Epidemiology, genomics and antimicrobial resistance of bacteria
Our work aims to understand the evolution, origins and transmission of bacteria between different host populations, with a focus on bacteria that are resistant to antimicrobial drugs.
We are particularly interested in understanding the relative contributions of animals, humans, the environment and food to the overall burden of disease caused by pathogenic bacteria and antimicrobial resistance (AMR). We also want to understand the importance of non-pathogenic bacteria, including those in the microbiome, as reservoirs of AMR genes.
By defining and quantifying the importance of different sources of bacteria and AMR, we aim to address gaps in our knowledge, identify points where interventions may be most effectively applied, improve food safety, and inform policy and surveillance.
We use a combination of approaches from epidemiology, ecology and genomics to understand where bacteria and AMR come from and how they spread. We work with partners in national reference laboratories, examining large, long-term bacterial collections to understand the population structure and evolution of bacteria, and are also working with the Food Standards Agency to investigate the diversity and epidemiology of bacteria and AMR in the food we eat. We use a variety of bioinformatics and statistical techniques to investigate these questions, including short read, long read, and metagenome sequencing approaches.