Dr. Hanage is interested in bacterial evolution, which his lab investigates using modern population genomic methods, applied to many different pathogens. To understand the variation we observe in pathogen populations, we need theory to explain what we expect under different evolutionary histories, and the lab actively works to develop these methods with a particular focus on recombination and horizontal gene transfer, which has the ability to transfer genetic material encoding important traits like drug resistance or virulence among strains. His current projects focus on ways to understand how major successful resistant lineages emerge and persist, and how genomic data can be used to reconstruct transmission trees. He maintains a long standing interest in the question of whether a useful species concept can be developed for bacteria. During his post-doctoral work at Imperial College London, he worked extensively on Multi-locus Sequence Typing (MLST) and remains a curator of the pneumococcal MLST database https://pubmlst.org/spneumoniae/. He has been awarded honors including the Fleming Prize for his work.