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Bacterial Analysis Group (BAG)

BAG is a group of scientists based in the Department of Statistics, Nuffield Department of Clinical Medicine (NDM) and Wellcome Trust Centre for Human Genetics (WTCHG), working on interesting problems involving techniques such as the large-scale sequencing and analysis of pathogen genomes.  

Publicity
Our work has attracted interest from scientific and mainstream media: 

Nature Medicine (2010) Sequencing of superbugs seen as key to combating their spread  

BBC News Website (2012) Bacterial disguise evades vaccine: coverage of Nature Genetics (2012) Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event 

What do we do?
Much of our work is as part of the UK-CRC Consortium Modernising Medical Microbiology collaborating with the group of Professor Derrick Crook at the Nuffield Department of Medicine and Oxford University Hospitals NHS Trust. Modern sequencing technologies have made possible studies of evolution, transmission and epidemiology of pathogens that just a few years ago could not be imagined. Whereas previously obtaining just one bacterial genome sequence took months and thousands of pounds, now we can realistically sequence dozens of genomes from one host to characterize the dynamics and evolution of the pathogen during infection, or hundreds from a population to investigate pathogen transmission or population structure. In conjunction with the High-Throughput Genomics Group at the WTCHG, we have sequenced thousands of bacterial genomes belonging to large population-, cohort- and cluster-based samples. We have developed an integrated pipeline for high-throughput data QC and mapping-based and de novo genome assembly, and a comprehensive sample database to support analysis. We are now completing research that will make a difference to how infections are tracked and treated within just a few years.  

Personnel
Publications

Opportunities
Job opportunities are always advertised on the relevant University and Departmental webpages. For research placements, studentships and potential fellowship opportunities, please contact senior members of the group.

Current projects and projects for potential students
• modelling carriage in S. aureus using unparalleled datasets
• modelling transmission in C. difficile with complete hospital movement data
• digital sequencing analysis of mixed infection
• within-host infection dynamics using deep whole-genome sequencing
• case-control studies of virulence
• bacterial genome-wide association studies
• tracking genetic exchange in bacterial populations
• predicting antibioitic resistance and other phenotypes from whole-genome sequence data
• reconstructing genomic re-arrangements from sequence data
• controlling for selection in phylogenetic reconstruction
• modelling natural and carriage populations
• worldwide spread of new antibiotic resistance genes
• selection and recombination in S. pneumoniae
• studies across organisms comparisons of evolution, population structure and epidemiology

Where are we?
We are in the Oxford Centre for Gene Function, situated in the Henry Wellcome Building for Gene Function, which can be found on this map. For visitors, access is via reception at the Sherrington Building next door. For general enquiries, contact bowden at stats.ox.ac.uk.