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
Kendall, Michelle, Ferretti, Luca, Wymant, Chris, Tsallis, Daphne, Petrie, James, Di Francia, Andrea, Di Lauro, Francesco, Abeler-Dörner, Lucie, Manley, Harrison, Panovska-Griffiths, Jasmina, Ledda, Alice, Didelot, Xavier and Fraser, Christophe (2024) Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements. Science, 385 (6710). eadm8103. doi:10.1126/science.adm8103 ISSN 0036-8075.
Osman, Roeann, Dema, Emily, David, Alexandra, Hughes, Gwenda, Field, Nigel, Cole, Michelle, Didelot, Xavier and Saunders, John (2024) Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea : a systematic review of WGS use on human pathogens in individual patient care. Journal of Infection, 88 (6). 106168. doi:10.1016/j.jinf.2024.106168 ISSN 0163-4453.
Nair, Satheesh, Barker, Clare R., Bird, Matthew, Greig, David R., Collins, Caitlin, Painset, Anaïs, Chattaway, Marie, Pickard, Derek, Larkin, Lesley, Gharbia, Saheer, Didelot, Xavier and Ribeca, Paolo (2024) Presence of phage-plasmids in multiple serovars of Salmonella enterica. Microbial Genomics, 10 (5). 001247. doi:10.1099/mgen.0.001247 ISSN 2057-5858.
Moore, Matthew P., Laager, Mirjam, Ribeca, Paolo and Didelot, Xavier (2024) KmerAperture : retaining k-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes. PLoS Genetics, 20 (4). e1011184. doi:10.1371/journal.pgen.1011184 ISSN 1553-7390.
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 and van Dorp, Lucy (2024) Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Medicine, 16 (1). 34. doi:10.1186/s13073-024-01289-5 ISSN 1756-994X.
Carson, Jake, Keeling, Matthew James, Wyllie, David, Ribeca, Paolo, Didelot, Xavier and Hepp, Crystal (2024) Inference of infectious disease transmission through a relaxed bottleneck using multiple genomes per host. Molecular Biology and Evolution, 41 (1). msad288. doi:10.1093/molbev/msad288 ISSN 0737-4038.
Fotopoulou, Emily T., Jenkins, Claire, Barker, Clare R., Painset, Anais, Didelot, Xavier, Simbo, Ameze, Douglas, Amy, Godbole, Gauri, Jorgensen, Frieda, Gharbia, Saheer and McLauchlin, Jim (2024) Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK. Microbial Genomics, 10 (1). doi:10.1099/mgen.0.001155 ISSN 2057-5858. (In Press)
Avila Cartes, Jorge, Bonizzoni, Paola, Ciccolella, Simone, Della Vedova, Gianluca, Denti, Luca, Didelot, Xavier, Monti, Davide, Pirola, Yuri and Valencia, Alfonso (2024) RecGraph: recombination-aware alignment of sequences to variation graphs. Bioinformatics . doi:10.1093/bioinformatics/btae292 ISSN 1367-4803. (In Press)
Medina-Aguayo, F. J., Didelot, Xavier and Everitt, Richard G. (2024) Speeding up inference of homologous recombination in bacteria. Bayesian Analysis . doi:10.1214/23-BA1388 ISSN 1931-6690. (In Press)
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 and Grandjean, Louis (2023) Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife, 12 . doi:10.7554/eLife.84384 ISSN 2050-084X.
Helekal, David, Keeling, Matthew James, Grad, Yonatan H. and Didelot, Xavier (2023) Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data. Journal of the Royal Society Interface, 20 (203). 20230074. doi:10.1098/rsif.2023.0074 ISSN 1742-5662.
Didelot, Xavier (2023) Phylogenetic analysis of bacterial pathogen genomes. In: Nordenfelt, P. and Collin, M., (eds.) Bacterial Pathogenesis. Methods in Molecular Biology, 2674 . New York, NY: Humana, pp. 87-99. ISBN 9781071632420
Didelot, Xavier, Franceschi, Vinicius, Frost, Simon D. W., Dennis, Ann and Volz, Erik M. (2023) Model design for nonparametric phylodynamic inference and applications to pathogen surveillance. Virus Evolution, 9 (1). vead028. doi:10.1093/ve/vead028 ISSN 2057-1577.
Samy, Abdallah M., Esquivel Gomez, Luis Roger, Savin, Cyril, Andrianaivoarimanana, Voahangy, Rahajandraibe, Soloandry, Randriantseheno, Lovasoa Nomena, Zhou, Zhemin, Kocher, Arthur, Didelot, Xavier, Rajerison, Minoarisoa and Kühnert, Denise (2023) Phylogenetic analysis of the origin and spread of plague in Madagascar. PLoS Neglected Tropical Diseases, 17 (5). e0010362. doi:10.1371/journal.pntd.0010362 ISSN 1935-2727.
Dingle, Kate E., Freeman, Jane, Didelot, Xavier, Quan, T. Phuong, Eyre, David W., Swann, Jeremy, Spittal, William D., Clark, Emma V., Jolley, Keith A., Walker, A. Sarah, Wilcox, Mark H. and Crook, Derrick W. (2023) Penicillin binding protein substitutions cooccur with fluoroquinolone resistance in epidemic lineages of multidrug-resistant Clostridioides difficile. mBio, 14 (2). e00243-23. doi:10.1128/mbio.00243-23 ISSN 2150-7511.
Kendall, Michelle, Tsallis, Daphne, Wymant, Chris, Di Francia, Andrea, Balogun, Yakubu, Didelot, Xavier, Ferretti, Luca and Fraser, Christophe (2023) Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year. Nature Communications, 14 (1). 858. doi:10.1038/s41467-023-36495-z ISSN 2041-1723.
Mughal, Sadaf Rasheed, Niazi, Sadia Ambreen, Do, Thuy, Gilbert, Steven C., Didelot, Xavier, Radford, David R. and Beighton, David (2023) Genomic diversity among Actinomyces naeslundii strains and closely related species. Microorganisms, 11 (2). 254. doi:10.3390/microorganisms11020254 ISSN 2076-2607.
Abdel-Glil, Mostafa Y., Hotzel, Helmut, Tomaso, Herbert, Didelot, Xavier, Brandt, Christian, Seyboldt, Christian, Linde, Jörg, Schwarz, Stefan, Neubauer, Heinrich and El-Adawy, Hosny (2023) Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany. Frontiers In Veterinary Science, 9 . 1069062. doi:10.3389/fvets.2022.1069062 ISSN 2297-1769.
Didelot, Xavier, Helekal, David, Kendall, Michelle, Ribeca, Paolo and Schwartz, Russell (2023) Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease. Bioinformatics, 39 (1). btac761. doi:10.1093/bioinformatics/btac761 ISSN 1367-4803.
Didelot, Xavier and Parkhill, Julian (2022) A scalable analytical approach from bacterial genomes to epidemiology. Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861). 20210246. doi:10.1098/rstb.2021.0246 ISSN 0962-8436.
Didelot, Xavier and Evans, Charles Morris (2022) London parochial burial records from 1563 to 1665 indicate higher plague death rates for males than females : some possible demographic and social explanations. PLoS One, 17 (8). e0272278. doi:10.1371/journal.pone.0272278 ISSN 1932-6203.
Whittles, Lilith K., Didelot, Xavier and 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, 22 (7). pp. 1030-1041. doi:10.1016/S1473-3099(21)00744-1 ISSN 1474-4457.
Volk, Denis, Yang-Turner, Fan, Didelot, Xavier, Crook, Derrick W. and Wyllie, David (2022) Catwalk : identifying closely related sequences in large microbial sequence databases. Microbial Genomics, 8 (6). 000850. doi:10.1099/mgen.0.000850 ISSN 2057-5858.
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. and 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). doi:10.1099/mgen.0.000675 ISSN 2057-5858.
Wang, Liang, Didelot, Xavier, Bi, Yuhai and Gao, George F. (2022) SARS-CoV-2 transmissibility compared between variants of concern and vaccination status. Briefings in Bioinformatics, 23 (2). bbab594. doi:10.1093/bib/bbab594 ISSN 1467-5463.
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 and Craft, Meggan E. (2022) Hunting alters viral transmission and evolution in a large carnivore. Nature Ecology & Evolution . pp. 174-182. doi:10.1038/s41559-021-01635-5 ISSN 2397-334X.
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 and Conlan, Andrew J. K. (2022) Transmission history of SARS-CoV-2 in humans and white-tailed deer. Scientific Reports, 12 (1). 12094. doi:10.1038/s41598-022-16071-z ISSN 2045-2322.
Torres Ortiz, Arturo, Coronel, Jorge, Vidal, Julia Rios, Bonilla, Cesar, Moore, David A. J., Gilman, Robert H., Balloux, Francois, Kon, Onn Min, Didelot, Xavier and Grandjean, Louis (2021) Genomic signatures of pre-resistance in Mycobacterium tuberculosis. Nature Communications, 12 (1). 7312. doi:10.1038/s41467-021-27616-7 ISSN 2041-1723.
Helekal, David, Ledda, Alice, Volz, Erik, Wyllie, David and Didelot, Xavier (2021) Bayesian inference of clonal expansions in a dated phylogeny. Systematic Biology, 71 (5). pp. 1073-1087. syab095. doi:10.1093/sysbio/syab095 ISSN 1076-836X.
Knight, Daniel R., Imwattana, Korakrit, Kullin, Brian, Guerrero-Araya, Enzo, Paredes-Sabja, Daniel, Didelot, Xavier, Dingle, Kate E., Eyre, David W., Rodríguez, César Cabrera and Riley, Thomas V. (2021) Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife, 10 . e64325. doi:10.7554/elife.64325 ISSN 2050-084X.
Wang, Liang, Didelot, Xavier, Bi, Yuhai and Gao, George F. (2021) Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants. The Innovation . 100128. doi:10.1016/j.xinn.2021.100128 ISSN 2666-6758.
Didelot, Xavier (2021) Phylogenetic methods for genome-wide association studies in bacteria. In: Mengoni, Alessio and Bacci, Giovanni and Fondi, Marco, (eds.) Bacterial Pangenomics : Methods and Protocols. Methods in Molecular Biology, 2242 . Springer US, pp. 205-220. ISBN 9781071610985
Didelot, Xavier, Kendall, Michelle, Xu, Yuanwei, White, Peter J. and McCarthy, Noel D. (2021) Genomic epidemiology analysis of infectious disease outbreaks using transPhylo. Current Protocols, 1 (2). e60. doi:10.1002/cpz1.60 ISSN 2691-1299.
Didelot, Xavier, Siveroni, Igor and 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. msaa193. doi:10.1093/molbev/msaa193 ISSN 1537-1719.
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. and 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). 126165. doi:10.1016/j.syapm.2020.126165 ISSN 0723-2020.
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 and Brisse, Sylvain (2020) Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Medicine, 12 (1). 107. doi:10.1186/s13073-020-00805-7 ISSN 1756-994X.
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. and Eldholm, Vegard (2020) Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway. Microbial Genomics, 6 (12). doi:10.1099/mgen.0.000480 ISSN 2057-5858.
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. and Gardiner, David (2020) Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. Eurosurveillance, 25 (43). doi:10.2807/1560-7917.ES.2020.25.43.1900210 ISSN 1560-7917.
Whittles, Lilith K., White, Peter J. and 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. ciz1241. doi:10.1093/cid/ciz1241 ISSN 1058-4838.
Janezic, Sandra, Dingle, Kate, Alvin, Joseph, Accetto, Tomaž, Didelot, Xavier, Crook, Derrick W., Lacy, D. Borden and Rupnik, Maja (2020) Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution. Microbial Genomics, 6 (10). doi:10.1099/mgen.0.000449 ISSN 2057-5858.
Wang, Liang, Didelot, Xavier, Yang, Jing, Wong, Gary, Shi, Yi, Liu, Wenjun, Gao, George F. and 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). 5006. doi:10.1038/s41467-020-18836-4 ISSN 2041-1723.
Volz, Erik M., Wiuf, Carsten, Grad, Yonatan H., Frost, Simon D. W., Dennis, Ann M. and Didelot, Xavier (2020) Identification of hidden population structure in time-scaled phylogenies. Systematic Biology, 69 (5). pp. 884-896. doi:10.1093/sysbio/syaa009 ISSN 1063-5157.
Fountain-Jones, Nicholas M., Appaw, Raima Carol, Carver, Scott, Didelot, Xavier, Volz, Erik and Charleston, Michael (2020) Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evolution, 6 (2). veaa082. doi:10.1093/ve/veaa082 ISSN 2057-1577.
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 and Georgiou, Pantelis (2020) Rapid detection of mobilized colistin resistance using a nucleic acid based lab-on-a-chip diagnostic system. Scientific Reports, 10 (1). 8448 . doi:10.1038/s41598-020-64612-1 ISSN 2045-2322.
Lassalle, Florent and Didelot, Xavier (2020) Bacterial microevolution and the Pangenome. In: Tettelin, H. and Medini, D., (eds.) The Pangenome. Cham: Springer, pp. 129-149. ISBN 9783030382803
Wang, Haoqiu, Yang, Chao, Sun, Zhou, Zheng, Wei, Zhang, Wei, Yu, Hua, Wu, Yarong, Didelot, Xavier, Yang, Ruifu, Pan, Jingcao and 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). e0008046. doi:10.1371/journal.pntd.0008046 ISSN 1935-2735.
Klinkenberg, Don, Colijn, Caroline and Didelot, Xavier (2019) Methods for outbreaks using genomic data. In: Held, Leonhard and Hens, Niel and O'Neill, Philip D. and Wallinga, Jacco, (eds.) Handbook of Infectious Disease Data Analysis. Chapman & Hall/CRC Handbooks of Modern Statistical Methods . Milton: CRC Press. ISBN 9781138626713
Zhao, Lin, Chen, Hongyou, Didelot, Xavier, Li, Zhenpeng, Li, Yinghui, Chen, Meiling, Du, Yu, Zhao, Hongqun, Liu, Jie, Hu, Qinghua, Kan, Biao, Chen, Min and Pang, Bo (2019) Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12. Microbial Genomics, 6 (12). doi:10.1099/mgen.0.000287 ISSN 2057-5858.
Criscuolo, Alexis, Issenhuth-Jeanjean, Sylvie, Didelot, Xavier, Thorell, Kaisa, Hale, James, Parkhill, Julian, Thomson, Nicholas R., Weill, François-Xavier, Falush, Daniel and Brisse, Sylvain (2019) The speciation and hybridization history of the genus Salmonella. Microbial Genomics, 5 (8). doi:10.1099/mgen.0.000284 ISSN 2057-5858.
Didelot, Xavier and Pouwels, Koen B. (2019) Machine-learning-assisted selection of antibiotic prescription. Nature Medicine, 25 (7). pp. 1033-1034. doi:10.1038/s41591-019-0517-0 ISSN 1078-8956.
Ailloud, Florent, Didelot, Xavier, Woltemate, Sabrina, Pfaffinger, Gudrun, Overmann, Jörg, Bader, Ruth Christiane, Schulz, Christian, Malfertheiner, Peter and Suerbaum, Sebastian (2019) Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nature Communications, 10 (1). 2273 . doi:10.1038/s41467-019-10050-1 ISSN 2041-1723.
Moniri, Ahmad, Rodriguez-Manzano, Jesus, Malpartida-Cardenas, Kenny, Yu, Ling-Shan, Didelot, Xavier, Holmes, Alison and Georgiou, Pantelis (2019) Framework for DNA quantification and outlier detection using multidimensional standard curves. Analytical Chemistry, 91 (11). pp. 7426-7434. doi:10.1021/acs.analchem.9b01466 ISSN 1520-6882.
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. and 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. doi:10.1016/j.ebiom.2019.04.038 ISSN 2352-3964.
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 and Wang, Hui (2019) Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains. Microbial Genomics, 5 (4). doi:10.1099/mgen.0.000263 ISSN 2057-5858.
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. and 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. e02790. doi:10.1128/mBio.02790-18 ISSN 2150-7511.
Ferrari, Matthew (Matt), Whittles, Lilith K., White, Peter J. and Didelot, Xavier (2019) A dynamic power-law sexual network model of gonorrhoea outbreaks. PLoS Computational Biology, 15 (3). e1006748. doi:10.1371/journal.pcbi.1006748 ISSN 1553-7358.
Ozer, Egon A., Nnah, Ekpeno, Didelot, Xavier, Whitaker, Rachel J. and 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. doi:10.1093/gbe/evz119 ISSN 1759-6653.
Didelot, Xavier, Croucher, Nicholas J., Bentley, Stephen D., Harris, Simon R. and Wilson, Daniel J. (2018) Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Research, 46 (22). e134. doi:10.1093/nar/gky783 ISSN 0305-1048.
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. and Read, Robert C. (2018) Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection. Nature Communications, 9 (1). 4753. doi:10.1038/s41467-018-07235-5 ISSN 2041-1723.
Campbell, Finlay, Didelot, Xavier, Fitzjohn, Rich, Ferguson, Neil, Cori, Anne and Jombart, Thibaut (2018) outbreaker2 : a modular platform for outbreak reconstruction. BMC Bioinformatics, 19 (Supplement 11). 363. doi:10.1186/s12859-018-2330-z ISSN 1471-2105.
Séraphin, Marie Nancy, Khan, Md. Siddiqur Rahman, Didelot, Xavier, Morris, J. Glenn, Nolan, David J., Murray, Ellen R., Salemi, Marco, Lauzardo, Michael and 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). doi:10.4269/ajtmh.17-0700 ISSN 0002-9637.
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 and Ohnishi, Makoto (2018) Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microbial Genomics, 4 (8). doi:10.1099/mgen.0.000205 ISSN 2057-5858.
Whittles, Lilith, White, Peter, Paul, John and Didelot, Xavier (2018) Epidemiological trends of antibiotic resistant Gonorrhoea in the United Kingdom. Antibiotics, 7 (3). 60. doi:10.3390/antibiotics7030060 ISSN 2079-6382.
Volz, Erik M. and 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. doi:10.1093/sysbio/syy007 ISSN 1063-5157.
Whittles, Lilith K., Didelot, Xavier, Grad, Yonatan H. and White, Peter J. (2018) Testing for gonorrhoea should routinely include the pharynx. The Lancet Infectious Diseases, 18 (7). pp. 716-717. doi:10.1016/S1473-3099(18)30341-4 ISSN 1473-3099.
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 and Balloux, Francois (2018) The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nature Communications, 9 (1). 1179. doi:10.1038/s41467-018-03205-z ISSN 2041-1723.
Collins, Caitlin and 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). e1005958. doi:10.1371/journal.pcbi.1005958 ISSN 1553-7358.
Whittles, Lilith K., White, Peter J. and 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). e1002416. doi:10.1371/journal.pmed.1002416 ISSN 1549-1277.
Peters, Joanna, Cresswell, Fiona, Amor, Lauren, Cole, Kevin, Dean, Gillian, Didelot, Xavier, De Silva, Dilrini, Eyre, David W. and 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. doi:10.1136/sextrans-2017-053198 ISSN 1472-3263.
Mostowy, Rafał J., Croucher, Nicholas J., De Maio, Nicola, Chewapreecha, Claire, Salter, Susannah J., Turner, Paul, Aanensen, David M., Bentley, Stephen D., Didelot, Xavier and 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. doi:10.1093/molbev/msx173 ISSN 0737-4038.
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. and 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. doi:10.1111/mec.14176 ISSN 0962-1083.
Pandey, Anish K., Cleary, David W., Laver, Jay R., Maiden, Martin C. J., Didelot, Xavier, Gorringe, Andrew and Read, Robert C. (2017) Neisseria lactamica Y92–1009 complete genome sequence. Standards in Genomic Sciences, 12 (1). 41. doi:10.1186/s40793-017-0250-6 ISSN 1944-3277.
Rosner, Bettina M., Schielke, Anika, Didelot, Xavier, Kops, Friederike, Breidenbach, Janina, Willrich, Niklas, Gölz, Greta, Alter, Thomas, Stingl, Kerstin, Josenhans, Christine, Suerbaum, Sebastian and Stark, Klaus (2017) A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011–2014. Scientific Reports, 7 (1). 5139. doi:10.1038/s41598-017-05227-x ISSN 2045-2322.
Klinkenberg, Don, Backer, Jantien A., Didelot, Xavier, Colijn, Caroline and Wallinga, Jacco (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Computational Biology, 13 (5). e1005495. doi:10.1371/journal.pcbi.1005495 ISSN 1553-7358.
Ledda, Alice, Price, James R., Cole, Kevin, Llewelyn, Martin J., Kearns, Angela M., Crook, Derrick W., Paul, John and Didelot, Xavier (2017) Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. Journal of Antimicrobial Chemotherapy, 72 (5). pp. 1285-1288. doi:10.1093/jac/dkw570 ISSN 0305-7453.
Didelot, Xavier, Fraser, Christophe, Gardy, Jennifer and Colijn, Caroline (2017) Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Molecular Biology and Evolution, 34 (4). pp. 997-1007. doi:10.1093/molbev/msw275 ISSN 0737-4038.
Yang, Shangxin, Hemarajata, Peera, Hindler, Janet, Li, Fan, Adisetiyo, Helty, Aldrovandi, Grace, Sebra, Robert, Kasarskis, Andrew, MacCannell, Duncan, Didelot, Xavier, Russell, Dana, Rubin, Zachary and 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. doi:10.1093/cid/ciw876 ISSN 1058-4838.
Didelot, Xavier, Whittles, Lilith K. and Hall, Ian (2017) Model-based analysis of an outbreak of bubonic plague in Cairo in 1801. Journal of The Royal Society Interface, 14 (131). 20170160. doi:10.1098/rsif.2017.0160 ISSN 1742-5689.
Collins, Caitlin and Didelot, Xavier (2016) Reconstructing the ancestral relationships between bacterial pathogen genomes. In: Nordenfelt, P. and Collin, M., (eds.) Bacterial Pathogenesis. Springer, pp. 109-137. ISBN 9781493966714
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 and 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. doi:10.1016/S1473-3099(16)30157-8 ISSN 1473-3099.
Didelot, Xavier (2016) Heroic sacrifice or tragic mistake? Revisiting the Eyam plague, 350 years on. Significance, 13 (5). pp. 20-25. doi:10.1111/j.1740-9713.2016.00961.x ISSN 1740-9705.
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. and Dean, Deborah (2016) Dynamics of genome change among Legionella species. Scientific Reports, 6 (1). 33442. doi:10.1038/srep33442 ISSN 2045-2322.
Ansari, M. Azim and Didelot, Xavier (2016) Bayesian inference of the evolution of a phenotype distribution on a phylogenetic tree. Genetics, 204 (1). pp. 89-98. doi:10.1534/genetics.116.190496 ISSN 0016-6731.
Eldholm, Vegard, Rieux, Adrien, Monteserin, Johana, Lopez, Julia Montana, Palmero, Domingo, Lopez, Beatriz, Ritacco, Viviana, Didelot, Xavier and Balloux, Francois (2016) Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis. eLife, 5 . doi:10.7554/eLife.16644 ISSN 2050-084X.
Joseph, Sandeep J., Marti, Hanna, Didelot, Xavier, Read, Timothy D. and 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. doi:10.1093/gbe/evw182 ISSN 1759-6653.
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. and Harris, Simon R. (2016) Genomic analysis and comparison of two Gonorrhea outbreaks. mBio, 7 (3). doi:10.1128/mBio.00525-16 ISSN 2150-7511.
Bubendorfer, Sebastian, Krebes, Juliane, Yang, Ines, Hage, Elias, Schulz, Thomas F., Bahlawane, Christelle, Didelot, Xavier and Suerbaum, Sebastian (2016) Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nature Communications, 7 . 11995. doi:10.1038/ncomms11995 ISSN 2041-1723.
Hatherell, Hollie-Ann, Tang, Patrick, Pollock, Sue L., Didelot, Xavier, Johnston, James C., Gardy, Jennifer L., Crisan, Anamaria and Colijn, Caroline (2016) Declaring a tuberculosis outbreak over with genomic epidemiology. Microbial Genomics, 2 (5). doi:10.1099/mgen.0.000060 ISSN 2057-5858.
Whittles, Lilith K. and Didelot, Xavier (2016) Epidemiological analysis of the Eyam plague outbreak of 1665–1666. Proceedings of the Royal Society B: Biological Sciences, 283 (1830). doi:10.1098/rspb.2016.0618 ISSN 0962-8452.
Wielgoss, Sébastien, Didelot, Xavier, Chaudhuri, Roy R, Liu, Xuan, Weedall, Gareth D, Velicer, Gregory J and 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. doi:10.1038/ismej.2016.34 ISSN 1751-7362.
Yahara, Koji, Didelot, Xavier, Jolley, Keith A., Kobayashi, Ichizo, Maiden, Martin C. J., Sheppard, Samuel K. and Falush, Daniel (2016) The landscape of realized homologous recombination in pathogenic bacteria. Molecular Biology and Evolution, 33 (2). pp. 456-471. doi:10.1093/molbev/msv237 ISSN 0737-4038.
Brown, Thomas, Didelot, Xavier, Maio, Nicola De and Wilson, Daniel J. (2016) SimBac : simulation of whole bacterial genomes with homologous recombination. Microbial Genomics, 2 (1). doi:10.1099/mgen.0.000044 ISSN 2057-5858.
Didelot, Xavier, Walker, A. Sarah, Peto, Tim E., Crook, Derrick W. and Wilson, Daniel J. (2016) Within-host evolution of bacterial pathogens. Nature Reviews Microbiology, 14 (3). pp. 150-162. doi:10.1038/nrmicro.2015.13 ISSN 1740-1526.
Joseph, Sandeep J., Marti, Hanna, Didelot, Xavier, Castillo-Ramirez, Santiago, Read, Timothy D. and 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. doi:10.1093/gbe/evv201 ISSN 1759-6653.
Achtman, Mark, Zhou, Zhemin and 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. e0134435. doi:10.1371/journal.pone.0134435 ISSN 1932-6203.
Montano, Valeria, Didelot, Xavier, Foll, Matthieu, Linz, Bodo, Reinhardt, Richard, Suerbaum, Sebastian, Moodley, Yoshan and Jensen, Jeffrey D. (2015) Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori. Genetics, 200 (3). pp. 947-963. doi:10.1534/genetics.115.176404 ISSN 0016-6731.
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 and 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. doi:10.1093/molbev/msv009 ISSN 0737-4038.
Biek, Roman, Pybus, Oliver G., Lloyd-Smith, James O. and Didelot, Xavier (2015) Measurably evolving pathogens in the genomic era. Trends in Ecology & Evolution, 30 (6). pp. 306-313. doi:10.1016/j.tree.2015.03.009 ISSN 0169-5347.
Didelot, Xavier, Pang, Bo, Zhou, Zhemin, McCann, Angela, Ni, Peixiang, Li, Dongfang, Achtman, Mark and Kan, Biao (2015) The role of China in the global spread of the current cholera pandemic. PLoS Genetics, Volume 11 (Number 3). pp. 1-14. Article number e1005072. doi:10.1371/journal.pgen.1005072 ISSN 1553-7390.
Prlic, Andreas, Didelot, Xavier and Wilson, Daniel J. (2015) ClonalFrameML : efficient inference of recombination in whole bacterial genomes. PLoS Computational Biology, 11 (2). e1004041. doi:10.1371/journal.pcbi.1004041 ISSN 1553-7358.
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 and 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. doi:10.1128/AAC.04292-14 ISSN 0066-4804.
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 and Read, Timothy D. (2015) Population structure of Neisseria gonorrhoeaebased on whole genome data and its relationship with antibiotic resistance. PeerJ, 3 . e806. doi:10.7717/peerj.806 ISSN 2167-8359.
Croucher, Nicholas J and Didelot, Xavier (2015) The application of genomics to tracing bacterial pathogen transmission. Current Opinion in Microbiology, 23 . pp. 62-67. doi:10.1016/j.mib.2014.11.004 ISSN 1369-5274.
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 and Zhang, Jianzhong (2015) Progressive genomic convergence of twoHelicobacter pyloristrains during mixed infection of a patient with chronic gastritis. Gut, 64 (4). pp. 554-561. doi:10.1136/gutjnl-2014-307345 ISSN 0017-5749.
Elliott, Briony, Dingle, Kate E., Didelot, Xavier, Crook, Derrick W. and 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. doi:10.1093/gbe/evu248 ISSN 1759-6653.
Krebes, Juliane, Didelot, Xavier, Kennemann, Lynn and 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. doi:10.1016/j.ijmm.2014.08.007 ISSN 1438-4221.
O'Brien, J. D., Didelot, Xavier, Iqbal, Z., Amenga-Etego, L., Ahiska, B. and Falush, D. (2014) A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics, 197 (3). pp. 925-937. doi:10.1534/genetics.114.161299 ISSN 0016-6731.
Didelot, Xavier, Gardy, Jennifer and Colijn, Caroline (2014) Bayesian inference of infectious disease transmission from whole-genome sequence data. Molecular Biology and Evolution, 31 (7). pp. 1869-1879. doi:10.1093/molbev/msu121 ISSN 0737-4038.
Yahara, Koji, Didelot, Xavier, Ansari, M. Azim, Sheppard, Samuel K. and Falush, Daniel (2014) Efficient inference of recombination hot regions in bacterial genomes. Molecular Biology and Evolution, 31 (6). pp. 1593-1605. doi:10.1093/molbev/msu082 ISSN 0737-4038.
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. and Wilson, Daniel J. (2014) Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nature Communications, 5 (1). 3956. doi:10.1038/ncomms4956 ISSN 2041-1723.
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. and 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. doi:10.1016/j.jhin.2013.11.007 ISSN 0195-6701.
Haase, Jana K., Didelot, Xavier, Lecuit, Marc, Korkeala, Hannu and Achtman, Mark (2014) The ubiquitous nature of Listeria monocytogenesclones : a large-scale Multilocus Sequence Typing study. Environmental Microbiology, Volume 16 (Number 2). pp. 405-416. doi:10.1111/1462-2920.12342 ISSN 1462-2912.
Tanaka, Mark M., Jombart, Thibaut, Cori, Anne, Didelot, Xavier, Cauchemez, Simon, Fraser, Christophe and Ferguson, Neil (2014) Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Computational Biology, 10 (1). e1003457. doi:10.1371/journal.pcbi.1003457 ISSN 1553-7358.
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. doi:10.1586/eri.13.15 ISSN 1478-7210.
Krause, David J., Didelot, Xavier, Cadillo-Quiroz, Hinsby and Whitaker, Rachel J. (2014) Recombination shapes genome architecture in an organism from the archaeal domain. Genome Biology and Evolution, 6 (1). pp. 170-178. doi:10.1093/gbe/evu003 ISSN 1759-6653.
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 and Didelot, Xavier (2014) Evolutionary history of the clostridium difficile pathogenicity locus. Genome Biology, 6 (1). pp. 36-52. doi:10.1093/gbe/evt204 ISSN 1474-7596.
Ansari, M. Azim and Didelot, Xavier (2014) Inference of the properties of the recombination process from whole bacterial genomes. Genetics, 196 (1). pp. 253-265. doi:10.1534/genetics.113.157172 ISSN 0016-6731.
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. and Didelot, Xavier (2013) Evolutionary history of the Clostridium difficile pathogenicity Locus. Genome Biology and Evolution, 6 (1). pp. 36-52. doi:10.1093/gbe/evt204 ISSN 1759-6653.
Price, J. R., Didelot, Xavier, Crook, D. W., Llewelyn, M. J. and Paul, J. (2013) Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. Journal of Hospital Infection, 83 (1). pp. 14-21. doi:10.1016/j.jhin.2012.10.003 ISSN 0195-6701.
Read, T. D., Joseph, S. J., Didelot, Xavier, Liang, B., Patel, L. and 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). doi:10.1128/mBio.00604-12 ISSN 2150-7511.
de Muinck, Eric J., Lagesen, Karin, Afset, Jan Egil, Didelot, Xavier, Rønningen, Kjersti S., Rudi, Knut, Stenseth, Nils Chr and Trosvik, Pål (2013) Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche. BMC Genomics, 14 (1). p. 81. doi:10.1186/1471-2164-14-81 ISSN 1471-2164.
Robinson, Esther R., Didelot, Xavier, Hood, Derek and Crook, Derrick (2013) Comparative phylogenetics of ICEHin1056 family reveals deep evolutionary associations of mobile genetic elements responsible for transfer of antibiotic resistance genes. In: Spring Meeting for Clinician Scientists in Training. Published in: The Lancet, 381 (S1). S93. doi:10.1016/S0140-6736(13)60533-4 ISSN 0140-6736.
Sheppard, S. K., Didelot, Xavier, Meric, G., Torralbo, A., Jolley, K. A., Kelly, D. J., Bentley, S. D., Maiden, M. C. J., Parkhill, J. and 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. doi:10.1073/pnas.1305559110 ISSN 0027-8424.
Didelot, Xavier, Nell, Sandra, Yang, Ines, Woltemate, Sabrina, van der Merwe, Schalk and 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. doi:10.1073/pnas.1304681110 ISSN 0027-8424.
Behrens, Wiebke, Schweinitzer, Tobias, Bal, Joena, Dorsch, Martina, Bleich, André, Kops, Friederike, Brenneke, Birgit, Didelot, Xavier, Suerbaum, Sebastian, Josenhans, Christine and 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. doi:10.1128/IAI.00750-13 ISSN 0019-9567.
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. and 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. doi:10.1093/infdis/jis734 ISSN 0022-1899.
Didelot, Xavier, Bowden, Rory, Wilson, Daniel J., Peto, Tim E. A. and Crook, Derrick W. (2012) Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics , 13 (9). pp. 601-612. doi:10.1038/nrg3226 ISSN 1471-0056.
Zhang, Liangfen, Thomas, Jonathan C., Didelot, Xavier and 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. doi:10.1007/s00239-012-9520-5 ISSN 0022-2844.
Achtman, Mark, Wain, John, Weill, François-Xavier, Nair, Satheesh, Zhou, Zhemin, Sangal, Vartul, Krauland, Mary G., Hale, James L., Harbottle, Heather, Uesbeck, Alexandra, Dougan, Gordon, Harrison, Lee H. and Brisse, Sylvain (2012) Multilocus sequence typing as a replacement for serotyping in salmonella enterica. PLoS Pathogens, Volume 8 (Number 6). Article number e1002776. doi:10.1371/journal.ppat.1002776 ISSN 1553-7374.
Didelot, Xavier, Méric, Guillaume, Falush, Daniel and Darling, Aaron E (2012) Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics, 13 (1). p. 256. doi:10.1186/1471-2164-13-256 ISSN 1471-2164.
Moccia, Claudia, Krebes, Juliane, Kulick, Stefan, Didelot, Xavier, Kraft, Christian, Bahlawane, Christelle and 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). 67. doi:10.1186/1471-2180-12-67 ISSN 1471-2180.
Barton, Nick H., Cadillo-Quiroz, Hinsby, Didelot, Xavier, Held, Nicole L., Herrera, Alfa, Darling, Aaron, Reno, Michael L., Krause, David J. and Whitaker, Rachel J. (2012) Patterns of gene flow define species of Thermophilic Archaea. PLoS Biology, 10 (2). e1001265. doi:10.1371/journal.pbio.1001265 ISSN 1545-7885.
Namouchi, A., Didelot, Xavier, Schock, U., Gicquel, B. and 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. doi:10.1101/gr.129544.111 ISSN 1088-9051.
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. and 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. doi:10.1101/gr.134437.111 ISSN 1088-9051.
Joseph, Sandeep J., Didelot, Xavier, Rothschild, James, de Vries, Henry J.C., Morré, Servaas A., Read, Timothy D. and 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. doi:10.1093/molbev/mss198 ISSN 0737-4038.
Joseph, Sandeep J., Didelot, Xavier, Gandhi, Khanjan, Dean, Deborah and Read, Timothy D. (2011) Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biology Direct, 6 (1). p. 28. doi:10.1186/1745-6150-6-28 ISSN 1745-6150.
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 and Crook, Derrick W. (2011) Clinical Clostridium difficile : clonality and pathogenicity locus diversity. PLoS One, 6 (5). e19993. doi:10.1371/journal.pone.0019993 ISSN 1932-6203.
Kennemann, L., Didelot, Xavier, Aebischer, T., Kuhn, S., Drescher, B., Droege, M., Reinhardt, R., Correa, P., Meyer, T. F., Josenhans, C., Falush, D. and Suerbaum, S. (2011) Helicobacter pylori genome evolution during human infection. Proceedings of the National Academy of Sciences, 108 (12). pp. 5033-5038. doi:10.1073/pnas.1018444108 ISSN 0027-8424.
Didelot, Xavier, Everitt, Richard G., Johansen, Adam M. and Lawson, Daniel J. (2011) Likelihood-free estimation of model evidence. Bayesian Analysis, Vol.6 (No.1). pp. 49-76. doi:10.1214/11-BA602 ISSN 1931-6690.
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 and Achtman, Mark (2011) Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing. Environmental Microbiology, 13 (12). pp. 3114-3127. doi:10.1111/j.1462-2920.2011.02588.x ISSN 1462-2912.
Didelot, Xavier, Bowden, Rory, Street, Teresa, Golubchik, Tanya, Spencer, Chris, McVean, Gil, Sangal, Vartul, Anjum, Muna F., Achtman, Mark, Falush, Daniel and Donnelly, Peter (2011) Recombination and population structure in salmonella enterica. PLoS Genetics, Volume 7 (Number 7). Article number e1002191. doi:10.1371/journal.pgen.1002191 ISSN 1553-7390.
Morelli, Giovanna, Didelot, Xavier, Kusecek, Barica, Schwarz, Sandra, Bahlawane, Christelle, Falush, Daniel, Suerbaum, Sebastian and Achtman, Mark (2010) Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PL o S Genetics, Vol.6 (No.7). doi:10.1371/journal.pgen.1001036 ISSN 1553-7390.
Didelot, Xavier and Maiden, Martin C. J. (2010) Impact of recombination on bacterial evolution. Trends in Microbiology, Vol.18 (No.7). pp. 315-322. ISSN 0966-842X doi:10.1016/j.tim.2010.04.002
Didelot, Xavier, Everitt, Richard G., Johansen, Adam M. and Lawson, Daniel J. (2010) Likelihood-free estimation of model evidence. Working Paper. Coventry: University of Warwick. Centre for Research in Statistical Methodology. Working papers, Vol.2010 (No.12).
Sangal, V., Harbottle, H., Mazzoni, C. J., Helmuth, R., Guerra, B., Didelot, Xavier, Paglietti, B., Rabsch, W., Brisse, S., Weill, F.-X., Roumagnac, P. and Achtman, M. (2010) Evolution and population structure of Salmonella enterica serovar Newport. Journal of Bacteriology, 192 (24). pp. 6465-6476. doi:10.1128/JB.00969-10 ISSN 0021-9193.
Didelot, Xavier, Lawson, D., Darling, A. and Falush, D. (2010) Inference of homologous recombination in bacteria using whole-genome sequences. Genetics, 186 (4). pp. 1435-1449. doi:10.1534/genetics.110.120121 ISSN 0016-6731.
Zhang, Junlong, Zhang, F. (Fang), Didelot, Xavier, Bruce, Kimberley D., Cagampang, Felino R., Vatish, Manu, Hanson, Mark A., Lehnert, Hendrik, Ceriello, Antonio and 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). doi:10.1186/1471-2164-10-478 ISSN 1471-2164.
Didelot, Xavier, Urwin, Rachel, Maiden, Martin C. J. and Falush, Daniel (2009) Genealogical typing of Neisseria meningitidis. Microbiology, Vol.15 (No.10). pp. 3176-3186. doi:10.1099/mic.0.031534-0 ISSN 1350-0872.
Didelot, Xavier, Lawson, Daniel J. and Falush, Daniel (2009) SimMLST: simulation of multi-locus sequence typing data under a neutral model. Bioinformatics, Vol.25 (No.11). pp. 1442-1444. doi:10.1093/bioinformatics/btp145 ISSN 1367-4803.
Didelot, Xavier, Barker, Margaret, Falush, Daniel and Priest, Fergus G. (2009) Evolution of pathogenicity in the Bacillus cereus group. Systematic and Applied Microbiology, Vol.32 (No.2). pp. 81-90. doi:10.1016/j.syapm.2009.01.001 ISSN 0723-2020.
Didelot, Xavier, Darling, Aaron and Falush, Daniel (2009) Inferring genomic flux in bacteria. Genome Research, Vol.19 (No.2). pp. 306-317. doi:10.1101/gr.082263.108 ISSN 1088-9051.
Vos, Michiel and Didelot, Xavier (2009) A comparison of homologous recombination rates in bacteria and archaea. ISME Journal, Vol.3 (No.2). pp. 199-208. doi:10.1038/ismej.2008.93 ISSN 1751-7362.
Vos, Michiel and Didelot, Xavier (2009) A comparison of homologous recombination rates in bacteria and archaea. The ISME Journal, 3 (2). pp. 199-208. doi:10.1038/ismej.2008.93 ISSN 1751-7362.
Kulick, Stefan, Moccia, Claudia, Didelot, Xavier, Falush, Daniel, Kraft, Christian and Suerbaum, Sebastian (2008) Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLOS One, Vol.3 (No.11). doi:10.1371/journal.pone.0003797 ISSN 1932-6203.
den Bakker, Henk C., Didelot, Xavier, Fortes, Esther D, Nightingale, Kendra K and Wiedmann, Martin (2008) Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evolutionary Biology, Vol. 8 (No. 27). doi:10.1186/1471-2148-8-277 ISSN 1471-2148.
Kennemann, L., Didelot, Xavier, Drescher, B., Kuhn, S., Olbermann, P., Falush, Daniel, Droege, M., Josenhans, C. and Suerbaum, Sebastian (2008) Genome plasticity during chronic infection with H-pylori. In: 60th Annual Meeting of the Deutschen-Gesellschaft-fur-Hygiene-und-Mikrobiologie, Dresden, Germany, Sep 21-24, 2008. Published in: International Journal of Medical Microbiology, Vol.298 (Suppl.2). p. 26. ISSN 1438-4221.
Moccia, C., Kulick, S., Didelot, Xavier, Ellrott, K., Kraft, C. and Suerbaum, Sebastian (2008) The role of Helicobacter pylori ruvA, ruvB and ruvC genes in homologous recombination and mutation. In: 60th Annual Meeting of the Deutschen-Gesellschaft-fur-Hygiene-und-Mikrobiologie, Dresden, Germany, Sep 21-24, 2008. Published in: International Journal of Medical Microbiology, Vol.298 (Suppl.2). p. 29. ISSN 1438-4221.
Didelot, Xavier and Falush, D. (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics, 175 (3). pp. 1251-1266. doi:10.1534/genetics.106.063305 ISSN 0016-6731.
Falush, D., Torpdahl, M., Didelot, Xavier, Conrad, D. F., Wilson, D. J. and 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. doi:10.1098/rstb.2006.1925 ISSN 0962-8436.
Didelot, Xavier, Achtman, Mark, Parkhill, J., Thomson, N. R. and 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. doi:10.1101/gr.5512906 ISSN 1088-9051.
Title | Funder | Award start | Award end |
---|---|---|---|
Broad species surveillance, sequencing, and transmission dynamics of SARS-CoV-2 in non-human animals | US Department of Agriculture Animal and Plant Health Inspection Service | 01 Aug 2023 | 31 Jul 2025 |
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.