Publications

2023

A Boonyasiri, A Myall, Y Wan, F Bolt, A Ledda, S Mookerjee, A Weisse, J Turton, H Abbas, R Prakapaite, A Sabnis, A Abdolrasouli, K Malpartida Cardenas, L Miglietta, H Donaldson, M Gilchrist, K Hopkins, M Ellington, J Otter, G Larrouy-Maumus, A Edwards, J Rodriguez Manzano, X Didelot, M Barahona, A Holmes, E Jauneikaite, and F Davies. Integrated Patient Network and Genomic Plasmid Analysis Reveal a Regional, Multi-Species Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and Mcr-9 Genes. medRxiv, 2023.
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X Didelot, L Geidelberg, COG-UK, and E Volz. Model Design for Non-Parametric Phylodynamic Inference and Applications to Pathogen Surveillance. bioRxiv, pp. 427056, 2023.
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X Didelot, D Helekal, M Kendall, and P Ribeca. Distinguishing Imported Cases from Locally Acquired Cases within a Geographically Limited Genomic Sample of an Infectious Disease. Bioinformatics, 23:btac761, 2023.
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X Didelot and P Ribeca. KPop : An Assembly-Free and Scalable Method for the Comparative Analysis of Microbial Genomes. bioRxiv, pp. 2022.06.22.497172, 2023.
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K Dingle, J Freeman, X Didelot, D Eyre, J Swan, W Spittal, E Clark, K Jolley, A Sarah Walker, M Wilcox, and D Crook. Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in Epidemic Lineages of Multi Drug-Resistant Clostridioides Difficile. bioRxiv, pp. 2022.05.23.493179, 2023.
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L Gomez, C Savin, V Andrianaivoarimanana, L Randriantseheno, Z Zhou, A Kocher, M Rajerison, X Didelot, and D Kühnert. Phylogenetic Analysis of the Origin and Spread of Plague in Madagascar. bioRxiv, pp. 2022.03.29.486186v1, 2023.
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D Helekal, M Keeling, Y Grad, and X Didelot. Estimating the Fitness Cost and Benefit of Antimicrobial Resistance from Pathogen Genomic Data. bioRxiv, pp. 2022.12.02.518824, 2023.
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M Kendall, D Tsallis, C Wymant, A Di Francia, Y Balogun, X Didelot, L Ferretti, and C Fraser. Epidemiological Impacts of the NHS COVID-19 App in England and Wales throughout Its First Year. Nat Commun, 14(1):858, 2023.
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M Moore, M Laager, and X Didelot. KmerAperture: Retaining k -Mer Synteny for Alignment-Free Estimation of within-Lineage Core and Accessory Differences. bioRxiv, pp. 2022.10.12.511870, 2023.
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S Mughal, S Niazi, T Do, S Gilbert, X Didelot, D Radford, and D Beighton. Genomic Diversity among Actinomyces Naeslundii Strains and Closely Related Species. Microorganisms, 11:254, 2023.
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A Ortiz, M Kendall, N Storey, J Hatcher, H Dunn, S Roy, R Williams, C Williams, R Goldstein, X Didelot, K Harris, J Breuer, and L Grandjean. Within-Host Diversity Improves Phylogenetic and Transmission Reconstruction of SARS-CoV-2 Outbreaks. bioRxiv, pp. 2022.06.07.495142, 2023.
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A Taylor, G Méric, K Yahara, B Pascoe, L Mageiros, E Mourkas, J Calland, S Puranen, M Hitchings, S Bayliss, K Jolley, C Kobras, N Williams, A van Vliet, J Parkhill, M Maiden, J Corander, D Falush, X Didelot, D Kelly, and S Sheppard. Cross-Species Evolutionary Rewiring in the Enteric Bacterium Campylobacter. bioRxiv, pp. 2021.03.15.435406, 2023.
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M Abdel-Glil, H Hotzel, H Tomaso, X Didelot, C Brandt, C Seyboldt, J Linde, S Schwarz, H Neubauer, and H El-Adawy. Genomic Epidemiology of Campylobacter Fetus Subsp. Venerealis from Germany. Front. Vet. Sci., 9:1069062, 2023.
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F Medina-Aguayo, X Didelot, and R Everitt. Speeding up Inference of Homologous Recombination in Bacteria. bioRXiv, pp. 087007, 2023.
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2022

J Carson, A Ledda, L Ferretti, M Keeling, and X Didelot. The Bounded Coalescent Model: Conditioning a Genealogy on a Minimum Root Date. Journal of Theoretical Biology, 548:111186, 2022.
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X Didelot and J Parkhill. A Scalable Analytical Approach from Bacterial Genomes to Epidemiology. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1861):20210246, 2022.
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X Didelot and C Evans. 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, 2022.
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J Larsen, C Raisen, X Ba, N Sadgrove, G Padilla-González, M Simmonds, I Loncaric, H Kerschner, P Apfalter, R Hartl, A Deplano, S Vandendriessche, B erná Bolf'iková, P Hulva, M Arendrup, R Hare, C Barnadas, M Stegger, R Sieber, R Skov, A Petersen, { Angen, S Rasmussen, C Espinosa-Gongora, F Aarestrup, L Lindholm, S Nykäsenoja, F Laurent, K Becker, B Walther, C Kehrenberg, C Cuny, F Layer, G Werner, W Witte, I Stamm, P Moroni, H Jørgensen, H de Lencastre, E Cercenado, F Garc'ia-Garrote, S Börjesson, S Hæggman, V Perreten, C Teale, A Waller, B Pichon, M Curran, M Ellington, J Welch, S Peacock, D Seilly, F Morgan, J Parkhill, N Hadjirin, J Lindsay, M Holden, G Edwards, G Foster, G Paterson, X Didelot, M Holmes, E Harrison, and A Larsen. Emergence of Methicillin Resistance Predates the Clinical Use of Antibiotics. Nature, 602:135–141, 2022.
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A Ledda, M Cummins, L Shaw, E Jauneikaite, K Cole, F Lasalle, D Barry, J Turton, C Rosmarin, S Anaraki, D Wareham, N Stoesser, J Paul, R Manuel, B Cherian, and X Didelot. Hospital Outbreak of Carbapenem-Resistant Enterobacterales Associated with a blaOXA-48 Plasmid Carried Mostly by Escherichia Coli ST399. Microbial Genomics, 8(4):1–11, 2022.
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D Volk, F Yang-Turner, X Didelot, D Crook, and D Wyllie. Catwalk: Identifying Closely Related Sequences in Large Microbial Sequence Databases. Microbial Genomics, 8(6):1–6, 2022.
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L Wang, X Didelot, Y Bi, and G Gao. SARS-CoV-2 Transmissibility Compared between Variants of Concern and Vaccination Status. Briefings in Bioinformatics, 23(2):1–12, 2022.
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L Whittles, X Didelot, and P White. Public Health Impact and Cost-Effectiveness of Gonorrhoea Vaccination: An Integrated Transmission-Dynamic Health-Economic Modelling Analysis. The Lancet Infectious Diseases, 22:1030–1041, 2022.
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K Willgert, X Didelot, M Surendran-Nair, S Kuchipudi, R Ruden, M Yon, R Nissly, K Vandegrift, R Nelli, L Li, B Jayarao, N Levine, R Olsen, J Davis, J Musser, P Hudson, V Kapur, and A Conlan. Transmission History of SARS-CoV-2 in Humans and White-Tailed Deer. Scientific Reports, 12(1):12094, 2022.
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N Fountain-Jones, S Kraberger, R Gagne, M Gilbertson, D Trumbo, M Charleston, P Salerno, W Chris Funk, K Crooks, K Logan, M Alldredge, S Dellicour, G Baele, X Didelot, S VandeWoude, S Carver, and M Craft. Hunting Alters Viral Transmission and Evolution in a Large Carnivore. Nature Ecology & Evolution, 6:174–182, 2022.
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2021

X Didelot, I Siveroni, and E Volz. Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies. Molecular Biology and Evolution, 38:307–317, 2021.
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X Didelot. Phylogenetic Methods for Genome-Wide Association Studies in Bacteria In Bacterial Pangenomics: Methods and Protocols, pp. 205–220, Springer Nature, 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. Current Protocols, 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, and F Balloux. Detection of a Bedaquiline / Clofazimine Resistance Reservoir in Mycobacterium Tuberculosis Predating the Antibiotic Era. bioRxiv, pp. 328799, 2021.
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D Helekal, A Ledda, E Volz, D Wyllie, and X Didelot. Bayesian Inference of Clonal Expansions in a Dated Phylogeny. Systematic Biology, pp. syab095, 2021.
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D Knight, K Imwattana, B Kullin, E Guerrero-Araya, D Paredes-Sabja, X Didelot, K Dingle, D Eyre, C Rodr'iguez, and T Riley. Major Genetic Discontinuity and Novel Toxigenic Species in Clostridioides Difficile Taxonomy. eLife, 10:e64325, 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. Systematic and Applied Microbiology, 44:126165, 2021.
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A Torres Ortiz, J Coronel, J Vidal, C Bonilla, D Moore, R Gilman, F Balloux, O Kon, X Didelot, and L Grandjean. Genomic Signatures of Pre-Resistance in Mycobacterium Tuberculosis. Nature Communications, 12(1):7312, 2021.
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L Wang, X Didelot, Y Bi, and G Gao. Assessing the Extent of Community Spread Caused by Mink-Derived SARS-CoV-2 Variants. The Innovation, 2(3):100128, 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

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 Medicine, 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. Microbial Genomics, pp. 10.1099/mgen.0.000449, 2020.
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F Lassalle and X Didelot. Bacterial Microevolution and the Pangenome In The Pangenome, Diversity, Dynamics and Evolution of 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. Microbial 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. Scientific Reports, 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 Surveillance, 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. Systematic Biology, 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. Nature Communications, 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 Neglected Tropical Diseases, 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. Clinical Infectious Diseases, 71:1912–1919, 2020.
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N Fountain-Jones, R Appaw, S Carver, X Didelot, E Volz, and M Charleston. Emerging Phylogenetic Structure of the SARS-CoV-2 Pandemic. Virus Evolution, 6:veaa082, 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. Nature Communications, 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. Microbial Genomics, 5:10.1099/mgen.0.000284, 2019.
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X Didelot and K Pouwels. Machine-Learning-Assisted Selection of Antibiotic Prescription. Nature Medicine, 25:1033–1034, 2019.
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X Didelot. Computational Methods in Microbial Population Genomics In M Polz and O Rajora, editors, Population Genomics: Microorganisms, 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, 2019.
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D Klinkenberg, C Colijn, and X Didelot. Methods for Outbreaks Using Genomic Data In Handbook of Infectious Disease Data Analysis, pp. 245–263, CRC Press, 2019.
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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. Analytical Chemistry, 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 Biology and Evolution, 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 Computational Biology, 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. Microbial 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. Microbial 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 Computational Biology, 14(2):e1005958, 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 Research, 46(22):e134–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. Nature Communications, 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. Nature Communications, 9(1):4753, 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. Sexually Transmitted Infections, 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. American Journal of Tropical Medicine and Hygiene, 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. Systematic Biology, 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. Nature Communications, 9(1):1179, 2018.
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L Whittles, X Didelot, Y Grad, and P White. Testing for Gonorrhoea Should Routinely Include the Pharynx. Lancet Infectious Diseases, 18(7):716–717, 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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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. Microbial 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 In Bacterial Pathogenesis: Methods and Protocols, pp. 109–137, Clifton, N.J., 2017.
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X Didelot, C Fraser, J Gardy, and C Colijn. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Molecular Biology and Evolution, 34:997–1007, 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. Journal of The Royal Society Interface, 14(131):20170160, 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 Infectious Diseases, 17(4):411–421, Elsevier, 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 Infectious Diseases, 17(5):478–479, Elsevier, 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 Computational Biology, 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. Journal Of Antimicrobial Chemotherapy, 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. Molecular Biology and Evolution, 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. Standards in Genomic Sciences, 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. Molecular Ecology, 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 Medical Officier Annual Report, 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. Molecular Biology and Evolution, 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. Scientific Reports, 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 Medicine, 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. Environmental Microbiology, 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. Clinical Infectious Diseases, 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, 2016.
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T Brown, X Didelot, D Wilson, and N De Maio. SimBac: Simulation of Whole Bacterial Genomes with Homologous Recombination. Microbial 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. Nature Communications, 7:11995, 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 Infectious Diseases, 16(11):1295–1303, Elsevier Ltd, 2016.
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X Didelot, A Walker, T Peto, D Crook, and D Wilson. Within-Host Evolution of Bacterial Pathogens. Nature Reviews Microbiology, 14:150–162, 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, 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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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. Microbial Genomics, 1:10.1099/mgen.0.000060, 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 Biology and Evolution, 8:2613–2623, 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. Scientific Reports, 6:33442, Nature Publishing Group, 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. Proceedings of the Royal Society 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 Journal, 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. Molecular Biology and Evolution, 33:456–471, 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 in Ecology & Evolution, 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. Current Opinion in Microbiology, 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. Molecular Biology and Evolution, 32:1396–1410, 2015.
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X Didelot and D Wilson. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Computational Biology, 11(2):e1004041, 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 Genetics, 11:e1005072, 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 Biology and Evolution, 7:3070–3084, 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. Antimicrobial agents and chemotherapy, 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 a. 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 Research, 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. Molecular Biology and Evolution, 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 Biology and Evolution, 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 Biology and Evolution, 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. Nature communications, 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. Environmental microbiology, 16:405–416, 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 Computational Biology, 10:e1003457, 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 a. 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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D Krause, X Didelot, H Cadillo-Quiroz, and R Whitaker. Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain. Genome biology and evolution, 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. International Journal of Medical Microbiology, 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. Journal of Hospital Infection, 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 a 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. Antimicrobial agents and chemotherapy, 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. Molecular biology and evolution, 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. Infection and Immunity, 81(10):3534–3551, 2013.
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X Didelot. Genomic Analysis to Improve the Management of Outbreaks of Bacterial Infection. Expert Review of Anti-infective Therapy, 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. Journal of Infectious Diseases, 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. New England Journal of Medicine, 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 a 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. Journal of Hospital Infection, 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. Molecular Ecology, 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 Pathogens, 8(6):e1002776, 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. Nature Reviews Genetics, 13:601–612, 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 Biology, 13:R118, 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 a Morré, T Read, and D Dean. Population Genomics of Chlamydia Trachomatis: Insights on Drift, Selection, Recombination and Population Structure. Molecular Biology and Evolution, 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 microbiology, 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 Research, 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. Journal Molecular Evolution, 75:43–54, 2012.
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M Zwick, S Joseph, X Didelot, P Chen, K a 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 Research, 22(8):1512–24, 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 Biology, 10(2):e1001265, 2012.
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2011

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 Genetics, 7(7):e1002191, 2011.
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X Didelot, R Everitt, A Johansen, and D Lawson. Likelihood-Free Estimation of Model Evidence. Bayesian Analysis, 6:48–76, 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. Biology 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. Environmental Microbiology, 13(12):3114–3127, 2011.
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2010

X Didelot. Sequence-Based Analysis of Bacterial Population Structures In D Robinson, D Falush, and E Feil, editors, Bacterial Population Genetics in Infectious Disease, pp. 37–60, John Wiley & Sons, Inc., 2010.
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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 in Microbiology, 18(7):315–322, 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 Genetics, 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. Journal of Bacteriology, 192(24):6465–76, 2010.
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2009

X Didelot, M Barker, D Falush, and F Priest. Evolution of Pathogenicity in the Bacillus Cereus Group. Systematic and Applied Microbiology, 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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X Didelot, R Urwin, M Maiden, and D Falush. Genealogical Typing of Neisseria Meningitidis. Microbiology, 155:3176–86, 2009.
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M Vos and X Didelot. A Comparison of Homologous Recombination Rates in Bacteria and Archaea. ISME Journal, 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, Horizontal Gene Transfer in the Evolution of Pathogenesis, pp. 23–46, Cambridge University Press, 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 Processes and Related Topics, 4:315–324, 2008.
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X Didelot, A Darling, and D Falush. Inferring Genomic Flux in Bacteria. Genome Research, 19(2):306–317, 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 Evolutionary Biology, 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 Research, 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. Philosophical Transactions of the Royal Society B, 361(1475):2045–53, 2006.
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