Professor Xavier Didelot

Job Title

Professor

Department

Life Sciences

Xavier.Didelot@warwick.ac.uk

Web Link

Didelot Website

Research Interests

My research is concerned with understanding the way bacterial pathogens evolve, spread and cause disease. I have analysed both epidemiological and genomic data from a wide range of bacteria. 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 cereus, Campylobacter jejuni and Helicobacter pylori).

I share my time equally between the School of Life Sciences and the Department of Statistics. I am also a member of the Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER).

I lead the recently created Health Protection Research Unit in Genomics and Enabling Data which is funded by the National Institute for Health Research (NIHR). This project is a partnership between the University of Warwick and the UK Health Security Agency, in collaboration with the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Our aim is to provide the methodological backbone required to improve national public health using large scale genomic and epidemiological data.

Biography

2004-2007: Doctorate in Statistical Genetics, Department of Statistics, University of Oxford
2007-2010: Research Fellow, Department of Statistics, University of Warwick
2010-2012: Leadership Fellow, Department of Statistics, University of Oxford
2012-2018: Senior Lecturer, School of Public Health, Imperial College London
2018-present: Professor of Statistical Epidemiology and Genomics, School of Life Sciences and Department of Statistics, University of Warwick

Larsen, Jesper, Raisen, Claire L., Ba, Xiaoliang, Sadgrove, Nicholas J., Padilla-González, Guillermo F., Simmonds, Monique S. J., Loncaric, Igor, Kerschner, Heidrun, Apfalter, Petra, Hartl, Rainer, Deplano, Ariane, Vandendriessche, Stien, Cerná Bolfíková, Barbora, Hulva, Pavel, Arendrup, Maiken C., Hare, Rasmus K., Barnadas, Céline, Stegger, Marc, Sieber, Raphael N., Skov, Robert L. et al (Select to open full list), 2022.

All authors for Emergence of methicillin resistance predates the clinical use of antibiotics

Larsen, Jesper, Raisen, Claire L., Ba, Xiaoliang, Sadgrove, Nicholas J., Padilla-González, Guillermo F., Simmonds, Monique S. J., Loncaric, Igor, Kerschner, Heidrun, Apfalter, Petra, Hartl, Rainer, Deplano, Ariane, Vandendriessche, Stien, Cerná Bolfíková, Barbora, Hulva, Pavel, Arendrup, Maiken C., Hare, Rasmus K., Barnadas, Céline, Stegger, Marc, Sieber, Raphael N., Skov, Robert L., Petersen, Andreas, Angen, Øystein, Rasmussen, Sophie L., Espinosa-Gongora, Carmen, Aarestrup, Frank M., Lindholm, Laura J., Nykäsenoja, Suvi M., Laurent, Frederic, Becker, Karsten, Walther, Birgit, Kehrenberg, Corinna, Cuny, Christiane, Layer, Franziska, Werner, Guido, Witte, Wolfgang, Stamm, Ivonne, Moroni, Paolo, Jørgensen, Hannah J., de Lencastre, Hermínia, Cercenado, Emilia, García-Garrote, Fernando, Börjesson, Stefan, Hæggman, Sara, Perreten, Vincent, Teale, Christopher J., Waller, Andrew S., Pichon, Bruno, Curran, Martin D., Ellington, Matthew J., Welch, John J., Peacock, Sharon J., Seilly, David J., Morgan, Fiona J. E., Parkhill, Julian, Hadjirin, Nazreen F., Lindsay, Jodi A., Holden, Matthew T. G., Edwards, Giles F., Foster, Geoffrey, Paterson, Gavin K., Didelot, Xavier, Holmes, Mark A., Harrison, Ewan M., Larsen, Anders R.

Emergence of methicillin resistance predates the clinical use of antibiotics. Nature
'Whittles, Lilith K., 'Didelot, Xavier, 'White, Peter J., 2022. 'Public health impact and cost-effectiveness of gonorrhoea vaccination : an integrated transmission-dynamic health-economic modelling analysis. The Lancet. Infectious diseases
'Willgert, Katriina, 'Didelot, Xavier, 'Surendran-Nair, Meera, 'Kuchipudi, Suresh V., 'Ruden, Rachel M., 'Yon, Michele, 'Nissly, Ruth H., 'Vandegrift, Kurt J., 'Nelli, Rahul K., 'Li, Lingling, 'Jayarao, Bhushan M., 'Levine, Nicole, 'Olsen, Randall J., 'Davis, James J., 'Musser, James M., 'Hudson, Peter J., 'Kapur, Vivek, 'Conlan, Andrew J. K., 2022. 'Transmission history of SARS-CoV-2 in humans and white-tailed deer. Scientific Reports, 12 (1)
'Wang, Liang, 'Didelot, Xavier, 'Bi, Yuhai, 'Gao, George F., 2022. 'SARS-CoV-2 transmissibility compared between variants of concern and vaccination status. Briefings in Bioinformatics, 23 (2)
'Volk, Denis, 'Yang-Turner, Fan, 'Didelot, Xavier, 'Crook, Derrick W., 'Wyllie, David, 2022. 'Catwalk : identifying closely related sequences in large microbial sequence databases. Microbial Genomics, 8 (6)
'Fountain-Jones, Nicholas M., 'Kraberger, Simona, 'Gagne, Roderick B., 'Gilbertson, Marie L. J., 'Trumbo, Daryl R., 'Charleston, Michael, 'Salerno, Patricia E., 'Chris Funk, W., 'Crooks, Kevin, 'Logan, Kenneth, 'Alldredge, Mathew, 'Dellicour, Simon, 'Baele, Guy, 'Didelot, Xavier, 'VandeWoude, Sue, 'Carver, Scott, 'Craft, Meggan E., 2022. 'Hunting alters viral transmission and evolution in a large carnivore. Nature Ecology & Evolution, pp. 174-182
'Ledda, Alice, 'Cummins, Martina, 'Shaw, Liam P., 'Jauneikaite, Elita, 'Cole, Kevin, 'Lasalle, Florent, 'Barry, Deborah, 'Turton, Jane, 'Rosmarin, Caryn, 'Anaraki, Sudy, 'Wareham, David, 'Stoesser, Nicole, 'Paul, John, 'Manuel, Rohini, 'Cherian, Benny P., 'Didelot, Xavier, 2022. 'Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399. Microbial Genomics, 8 (4)
'Didelot, Xavier, 'Parkhill, Julian, 2022. 'A scalable analytical approach from bacterial genomes to epidemiology. Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861)
Didelot, Xavier, Kendall, Michelle, Xu, Yuanwei, White, Peter J., McCarthy, Noel D., 2021. Genomic epidemiology analysis of infectious disease outbreaks using transPhylo. Current Protocols, 1 (2)
Didelot, Xavier, Siveroni, Igor, Volz, Erik M., 2021. Additive uncorrelated relaxed clock models for the dating of genomic epidemiology phylogenies. Molecular Biology and Evolution, 38 (1), pp. 307-317
Didelot, Xavier, Kendall, Michelle, Xu, Yuanwei, White, Peter J., McCarthy, Noel D., 2021. Genomic epidemiology analysis of infectious disease outbreaks using transPhylo. Current Protocols, 1 (2)
Lassalle, Florent, Dastgheib, Seyed M. M., Zhao, Fang-Jie, Zhang, Jun, Verbarg, Susanne, Frühling, Anja, Brinkmann, Henner, Osborne, Thomas H., Sikorski, Johannes, Balloux, Francois, Didelot, Xavier, Santini, Joanne M., Petersen, Jörn, 2021. Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Systematic and Applied Microbiology, 44 (1)
'Helekal, David, 'Ledda, Alice, 'Volz, Erik, 'Wyllie, David, 'Didelot, Xavier, 2021. 'Bayesian inference of clonal expansions in a dated phylogeny. Systematic Biology, 71 (5), pp. 1073-1087
Knight, Daniel R., Imwattana, Korakrit, Kullin, Brian, Guerrero-Araya, Enzo, Paredes-Sabja, Daniel, Didelot, Xavier, Dingle, Kate E., Eyre, David W., Rodríguez, César Cabrera, Riley, Thomas V., 2021. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife, 10
Wang, Liang, Didelot, Xavier, Bi, Yuhai, Gao, George F., 2021. Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants. The Innovation
Torres Ortiz, Arturo, Coronel, Jorge, Vidal, Julia Rios, Bonilla, Cesar, Moore, David A. J., Gilman, Robert H., Balloux, Francois, Kon, Onn Min, Didelot, Xavier, Grandjean, Louis, 2021. Genomic signatures of pre-resistance in Mycobacterium tuberculosis. Nature Communications, 12 (1)
Osnes, Magnus N., Didelot, Xavier, Korne-Elenbaas, Jolinda de, Alfsnes, Kristian, Brynildsrud, Ola B., Syversen, Gaute, Nilsen, Øivind Jul, De Blasio, Birgitte Freiesleben, Caugant, Dominique A., Eldholm, Vegard, 2020. Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway. Microbial Genomics, 6 (12)
Fountain-Jones, Nicholas M, Appaw, Raima Carol, Carver, Scott, Didelot, Xavier, Volz, Erik, Charleston, Michael, 2020. Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evolution
Janezic, Sandra, Dingle, Kate, Alvin, Joseph, Accetto, Toma?, Didelot, Xavier, Crook, Derrick W., Lacy, D. Borden, Rupnik, Maja, 2020. Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution. Microbial Genomics, 6 (10)
Wang, Haoqiu, Yang, Chao, Sun, Zhou, Zheng, Wei, Zhang, Wei, Yu, Hua, Wu, Yarong, Didelot, Xavier, Yang, Ruifu, Pan, Jingcao, Cui, Yujun, 2020. Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages. PLOS Neglected Tropical Diseases, 14 (2)
Rodriguez-Manzano, Jesus, Moser, Nicolas, Malpartida-Cardenas, Kenny, Moniri, Ahmad, Fisarova, Lenka, Pennisi, Ivana, Boonyasiri, Adhiratha, Jauneikaite, Elita, Abdolrasouli, Alireza, Otter, Jonathan A., Bolt, Frances, Davies, Frances, Didelot, Xavier, Holmes, Alison, Georgiou, Pantelis, 2020. Rapid detection of mobilized colistin resistance using a nucleic acid based lab-on-a-chip diagnostic system. Scientific Reports, 10 (1)
Volz, Erik M., Wiuf, Carsten, Grad, Yonatan H., Frost, Simon D. W., Dennis, Ann M., Didelot, Xavier, 2020. Identification of hidden population structure in time-scaled phylogenies. Systematic Biology, 69 (5), pp. 884-896
Whittles, Lilith K., White, Peter J., Didelot, Xavier, 2020. Assessment of the potential of vaccination to combat antibiotic resistance in gonorrhea : a modeling analysis to determine preferred product characteristics. Clinical Infectious Diseases, 71 (8), pp. 1912-1919
Vegvari, Carolin, Grad, Yonatan H., White, Peter J., Didelot, Xavier, Whittles, Lilith K., Scangarella-Oman, Nicole E., Mitrani-Gold, Fanny S., Dumont, Etienne, Perry, Caroline R., Gilchrist, Kim, Hossain, Mohammad, Mortimer, Tatum D., Anderson, Roy M., Gardiner, David, 2020. Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. Eurosurveillance, 25 (43)
Hennart, Melanie, Panunzi, Leonardo G., Rodrigues, Carla, Gaday, Quentin, Baines, Sarah L., Barros-Pinkelnig, Marina, Carmi-Leroy, Annick, Dazas, Melody, Wehenkel, Anne Marie, Didelot, Xavier, Toubiana, Julie, Badell, Edgar, Brisse, Sylvain, 2020. Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Medicine, 12 (1)
Wang, Liang, Didelot, Xavier, Yang, Jing, Wong, Gary, Shi, Yi, Liu, Wenjun, Gao, George F., Bi, Yuhai, 2020. Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase. Nature Communications, 11 (1)
Ferrari, Matthew (Matt), Whittles, Lilith K., White, Peter J., Didelot, Xavier, 2019. A dynamic power-law sexual network model of gonorrhoea outbreaks. PLoS Computational Biology, 15 (3)
Ozer, Egon A., Nnah, Ekpeno, Didelot, Xavier, Whitaker, Rachel J., Hauser, Alan R., 2019. The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages. Genome Biology and Evolution, 11 (1), pp. 1780-1796
Criscuolo, Alexis, Issenhuth-Jeanjean, Sylvie, Didelot, Xavier, Thorell, Kaisa, Hale, James, Parkhill, Julian, Thomson, Nicholas R., Weill, François-Xavier, Falush, Daniel, Brisse, Sylvain, 2019. The speciation and hybridization history of the genus Salmonella. Microbial Genomics, 5 (8)
Dorp, Lucy van, Wang, Qi, Shaw, Liam P., Acman, Mislav, Brynildsrud, Ola B., Eldholm, Vegard, Wang, Ruobing, Gao, Hua, Yin, Yuyao, Chen, Hongbin, Ding, Chuling, Farrer, Rhys A., Didelot, Xavier, Balloux, Francois, Wang, Hui, 2019. Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains. Microbial Genomics, 5 (4)
Zhao, Lin, Chen, Hongyou, Didelot, Xavier, Li, Zhenpeng, Li, Yinghui, Chen, Meiling, Du, Yu, Zhao, Hongqun, Liu, Jie, Hu, Qinghua, Kan, Biao, Chen, Min, Pang, Bo, 2019. Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12. Microbial Genomics, 6 (12)
Didelot, Xavier, Pouwels, Koen B., 2019. Machine-learning-assisted selection of antibiotic prescription. Nature Medicine, 25 (7), pp. 1033-1034
Dingle, Kate E., Didelot, Xavier, Quan, T. Phuong, Eyre, David W., Stoesser, Nicole, Marwick, Charis A., Coia, John, Brown, Derek, Buchanan, Sarah, Ijaz, Umer Z., Goswami, Cosmika, Douce, Gill, Fawley, Warren N., Wilcox, Mark H., Peto, Timothy E. A., Walker, A. Sarah, Crook, Derrick W., Keim, Paul, 2019. A role for tetracycline selection in recent evolution of agriculture-associated clostridium difficile PCR ribotype 078. mBio, 10 (2), pp. 1-19
Ailloud, Florent, Didelot, Xavier, Woltemate, Sabrina, Pfaffinger, Gudrun, Overmann, Jörg, Bader, Ruth Christiane, Schulz, Christian, Malfertheiner, Peter, Suerbaum, Sebastian, 2019. Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nature Communications, 10 (1)
Moniri, Ahmad, Rodriguez-Manzano, Jesus, Malpartida-Cardenas, Kenny, Yu, Ling-Shan, Didelot, Xavier, Holmes, Alison, Georgiou, Pantelis, 2019. Framework for DNA quantification and outlier detection using multidimensional standard curves. Analytical Chemistry, 91 (11), pp. 7426-7434
Eyre, David W., Didelot, Xavier, Buckley, Anthony M., Freeman, Jane, Moura, Ines B., Crook, Derrick W., Peto, Tim E.A., Walker, A. Sarah, Wilcox, Mark H., Dingle, Kate E., 2019. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine, 43, pp. 347-355
Didelot, Xavier, Croucher, Nicholas J., Bentley, Stephen D., Harris, Simon R., Wilson, Daniel J., 2018. Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Research, 46 (22)
Challagundla, Lavanya, Luo, Xiao, Tickler, Isabella A., Didelot, Xavier, Coleman, David C., Shore, Anna C., Coombs, Geoffrey W., Sordelli, Daniel O., Brown, Eric L., Skov, Robert, Larsen, Anders Rhod, Reyes, Jinnethe, Robledo, Iraida E., Vazquez, Guillermo J., Rivera, Raul, Fey, Paul D., Stevenson, Kurt, Wang, Shu-Hua, Kreiswirth, Barry N., Mediavilla, Jose R. et al (Select to open full list), 2018.

All authors for Range expansion and the origin of USA300 North American epidemic methicillin-resistant staphylococcus aureus

Challagundla, Lavanya, Luo, Xiao, Tickler, Isabella A., Didelot, Xavier, Coleman, David C., Shore, Anna C., Coombs, Geoffrey W., Sordelli, Daniel O., Brown, Eric L., Skov, Robert, Larsen, Anders Rhod, Reyes, Jinnethe, Robledo, Iraida E., Vazquez, Guillermo J., Rivera, Raul, Fey, Paul D., Stevenson, Kurt, Wang, Shu-Hua, Kreiswirth, Barry N., Mediavilla, Jose R., Arias, Cesar A., Planet, Paul J., Nolan, Rathel L., Tenover, Fred C., Goering, Richard V., Robinson, D. Ashley

Range expansion and the origin of USA300 North American epidemic methicillin-resistant staphylococcus aureus. mBio, 9 (1)
Whittles, Lilith, White, Peter, Paul, John, Didelot, Xavier, 2018. Epidemiological trends of antibiotic resistant Gonorrhoea in the United Kingdom. Antibiotics, 7 (3)
Collins, Caitlin, Didelot, Xavier, 2018. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. PLoS Computational Biology, 14 (2)
Méric, Guillaume, Mageiros, Leonardos, Pensar, Johan, Laabei, Maisem, Yahara, Koji, Pascoe, Ben, Kittiwan, Nattinee, Tadee, Phacharaporn, Post, Virginia, Lamble, Sarah, Bowden, Rory, Bray, James E., Morgenstern, Mario, Jolley, Keith A., Maiden, Martin C. J., Feil, Edward J., Didelot, Xavier, Miragaia, Maria, de Lencastre, Herminia, Moriarty, T. Fintan et al (Select to open full list), 2018.

All authors for Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Méric, Guillaume, Mageiros, Leonardos, Pensar, Johan, Laabei, Maisem, Yahara, Koji, Pascoe, Ben, Kittiwan, Nattinee, Tadee, Phacharaporn, Post, Virginia, Lamble, Sarah, Bowden, Rory, Bray, James E., Morgenstern, Mario, Jolley, Keith A., Maiden, Martin C. J., Feil, Edward J., Didelot, Xavier, Miragaia, Maria, de Lencastre, Herminia, Moriarty, T. Fintan, Rohde, Holger, Massey, Ruth, Mack, Dietrich, Corander, Jukka, Sheppard, Samuel K.

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications, 9 (1)
Yahara, Koji, Nakayama, Shu-ichi, Shimuta, Ken, Lee, Ken-ichi, Morita, Masatomo, Kawahata, Takuya, Kuroki, Toshiro, Watanabe, Yuko, Ohya, Hitomi, Yasuda, Mitsuru, Deguchi, Takashi, Didelot, Xavier, Ohnishi, Makoto, 2018. Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microbial Genomics, 4 (8)
Wang, Ruobing, van Dorp, Lucy, Shaw, Liam P., Bradley, Phelim, Wang, Qi, Wang, Xiaojuan, Jin, Longyang, Zhang, Qing, Liu, Yuqing, Rieux, Adrien, Dorai-Schneiders, Thamarai, Weinert, Lucy Anne, Iqbal, Zamin, Didelot, Xavier, Wang, Hui, Balloux, Francois, 2018. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nature Communications, 9 (1)
Séraphin, Marie Nancy, Khan, Md. Siddiqur Rahman, Didelot, Xavier, Morris, J. Glenn, Nolan, David J., Murray, Ellen R., Salemi, Marco, Lauzardo, Michael, May, Justin R., 2018. Genomic investigation of a Mycobacterium tuberculosis outbreak involving prison and community cases in Florida, United States. The American Journal of Tropical Medicine and Hygiene, 99 (4)
Volz, Erik M., Didelot, Xavier, 2018. Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance. Systematic Biology, 67 (4), pp. 719-728
Pandey, Anish, Cleary, David W., Laver, Jay R., Gorringe, Andrew, Deasy, Alice M., Dale, Adam P., Morris, Paul D., Didelot, Xavier, Maiden, Martin C. J., Read, Robert C., 2018. Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection. Nature Communications, 9 (1)
Campbell, Finlay, Didelot, Xavier, Fitzjohn, Rich, Ferguson, Neil, Cori, Anne, Jombart, Thibaut, 2018. outbreaker2 : a modular platform for outbreak reconstruction. BMC Bioinformatics, 19 (Supplement 11)
Pandey, Anish, Cleary, David W., Laver, Jay R., Gorringe, Andrew, Deasy, Alice M., Dale, Adam P., Morris, Paul D., Didelot, Xavier, Maiden, Martin C. J., Read, Robert C., 2018. Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection. Nature Communications, 9 (1)
Whittles, Lilith K., Didelot, Xavier, Grad, Yonatan H., White, Peter J., 2018. Testing for gonorrhoea should routinely include the pharynx. The Lancet Infectious Diseases, 18 (7), pp. 716-717
Didelot, Xavier, Fraser, Christophe, Gardy, Jennifer, Colijn, Caroline, 2017. Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Molecular Biology and Evolution, 34 (4), pp. 997-1007
Pandey, Anish K., Cleary, David W., Laver, Jay R., Maiden, Martin C. J., Didelot, Xavier, Gorringe, Andrew, Read, Robert C., 2017. Neisseria lactamica Y92?1009 complete genome sequence. Standards in Genomic Sciences, 12 (1)
Peters, Joanna, Cresswell, Fiona, Amor, Lauren, Cole, Kevin, Dean, Gillian, Didelot, Xavier, De Silva, Dilrini, Eyre, David W., Paul, John, 2017. Whole genome sequencing of Neisseria gonorrhoeae reveals transmission clusters involving patients of mixed HIV serostatus. Sexually Transmitted Infections, 94 (2), pp. 138-143
Mostowy, Rafal J., Croucher, Nicholas J., De Maio, Nicola, Chewapreecha, Claire, Salter, Susannah J., Turner, Paul, Aanensen, David M., Bentley, Stephen D., Didelot, Xavier, Fraser, Christophe, 2017. Pneumococcal capsule synthesis locus cps as evolutionary hotspot with potential to generate novel serotypes by recombination. Molecular Biology and Evolution, 34 (10), pp. 2537-2554
Whittles, Lilith K., White, Peter J., Didelot, Xavier, 2017. Estimating the fitness cost and benefit of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy : a modelling study. PLoS Medicine, 14 (10)
Pascoe, Ben, Méric, Guillaume, Yahara, Koji, Wimalarathna, Helen, Murray, Susan, Hitchings, Matthew D., Sproston, Emma L., Carrillo, Catherine D., Taboada, Eduardo N., Cooper, Kerry K., Huynh, Steven, Cody, Alison J., Jolley, Keith A., Maiden, Martin C. J., McCarthy, Noel D., Didelot, Xavier, Parker, Craig T., Sheppard, Samuel K., 2017. Local genes for local bacteria : evidence of allopatry in the genomes of transatlantic Campylobacter populations. Molecular Ecology, 26 (17), pp. 4497-4508
Yahara, Koji, Méric, Guillaume, Taylor, Aidan J., de Vries, Stefan P. W., Murray, Susan, Pascoe, Ben, Mageiros, Leonardos, Torralbo, Alicia, Vidal, Ana, Ridley, Anne, Komukai, Sho, Wimalarathna, Helen, Cody, Alison J., Colles, Frances M., McCarthy, Noel, Harris, David, Bray, James E., Jolley, Keith A., Maiden, Martin C. J., Bentley, Stephen D. et al (Select to open full list), 2017.

All authors for Genome-wide association of functional traits linked with Campylobacter jejunisurvival from farm to fork

Yahara, Koji, Méric, Guillaume, Taylor, Aidan J., de Vries, Stefan P. W., Murray, Susan, Pascoe, Ben, Mageiros, Leonardos, Torralbo, Alicia, Vidal, Ana, Ridley, Anne, Komukai, Sho, Wimalarathna, Helen, Cody, Alison J., Colles, Frances M., McCarthy, Noel, Harris, David, Bray, James E., Jolley, Keith A., Maiden, Martin C. J., Bentley, Stephen D., Parkhill, Julian, Bayliss, Christopher D., Grant, Andrew, Maskell, Duncan, Didelot, Xavier, Kelly, David J., Sheppard, Samuel K.

Genome-wide association of functional traits linked with Campylobacter jejunisurvival from farm to fork. Environmental Microbiology, 19 (1), pp. 361-380
Rosner, Bettina M., Schielke, Anika, Didelot, Xavier, Kops, Friederike, Breidenbach, Janina, Willrich, Niklas, Gölz, Greta, Alter, Thomas, Stingl, Kerstin, Josenhans, Christine, Suerbaum, Sebastian, Stark, Klaus, 2017. A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011?2014. Scientific Reports, 7 (1)
Klinkenberg, Don, Backer, Jantien A., Didelot, Xavier, Colijn, Caroline, Wallinga, Jacco, 2017. Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Computational Biology, 13 (5)
Dingle, Kate E., Didelot, Xavier, Quan, T Phuong, Eyre, David W., Stoesser, Nicole, Golubchik, Tanya, Harding, Rosalind M., Wilson, Daniel J., Griffiths, David, Vaughan, Alison, Finney, John M., Wyllie, David H., Oakley, Sarah J., Fawley, Warren N., Freeman, Jane, Morris, Kirsti, Martin, Jessica, Howard, Philip, Gorbach, Sherwood, Goldstein, Ellie J. C. et al (Select to open full list), 2017.

All authors for Effects of control interventions on Clostridium difficile infection in England : an observational study

Dingle, Kate E., Didelot, Xavier, Quan, T Phuong, Eyre, David W., Stoesser, Nicole, Golubchik, Tanya, Harding, Rosalind M., Wilson, Daniel J., Griffiths, David, Vaughan, Alison, Finney, John M., Wyllie, David H., Oakley, Sarah J., Fawley, Warren N., Freeman, Jane, Morris, Kirsti, Martin, Jessica, Howard, Philip, Gorbach, Sherwood, Goldstein, Ellie J. C., Citron, Diane M., Hopkins, Susan, Hope, Russell, Johnson, Alan P., Wilcox, Mark H., Peto, Timothy E. A., Walker, A Sarah, Crook, Derrick W., Del Ojo Elias, Carlos, Crichton, Charles, Kostiou, Vasiliki, Giess, Adam, Davies, Jim

Effects of control interventions on Clostridium difficile infection in England : an observational study. The Lancet Infectious Diseases, 17 (4), pp. 411-421
Ledda, Alice, Price, James R., Cole, Kevin, Llewelyn, Martin J., Kearns, Angela M., Crook, Derrick W., Paul, John, Didelot, Xavier, 2017. Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. Journal of Antimicrobial Chemotherapy, 72 (5), pp. 1285-1288
Yang, Shangxin, Hemarajata, Peera, Hindler, Janet, Li, Fan, Adisetiyo, Helty, Aldrovandi, Grace, Sebra, Robert, Kasarskis, Andrew, MacCannell, Duncan, Didelot, Xavier, Russell, Dana, Rubin, Zachary, Humphries, Romney, 2017. Evolution and transmission of carbapenem-resistant Klebsiella pneumoniae expressing the blaOXA-232 gene during an institutional outbreak associated with endoscopic retrograde cholangiopancreatography. Clinical Infectious Diseases, 64 (7), pp. 894-901
Ratmann, Oliver, Hodcroft, Emma B., Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon, Hossain, A.S. Md Mukarram, Joy, Jeffrey B., Kendall, Michelle, Kühnert, Denise, Leventhal, Gabriel E., Liang, Richard, Plazzotta, Giacomo, Poon, Art F.Y., Rasmussen, David A., Stadler, Tanja et al (Select to open full list), 2017.

All authors for Phylogenetic tools for generalized HIV-1 epidemics : findings from the PANGEA-HIV methods comparison

Ratmann, Oliver, Hodcroft, Emma B., Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon, Hossain, A.S. Md Mukarram, Joy, Jeffrey B., Kendall, Michelle, Kühnert, Denise, Leventhal, Gabriel E., Liang, Richard, Plazzotta, Giacomo, Poon, Art F.Y., Rasmussen, David A., Stadler, Tanja, Volz, Erik, Weis, Caroline, Leigh Brown, Andrew J., Fraser, Christophe

Phylogenetic tools for generalized HIV-1 epidemics : findings from the PANGEA-HIV methods comparison. Molecular Biology and Evolution, 34 (1), pp. 185-203
Didelot, Xavier, Whittles, Lilith K., Hall, Ian, 2017. Model-based analysis of an outbreak of bubonic plague in Cairo in 1801. Journal of The Royal Society Interface, 14 (131)
De Silva, Dilrini, Peters, Joanna, Cole, Kevin, Cole, Michelle J, Cresswell, Fiona, Dean, Gillian, Dave, Jayshree, Thomas, Daniel Rh, Foster, Kirsty, Waldram, Alison, Wilson, Daniel J, Didelot, Xavier, Grad, Yonatan H, Crook, Derrick W, Peto, Tim E A, Walker, A Sarah, Paul, John, Eyre, David W, 2016. Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae : an observational study. The Lancet Infectious Diseases, 16 (11), pp. 1295-1303
Bubendorfer, Sebastian, Krebes, Juliane, Yang, Ines, Hage, Elias, Schulz, Thomas F., Bahlawane, Christelle, Didelot, Xavier, Suerbaum, Sebastian, 2016. Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nature Communications, 7
Joseph, Sandeep J., Marti, Hanna, Didelot, Xavier, Read, Timothy D., Dean, Deborah, 2016. Tetracycline selective pressure and homologous recombination shape the evolution of Chlamydia suis : a recently identified zoonotic pathogen. Genome Biology and Evolution, 8 (8), pp. 2613-2623
Didelot, Xavier, Walker, A. Sarah, Peto, Tim E., Crook, Derrick W., Wilson, Daniel J., 2016. Within-host evolution of bacterial pathogens. Nature Reviews Microbiology, 14 (3), pp. 150-162
Hatherell, Hollie-Ann, Tang, Patrick, Pollock, Sue L., Didelot, Xavier, Johnston, James C., Gardy, Jennifer L., Crisan, Anamaria, Colijn, Caroline, 2016. Declaring a tuberculosis outbreak over with genomic epidemiology. Microbial Genomics, 2 (5)
Stoesser, Nicole, Sheppard, Anna E., Pankhurst, Louise, De Maio, Nicola, Moore, Catrin E., Sebra, Robert, Turner, Paul, Anson, Luke W., Kasarskis, Andrew, Batty, Elizabeth M., Kos, Veronica, Wilson, Daniel J., Phetsouvanh, Rattanaphone, Wyllie, David, Sokurenko, Evgeni, Manges, Amee R., Johnson, Timothy J., Price, Lance B., Peto, Timothy E. A., Johnson, James R. et al (Select to open full list), 2016.

All authors for Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

Stoesser, Nicole, Sheppard, Anna E., Pankhurst, Louise, De Maio, Nicola, Moore, Catrin E., Sebra, Robert, Turner, Paul, Anson, Luke W., Kasarskis, Andrew, Batty, Elizabeth M., Kos, Veronica, Wilson, Daniel J., Phetsouvanh, Rattanaphone, Wyllie, David, Sokurenko, Evgeni, Manges, Amee R., Johnson, Timothy J., Price, Lance B., Peto, Timothy E. A., Johnson, James R., Didelot, Xavier, Walker, A. Sarah, Crook, Derrick W.

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131. mBio, 7 (2)
Eldholm, Vegard, Rieux, Adrien, Monteserin, Johana, Lopez, Julia Montana, Palmero, Domingo, Lopez, Beatriz, Ritacco, Viviana, Didelot, Xavier, Balloux, Francois, 2016. Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis. eLife, 5
Whittles, Lilith K., Didelot, Xavier, 2016. Epidemiological analysis of the Eyam plague outbreak of 1665?1666. Proceedings of the Royal Society B: Biological Sciences, 283 (1830)
Yahara, Koji, Didelot, Xavier, Jolley, Keith A., Kobayashi, Ichizo, Maiden, Martin C. J., Sheppard, Samuel K., Falush, Daniel, 2016. The landscape of realized homologous recombination in pathogenic bacteria. Molecular Biology and Evolution, 33 (2), pp. 456-471
Wielgoss, Sébastien, Didelot, Xavier, Chaudhuri, Roy R, Liu, Xuan, Weedall, Gareth D, Velicer, Gregory J, Vos, Michiel, 2016. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. The ISME Journal, 10 (10), pp. 2468-2477
Brown, Thomas, Didelot, Xavier, Maio, Nicola De, Wilson, Daniel J., 2016. SimBac : simulation of whole bacterial genomes with homologous recombination. Microbial Genomics, 2 (1)
Didelot, Xavier, 2016. Heroic sacrifice or tragic mistake? Revisiting the Eyam plague, 350 years on. Significance, 13 (5), pp. 20-25
Joseph, Sandeep J., Cox, Daniel, Wolff, Bernard, Morrison, Shatavia S., Kozak-Muiznieks, Natalia A., Frace, Michael, Didelot, Xavier, Castillo-Ramirez, Santiago, Winchell, Jonas, Read, Timothy D., Dean, Deborah, 2016. Dynamics of genome change among Legionella species. Scientific Reports, 6 (1)
Didelot, Xavier, Dordel, Janina, Whittles, Lilith K., Collins, Caitlin, Bilek, Nicole, Bishop, Cynthia J., White, Peter J., Aanensen, David M., Parkhill, Julian, Bentley, Stephen D., Spratt, Brian G., Harris, Simon R., 2016. Genomic analysis and comparison of two Gonorrhea outbreaks. mBio, 7 (3)
Ansari, M. Azim, Didelot, Xavier, 2016. Bayesian inference of the evolution of a phenotype distribution on a phylogenetic tree. Genetics, 204 (1), pp. 89-98
Cui, Yujun, Yang, Xianwei, Didelot, Xavier, Guo, Chenyi, Li, Dongfang, Yan, Yanfeng, Zhang, Yiquan, Yuan, Yanting, Yang, Huanming, Wang, Jian, Wang, Jun, Song, Yajun, Zhou, Dongsheng, Falush, Daniel, Yang, Ruifu, 2015. Epidemic clones, oceanic gene pools, and eco-LD in the free living Marine pathogen vibrio parahaemolyticus. Molecular Biology and Evolution, 32 (6), pp. 1396-1410
Prlic, Andreas, Didelot, Xavier, Wilson, Daniel J., 2015. ClonalFrameML : efficient inference of recombination in whole bacterial genomes. PLoS Computational Biology, 11 (2)
Joseph, Sandeep J., Marti, Hanna, Didelot, Xavier, Castillo-Ramirez, Santiago, Read, Timothy D., Dean, Deborah, 2015. Chlamydiaceae genomics reveals interspecies admixture and the recent evolution of Chlamydia abortus infecting lower mammalian species and humans. Genome Biology and Evolution, 7 (11), pp. 3070-3084
Mathers, Amy J., Stoesser, Nicole, Sheppard, Anna E., Pankhurst, Louise, Giess, Adam, Yeh, Anthony J., Didelot, Xavier, Turner, Stephen D., Sebra, Robert, Kasarskis, Andrew, Peto, Tim, Crook, Derrick, Sifri, Costi D., 2015. Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution : insights into endemicity from whole-genome sequencing. Antimicrobial Agents and Chemotherapy, 59 (3), pp. 1656-1663
Didelot, Xavier, Pang, Bo, Zhou, Zhemin, McCann, Angela, Ni, Peixiang, Li, Dongfang, Achtman, Mark, Kan, Biao, 2015. The role of China in the global spread of the current cholera pandemic. PLoS Genetics, 11 (3), pp. 1-14
Montano, Valeria, Didelot, Xavier, Foll, Matthieu, Linz, Bodo, Reinhardt, Richard, Suerbaum, Sebastian, Moodley, Yoshan, Jensen, Jeffrey D., 2015. Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori. Genetics, 200 (3), pp. 947-963
Cao, Qizhi, Didelot, Xavier, Wu, Zhongbiao, Li, Zongwei, He, Lihua, Li, Yunsheng, Ni, Ming, You, Yuanhai, Lin, Xi, Li, Zhen, Gong, Yanan, Zheng, Minqiao, Zhang, Minli, Liu, Jie, Wang, Weijun, Bo, Xiaochen, Falush, Daniel, Wang, Shengqi, Zhang, Jianzhong, 2015. Progressive genomic convergence of twoHelicobacter pyloristrains during mixed infection of a patient with chronic gastritis. Gut, 64 (4), pp. 554-561
Achtman, Mark, Zhou, Zhemin, Didelot, Xavier, 2015. Formal comment to Pettengill : the time to most recent common ancestor does not (usually) approximate the date of divergence. PLoS One, 10 (8), pp. 1-11
Ezewudo, Matthew N., Joseph, Sandeep J., Castillo-Ramirez, Santiago, Dean, Deborah, del Rio, Carlos, Didelot, Xavier, Dillon, Jo-Anne, Selden, Richard F., Shafer, William M., Turingan, Rosemary S., Unemo, Magnus, Read, Timothy D., 2015. Population structure of Neisseria gonorrhoeaebased on whole genome data and its relationship with antibiotic resistance. PeerJ, 3
Croucher, Nicholas J, Didelot, Xavier, 2015. The application of genomics to tracing bacterial pathogen transmission. Current Opinion in Microbiology, 23, pp. 62-67
Biek, Roman, Pybus, Oliver G., Lloyd-Smith, James O., Didelot, Xavier, 2015. Measurably evolving pathogens in the genomic era. Trends in Ecology & Evolution, 30 (6), pp. 306-313
Elliott, Briony, Dingle, Kate E., Didelot, Xavier, Crook, Derrick W., Riley, Thomas V., 2014. The complexity and diversity of the pathogenicity locus in Clostridium difficile clade 5. Genome Biology and Evolution, 6 (12), pp. 3159-3170
Nandi, Tannistha, Holden, Matthew T. G., Didelot, Xavier, Mehershahi, Kurosh, Boddey, Justin A., Beacham, Ifor, Peak, Ian, Harting, John, Baybayan, Primo, Guo, Yan, Wang, Susana, How, Lee Chee, Sim, Bernice, Essex-Lopresti, Angela, Sarkar-Tyson, Mitali, Nelson, Michelle, Smither, Sophie, Ong, Catherine, Aw, Lay Tin, Hoon, Chua Hui et al (Select to open full list), 2014.

All authors for Burkholderia pseudomalleisequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Nandi, Tannistha, Holden, Matthew T. G., Didelot, Xavier, Mehershahi, Kurosh, Boddey, Justin A., Beacham, Ifor, Peak, Ian, Harting, John, Baybayan, Primo, Guo, Yan, Wang, Susana, How, Lee Chee, Sim, Bernice, Essex-Lopresti, Angela, Sarkar-Tyson, Mitali, Nelson, Michelle, Smither, Sophie, Ong, Catherine, Aw, Lay Tin, Hoon, Chua Hui, Michell, Stephen, Studholme, David J., Titball, Richard, Chen, Swaine L., Parkhill, Julian, Tan, Patrick

Burkholderia pseudomalleisequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles. Genome Research, 25 (1), pp. 129-141
Everitt, Richard G., Didelot, Xavier, Batty, Elizabeth M., Miller, Ruth R, Knox, Kyle, Young, Bernadette C., Bowden, Rory, Auton, Adam, Votintseva, Antonina, Larner-Svensson, Hanna, Charlesworth, Jane, Golubchik, Tanya, Ip, Camilla L. C., Godwin, Heather, Fung, Rowena, Peto, Tim E. A., Walker, A. Sarah, Crook, Derrick W., Wilson, Daniel J., 2014. Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nature Communications, 5 (1)
Tanaka, Mark M., Jombart, Thibaut, Cori, Anne, Didelot, Xavier, Cauchemez, Simon, Fraser, Christophe, Ferguson, Neil, 2014. Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Computational Biology, 10 (1)
Haase, Jana K., Didelot, Xavier, Lecuit, Marc, Korkeala, Hannu, Achtman, Mark, 2014. The ubiquitous nature of Listeria monocytogenesclones : a large-scale Multilocus Sequence Typing study. Environmental Microbiology, 16 (2), pp. 405-416
Didelot, Xavier, 2014. Genomic analysis to improve the management of outbreaks of bacterial infection. Expert Review of Anti-infective Therapy, 11 (4), pp. 335-337
Ansari, M. Azim, Didelot, Xavier, 2014. Inference of the properties of the recombination process from whole bacterial genomes. Genetics, 196 (1), pp. 253-265
Yahara, Koji, Didelot, Xavier, Ansari, M. Azim, Sheppard, Samuel K., Falush, Daniel, 2014. Efficient inference of recombination hot regions in bacterial genomes. Molecular Biology and Evolution, 31 (6), pp. 1593-1605
Stoesser, N., Giess, A., Batty, E. M., Sheppard, A. E., Walker, A. S., Wilson, D. J., Didelot, Xavier, Bashir, A., Sebra, R., Kasarskis, A., Sthapit, B., Shakya, M., Kelly, D., Pollard, A. J., Peto, T. E. A., Crook, D. W., Donnelly, P., Thorson, S., Amatya, P., Joshi, S., 2014. Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting. Antimicrobial Agents and Chemotherapy, 58 (12), pp. 7347-7357
Didelot, Xavier, Gardy, Jennifer, Colijn, Caroline, 2014. Bayesian inference of infectious disease transmission from whole-genome sequence data. Molecular Biology and Evolution, 31 (7), pp. 1869-1879
Jombart, Thibaut, Aanensen, David M., Baguelin, Marc, Birrell, Paul, Cauchemez, Simon, Camacho, Anton, Colijn, Caroline, Collins, Caitlin, Cori, Anne, Didelot, Xavier, Fraser, Christophe, Frost, Simon, Hens, Niel, Hugues, Joseph, Höhle, Michael, Opatowski, Lulla, Rambaut, Andrew, Ratmann, Oliver, Soubeyrand, Samuel, Suchard, Marc A. et al (Select to open full list), 2014.

All authors for OutbreakTools : a new platform for disease outbreak analysis using the R software

Jombart, Thibaut, Aanensen, David M., Baguelin, Marc, Birrell, Paul, Cauchemez, Simon, Camacho, Anton, Colijn, Caroline, Collins, Caitlin, Cori, Anne, Didelot, Xavier, Fraser, Christophe, Frost, Simon, Hens, Niel, Hugues, Joseph, Höhle, Michael, Opatowski, Lulla, Rambaut, Andrew, Ratmann, Oliver, Soubeyrand, Samuel, Suchard, Marc A., Wallinga, Jacco, Ypma, Rolf, Ferguson, Neil

OutbreakTools : a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34
O'Brien, J. D., Didelot, Xavier, Iqbal, Z., Amenga-Etego, L., Ahiska, B., Falush, D., 2014. A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics, 197 (3), pp. 925-937
Miller, R. R., Price, J. R., Batty, E. M., Didelot, Xavier, Wyllie, D., Golubchik, T., Crook, D. W., Paul, J., Peto, T. E. A., Wilson, D. J., Cule, M., Ip, C. L. C., Day, N. P. J., Moore, C. E., Bowden, R., Llewelyn, M. J., 2014. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia : role of a cryptic variant of an epidemic clone. Journal of Hospital Infection, 86 (2), pp. 83-89
Dingle, K. E., Elliott, Bryony Clare, Robinson, Esther R., Griffiths, David, Eyre, D. W., Stoesser, N., Vaughan, A., Golubchik, Tanya, Fawley, W. N., Wilcox, M., Peto, T. E., Walker, S. A., Riley, T, Crook, Derrick, Didelot, Xavier, 2014. Evolutionary history of the clostridium difficile pathogenicity locus. Genome Biology, 6 (1), pp. 36-52
Krebes, Juliane, Didelot, Xavier, Kennemann, Lynn, Suerbaum, Sebastian, 2014. Bidirectional genomic exchange between Helicobacter pylori strains from a family in Coventry, United Kingdom. International Journal of Medical Microbiology, 304 (8), pp. 1135-1146
Sheppard, S. K., Didelot, Xavier, Meric, G., Torralbo, A., Jolley, K. A., Kelly, D. J., Bentley, S. D., Maiden, M. C. J., Parkhill, J., Falush, D., 2013. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proceedings of the National Academy of Sciences, 110 (29), pp. 11923-11927
Didelot, Xavier, Nell, Sandra, Yang, Ines, Woltemate, Sabrina, van der Merwe, Schalk, Suerbaum, Sebastian, 2013. Genomic evolution and transmission of Helicobacter pyloriin two South African families. Proceedings of the National Academy of Sciences of the United States of America, 110 (34), pp. 13880-13885
Aziz, Ramy K., Golubchik, Tanya, Batty, Elizabeth M., Miller, Ruth R., Farr, Helen, Young, Bernadette C., Larner-Svensson, Hanna, Fung, Rowena, Godwin, Heather, Knox, Kyle, Votintseva, Antonina, Everitt, Richard G., Street, Teresa, Cule, Madeleine, Ip, Camilla L. C., Didelot, Xavier, Peto, Timothy E. A., Harding, Rosalind M., Wilson, Daniel J., Crook, Derrick W. et al (Select to open full list), 2013.

All authors for Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Aziz, Ramy K., Golubchik, Tanya, Batty, Elizabeth M., Miller, Ruth R., Farr, Helen, Young, Bernadette C., Larner-Svensson, Hanna, Fung, Rowena, Godwin, Heather, Knox, Kyle, Votintseva, Antonina, Everitt, Richard G., Street, Teresa, Cule, Madeleine, Ip, Camilla L. C., Didelot, Xavier, Peto, Timothy E. A., Harding, Rosalind M., Wilson, Daniel J., Crook, Derrick W., Bowden, Rory

Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS One, 8 (5)
Behrens, Wiebke, Schweinitzer, Tobias, Bal, Joena, Dorsch, Martina, Bleich, André, Kops, Friederike, Brenneke, Birgit, Didelot, Xavier, Suerbaum, Sebastian, Josenhans, Christine, Blanke, S. R., 2013. Role of energy sensor TlpD of Helicobacter pylori in gerbil colonization and genome analyses after adaptation in the gerbil. Infection and Immunity, 81 (10), pp. 3534-3551
Eyre, David W., Cule, Madeleine L., Wilson, Daniel J., Griffiths, David, Vaughan, Alison, O'Connor, Lily, Ip, Camilla L. C., Golubchik, Tanya, Batty, Elizabeth M., Finney, John M., Wyllie, David H., Didelot, Xavier, Piazza, Paolo, Bowden, Rory, Dingle, Kate E., Harding, Rosalind M., Crook, Derrick W., Wilcox, Mark H., Peto, Tim E.A., Walker, A. Sarah, 2013. Diverse sources of C. difficile infection identified on whole-genome sequencing. New England Journal Of Medicine, 369 (13), pp. 1195-1205
Price, J. R., Didelot, Xavier, Crook, D. W., Llewelyn, M. J., Paul, J., 2013. Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. Journal of Hospital Infection, 83 (1), pp. 14-21
Dingle, Kate E., Elliott, Briony, Robinson, Esther, Griffiths, David, Eyre, David W., Stoesser, Nicole, Vaughan, Alison, Golubchik, Tanya, Fawley, Warren N., Wilcox, Mark H., Peto, Timothy E., Walker, A. Sarah, Riley, Thomas V., Crook, Derrick W., Didelot, Xavier, 2013. Evolutionary history of the Clostridium difficile pathogenicity Locus. Genome Biology and Evolution, 6 (1), pp. 36-52
Read, T. D., Joseph, S. J., Didelot, Xavier, Liang, B., Patel, L., Dean, D., 2013. Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range. mBio, 4 (2)
de Muinck, Eric J., Lagesen, Karin, Afset, Jan Egil, Didelot, Xavier, Rønningen, Kjersti S., Rudi, Knut, Stenseth, Nils Chr, Trosvik, Pål, 2013. Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche. BMC Genomics, 14 (1)
Didelot, Xavier, Bowden, Rory, Wilson, Daniel J., Peto, Tim E. A., Crook, Derrick W., 2012. Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics, 13 (9), pp. 601-612
Didelot, Xavier, Eyre, David W., Cule, Madeleine, Ip, Camilla L. C., Ansari, M, Griffiths, David, Vaughan, Alison, O'Connor, Lily, Golubchik, Tanya, Batty, Elizabeth M., Piazza, Paolo, Wilson, Daniel J., Bowden, Rory, Donnelly, Peter J., Dingle, Kate E., Wilcox, Mark, Walker, A, Crook, Derrick W., A Peto, Tim E., Harding, Rosalind M., 2012. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biology, 13 (12)
Zwick, M. E., Joseph, S. J., Didelot, Xavier, Chen, P. E., Bishop-Lilly, K. A., Stewart, A. C., Willner, K., Nolan, N., Lentz, S., Thomason, M. K., Sozhamannan, S., Mateczun, A. J., Du, L., Read, T. D., 2012. Genomic characterization of the Bacillus cereus sensu lato species : backdrop to the evolution of Bacillus anthracis. Genome Research, 22 (8), pp. 1512-1524
Barton, Nick H., Cadillo-Quiroz, Hinsby, Didelot, Xavier, Held, Nicole L., Herrera, Alfa, Darling, Aaron, Reno, Michael L., Krause, David J., Whitaker, Rachel J., 2012. Patterns of gene flow define species of Thermophilic Archaea. PLoS Biology, 10 (2)
Namouchi, A., Didelot, Xavier, Schock, U., Gicquel, B., Rocha, E. P. C., 2012. After the bottleneck : genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Research, 22 (4), pp. 721-734
Eyre, David W., Golubchik, Tanya, Gordon, N Claire, Bowden, Rory, Piazza, Paolo, Batty, Elizabeth M., Ip, Camilla L. C., Wilson, Daniel J., Didelot, Xavier, O'Connor, Lily, Lay, Rochelle, Buck, David, Kearns, Angela M., Shaw, Angela, Paul, John, Wilcox, Mark H., Donnelly, Peter J., Peto, Tim E. A., Walker, A Sarah, Crook, Derrick W., 2012. A pilot study of rapid benchtop sequencing of Staphylococcus aureusand Clostridium difficilefor outbreak detection and surveillance. BMJ Open, 2 (3)
Young, B. C., Golubchik, T., Batty, E. M., Fung, R., Larner-Svensson, H., Votintseva, A. A., Miller, R. R., Godwin, H., Knox, K., Everitt, R. G., Iqbal, Z., Rimmer, A. J., Cule, M., Ip, C. L. C., Didelot, Xavier, Harding, R. M., Donnelly, P., Peto, T. E., Crook, D. W., Bowden, R. et al (Select to open full list), 2012.

All authors for Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Young, B. C., Golubchik, T., Batty, E. M., Fung, R., Larner-Svensson, H., Votintseva, A. A., Miller, R. R., Godwin, H., Knox, K., Everitt, R. G., Iqbal, Z., Rimmer, A. J., Cule, M., Ip, C. L. C., Didelot, Xavier, Harding, R. M., Donnelly, P., Peto, T. E., Crook, D. W., Bowden, R., Wilson, D. J.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proceedings of the National Academy of Sciences of the United States of America, 109 (12), pp. 4550-4555
Sheppard, Samuel K., Didelot, Xavier, Jolley, Keith A., Darling, Aaron E., Pascoe, Ben, Meric, Guillaume, Kelly, David J., Cody, Alison, Colles, Frances M., Strachan, Norval J. C., Ogden, Iain D., Forbes, Ken, French, Nigel P., Carter, Philip, Miller, William G., McCarthy, Noel D., Owen, Robert, Litrup, Eva, Egholm, Michael, Affourtit, Jason P. et al (Select to open full list), 2012.

All authors for Progressive genome-wide introgression in agricultural Campylobacter coli

Sheppard, Samuel K., Didelot, Xavier, Jolley, Keith A., Darling, Aaron E., Pascoe, Ben, Meric, Guillaume, Kelly, David J., Cody, Alison, Colles, Frances M., Strachan, Norval J. C., Ogden, Iain D., Forbes, Ken, French, Nigel P., Carter, Philip, Miller, William G., McCarthy, Noel D., Owen, Robert, Litrup, Eva, Egholm, Michael, Affourtit, Jason P., Bentley, Stephen D., Parkhill, Julian, Maiden, Martin C. J., Falush, Daniel

Progressive genome-wide introgression in agricultural Campylobacter coli. Molecular Ecology, 22 (4), pp. 1051-1064
Dingle, Kate E., Didelot, Xavier, Ansari, M. Azim, Eyre, David W., Vaughan, Alison, Griffiths, David, Ip, Camilla L. C., Batty, Elizabeth M., Golubchik, Tanya, Bowden, Rory, Jolley, Keith A., Hood, Derek W., Fawley, Warren N., Walker, A. Sarah, Peto, Timothy E., Wilcox, Mark H., Crook, Derrick W., 2012. Recombinational switching of the Clostridium difficile S-Layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. The Journal of Infectious Diseases, 207 (4), pp. 675-686
Joseph, Sandeep J., Didelot, Xavier, Rothschild, James, de Vries, Henry J.C., Morré, Servaas A., Read, Timothy D., Dean, Deborah, 2012. Population genomics of Chlamydia trachomatis : insights on drift, selection, recombination, and population structure. Molecular Biology and Evolution, 29 (12), pp. 3933-3946
Didelot, Xavier, Méric, Guillaume, Falush, Daniel, Darling, Aaron E, 2012. Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics, 13 (1)
Moccia, Claudia, Krebes, Juliane, Kulick, Stefan, Didelot, Xavier, Kraft, Christian, Bahlawane, Christelle, Suerbaum, Sebastian, 2012. The nucleotide excision repair (NER) system of Helicobacter pylori : role in mutation prevention and chromosomal import patterns after natural transformation. BMC Microbiology, 12 (1)
Zhang, Liangfen, Thomas, Jonathan C., Didelot, Xavier, Robinson, D. Ashley, 2012. Molecular signatures identify a candidate target of balancing selection in an arcD-Like gene of Staphylococcus epidermidis. Journal of Molecular Evolution, 75 (1-2), pp. 43-54
Dingle, Kate E., Griffiths, David, Didelot, Xavier, Evans, Jessica, Vaughan, Alison, Kachrimanidou, Melina, Stoesser, Nicole, Jolley, Keith A., Golubchik, Tanya, Harding, Rosalind M., Peto, Tim E., Fawley, Warren, Walker, A. Sarah, Wilcox, Mark, Crook, Derrick W., 2011. Clinical Clostridium difficile : clonality and pathogenicity locus diversity. PLoS One, 6 (5)
Didelot, Xavier, Bowden, Rory, Street, Teresa, Golubchik, Tanya, Spencer, Chris, McVean, Gil, Sangal, Vartul, Anjum, Muna F., Achtman, Mark, Falush, Daniel, Donnelly, Peter, 2011. Recombination and population structure in salmonella enterica. PLoS Genetics, 7 (7)
Gripp, Eugenia, Hlahla, Daniela, Didelot, Xavier, Kops, Friederike, Maurischat, Sven, Tedin, Karsten, Alter, Thomas, Ellerbroek, Lüppo, Schreiber, Kerstin, Schomburg, Dietmar, Janssen, Traute, Bartholomäus, Patrick, Hofreuter, Dirk, Woltemate, Sabrina, Uhr, Markus, Brenneke, Birgit, Grüning, Petra, Gerlach, Gerald, Wieler, Lothar, Suerbaum, Sebastian et al (Select to open full list), 2011.

All authors for Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle

Gripp, Eugenia, Hlahla, Daniela, Didelot, Xavier, Kops, Friederike, Maurischat, Sven, Tedin, Karsten, Alter, Thomas, Ellerbroek, Lüppo, Schreiber, Kerstin, Schomburg, Dietmar, Janssen, Traute, Bartholomäus, Patrick, Hofreuter, Dirk, Woltemate, Sabrina, Uhr, Markus, Brenneke, Birgit, Grüning, Petra, Gerlach, Gerald, Wieler, Lothar, Suerbaum, Sebastian, Josenhans, Christine

Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics, 12 (1)
Joseph, Sandeep J., Didelot, Xavier, Gandhi, Khanjan, Dean, Deborah, Read, Timothy D., 2011. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biology Direct, 6 (1)
Laukkanen-Ninios, Riikka, Didelot, Xavier, Jolley, Keith A., Morelli, Giovanna, Sangal, Vartul, Kristo, Paula, Brehony, Carina, Imori, Priscilla F. M., Fukushima, Hiroshi, Siitonen, Anja, Tseneva, Galina, Voskressenskaya, Ekaterina, Falcao, Juliana P., Korkeala, Hannu, Maiden, Martin C. J., Mazzoni, Camila, Carniel, Elisabeth, Skurnik, Mikael, Achtman, Mark, 2011. Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing. Environmental Microbiology, 13 (12), pp. 3114-3127
Kennemann, L., Didelot, Xavier, Aebischer, T., Kuhn, S., Drescher, B., Droege, M., Reinhardt, R., Correa, P., Meyer, T. F., Josenhans, C., Falush, D., Suerbaum, S., 2011. Helicobacter pylori genome evolution during human infection. Proceedings of the National Academy of Sciences, 108 (12), pp. 5033-5038
Didelot, Xavier, Everitt, Richard G., Johansen, Adam M., Lawson, Daniel J., 2011. Likelihood-free estimation of model evidence. Bayesian Analysis, Vol.6 (No.1), pp. 49-76
Morelli, Giovanna, Didelot, Xavier, Kusecek, Barica, Schwarz, Sandra, Bahlawane, Christelle, Falush, Daniel, Suerbaum, Sebastian, Achtman, Mark, 2010. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PL o S Genetics, Vol.6 (No.7)
Didelot, Xavier, Lawson, D., Darling, A., Falush, D., 2010. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics, 186 (4), pp. 1435-1449
Sangal, V., Harbottle, H., Mazzoni, C. J., Helmuth, R., Guerra, B., Didelot, Xavier, Paglietti, B., Rabsch, W., Brisse, S., Weill, F.-X., Roumagnac, P., Achtman, M., 2010. Evolution and population structure of Salmonella enterica serovar Newport. Journal of Bacteriology, 192 (24), pp. 6465-6476
Didelot, Xavier, Darling, Aaron, Falush, Daniel, 2009. Inferring genomic flux in bacteria. Genome Research, Vol.19 (No.2), pp. 306-317
Vos, Michiel, Didelot, Xavier, 2009. A comparison of homologous recombination rates in bacteria and archaea. The ISME Journal, 3 (2), pp. 199-208
Didelot, Xavier, Urwin, Rachel, Maiden, Martin C. J., Falush, Daniel, 2009. Genealogical typing of Neisseria meningitidis. Microbiology, Vol.15 (No.10), pp. 3176-3186
Zhang, Junlong, Zhang, F. (Fang), Didelot, Xavier, Bruce, Kimberley D., Cagampang, Felino R., Vatish, Manu, Hanson, Mark A., Lehnert, Hendrik, Ceriello, Antonio, Byrne, Christopher D., 2009. Maternal high fat diet during pregnancy and lactation alters hepatic expression of insulin like growth factor-2 and key microRNAs in the adult offspring. BMC Genomics, Vol.10 (No.478)
Vos, Michiel, Didelot, Xavier, 2009. A comparison of homologous recombination rates in bacteria and archaea. ISME Journal, Vol.3 (No.2), pp. 199-208
Didelot, Xavier, Barker, Margaret, Falush, Daniel, Priest, Fergus G., 2009. Evolution of pathogenicity in the Bacillus cereus group. Systematic and Applied Microbiology, Vol.32 (No.2), pp. 81-90
Didelot, Xavier, Lawson, Daniel J., Falush, Daniel, 2009. SimMLST: simulation of multi-locus sequence typing data under a neutral model. Bioinformatics, Vol.25 (No.11), pp. 1442-1444
den Bakker, Henk C., Didelot, Xavier, Fortes, Esther D, Nightingale, Kendra K, Wiedmann, Martin, 2008. Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evolutionary Biology, Vol. 8 (No. 27)
Kulick, Stefan, Moccia, Claudia, Didelot, Xavier, Falush, Daniel, Kraft, Christian, Suerbaum, Sebastian, 2008. Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLOS One, Vol.3 (No.11)
Didelot, Xavier, Falush, D., 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics, 175 (3), pp. 1251-1266
Falush, D., Torpdahl, M., Didelot, Xavier, Conrad, D. F., Wilson, D. J., Achtman, Mark, 2006. Mismatch induced speciation in Salmonella : model and data. Philosophical Transactions of the Royal Society B: Biological Sciences, 361 (1475), pp. 2045-2053
Didelot, Xavier, Achtman, Mark, Parkhill, J., Thomson, N. R., Falush, D., 2006. A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes : convergence or divergence by homologous recombination?. Genome Research, 17 (1), pp. 61-68

Didelot, Xavier, 2021. Phylogenetic methods for genome-wide association studies in bacteria. In Mengoni, Alessio; Bacci, Giovanni; Fondi, Marco (eds.), Bacterial Pangenomics : Methods and Protocols, Springer US, pp. 205-220
Lassalle, Florent, Didelot, Xavier, 2020. Bacterial microevolution and the Pangenome. In Tettelin, H.; Medini, D. (eds.), The Pangenome, Cham, Springer, pp. 129-149
Klinkenberg, Don, Colijn, Caroline, Didelot, Xavier, 2019. Methods for outbreaks using genomic data. Held, Leonhard; Hens, Niel; O'Neill, Philip D.; Wallinga, Jacco (eds.), Handbook of Infectious Disease Data Analysis, Milton, CRC Press
Collins, Caitlin, Didelot, Xavier, 2016. Reconstructing the ancestral relationships between bacterial pathogen genomes. In Nordenfelt, P.; Collin, M. (eds.), Bacterial Pathogenesis, Springer, pp. 109-137

Robinson, Esther R., Didelot, Xavier, Hood, Derek, Crook, Derrick, 2013. Comparative phylogenetics of ICEHin1056 family reveals deep evolutionary associations of mobile genetic elements responsible for transfer of antibiotic resistance genes. Spring Meeting for Clinician Scientists in Training, Published in The Lancet
Kennemann, L., Didelot, Xavier, Drescher, B., Kuhn, S., Olbermann, P., Falush, Daniel, Droege, M., Josenhans, C., Suerbaum, Sebastian, 2008. Genome plasticity during chronic infection with H-pylori. 60th Annual Meeting of the Deutschen-Gesellschaft-fur-Hygiene-und-Mikrobiologie, Dresden, Germany, Sep 21-24, 2008, Published in International Journal of Medical Microbiology, pp. 26-26
Moccia, C., Kulick, S., Didelot, Xavier, Ellrott, K., Kraft, C., Suerbaum, Sebastian, 2008. The role of Helicobacter pylori ruvA, ruvB and ruvC genes in homologous recombination and mutation. 60th Annual Meeting of the Deutschen-Gesellschaft-fur-Hygiene-und-Mikrobiologie, Dresden, Germany, Sep 21-24, 2008, Published in International Journal of Medical Microbiology, pp. 29-29

Didelot, Xavier, Maiden, Martin C. J., 2010. Impact of recombination on bacterial evolution. Trends in Microbiology, Elsevier Ltd, pp. 315-322
Didelot, Xavier, Everitt, Richard G., Johansen, Adam M., Lawson, Daniel J., 2010. Likelihood-free estimation of model evidence. University of Warwick. Centre for Research in Statistical Methodology

Title	Funder	Award start	Award end
NIHR HPRU in Gastrointestinal Infections	National Institute for Health Research (DoH)	01 Apr 2020	31 Mar 2025
HPRU in Genomics and Enabling at University of Warwick	National Institute for Health Research (DoH)	01 Apr 2020	31 Mar 2025
Real-time phylogenetics using sequential Monte Carlo with tree sequences	EPSRC	01 Jun 2022	31 May 2023
COVID-19 Intervention modelling for East Africa (CIMEA) (linked to 67166)	Wellcome Trust	27 May 2020	26 May 2022

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