2021

  • X Didelot and E Volz. Maximum likelihood inference of pathogen population size history from a phylogeny. bioRxiv, pp. 427056, 2021.
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  • X Didelot, I Siveroni, and E Volz. Additive uncorrelated relaxed clock models for the dating of genomic epidemiology phylogenies. Mol. Biol. Evol., 38:307–317, 2021.
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  • X Didelot, M Kendall, Y Xu, P White, and N McCarthy. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo. Curr. Protoc., 1:1–23, 2021.
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  • L Dorp, C Nimmo, A Ortiz, J Pang, M Acman, C Tan, J Millard, N Padayatchi, A Grant, A Pym, V Eldholm, L Grandjean, X Didelot, S Africa, G Health, and S Africa. Detection of a bedaquiline / clofazimine resistance reservoir in Mycobacterium tuberculosis predating the antibiotic era. bioRxiv, pp. 328799, 2021.
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  • D Knight, K Imwattana, B Kullin, E Guerrero-araya, D Paredes-Sabja, X Didelot, K Dingle, D Eyre, R Cesar, and T Riley. The Clostridioides difficile species problem : global phylogenomic analysis uncovers three ancient , toxigenic , genomospecies. bioRxiv, pp. 101101, 2021.
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  • F Lassalle, P Veber, E Jauneikaite, and X Didelot. Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel. bioRxiv, pp. 586495, 2021.
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  • F Lassalle, S Dastgheib, F Zhao, J Zhang, S Verbarg, A Fruhling, H Brinkmann, T Osborne, J Sikorski, F Balloux, X Didelot, J Santini, and J Petersen. Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Syst. Appl. Microbiol., 44:126165, 2021.
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  • A Ledda, M Cummins, L Shaw, E Jauneikaite, K Cole, F Lassalle, D Barry, C Rosmarin, S Anaraki, D Wareham, N Stoesser, J Paul, R Manuel, B Cherian, and X Didelot. Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by ​ Escherichia coli. bioRxiv, pp. 148189, 2021.
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  • F Medina-Aguayo, X Didelot, and R Everitt. Speeding up Inference of Homologous Recombination in Bacteria. bioRXiv, pp. 087007, 2021.
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  • C Yang, Y Cui, X Didelot, R Yang, and D Falush. Why panmictic bacteria are rare. bioRxiv, pp. 385336, 2021.
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2020

  • N Fountain-Jones, R Appaw, S Carver, X Didelot, E Volz, and M Charleston. Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evol., 6:veaa082, 2020.
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  • M Hennart, L Panunzi, C Rodrigues, Q Gaday, S Baines, M Barros-Pinkelnig, A Carmi-Leroy, M Dazas, A Wehenkel, X Didelot, J Toubiana, E Badell, and S Brisse. Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Med., 12:107, 2020.
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  • S Janezic, K Dingle, J Alvin, T Accetto, X Didelot, D Crook, D Lacy, and M Rupnik. Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution. Microb. Genomics, pp. 10.1099/mgen.0.000449, 2020.
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  • F Lassalle and X Didelot. Bacterial Microevolution and the Pangenome In Pangenome, Divers. Dyn. Evol. Genomes, pp. 129–149, 2020.
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  • M Osnes, X Didelot, J de Korne-Elenbaas, K Alfsnes, O Brynildsrud, G Syversen, { Nilsen, B De Blasio, D Caugant, and V Eldholm. Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway. Microb. Genomics, pp. 10.1099/mgen.0.000480, 2020.
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  • M Rodriguez, N Moser, C Malpartida, A Moniri, L Fisarova, I Pennisi, A Boonyasiri, E Jauneikaite, A Abdolrasouli, J Otter, F Bolt, F Davies, X Didelot, A Holmes, and P Georgiou. Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System. Sci. Rep., 10:8448, 2020.
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  • C Vegvari, Y Grad, P White, X Didelot, L Whittles, N Scangarella-oman, F Mitrani-gold, E Dumont, C Perry, K Gilchrist, M Hossain, T Mortimer, M Roy, and D Gardiner. Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. Euro Surveill., 25:1900210, 2020.
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  • E Volz, C Wiuf, Y Grad, S Frost, A Dennis, and X Didelot. Identification of hidden population structure in time-scaled phylogenies. Syst. Biol., 69:884–896, 2020.
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  • L Wang, X Didelot, J Yang, G Wong, Y Shi, W Liu, G Gao, and Y Bi. Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase. Nat. Commun., 11:5006, 2020.
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  • H Wang, C Yang, Z Sun, W Zheng, W Zhang, H Yu, Y Wu, X Didelot, R Yang, J Pan, and Y Cui. Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages. PLoS Negl. Trop. Dis., 14(2):e0008046, 2020.
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  • L Whittles, P White, and X Didelot. Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics. Clin. Infect. Dis., 71:1912–1919, 2020.
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2019

  • F Ailloud, X Didelot, S Woltemate, G Pfaffinger, J Overmann, R Bader, C Schulz, P Malfertheiner, and S Suerbaum. Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nat. Commun., 10(1):2273, 2019.
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  • A Criscuolo, S Issenhuth-Jeanjean, X Didelot, K Thorell, J Hale, J Parkhill, N Thomson, F Weill, D Falush, and S Brisse. The speciation and hybridization history of the genus Salmonella. Microb. Genomics, 5:10.1099/mgen.0.000284, jul 2019.
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  • X Didelot and K Pouwels. Machine-learning-assisted selection of antibiotic prescription. Nat. Med., 25:1033–1034, Springer US, 2019.
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  • X Didelot. Computational Methods in Microbial Population Genomics In M Polz and O Rajora, editors, Popul. Genomics Microorg., pp. 3–29, Springer International Publishing, 2019.
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  • K Dingle, X Didelot, T Quan, D Eyre, N Stoesser, C Marwick, J Coia, D Brown, S Buchanan, U Ijaz, C Goswami, G Douce, W Fawley, M Wilcox, T Peto, A Walker, and D Crook. A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078. MBio, 10(2):e02790–18, 2019.
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  • D Eyre, X Didelot, A Buckley, J Freeman, I Moura, D Crook, T Peto, A Walker, M Wilcox, and K Dingle. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine, 43:347–355, Elsevier, 2019.
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  • D Klinkenberg, C Colijn, and X Didelot. Methods for Outbreaks Using Genomic Data In Handb. Infect. Dis. Data Anal., pp. 245–263, CRC Press, 2019.
    (unavailable)
  • A Moniri, J Rodriguez-Manzano, K Malpartida-Cardenas, L Yu, X Didelot, A Holmes, and P Georgiou. Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves. Anal. Chem., 91:7426–7434, 2019.
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  • E Ozer, E Nnah, X Didelot, R Whitaker, and A Hauser. The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages. Genome Biol. Evol., 11:1780–1796, 2019.
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  • L Whittles, P White, and X Didelot. A dynamic power-law sexual network model of gonorrhoea outbreaks. PLoS Comput. Biol., 15(3):e1006748, 2019.
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  • L Zhao, H Chen, X Didelot, Z Li, Y Li, M Chen, Y Du, H Zhao, J Li, Q Hu, B Kan, M Chen, and B Pang. Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12. Microb. Genomics, 5:10.1099/mgen.0.000287, 2019.
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  • L van Dorp, Q Wang, L Shaw, M Acman, O Brynildsrud, V Eldholm, R Wang, H Gao, Y Yin, H Chen, C Ding, R Farrer, X Didelot, F Balloux, and H Wang. Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains. Microb. Genomics, 5:10.1099/mgen.0.000263, 2019.
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2018

  • F Campbell, X Didelot, R Fitzjohn, N Ferguson, A Cori, and T Jombart. Outbreaker2: a Modular Platform for Outbreak Reconstruction. BMC Bioinformatics, 19:363, 2018.
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  • L Challagundla, X Luo, I Tickler, X Didelot, D Coleman, A Shore, G Coombs, D Sordelli, E Brown, R Skov, R Larsen, J Reyes, I Robledo, G Vazquez, R Rivera, P Fey, K Stevenson, S Wang, B Kreiswirth, J Mediavilla, C Arias, P Planet, R Nolan, F Tenover, R Goering, and D Robinson. Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus. MBio, 9(1):e02016–17, 2018.
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  • C Collins and X Didelot. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. PLoS Comput. Biol., 14(2):e1005958, feb 2018.
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  • X Didelot, N Croucher, S Bentley, S Harris, and D Wilson. Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Res., 46:e134, 2018.
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  • G Méric, L Mageiros, J Pensar, M Laabei, K Yahara, B Pascoe, N Kittiwan, P Tadee, V Post, S Lamble, R Bowden, J Bray, M Morgenstern, K Jolley, M Maiden, E Feil, X Didelot, M Miragaia, H de Lencastre, T Moriarty, H Rohde, R Massey, D Mack, J Corander, and S Sheppard. Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nat. Commun., 9(1):5034, 2018.
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  • A Pandey, D Cleary, J Laver, A Gorringe, A Deasy, A Dale, P Morris, X Didelot, M Maiden, and R Read. Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection. Nat. Commun., 9(1):4753, Springer US, 2018.
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  • J Peters, F Cresswell, L Amor, K Cole, G Dean, X Didelot, D De Silva, D Eyre, and J Paul. Whole genome sequencing of Neisseria gonorrhoeae reveals transmission clusters involving patients of mixed HIV serostatus. Sex. Transm. Infect., 94:138–143, 2018.
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  • M Séraphin, X Didelot, D Nolan, J May, M Khan, E Murray, M Salemi, J Morris, and M Lauzardo. Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States. Am. J. Trop. Med. Hyg., 99:867–874, 2018.
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  • E Volz and X Didelot. Modeling the Growth and Decline of Pathogen Effective Population Size Provides Insight into Epidemic Dynamics and Drivers of Antimicrobial Resistance. Syst. Biol., 67(4):719–728, 2018.
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  • R Wang, L Van Dorp, L Shaw, P Bradley, Q Wang, X Wang, L Jin, Q Zhang, Y Liu, A Rieux, T Dorai-Schneiders, L Weinert, Z Iqbal, X Didelot, H Wang, and F Balloux. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun., 9(1):1179, 2018.
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  • L Whittles, P White, J Paul, and X Didelot. Epidemiological Trends of Antibiotic Resistant Gonorrhea in the United Kingdom. Antibiotics, 7(3):60, 2018.
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  • L Whittles, X Didelot, Y Grad, and P White. Testing for gonorrhoea should routinely include the pharynx. Lancet Infect. Dis., 18(7):716–717, 2018.
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  • K Yahara, S Nakayama, K Shimuta, K Lee, M Morita, T Kawahata, T Kuroki, Y Watanabe, H Ohya, M Yasuda, T Deguchi, X Didelot, and M Ohnishi. Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microb. Genomics, 4:10.1099/mgen.0.000205, 2018.
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2017

  • C Collins and X Didelot. Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes. Methods Mol. Biol., 1535:109–137, Clifton, N.J., 2017.
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  • X Didelot, L Whittles, and I Hall. Model-based analysis of an outbreak of bubonic plague in Cairo in 1801. J. R. Soc. Interface, 14(131):20170160, jun 2017.
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  • X Didelot, C Fraser, J Gardy, and C Colijn. Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Mol. Biol. Evol., 34:997–1007, 2017.
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  • K Dingle, X Didelot, T Quan, D Eyre, N Stoesser, T Golubchik, R Harding, D Wilson, D Griffiths, A Vaughan, J Finney, D Wyllie, S Oakley, W Fawley, J Freeman, K Morris, J Martin, P Howard, S Gorbach, E Goldstein, D Citron, S Hopkins, R Hope, A Johnson, M Wilcox, T Peto, A Walker, D Crook, C Del Ojo Elias, C Crichton, V Kostiou, A Giess, and J Davies. Effects of control interventions on Clostridium difficile infection in England: an observational study. Lancet Infect. Dis., 17(4):411–421, Elsevier, apr 2017.
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  • D Eyre, K Dingle, X Didelot, T Quan, T Peto, M Wilcox, A Walker, and D Crook. Clostridium difficile in England: can we stop washing our hands? – Authors’ reply. Lancet Infect. Dis., 17(5):478–479, Elsevier, may 2017.
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  • D Klinkenberg, J Backer, X Didelot, C Colijn, and J Wallinga. Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput. Biol., 13(5):e1005495, 2017.
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  • A Ledda, J Price, K Cole, M Llewelyn, A Kearns, D Crook, J Paul, and X Didelot. Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. J. Antimicrob. Chemother., 72:1285–1288, Oxford University Press (OUP): Policy B - Oxford Open Option B, 2017.
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  • R Mostowy, N Croucher, N De Maio, C Chewapreecha, S Salter, P Turner, D Aanensen, S Bentley, X Didelot, and C Fraser. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol. Biol. Evol., 34(10):2537–2554, 2017.
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  • A Pandey, D Cleary, J Laver, M Maiden, X Didelot, A Gorringe, and R Read. Neisseria lactamica Y92-1009 complete genome sequence. Stand. Genomic Sci., 12(1):41, Standards in Genomic Sciences, 2017.
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  • B Pascoe, G Méric, K Yahara, H Wimalarathna, S Murray, M Hitchings, E Sproston, C Carrillo, E Taboada, K Cooper, S Huynh, A Cody, K Jolley, M Maiden, N McCarthy, X Didelot, C Parker, S Sheppard, G Meric, K Yahara, H Wimaralathna, S Murray, M Hitchings, E Sproston, C Carrillo, E Taboada, K Cooper, S Huynh, A Cody, K Jolley, M Maiden, N McCarthy, X Didelot, C Parker, and S Sheppard. Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations. Mol. Ecol., 26(17):4497–4508, 2017.
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  • S Peacock, E Barnes, J Breuer, M Carroll, D Crook, X Didelot, M Fife, A Fox, J Greatorex, I Goodfellow, P Kellam, D Kind, J Parkhill, and T Walker. Pathogen genomics In Chief Med. Off. Annu. Rep., pp. 134–153, 2017.
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  • O Ratmann, E Hodcroft, M Pickles, A Cori, M Hall, S Lycett, C Colijn, B Dearlove, X Didelot, S Frost, M Hossain, J Joy, M Kendall, D Kühnert, G Leventhal, R Liang, G Plazzotta, A Poon, D Rasmussen, T Stadler, E Volz, C Weis, A Leigh Brown, C Fraser, and on behalf of the PANGEA-HIV consortium. Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Mol. Biol. Evol., 34:185–203, 2017.
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  • B Rosner, A Schielke, X Didelot, F Kops, J Breidenbach, N Willrich, G Gölz, T Alter, K Stingl, C Josenhans, S Suerbaum, and K Stark. A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011–2014. Sci. Rep., 7(1):5139, 2017.
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  • L Whittles, P White, and X Didelot. Estimating the fitness benefit and cost of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy: A modelling study. PLoS Med., 14(10):e1002416, 2017.
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  • K Yahara, G Méric, A Taylor, S de Vries, S Murray, B Pascoe, L Mageiros, A Torralbo, A Vidal, A Ridley, S Komukai, H Wimalarathna, A Cody, F Colles, N McCarthy, D Harris, J Bray, K Jolley, M Maiden, S Bentley, J Parkhill, C Bayliss, A Grant, D Maskell, X Didelot, D Kelly, and S Sheppard. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. Environ. Microbiol., 19:361–380, 2017.
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  • S Yang, P Hemarajata, J Hindler, F Li, H Adisetiyo, G Aldrovandi, R Sebra, A Kasarskis, D MacCannell, X Didelot, D Russell, Z Rubin, and R Humphries. Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography. Clin. Infect. Dis., 64:894–901, 2017.
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2016

  • M Ansari and X Didelot. Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree. Genetics, 204(1):89–98, sep 2016.
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  • T Brown, X Didelot, D Wilson, and N De Maio. SimBac: simulation of whole bacterial genomes with homologous recombination. Microb. Genomics, 2:10.1099/mgen.0.000044, 2016.
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  • S Bubendorfer, J Krebes, I Yang, E Hage, T Schulz, C Bahlawane, X Didelot, and S Suerbaum. Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nat. Commun., 7:11995, 2016.
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  • X Didelot, J Dordel, L Whittles, C Collins, N Bilek, C Bishop, P White, D Aanensen, J Parkhill, S Bentley, B Spratt, and S Harris. Genomic Analysis and Comparison of Two Gonorrhea Outbreaks. MBio, 7(3):e00525–16, jul 2016.
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  • X Didelot. Heroic sacrifice or tragic mistake? Revisiting the Eyam plague, 350 years on. Significance, 13(5):20–25, 2016.
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  • X Didelot, A Walker, T Peto, D Crook, and D Wilson. Within-host evolution of bacterial pathogens. Nat. Rev. Microbiol., 14:150–162, 2016.
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  • V Eldholm, A Rieux, J Monteserin, J Lopez, D Palmero, B Lopez, V Ritacco, X Didelot, and F Balloux. Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis. Elife, 5:e16644, 2016.
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  • H Hatherell, X Didelot, S Pollock, P Tang, A Crisan, J Johnston, C Colijn, and J Gardy. Declaring a tuberculosis outbreak over with genomic epidemiology. Microb. Genomics, 1:10.1099/mgen.0.000060, 2016.
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  • S Joseph, D Cox, B Wolff, S Morrison, N Kozak-Muiznieks, M Frace, X Didelot, S Castillo-Ramirez, J Winchell, T Read, and D Dean. Dynamics of genome change among Legionella species. Sci. Rep., 6:33442, Nature Publishing Group, 2016.
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  • S Joseph, H Marti, X Didelot, T Read, and D Dean. Tetracycline selective pressure and homologous recombination shape the evolution of Chlamydia suis: a recently identified zoonotic pathogen. Genome Biol. Evol., 8:2613–2623, 2016.
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  • N Stoesser, A Sheppard, L Pankhurst, N de Maio, C Moore, R Sebra, P Turner, L Anson, A Kasarskis, E Batty, V Kos, D Wilson, R Phetsouvanh, D Wyllie, E Sokurenko, A Manges, T Johnson, L Price, T Peto, J Johnson, X Didelot, A Walker, and D Crook. Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131. MBio, 7(2):e02162–15, 2016.
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  • L Whittles and X Didelot. Epidemiological analysis of the Eyam plague outbreak of 1665-1666. Proc. R. Soc. B, 283:20160618, 2016.
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  • S Wielgoss, X Didelot, R Chaudhuri, X Liu, G Weedall, G Velicer, and M Vos. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. ISME J., 10:2468–2477, 2016.
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  • K Yahara, X Didelot, K Jolley, I Kobayashi, M Maiden, S Sheppard, and D Falush. The landscape of realized homologous recombination in pathogenic bacteria. Mol. Biol. Evol., 33:456–471, 2016.
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  • D De Silva, J Peters, K Cole, M Cole, F Cresswell, G Dean, J Dave, D Thomas, K Foster, A Waldram, D Wilson, X Didelot, Y Grad, D Crook, T Peto, A Walker, J Paul, and D Eyre. Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study. Lancet Infect. Dis., 16(11):1295–1303, Elsevier Ltd, 2016.
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2015

  • M Achtman, Z Zhou, and X Didelot. Formal Comment to Pettengill. PLoS One, 10(8):e0134435, 2015.
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  • R Biek, O Pybus, J Lloyd-Smith, and X Didelot. Measurably evolving pathogens in the genomic era. Trends Ecol. Evol., 30:306–313, Elsevier Ltd, 2015.
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  • Q Cao, X Didelot, Z Wu, Z Li, L He, Y Li, M Ni, Y You, X Lin, Z Li, Y Gong, M Zheng, M Zhang, J Liu, W Wang, X Bo, D Falush, S Wang, and J Zhang. Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut, 64:554–61, 2015.
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  • N Croucher and X Didelot. The application of genomics to tracing bacterial pathogen transmission. Curr. Opin. Microbiol., 23:62–67, 2015.
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  • Y Cui, X Yang, X Didelot, C Guo, D Li, Y Yan, Y Zhang, Y Yuan, H Yang, J Wang, J Wang, Y Song, D Zhou, D Falush, and R Yang. Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus. Mol. Biol. Evol., 32:1396–1410, 2015.
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  • X Didelot, B Pang, Z Zhou, A McCann, P Ni, D Li, M Achtman, and B Kan. The Role of China in the Global Spread of the Current Cholera Pandemic. PLoS Genet., 11:e1005072, 2015.
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  • X Didelot and D Wilson. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput. Biol., 11(2):e1004041, feb 2015.
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  • M Ezewudo, S Joseph, S Castillo-Ramirez, D Dean, C Rio, X Didelot, R Selden, W Shafer, R Turingan, M Unemo, and T Read. Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ, 3:e806, 2015.
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  • S Joseph, H Marti, X Didelot, S Castillo-Ramirez, T Read, and D Dean. Chlamydiaceae genomics reveals interspecies admixture and the recent evolution of Chlamydia abortus infecting lower mammalian species and humans. Genome Biol. Evol., 7:3070–3084, oct 2015.
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  • A Mathers, N Stoesser, A Sheppard, L Pankhurst, A Giess, A Yeh, X Didelot, S Turner, R Sebra, A Kasarskis, T Peto, D Crook, and C Sifri. Klebsiella pneumoniae carbapenemase (KPC) producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole Genome Sequencing. Antimicrob. Agents Chemother., 59:1656–1663, 2015.
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  • V Montano, X Didelot, M Foll, B Linz, R Reinhardt, S Suerbaum, Y Moodley, and J Jensen. Worldwide Population Structure, Long Term Demography, and Local Adaptation of Helicobacter pylori. Genetics, 200:947–963, 2015.
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  • T Nandi, M Holden, X Didelot, K Mehershahi, J Boddey, I Beacham, I Peak, J Harting, P Baybayan, Y Guo, S Wang, C Lee, B Sim, A Essex-Lopresti, M Sarkar-Tyson, M Nelson, S Smither, C Ong, L Aw, H Chua, S Michell, D Studholme, R Titball, S Chen, J Parkhill, and P Tan. Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory and epigenetic profiles. Genome Res., 25:129–141, 2015.
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2014

  • M Ansari and X Didelot. Inference of the Properties of the Recombination Process from Whole Bacterial Genomes. Genetics, 196:253–265, 2014.
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  • X Didelot, J Gardy, and C Colijn. Bayesian inference of infectious disease transmission from whole genome sequence data. Mol. Biol. Evol., 31:1869–1879, 2014.
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  • K Dingle, B Elliott, E Robinson, D Griffiths, D Eyre, N Stoesser, A Vaughan, T Golubchik, W Fawley, M Wilcox, T Peto, A Walker, T Riley, D Crook, and X Didelot. Evolutionary History of the Clostridium difficile Pathogenicity Locus. Genome Biol. Evol., 6:36–52, 2014.
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  • B Elliott, K Dingle, X Didelot, D Crook, and T Riley. The complexity and diversity of the Pathogenicity locus in Clostridium difficile clade 5. Genome Biol. Evol., 6:3159–3170, 2014.
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  • R Everitt, X Didelot, E Batty, R Miller, K Knox, B Young, R Bowden, A Auton, A Votintseva, H Larner-Svensson, J Charlesworth, T Golubchik, C Ip, H Godwin, R Fung, T Peto, A Walker, D Crook, and D Wilson. Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nat. Commun., 5:3956, 2014.
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  • J Haase, X Didelot, M Lecuit, H Korkeala, and M Achtman. The ubiquitous nature of Listeria monocytogenes clones: a large scale MultiLocus Sequence Typing study. Environ. Microbiol., 16:405–416, 2014.
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  • T Jombart, D Aanensen, M Baguelin, P Birrell, S Cauchemez, A Camacho, C Colijn, C Collins, A Cori, X Didelot, C Fraser, S Frost, N Hens, J Hugues, M Höhle, L Opatowski, A Rambaut, O Ratmann, S Soubeyrand, M Suchard, J Wallinga, R Ypma, and N Ferguson. OutbreakTools: A new platform for disease outbreak analysis using the R software. Epidemics, 7:28–34, 2014.
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  • T Jombart, A Cori, X Didelot, S Cauchemez, C Fraser, and N Ferguson. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLoS Comput. Biol., 10:e1003457, 2014.
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  • D Krause, X Didelot, H Cadillo-Quiroz, and R Whitaker. Recombination shapes genome architecture in an organism from the Archaeal domain. Genome Biol. Evol., 6:170–178, 2014.
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  • J Krebes, X Didelot, L Kennemann, and S Suerbaum. Bidirectional genomic exchange between Helicobacter pylori strains from a family in Coventry, United Kingdom. Int. J. Med. Microbiol., 304:1135–1146, 2014.
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  • R Miller, J Price, E Batty, X Didelot, D Wyllie, T Golubchik, D Crook, J Paul, T Peto, D Wilson, M Cule, C Ip, N Day, C Moore, R Bowden, and M Llewelyn. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. J. Hosp. Infect., 86:83–89, 2014.
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  • J O’Brien, X Didelot, Z Iqbal, L Amenga-Etego, B Ahiska, and D Falush. A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics, 197:925–937, 2014.
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  • N Stoesser, A Giess, E Batty, A Sheppard, A Walker, D Wilson, X Didelot, A Bashir, R Sebra, A Kasarskis, B Sthapit, M Shakya, D Kelly, a Pollard, T Peto, D Crook, P Donnelly, S Thorson, P Amatya, and S Joshi. Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community Versus Hospital-associated Transmission in an Endemic Setting. Antimicrob. Agents Chemother., 58:7347–57, 2014.
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  • K Yahara, X Didelot, M Ansari, S Sheppard, and D Falush. Efficient inference of recombination hot regions in bacterial genomes. Mol. Biol. Evol., 31:1593–605, 2014.
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2013

  • W Behrens, T Schweinitzer, J Bal, M Dorsch, A Bleich, F Kops, B Brenneke, X Didelot, S Suerbaum, and C Josenhans. Role of energy sensor TlpD of Helicobacter pylori in gerbil colonization and genome analyses after adaptation in the gerbil. Infect. Immun., 81(10):3534–3551, 2013.
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  • X Didelot. Genomic analysis to improve the management of outbreaks of bacterial infection. Expert Rev. Anti. Infect. Ther., 11(4):335–337, 2013.
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  • X Didelot, S Nell, I Yang, S Woltemate, S van der Merwe, and S Suerbaum. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc Natl Acad Sci USA, 110(34):13880–13885, 2013.
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  • K Dingle, X Didelot, M Ansari, D Eyre, A Vaughan, D Griffiths, C Ip, E Batty, T Golubchik, R Bowden, K Jolley, D Hood, W Fawley, A Walker, T Peto, M Wilcox, and D Crook. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large scale whole genome sequencing. J. Infect. Dis., 207:675–686, 2013.
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  • D Eyre, M Cule, D Wilson, D Griffiths, A Vaughan, L O’Connor, C Ip, T Golubchik, E Batty, J Finney, D Wyllie, X Didelot, P Piazza, R Bowden, K Dingle, R Harding, D Crook, M Wilcox, T Peto, and A Walker. Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing. N. Engl. J. Med., 369(13):1195–1205, 2013.
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  • T Golubchik, E Batty, R Miller, H Farr, B Young, H Larner-Svensson, R Fung, H Godwin, K Knox, A Votintseva, R Everitt, T Street, M Cule, C Ip, X Didelot, T Peto, R Harding, D Wilson, D Crook, and R Bowden. Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage. PLoS One, 8(5):e61319, 2013.
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  • J Price, X Didelot, D Crook, M Llewelyn, and J Paul. Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. J. Hosp. Infect., 83:14–21, 2013.
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  • T Read, S Joseph, X Didelot, B Liang, L Patel, and D Dean. Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range. MBio, 4(2):e00604–12, 2013.
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  • S Sheppard, X Didelot, K Jolley, A Darling, B Pascoe, G Meric, D Kelly, A Cody, F Colles, N Strachan, I Ogden, K Forbes, N French, P Carter, W Miller, N McCarthy, R Owen, E Litrup, M Egholm, J Affourtit, S Bentley, J Parkhill, M Maiden, and D Falush. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol. Ecol., 22:1051–1064, 2013.
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  • S Sheppard, X Didelot, G Meric, A Torralbo, K Jolley, D Kelly, S Bentley, M Maiden, J Parkhill, and D Falush. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci USA, 110(29):11923–7, 2013.
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  • E de Muinck, K Lagesen, J Afset, X Didelot, K Rønningen, K Rudi, N Stenseth, and P Trosvik. Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche. BMC Genomics, 14:81, 2013.
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2012

  • M Achtman, J Wain, F Weill, S Nair, Z Zhou, V Sangal, M Krauland, J Hale, H Harbottle, A Uesbeck, G Dougan, L Harrison, S Brisse, and T S. enterica MLST study group. Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica. PLoS Pathog., 8(6):e1002776, 2012.
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  • H Cadillo-Quiroz, X Didelot, N Held, A Herrera, A Darling, M Reno, D Krause, and R Whitaker. Patterns of Gene Flow Define Species of Thermophilic Archaea. PLoS Biol., 10(2):e1001265, 2012.
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  • X Didelot, D Eyre, M Cule, C Ip, M Ansari, D Griffiths, A Vaughan, L O’Connor, T Golubchik, E Batty, P Piazza, D Wilson, R Bowden, P Donnelly, K Dingle, M Wilcox, A Walker, D Crook, T Peto, and R Harding. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol., 13:R118, 2012.
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  • X Didelot, G Méric, D Falush, and A Darling. Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics, 13(1):256, 2012.
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  • X Didelot, R Bowden, D Wilson, T Peto, and D Crook. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet., 13:601–612, 2012.
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  • D Eyre, T Golubchik, N Gordon, R Bowden, P Piazza, E Batty, C Ip, D Wilson, X Didelot, L O’Connor, R Lay, D Buck, A Kearns, A Shaw, J Paul, M Wilcox, P Donnelly, T Peto, A Walker, and D Crook. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open, 2:e001124, 2012.
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  • S Joseph, X Didelot, J Rothschild, H de Vries, S Morré, T Read, and D Dean. Population Genomics of Chlamydia trachomatis: Insights on Drift, Selection, Recombination and Population Structure. Mol. Biol. Evol., 29:3933–46, 2012.
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  • C Moccia, J Krebes, S Kulick, X Didelot, C Kraft, C Bahlawane, and S Suerbaum. The nucleotide excision repair (NER) system of Helicobacter pylori: Role in mutation prevention and chromosomal import patterns after natural transformation. BMC Microbiol., 12:67, 2012.
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  • A Namouchi, X Didelot, U Scho, B Gicquel, and E Rocha. After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res., 22:721–34, 2012.
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  • B Young, T Golubchik, E Batty, R Fung, H Larner-svensson, A Votintseva, R Miller, H Godwin, K Knox, R Everitt, Z Iqbal, A Rimmer, M Cule, C Ip, X Didelot, R Harding, P Donnelly, T Peto, D Crook, R Bowden, and D Wilson. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci USA, 109:4550–4555, 2012.
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  • L Zhang, J Thomas, X Didelot, and D Robinson. Molecular Signatures Identify a Candidate Target of Balancing Selection in an arcD-Like Gene of Staphylococcus epidermidis. J. Mol. Evol., 75:43–54, 2012.
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  • M Zwick, S Joseph, X Didelot, P Chen, K Bishop-Lilly, A Stewart, K Willner, S Lentz, N Nolan, M Thomason, S Sozhamannan, A Mateczun, L Du, and T Read. Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis. Genome Res., 22(8):1512–24, 2012.
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2011

  • X Didelot, R Everitt, A Johansen, and D Lawson. Likelihood-free estimation of model evidence. Bayesian Anal., 6:48–76, 2011.
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  • X Didelot, R Bowden, T Street, T Golubchik, C Spencer, G McVean, V Sangal, M Anjum, M Achtman, D Falush, and P Donnelly. Recombination and Population Structure in Salmonella enterica. PLoS Genet., 7(7):e1002191, 2011.
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  • K Dingle, D Griffiths, X Didelot, J Evans, A Vaughan, M Kachrimanidou, N Stoesser, K Jolley, T Golubchik, R Harding, T Peto, W Fawley, A Walker, M Wilcox, and D Crook. Clinical Clostridium difficile: Clonality and Pathogenicity Locus diversity. PLoS One, 6(5):e19993, 2011.
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  • E Gripp, D Hlahla, X Didelot, F Kops, S Maurischat, K Tedin, T Alter, L Ellerbroek, K Schreiber, D Schomburg, T Janssen, P Bartholomäus, D Hofreuter, S Woltemate, M Uhr, B Brenneke, P Grüning, G Gerlach, L Wieler, S Suerbaum, and C Josenhans. Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics, 12(1):584, 2011.
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  • S Joseph, X Didelot, K Gandhi, D Dean, and T Read. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biol. Direct, 6:28, 2011.
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  • L Kennemann, X Didelot, T Aebischer, S Kuhn, B Drescher, M Droege, R Reinhardt, P Correa, T Meyer, C Josenhans, D Falush, and S Suerbaum. Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA, 108(12):5033–5038, 2011.
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  • R Laukkanen-Ninios, X Didelot, K Jolley, G Morelli, V Sangal, P Kristo, C Brehony, P Imori, H Fukushima, A Siitonen, G Tseneva, E Voskressenskaya, J Falcao, H Korkeala, M Maiden, C Mazzoni, E Carniel, M Skurnik, and M Achtman. Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing. Environ. Microbiol., 13(12):3114–3127, 2011.
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2010

  • X Didelot, D Lawson, A Darling, and D Falush. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics, 186(4):1435–49, 2010.
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  • X Didelot and M Maiden. Impact of recombination on bacterial evolution. Trends Microbiol., 18(7):315–322, 2010.
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  • X Didelot. Sequence-based analysis of bacterial population structures In D Robinson, D Falush, and E Feil, editors, Bact. Popul. Genet. Infect. Dis., pp. 37–60, John Wiley & Sons, Inc., 2010.
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  • G Morelli, X Didelot, B Kusecek, S Schwarz, C Bahlawane, D Falush, S Suerbaum, and M Achtman. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet., 6(7):e1001036, 2010.
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  • V Sangal, H Harbottle, C Mazzoni, R Helmuth, B Guerra, X Didelot, B Paglietti, W Rabsch, S Brisse, F Weill, P Roumagnac, and M Achtman. Evolution and Population Structure of Salmonella enterica Serovar Newport. J. Bacteriol., 192(24):6465–76, 2010.
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2009

  • X Didelot, R Urwin, M Maiden, and D Falush. Genealogical typing of Neisseria meningitidis. Microbiology, 155:3176–86, 2009.
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  • X Didelot, M Barker, D Falush, and F Priest. Evolution of pathogenicity in the Bacillus cereus group. Syst. Appl. Microbiol., 32(2):81–90, 2009.
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  • X Didelot, D Lawson, and D Falush. SimMLST: simulation of multi-locus sequence typing data under a neutral model. Bioinformatics, 25(11):1442–4, 2009.
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  • M Vos and X Didelot. A comparison of homologous recombination rates in bacteria and archaea. ISME J., 3(2):199–208, 2009.
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  • J Zhang, F Zhang, X Didelot, K Bruce, F Cagampang, M Vatish, M Hanson, H Lehnert, A Ceriello, and C Byrne. 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, 10:478, 2009.
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2008

  • X Didelot and D Falush. Bacterial Recombination in vivo In M Hensel and H Schmidt, editors, Horiz. Gene Transf. Evol. Pathog., pp. 23–46, Cambridge University Press, 2008.
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  • X Didelot, A Darling, and D Falush. Inferring genomic flux in bacteria. Genome Res., 19(2):306–317, dec 2008.
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  • X Didelot, J Taylor, and J Watkins. A Duality Identity between a Model of Bacterial Recombination and the Wright-Fisher Diffusion. Markov Process. Relat. Top., 4:315–324, 2008.
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  • S Kulick, C Moccia, X Didelot, D Falush, C Kraft, and S Suerbaum. Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLoS One, 3(11):e3797, 2008.
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  • H den Bakker, X Didelot, E Fortes, K Nightingale, and M Wiedmann. Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evol. Biol., 8:277, 2008.
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2007

  • X Didelot, M Achtman, J Parkhill, N Thomson, and D Falush. A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?. Genome Res., 17(1):61–8, 2007.
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  • X Didelot and D Falush. Inference of bacterial microevolution using multilocus sequence data. Genetics, 175(3):1251–66, 2007.
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2006

  • D Falush, M Torpdahl, X Didelot, D Conrad, D Wilson, and M Achtman. Mismatch induced speciation in Salmonella: model and data. Philos. Trans. R. Soc. B, 361(1475):2045–53, 2006.
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