transferred between bacteria?” to the identification of potential diagnostic and vaccine targets and the development of software tools to enable integrated analysis of 100’s or 1000’s of bacterial genomes.

Recent research highlights

NHMRC Funding

Congratulations to Dr Scott Beatson on being awarded a Level 2 NHMRC Career Development Fellowship. The project was titled “Bacterial Pathogenomics: whole-genome sequencing to investigate infection transmission, pathogenesis and antibiotic resistance”. A total of $455 452 was awarded and will begin in 2015.

Complete genome of representative ST131 strain

We determined the complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. We used a 3rd generation sequencing technology, PacBio SMRT sequencing to determine this genome and associated plasmids. We declare that “Large discrepancies between ST131 genomes are likely due to misassembly of E. coli NA114″. [Link]

Escherichia coli ST131

In April 2014 we had a large scale study of E. coli ST131 published in PNAS. We wrote a blog post about the importance of this study. Both UQ News and 7 News presented a news articles about this study. The data is available on GitHub.

Collaborations

National: Prof Mark Schembri (UQ), Prof Mark Walker (UQ), A/Prof Andrew Barnes (UQ), A/Prof Mark Turner (UQ), A/Prof Glen Ulett (Griffith), Dr Kari Gobius (CSIRO), Prof David Paterson (UQ), Prof Scott Bell (QHealth/QIMRB), A/Prof Claire Wainwright (QHealth), Prof Elizabeth Hartland (UMel), Prof James Paton (UAdelaide), Dr Paul Bartley (Wesley Hospital), A/Prof Darren Trott (UAdelaide), Dr Nick West (UQ).

International: A/Prof Mat Upton (Manchester), Prof David Gally (Edinburgh), Dr Andrew Roe (Glasgow), Prof Tim Walsh (Cardiff), Dr Kok Gan Chan (Malaysia), Prof Ian Henderson (Birmingham), Dr Tim Dallman (PHE).

 

Read more about our research in our blog.

Have a look at some photos of recent activities.

Available projects

Briefly, projects include:

  • Developing software for Next-Gen bacterial genome and meta-genome assembly, annotation and analysis
  • Investigating the role of positive selection in the evolution of bacterial pathogenesis
  • Genomic epidemiology: investigating outbreaks using genome sequencing
  • Reverse vaccinology: identifying candidate bacterial vaccine candidates
  • Investigating the role of bacteriophage in mobilizing virulence genes
  • PacBio SMRT genome assembly and methylome analysis
  • Antibiotic resistance and virulence gene profiling from Illumina sequence data

 

We have ongoing projects to study the the following organisms:

  • Escherichia coli ST131 and other global pandemic E. coli sequence types
  • Carbapenem Resistant Enterobacteriaceae (CRE)
  • Pseudomonas aeruginosa
  • Group A and Group B Streptococcus
  • Mycobacterium tuberculosis

More information on projects can be found here.

Please contact Scott directly (scott.beatson@uq.edu.au) to enquire about specific opportunities for Undergraduate, Masters, Honours or PHD projects at The University of Queensland.