The Beatson 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 interest 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 2000 citations (GS 28/01/20). Recent software projects include an interactive web-based visualiser for communicating genomic and epidemiological data for Healthcare-associated infections (HAIviz (Budi Permana)).
Read more about our research in our blog.
For a complete list of publications and grants see here.
For collaborations, teaching and other information see here.
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 ([s.beatson@uq.edu.au]) to enquire about specific opportunities for Undergraduate, Masters, Honours or PhD projects at The University of Queensland.
