My research interests lie in using sequence data to study bacterial pathogens, both from a point of view of managing infections (molecular epidemiology) but also in terms of understanding fundamental evolutionary dynamics. The early part of my research career was spent generating and interpreting multilocus sequence typing (MLST) data for numerous species. I developed the BURST algorithm to help visualise these datasets (J Bacteriol. 186(5):1518-30). More recently, I have focussed on whole genome sequence (WGS) data, and was joint lead author on the first demonstration of WGS data for molecular epidemiology (Science 327: 5964 469-474). I am currently a PI on a large CRCUK project, headed by Prof Sharon Peacock, looking at implementing this technology into routine epidemiological surveillance, and was previously a work package leader on the FP7 Project TROCAR, headed by Prof Jordi Villa, which aimed to characterise and manage high risk antibiotic resistant clones in Europe.
I also have a strong interest in using whole genome sequencing (WGS) to understand and manage the spread of bacterial pathogens in animals. I was a PI on consortium funded under the insect pollinator initiative looking at the epidemiology of European Foul Brood in honeybees, and am currently PI on the BBSRC/NERC funded project wgs-aqua.net, which aims to deploy WGS to manage bacterial pathogens of aquaculture (in collaboration with Cefas, Weymouth, the University of Stirling and the Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute).
In addition to molecular epidemiology, WGS data of bacterial pathogens can shed light on basic evolutionary questions concerning diversification; mutation, recombination and selection. Research questions include the strength of selection on intergenic sites, codon bias, context dependant mutation, the maintenance of GC content, INDEL formation, and gene essentiality.
I was awarded the Zoological Society of London Scientific Medal in 2010, and am an ISI highly cited researcher for 2015.