Imperial College London


Faculty of MedicineSchool of Public Health

Senior Lecturer



+44 (0)20 7594 3622x.didelot




G30Medical SchoolSt Mary's Campus





I am a senior lecturer in the Department of Infectious Disease Epidemiology within the School of Public Health at Imperial College London. I am also a principal investigator of the MRC Centre for Outbreak Analysis and Modelling and of the NIHR Health Protection Research Unit in Modelling Methodology.

Research Interests

My research is focused on the analysis of genomic data in order to improve our understanding of bacterial evolution, epidemiology, ecology and pathogenicity. A key aim is to develop new bioinformatics and statistical methods that can handle the very large amounts of data made available by novel high-throughput sequencing techniques.

Because of the interdisciplinary nature of my work, I have broad interests in a variety of subjects, including theoretical topics such as mathematical population genetics, Bayesian statistics or Monte-Carlo methods, and biological topics such as bacterial evolutionary processes or pathogen epidemiology.

I have worked on a wide range of bacterial pathogens, especially those causing healthcare associated infections (eg Clostridium difficile and Staphylococcus aureus) and gastrointestinal infections (eg Salmonella enterica, Bacillus cereusCampylobacter jejuni and Helicobacter pylori).

Biographical Sketch

In 2007, I completed a doctorate in Statistical Genetics in the Department of Statistics, University of Oxford. I then spent three years as a postdoctoral research fellow in the Department of Statistics, University of Warwick. In 2010, I moved back to the University of Oxford as a leadership fellow in genomic microbiology before taking my current appointment with Imperial College London in April 2012.


I have developed the following computer software, all of which are freely available on the internet: 

ClonalFrame: inference of bacterial microevolution using sequence data
GenoPlast: analysis of genomic plasticity in bacteria
SimMLST: Simulation of genetic data under a neutral model
ClonalOrigin: inference of homologous recombination in bacteria using whole genome sequences
TransPhylo: inference of a pathogen transmission tree given a phylogeny
- TreeBreaker: evolutionary inference of a phenotype distribution
ClonalFrameML: efficient inference of recombination in whole bacterial genomes


I collaborate with the Modernising Medical Microbiology consortium which brings together the University of Oxford, Public Health England, the Sanger Institute and the NHS, with the aim of revolutionising our understanding of human pathogens through the use of whole-genome sequencing technology. Three major bacterial pathogens are under particular investigation: Staphylococcus aureus, Clostridium difficile and Mycobacterium tuberculosis

Other frequent collaborators include:

Mark Achtman (University of Warwick)
- Caroline Colijn (Imperial College London)
- Derrick Crook (Public Health England)
Aaron Darling (University of Technology Sydney)
Daniel Falush (University of Bath)
- Jennifer Gardy (BC Centre for Disease Control)
Dan Lawson (University of Bristol)
Martin Maiden (University of Oxford)
- John Paul (Public Health England)
Tim Read (Emory University)
Sam Sheppard ( University of Bath)
Sebastian Suerbaum (University of Munich)
Danny Wilson (University of Oxford)

Selected Publications

Journal Articles

Dingle KE, Didelot X, Quan TP, et al., 2017, Effects of control interventions on Clostridium difficile infection in England: an observational study., Lancet Infect Dis

Ledda A, Price JR, Cole K, et al., 2017, Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus., J Antimicrob Chemother

Didelot X, Fraser C, Gardy J, et al., 2017, Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks., Mol Biol Evol

Ansari MA, Didelot X, 2016, Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree, Genetics, Vol:204, ISSN:0016-6731, Pages:89-+

Didelot X, Dordel J, Whittles LK, et al., 2016, Genomic Analysis and Comparison of Two Gonorrhea Outbreaks, MBIO, Vol:7, ISSN:2150-7511

Whittles LK, Didelot X, 2016, Epidemiological analysis of the Eyam plague outbreak of 1665-1666, Proceedings of the Royal Society B: Biological Sciences, Vol:283, ISSN:0962-8452

Didelot X, Walker AS, Peto TE, et al., 2016, Within-host evolution of bacterial pathogens, Nature Reviews Microbiology, Vol:14, ISSN:1740-1526, Pages:150-162

More Publications