Professor Xavier Didelot
Professor of Statistical Epidemiology and Genomics
Email:
Phone: 024 765 72827
Office: (Mathematical Sciences) MB5.16
Twitter: @XavierDidelot
Didelot webpage
Research Clusters
Microbiology & Infectious Disease
Warwick Centres and GRPs
Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER)
Health Protection Research Unit (HPRU) in Genomics and Enabling Data
Vacancies and Opportunities
For PhD and postdoctoral opportunities, and interest in potential collaborations, please contact me at the above email address.
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.
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).
My work often requires to develop new statistical methods of analysis, which I release as open source software in the hope that they will be useful to other researchers. A list of free software tools I have developed or contributed to.
Research: Technical Summary
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 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 Health Protection Research Unit in Genomics and Enabling Data which is funded by the National Institute for Health Research (NIHR) for 2020-25. 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.
- 2018-present: Professor of Statistical Epidemiology and Genomics, School of Life Sciences and Department of Statistics, University of Warwick
- 2012-2018: Senior Lecturer, School of Public Health, Imperial College London
- 2010-2012: Leadership Fellow, Department of Statistics, University of Oxford
- 2007-2010: Research Fellow, Department of Statistics, University of Warwick
- 2004-2007: Doctorate in Statistical Genetics, Department of Statistics, University of Oxford
- Fotopoulou, Emily T., Jenkins, Claire, Barker, Clare R., Painset, Anais, Didelot, Xavier, Simbo, Ameze, Douglas, Amy, Godbole, Gauri, Jorgensen, Frieda, Gharbia, Saheer, McLauchlin, Jim, 2024. Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK. Microbial Genomics, 10 (1)
- Carson, Jake, Keeling, Matthew James, Wyllie, David, Ribeca, Paolo, Didelot, Xavier, Hepp, Crystal, 2024. Inference of infectious disease transmission through a relaxed bottleneck using multiple genomes per host. Molecular Biology and Evolution, 41 (1)
- Wan, Yu, Myall, Ashleigh C., Boonyasiri, Adhiratha, Bolt, Frances, Ledda, Alice, Mookerjee, Siddharth, Weiße, Andrea Y., Getino, Maria, Turton, Jane F., Abbas, Hala, Prakapaite, Ruta, Sabnis, Akshay, Abdolrasouli, Alireza, Malpartida-Cardenas, Kenny, Miglietta, Luca, Donaldson, Hugo, Gilchrist, Mark, Hopkins, Katie L., Ellington, Matthew J., Otter, Jonathan A. et al (Select to open full list), 2024. Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. The Journal of Infectious Diseases
- Medina-Aguayo, F. J., Didelot, Xavier, Everitt, Richard G., 2024. Speeding up inference of homologous recombination in bacteria. Bayesian Analysis
- Nimmo, Camus, Ortiz, Arturo Torres, Tan, Cedric C. S., Pang, Juanita, Acman, Mislav, Millard, James, Padayatchi, Nesri, Grant, Alison D., O?Donnell, Max, Pym, Alex, Brynildsrud, Ola B., Eldholm, Vegard, Grandjean, Louis, Didelot, Xavier, Balloux, François, van Dorp, Lucy, 2024. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Medicine, 16 (1)
- Helekal, David, Keeling, Matthew James, Grad, Yonatan H., Didelot, Xavier, 2023. Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data. Journal of the Royal Society Interface, 20 (203)
- Didelot, Xavier, Franceschi, Vinicius, Frost, Simon D. W., Dennis, Ann, Volz, Erik M., 2023. Model design for nonparametric phylodynamic inference and applications to pathogen surveillance. Virus Evolution, 9 (1)
- Samy, Abdallah M., Esquivel Gomez, Luis Roger, Savin, Cyril, Andrianaivoarimanana, Voahangy, Rahajandraibe, Soloandry, Randriantseheno, Lovasoa Nomena, Zhou, Zhemin, Kocher, Arthur, Didelot, Xavier, Rajerison, Minoarisoa, Kühnert, Denise, 2023. Phylogenetic analysis of the origin and spread of plague in Madagascar. PLoS Neglected Tropical Diseases, 17 (5)
- Chase-Topping, Margo, Dallman, Timothy J., Allison, Lesley, Lupolova, Nadejda, Matthews, Louise, Mitchell, Sonia, Banks, Christopher J., Prentice, Jamie, Brown, Helen, Tongue, Sue, Henry, Madeleine, Evans, Judith, Gunn, George, Hoyle, Deborah, McNeilly, Tom N., Fitzgerald, Stephen, Smith-Palmer, Alison, Shaaban, Sharif, Holmes, Anne, Hanson, Mary et al (Select to open full list), 2023. Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales : implications for human health. Microbial Genomics, 9 (9)
- Torres Ortiz, Arturo, Kendall, Michelle, Storey, Nathaniel, Hatcher, James, Dunn, Helen, Roy, Sunando, Williams, Rachel, Williams, Charlotte, Goldstein, Richard A., Didelot, Xavier, Harris, Kathryn, Breuer, Judith, Grandjean, Louis, 2023. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife, 12
- Yenew, Bazezew, Ghodousi, Arash, Diriba, Getu, Tesfaye, Ephrem, Cabibbe, Andrea Maurizio, Amare, Misikir, Moga, Shewki, Alemu, Ayinalem, Dagne, Binyam, Sinshaw, Waganeh, Mollalign, Hilina, Meaza, Abyot, Tadesse, Mengistu, Gamtesa, Dinka Fikadu, Abebaw, Yeshiwork, Seid, Getachew, Zerihun, Betselot, Getu, Melak, Chiacchiaretta, Matteo, Gaudin, Cyril et al (Select to open full list), 2023. A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex. Nature Communications, 14 (1)
- Thorell, Kaisa, Muñoz-Ramírez, Zilia Y., Wang, Difei, Sandoval-Motta, Santiago, Boscolo Agostini, Rajiv, Ghirotto, Silvia, Torres, Roberto C., Romero-Gallo, Judith, Krishna, Uma, Peek, Richard M., Piazuelo, M. Blanca, Raaf, Naïma, Bentolila, Federico, Aftab, Hafeza, Akada, Junko, Matsumoto, Takashi, Haesebrouck, Freddy, Colanzi, Rony P., Bartelli, Thais F., Nunes, Diana Noronha et al (Select to open full list), 2023. The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nature Communications, 14 (1)
- 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. 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)
- '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
- 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)
- 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
- 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)
- 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
- 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
- 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
- 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)
- 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)
- 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 |
---|---|---|---|
HPRU in Genomics and Enabling at University of Warwick | National Institute for Health Research (DoH) | 01 Apr 2020 | 31 Mar 2025 |
NIHR HPRU in Gastrointestinal Infections | 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 |
I am happy to receive enquires about PG Research projects in my group, please contact me at the above email address.