Historically my research has been on pathogenic members of the Enterobacteriaceae including Salmonella, pathogenic E. coli, Shigella, Citrobacter and Yersinia, although I have also studied the genetic makeup and diversity of non-enteric pathogens including Chlamydia. My work has progressed from generating reference genomes through to large-scale comparative phylogenomic projects, with my team now focusing largely on population-based studies including both national and international research collaborations. We have also focussed on defining the evolutionary signatures that mark long term evolution of the Yersinia genus, or lineages of Salmonella, that have moved from being broad host range pathogens to becoming restricted to a particular host(s) or niche.
A strong theme in my work is the application of phylogeny to understand the contemporary or historical distribution of bacterial pathogens causing diarrheal disease or sexually transmitted pathogens, including Shigella sonnei (Nature Genetics, 2012) Shigella flexneri (eLife, 2015) and Vibrio cholerae (Nature, 2011, 2017, 2018, 2019), as well as antimicrobial resistance. In Salmonella we focused on the course of the epidemic of the zoonotic pathogen Salmonella Typhimurium DT104 in Scotland, isolated from both humans and farm animals over a 22-year period (Science, 2013).
My group has also developed different approaches to enable sequence bacterial genomes directly from uncultured discarded clinical samples (Genome Res, 2013; Nature Protocols 2013, CID 2017) enabling my group to extend our population based studies without the need for culture. This methodology has broad applications in clinical microbiology.