The research of my group focusses on the evolution of bacterial pathogens; their origin, transmission and adaptation to selective pressure. I primarily use genomic and phylogenetic approaches to address these, and over the last few years my group has used large-scale population genomics to identify the global origin and routes of spread of many human and animal pathogens. Overlaid on the phylogeny, we look for signatures of adaptation to the host, to antibiotics and to vaccine pressure, most recently developing bacterial genome-wide association approaches to identify genetic determinants responsible for this adaptation. In addition to informatics approaches, we develop and apply genome-wide experimental tools, studying interaction with the host and antimicrobial resistance mechanisms. We have an interest in metagenomics, currently studying the microbiota in the gut, the lung, the nasopharynx and the placenta (which doesn’t have one). We often work at an international level, with many collaborations in Low- and Middle-Income countries.
Our work has clear translational benefits for tracking transmission at the hospital level and more broadly. To enable this translation, we have been collaborating with local hospitals, and national and international health-protection agencies, as well as the commercial sector.