Nair S, Barker CR, Bird M, Greig DR, Collins C, Painset A, Chattaway M, Pickard D, Larkin L, Gharbia S, Didelot X, Ribeca P (2024).“Presence of Phage-Plasmids in Multiple Serovars of Salmonella Enterica.”bioRxiv, 10.1101/2024.02.02.574330.doi:10.1101/2024.02.02.574330.
Gill A, Koskela J, Didelot X, Everitt RG (2024).“Bayesian Inference of Reproduction Number from Epidemiological and Genetic Data Using Particle MCMC.”arXiv, 10.48550/arXiv.2311.09838.doi:10.48550/arXiv.2311.09838.
Hoefer A, Seth-Smith H, Palma F, Schindler S, Freschi L, Dangel A, Berger A, D’Aeth J, Indra A, Fry NK, Palm D, Sing A, Brisse S, Egli A, the 2022 European diphtheria Consortium (2024).“Phenotypic and Genomic Analysis of a Large-Scale Corynebacterium Diphtheriae Outbreak among Migrant Populations in Europe.”medRxiv, 10.1101/2023.11.10.23297228.doi:10.1101/2023.11.10.23297228.
Karah N, Faille N, Grenier F, Abou-Fayad A, Higgins PG, Al-Hassan L, Evans BA, Poirel L, Bonnin R, Hammerum AM, Hansen F, Rafei R, Hamze M, Didelot X, Castillo-Ram'irez S, Lévesque S, Rodrigue S, Uhlin BE, Haraoui L (2024).“Emergence of Acinetobacter Baumannii International Clone 10 Predominantly Found in the Middle East.”bioRxiv, 10.1101/2023.10.09.561570.doi:10.1101/2023.10.09.561570.
Helekal D, Koskela J, Didelot X (2024).“Inference of Multiple Mergers While Dating a Pathogen Phylogeny.”bioRxiv, 2023.09.12.557403.doi:10.1101/2023.09.12.557403.
Osnes MN, Brynildsrud OB, Alfsnes K, Van Dorp L, McKeand SA, Ross J, Town K, DeKorne-Elenbaas J, Van Dam A, Bruisten S, De Blasio BF, Caugant DA, Grad YH, Williamson DA, Balloux F, Didelot X, Eldholm V (2024).“The Inter-Continental Population Dynamics of Neisseria Gonorrhoeae.”bioRxiv, 2023.08.02.551601.doi:10.1101/2023.08.02.551601.
Moore MP, Laager M, Ribeca P, Didelot X (2024).“KmerAperture: Retaining k -Mer Synteny for Alignment-Free Estimation of within-Lineage Core and Accessory Differences.”bioRxiv, 2022.10.12.511870.doi:10.1101/2022.10.12.511870.
Didelot X, Ribeca P (2024).“KPop : An Assembly-Free and Scalable Method for the Comparative Analysis of Microbial Genomes.”bioRxiv, 2022.06.22.497172.doi:10.1101/2022.06.22.497172.
Taylor AJ, Yahara K, Pascoe B, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss S, Williams NJ, Van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ, Sheppard SK (2024).“A Two-Hit Epistasis Model Prevents Core Genome Disharmony in Recombining Bacteria.”bioRxiv, 2021.03.15.435406.doi:10.1101/2021.03.15.435406.
Carson J, Keeling M, Wyllie D, Ribeca P, Didelot X (2024).“Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes per Host.”Molecular Biology and Evolution, 41, msad288.doi:10.1093/molbev/msad288.
Fotopoulou ET, Jenkins C, Barker CR, Painset A, Didelot X, Simbo A, Douglas A, Godbole G, Jorgensen F, Gharbia S, McLauchlin J (2024).“Genomic Epidemiology of the Clinically Dominant Clonal Complex 1 in the Listeria Monocytogenes Population in the UK.”Microbial Genomics, 10(1).doi:10.1099/mgen.0.001155.
Wan Y, Myall AC, Boonyasiri A, Bolt F, Ledda A, Mookerjee S, Weiße AY, Getino M, Turton JF, Abbas H, Prakapaite R, Sabnis A, Abdolrasouli A, Malpartida-Cardenas K, Miglietta L, Donaldson H, Gilchrist M, Hopkins KL, Ellington MJ, Otter JA, Larrouy-Maumus G, Edwards AM, Rodriguez-Manzano J, Didelot X, Barahona M, Holmes AH, Jauneikaite E, Davies F (2024).“Integrated Analysis of Patient Networks and Plasmid Genomes Reveals a Regional, Multi-Species Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and Mcr-9 Genes.”The Journal of Infectious Diseases, jiae019.doi:10.1093/infdis/jiae019.
Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O’Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, vanDorp L (2024).“Detection of a Historic Reservoir of Bedaquiline/Clofazimine Resistance-Associated Variants in Mycobacterium Tuberculosis.”Genome Medicine, 16(1), 34.doi:10.1186/s13073-024-01289-5.
Didelot X, Helekal D, Kendall M, Ribeca P (2023).“Distinguishing Imported Cases from Locally Acquired Cases within a Geographically Limited Genomic Sample of an Infectious Disease.”Bioinformatics, 23, btac761.doi:10.1093/bioinformatics/btac761.
Didelot X, Franceschi V, Frost SDW, Dennis A, Volz EM (2023).“Model Design for Non-Parametric Phylodynamic Inference and Applications to Pathogen Surveillance.”Virus Evolution, 9, vead028.doi:10.1093/ve/vead028.
Didelot X (2023).“Phylogenetic Analysis of Bacterial Pathogen Genomes.”In Nordenfelt P, Collin M (eds.), Bacterial Pathogenesis: Methods and Protocols, 87–99.Springer US, New York, NY.ISBN 978-1-07-163243-7, doi:10.1007/978-1-0716-3243-7_6.
Helekal D, Keeling M, Grad YH, Didelot X (2023).“Estimating the Fitness Cost and Benefit of Antimicrobial Resistance from Pathogen Genomic Data.”Journal of The Royal Society Interface, 20, 20230074.doi:10.1098/rsif.2023.0074.
Kendall M, Tsallis D, Wymant C, Di Francia A, Balogun Y, Didelot X, Ferretti L, Fraser C (2023).“Epidemiological Impacts of the NHS COVID-19 App in England and Wales throughout Its First Year.”Nat Commun, 14, 858.doi:10.1038/s41467-023-36495-z.
Mughal SR, Niazi SA, Do T, Gilbert SC, Didelot X, Radford DR, Beighton D (2023).“Genomic Diversity among Actinomyces Naeslundii Strains and Closely Related Species.”Microorganisms, 11, 254.doi:10.3390/microorganisms11020254.
Abdel-Glil MY, Hotzel H, Tomaso H, Didelot X, Brandt C, Seyboldt C, Linde J, Schwarz S, Neubauer H, El-Adawy H (2023).“Genomic Epidemiology of Campylobacter Fetus Subsp. Venerealis from Germany.”Front. Vet. Sci., 9, 1069062.doi:10.3389/fvets.2022.1069062.
Dingle KE, Freeman J, Didelot X, Quan TP, Eyre DW, Swann J, Spittal WD, Clark EV, Jolley KA, Walker AS, Wilcox MH, Crook DW (2023).“Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides Difficile.”mBio, e00243-23.doi:10.1128/mbio.00243-23.
Gomez LRE, Savin C, Andrianaivoarimanana V, Randriantseheno LN, Zhou Z, Kocher A, Didelot X, Rajerison M, Kühnert D (2023).“Phylogenetic Analysis of the Origin and Spread of Plague in Madagascar.”PLoS Neglected Tropical Diseases, 17(5), e0010362.doi:10.1371/journal.pntd.0010362.
Medina-Aguayo FJ, Didelot X, Everitt RG (2023).“Speeding up Inference of Homologous Recombination in Bacteria.”Bayesian Anal., -1(-1).doi:10.1214/23-BA1388.
Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL (2023).“Analysis of Escherichia Coli O157 Strains in Cattle and Humans between Scotland and England & Wales: Implications for Human Health.”Microbial Genomics, 9, 001090.doi:10.1099/mgen.0.001090.
Torres Ortiz A, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L (2023).“Within-Host Diversity Improves Phylogenetic and Transmission Reconstruction of SARS-CoV-2 Outbreaks.”eLife, 12, e84384.doi:10.7554/eLife.84384.
Yenew B, Ghodousi A, Diriba G, Tesfaye E, Cabibbe AM, Amare M, Moga S, Alemu A, Dagne B, Sinshaw W, Mollalign H, Meaza A, Tadesse M, Gamtesa DF, Abebaw Y, Seid G, Zerihun B, Getu M, Chiacchiaretta M, Gaudin C, Marceau M, Didelot X, Tolera G, Abdella S, Kebede A, Getahun M, Mehammed Z, Supply P, Cirillo DM (2023).“A Smooth Tubercle Bacillus from Ethiopia Phylogenetically Close to the Mycobacterium Tuberculosis Complex.”Nat Commun, 14(1), 7519.doi:10.1038/s41467-023-42755-9.
Thorell K, Muñoz-Ram'irez ZY, Wang D, Sandoval-Motta S, Boscolo Agostini R, Ghirotto S, Torres RC, HpGP Research Network, Romero-Gallo J, Krishna U, Peek RM, Piazuelo MB, Raaf N, Bentolila F, Aftab H, Akada J, Matsumoto T, Haesebrouck F, Colanzi RP, Bartelli TF, Nunes DN, Pelosof A, Sztokfisz CZ, Dias-Neto E, Assumpção PP, Tishkov I, Mabeku LBK, Goodman KJ, Geary J, Cromarty TJ, Price NL, Quilty D, Corvalan AH, Serrano CA, Gonzalez R, Riquelme A, Garc'ia-Cancino A, Parra-Sepúlveda C, Bernal G, Castillo F, Goldstein AM, Hu N, Taylor PR, Bravo MM, Pazos A, Bravo LE, Wilson KT, Fox JG, Ram'irez-Mayorga V, Molina-Castro S, Durán-Bermúdez S, Campos-Núñez C, Chaves-Cervantes M, Tshibangu-Kabamba E, Tumba GD, Tshimpi-Wola A, DeJesusNgoma-Kisoko P, Ngoyi DM, Cruz M, Hosking C, Abreu JJ, Varon C, Benejat L, Secka O, Link A, Malfertheiner P, Adinortey MB, Bockarie AS, Adinortey CA, Ofori EG, Sgouras DN, Martinez-Gonzalez B, Michopoulos S, Georgopoulos S, Hernandez E, Tacatic BV, Aguilar M, Dominguez RL, Morgan DR, Harðardóttir H, Gunnarsdóttir AI, Guðjónsson H, Jónasson JG, Björnsson ES, Ballal M, Shetty V, Miftahussurur M, Sugihartono T, Alfaray RI, Waskito LA, Fauzia KA, Syam AF, Maulahela H, Malekzadeh R, Sotoudeh M, Peretz A, Azrad M, On A, De Re V, Zanussi S, Cannizzaro R, Canzonieri V, Shimura T, Tokunaga K, Osaki T, Kamiya S, Jadallah K, Matalka I, Igissinov N, Moldobaeva MS, Rakhat A, Choi IJ, Kim JG, Kim N, Song M, Leja M, Vangravs R, Š, Rudz=ite D, R=udule A, Vanags A, Kikuste I, Kupcinskas J, Skieceviciene J, Jonaitis L, Kiudelis G, Jonaitis P, Kiudelis V, Varkalaite G, Vadivelu J, Loke MF, Vellasamy KM, Herrera-Goepfert R, Alonso-Larraga JO, Yee TT, Htet K, Matsuhisa T, Shrestha PK, Ansari S, Abiodun O, Jemilohun C, Akande KO, Olu-Abiodun O, Magaji FA, Omotoso A, Osuagwu CC, Okonkwo U, Owoseni OO, Castaneda C, Castillo M, Velapatino B, Gilman RH, Krzyżek P, Gościniak G, Pawełka D, Korona-Glowniak I, Cichoz-Lach H, Oleastro M, Figueiredo C, Machado JC, Ferreira RM, Bordin DS, Livzan MA, Tsukanov VV, Tan P, Yeoh KG, Zhu F, Ally R, Haas R, Montes M, Fernández-Reyes M, Tamayo E, Lizasoain J, Bujanda L, Lario S, Ram'irez-Lázaro MJ, Calvet X, Brunet-Mas E, Domper-Arnal MJ, Garc'ia-Mateo S, Abad-Baroja D, Delgado-Guillena P, Moreira L, Botargues J, Pérez-Mart'inez I, Barreiro-Alonso E, Flores V, Gisbert JP, Muro EA, Linares P, Martin V, Alcoba L, Fleitas-Kanonnikoff T, Altayeb HN, Engstrand L, Enroth H, Keller PM, Wagner K, Pohl D, Lee Y, Liou J, Wu M, Kocazeybek B, Sarıbas S, Tasçı İ, Demiryas S, Kepil N, Quiel L, Villagra M, Norton M, Johnson D, Huang RJ, Hwang JH, Szymczak W, Rajagopalan S, Asare E, Jacobs WR, In H, Bollag R, Lopez A, Kruse EJ, White J, Graham DY, Lane C, Gao Y, Fields PI, Gold BD, Cruz-Correa M, González-Pons M, Rodriguez LM, Tuan VP, Dung HDQ, Binh TT, Trang TTH, Van Khien V, Chen X, Raley C, Kessing B, Zhao Y, Tran B, Gutiérrez-Escobar AJ, Wan Y, Hicks B, Zhu B, Yu K, Zhu B, Yeager M, Hutchinson A, Teshome K, Jones K, Luo W, Jehanne Q, Katsura Y, Gonzalez-Hormazabal P, Didelot X, Sheppard S, Tarazona-Santos E, Mariño-Ram'irez L, Loh JT, Backert S, Naumann M, Abnet CC, Smet A, Berg DE, Chiner-Oms Á, Comas I, Mart'inez-Mart'inez FJ, Zamudio R, Lehours P, Megraud F, Yahara K, Blaser MJ, Vincze T, Morgan RD, Roberts RJ, Chanock SJ, Dekker JP, Torres J, Cover TL, Noureen M, Fischer W, Vale FF, Cherry JL, Osada N, Fukuyo M, Arita M, Yamaoka Y, Kobayashi I, Uchiyama I, Falush D, Camargo MC, Rabkin CS (2023).“The Helicobacter Pylori Genome Project: Insights into H. Pylori Population Structure from Analysis of a Worldwide Collection of Complete Genomes.”Nat Commun, 14(1), 8184.doi:10.1038/s41467-023-43562-y.
Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, ČernáBolf'iková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, deLencastre H, Cercenado E, Garc'ia-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR (2022).“Emergence of Methicillin Resistance Predates the Clinical Use of Antibiotics.”Nature, 602, 135–141.doi:10.1038/s41586-021-04265-w.
Wang L, Didelot X, Bi Y, Gao GF (2022).“SARS-CoV-2 Transmissibility Compared between Variants of Concern and Vaccination Status.”Briefings in Bioinformatics, 23(2), 1–12.doi:10.1093/bib/bbab594.
Fountain-Jones NM, Kraberger S, Gagne RB, Gilbertson MLJ, Trumbo DR, Charleston M, Salerno PE, Chris Funk W, Crooks K, Logan K, Alldredge M, Dellicour S, Baele G, Didelot X, VandeWoude S, Carver S, Craft ME (2022).“Hunting Alters Viral Transmission and Evolution in a Large Carnivore.”Nature Ecology & Evolution, 6, 174–182.doi:10.1038/s41559-021-01635-5.
Ledda A, Cummins M, Shaw LP, Jauneikaite E, Cole K, Lasalle F, Barry D, Turton J, Rosmarin C, Anaraki S, Wareham D, Stoesser N, Paul J, Manuel R, Cherian BP, Didelot X (2022).“Hospital Outbreak of Carbapenem-Resistant Enterobacterales Associated with a blaOXA-48 Plasmid Carried Mostly by Escherichia Coli ST399.”Microbial Genomics, 8(4), 1–11.doi:10.1099/mgen.0.000675.
Whittles LK, Didelot X, White PJ (2022).“Public Health Impact and Cost-Effectiveness of Gonorrhoea Vaccination: An Integrated Transmission-Dynamic Health-Economic Modelling Analysis.”Lancet Infectious Diseases, 22, 1030–1041.doi:10.1016/s1473-3099(21)00744-1.
Carson J, Ledda A, Ferretti L, Keeling M, Didelot X (2022).“The Bounded Coalescent Model: Conditioning a Genealogy on a Minimum Root Date.”Journal of Theoretical Biology, 548, 111186.doi:10.1016/j.jtbi.2022.111186.
Volk D, Yang-Turner F, Didelot X, Crook DW, Wyllie D (2022).“Catwalk: Identifying Closely Related Sequences in Large Microbial Sequence Databases.”Microbial Genomics, 8(6), 1–6.doi:10.1099/mgen.0.000850.
Willgert K, Didelot X, Surendran-Nair M, Kuchipudi SV, Ruden RM, Yon M, Nissly RH, Vandegrift KJ, Nelli RK, Li L, Jayarao BM, Levine N, Olsen RJ, Davis JJ, Musser JM, Hudson PJ, Kapur V, Conlan AJK (2022).“Transmission History of SARS-CoV-2 in Humans and White-Tailed Deer.”Scientific Reports, 12(1), 12094.doi:10.1038/s41598-022-16071-z.
Didelot X, Evans CM (2022).“London Parochial Burial Records from 1563 to 1665 Indicate Higher Plague Death Rates for Males than Females: Some Possible Demographic and Social Explanations.”PLoS One, 17(8), e0272278.doi:10.1371/journal.pone.0272278.
Didelot X, Parkhill J (2022).“A Scalable Analytical Approach from Bacterial Genomes to Epidemiology.”Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1861), 20210246.doi:10.1098/rstb.2021.0246.
Didelot X, Siveroni I, Volz EM (2021).“Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies.”Molecular Biology and Evolution, 38, 307–317.doi:10.1093/molbev/msaa193.
Didelot X, Kendall M, Xu Y, White PJ, McCarthy N (2021).“Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo.”Current Protocols, 1, e60.doi:10.1002/cpz1.60.
Didelot X (2021).“Phylogenetic Methods for Genome-Wide Association Studies in Bacteria.”In Bacterial Pangenomics: Methods and Protocols, volume 2242, 205–220.Springer Nature.ISBN 978-1-07-161099-2, doi:10.1007/978-1-0716-1099-2_13.
Lassalle F, Dastgheib SMM, Zhao F, Zhang J, Verbarg S, Fruhling A, Brinkmann H, Osborne TH, Sikorski J, Balloux F, Didelot X, Santini JM, Petersen J (2021).“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.doi:10.1016/j.syapm.2020.126165.
Wang L, Didelot X, Bi Y, Gao GF (2021).“Assessing the Extent of Community Spread Caused by Mink-Derived SARS-CoV-2 Variants.”The Innovation, 2(3), 100128.doi:10.1016/j.xinn.2021.100128.
Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV (2021).“Major Genetic Discontinuity and Novel Toxigenic Species in Clostridioides Difficile Taxonomy.”eLife, 10, e64325.doi:10.7554/eLife.64325.
Helekal D, Ledda A, Volz E, Wyllie D, Didelot X (2021).“Bayesian Inference of Clonal Expansions in a Dated Phylogeny.”Systematic Biology, syab095.doi:10.1093/sysbio/syab095.
Torres Ortiz A, Coronel J, Vidal JR, Bonilla C, Moore DAJ, Gilman RH, Balloux F, Kon OM, Didelot X, Grandjean L (2021).“Genomic Signatures of Pre-Resistance in Mycobacterium Tuberculosis.”Nature Communications, 12(1), 7312.doi:10.1038/s41467-021-27616-7.
Yang C, Cui Y, Didelot X, Yang R, Falush D (2021).“Why Panmictic Bacteria Are Rare.”bioRxiv, 385336.doi:10.1101/385336.
Lassalle F, Veber P, Jauneikaite E, Didelot X (2021).“Automated Reconstruction of All Gene Histories in Large Bacterial Pangenome Datasets and Search for Co-Evolved Gene Modules with Pantagruel.”bioRxiv, 586495.doi:10.1101/586495.
Whittles LK, White PJ, Didelot X (2020).“Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics.”Clinical Infectious Diseases, 71, 1912–1919.doi:10.1093/cid/ciz1241.
Volz EM, Wiuf C, Grad YH, Frost SDW, Dennis AM, Didelot X (2020).“Identification of Hidden Population Structure in Time-Scaled Phylogenies.”Systematic Biology, 69, 884–896.doi:10.1093/sysbio/syaa009.
Wang H, Yang C, Sun Z, Zheng W, Zhang W, Yu H, Wu Y, Didelot X, Yang R, Pan J, Cui Y (2020).“Genomic Epidemiology of Vibrio Cholerae Reveals the Regional and Global Spread of Two Epidemic Non-Toxigenic Lineages.”PLoS Neglected Tropical Diseases, 14(2), e0008046.doi:10.1371/journal.pntd.0008046.
Lassalle F, Didelot X (2020).“Bacterial Microevolution and the Pangenome.”In The Pangenome, Diversity, Dynamics and Evolution of Genomes, 129–149.Springer.ISBN 978-3-030-38281-0, doi:10.1007/978-3-030-38281-0_6.
Rodriguez MJ, Moser N, Malpartida CK, Moniri A, Fisarova L, Pennisi I, Boonyasiri A, Jauneikaite E, Abdolrasouli A, Otter J, Bolt F, Davies F, Didelot X, Holmes A, Georgiou P (2020).“Rapid Detection of Mobilized Colistin Resistance Using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System.”Scientific Reports, 10, 8448.doi:10.1038/s41598-020-64612-1.
Wang L, Didelot X, Yang J, Wong G, Shi Y, Liu W, Gao GF, Bi Y (2020).“Inference of Person-to-Person Transmission of COVID-19 Reveals Hidden Super-Spreading Events during the Early Outbreak Phase.”Nature Communications, 11, 5006.doi:10.1038/s41467-020-18836-4.
Janezic S, Dingle K, Alvin J, Accetto T, Didelot X, Crook DW, Lacy DB, Rupnik M (2020).“Comparative Genomics of Clostridioides Difficile Toxinotypes Identifies Module-Based Toxin Gene Evolution.”Microbial Genomics, 10.1099/mgen.0.000449.doi:10.1099/mgen.0.000449.
Vegvari C, Grad YH, White PJ, Didelot X, Whittles LK, Scangarella-oman NE, Mitrani-gold FS, Dumont E, Perry CR, Gilchrist K, Hossain M, Mortimer TD, Anderson RM, Gardiner D (2020).“Using Rapid Point-of-Care Tests to Inform Antibiotic Choice to Mitigate Drug Resistance in Gonorrhoea.”Euro Surveillance, 25, 1900210.doi:10.2807/1560-7917.ES.2020.25.43.1900210.
Fountain-Jones NM, Appaw RC, Carver S, Didelot X, Volz E, Charleston M (2020).“Emerging Phylogenetic Structure of the SARS-CoV-2 Pandemic.”Virus Evolution, 6, veaa082.doi:10.1093/ve/veaa082.
Osnes MN, Didelot X, deKorne-Elenbaas J, Alfsnes K, Brynildsrud OB, Syversen G, Nilsen ØJ, De Blasio BF, Caugant DA, Eldholm V (2020).“Sudden Emergence of a Neisseria Gonorrhoeae Clade with Reduced Susceptibility to Extended-Spectrum Cephalosporins, Norway.”Microbial Genomics, 10.1099/mgen.0.000480.doi:10.1099/mgen.0.000480.
Hennart M, Panunzi L, Rodrigues C, Gaday Q, Baines S, Barros-Pinkelnig M, Carmi-Leroy A, Dazas M, Wehenkel A, Didelot X, Toubiana J, Badell E, Brisse S (2020).“Population Genomics and Antimicrobial Resistance in Corynebacterium Diphtheriae.”Genome Medicine, 12, 107.doi:10.1101/2020.05.19.101030.
Whittles LK, White PJ, Didelot X (2019).“A Dynamic Power-Law Sexual Network Model of Gonorrhoea Outbreaks.”PLoS Computational Biology, 15(3), e1006748.doi:10.1371/journal.pcbi.1006748.
Didelot X (2019).“Computational Methods in Microbial Population Genomics.”In Polz MF, Rajora OP (eds.), Population Genomics: Microorganisms, 3–29.Springer International Publishing.doi:10.1007/13836_2017_3.
Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Marwick CA, Coia J, Brown D, Buchanan S, Ijaz UZ, Goswami C, Douce G, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Crook DW (2019).“A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium Difficile PCR Ribotype 078.”mBio, 10(2), e02790-18.doi:10.1128/mBio.02790-18.
vanDorp L, Wang Q, Shaw LP, Acman M, Brynildsrud OB, Eldholm V, Wang R, Gao H, Yin Y, Chen H, Ding C, Farrer RA, Didelot X, Balloux F, Wang H (2019).“Rapid Phenotypic Evolution in Multidrug-Resistant Klebsiella Pneumoniae Hospital Outbreak Strains.”Microbial Genomics, 5, 10.1099/mgen.0.000263.doi:10.1099/mgen.0.000263.
Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TE, Walker AS, Wilcox MH, Dingle KE (2019).“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.doi:10.1016/j.ebiom.2019.04.038.
Moniri A, Rodriguez-Manzano J, Malpartida-Cardenas K, Yu L, Didelot X, Holmes A, Georgiou P (2019).“Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves.”Analytical Chemistry, 91, 7426–7434.doi:10.1021/acs.analchem.9b01466.
Ailloud F, Didelot X, Woltemate S, Pfaffinger G, Overmann J, Bader RC, Schulz C, Malfertheiner P, Suerbaum S (2019).“Within-Host Evolution of Helicobacter Pylori Shaped by Niche-Specific Adaptation, Intragastric Migrations and Selective Sweeps.”Nature Communications, 10(1), 2273.doi:10.1038/s41467-019-10050-1.
Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR (2019).“The Population Structure of Pseudomonas Aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages.”Genome Biology and Evolution, 11, 1780–1796.doi:10.1093/gbe/evz119.
Didelot X, Pouwels KB (2019).“Machine-Learning-Assisted Selection of Antibiotic Prescription.”Nature Medicine, 25, 1033–1034.doi:10.1038/s41591-019-0517-0.
Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill F, Falush D, Brisse S (2019).“The Speciation and Hybridization History of the Genus Salmonella.”Microbial Genomics, 5, 10.1099/mgen.0.000284.doi:10.1099/mgen.0.000284.
Zhao L, Chen H, Didelot X, Li Z, Li Y, Chen M, Du Y, Zhao H, Li J, Hu Q, Kan B, Chen M, Pang B (2019).“Co-Existence of Multiple Distinct Lineages in Vibrio Parahaemolyticus Serotype O4:K12.”Microbial Genomics, 5, 10.1099/mgen.0.000287.doi:10.1099/mgen.0.000287.
Klinkenberg D, Colijn C, Didelot X (2019).“Methods for Outbreaks Using Genomic Data.”In Handbook of Infectious Disease Data Analysis, 245–263.CRC Press.doi:10.1201/9781315222912.
Didelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ (2018).“Bayesian Inference of Ancestral Dates on Bacterial Phylogenetic Trees.”Nucleic Acids Research, 46(22), e134-e134.doi:10.1093/nar/gky783.
Collins C, Didelot X (2018).“A Phylogenetic Method to Perform Genome-Wide Association Studies in Microbes That Accounts for Population Structure and Recombination.”PLoS Computational Biology, 14(2), e1005958.doi:10.1371/journal.pcbi.1005958.
Volz EM, Didelot X (2018).“Modeling the Growth and Decline of Pathogen Effective Population Size Provides Insight into Epidemic Dynamics and Drivers of Antimicrobial Resistance.”Systematic Biology, 67(4), 719–728.doi:10.1093/sysbio/syy007.
Challagundla L, Luo X, Tickler IA, Didelot X, Coleman DC, Shore AC, Coombs GW, Sordelli DO, Brown EL, Skov R, Larsen R, Reyes J, Robledo IE, Vazquez GJ, Rivera R, Fey PD, Stevenson K, Wang S, Kreiswirth BN, Mediavilla JR, Arias CA, Planet PJ, Nolan RL, Tenover FC, Goering RV, Robinson DA (2018).“Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus Aureus.”mBio, 9(1), e02016-17.doi:10.1128/mBio.02016-17.
Peters J, Cresswell F, Amor L, Cole K, Dean G, Didelot X, De Silva D, Eyre DW, Paul J (2018).“Whole Genome Sequencing of Neisseria Gonorrhoeae Reveals Transmission Clusters Involving Patients of Mixed HIV Serostatus.”Sexually Transmitted Infections, 94, 138–143.doi:10.1136/sextrans-2017-053198.
Wang R, Van Dorp L, Shaw LP, Bradley P, Wang Q, Wang X, Jin L, Zhang Q, Liu Y, Rieux A, Dorai-Schneiders T, Weinert LA, Iqbal Z, Didelot X, Wang H, Balloux F (2018).“The Global Distribution and Spread of the Mobilized Colistin Resistance Gene Mcr-1.”Nature Communications, 9(1), 1179.doi:10.1038/s41467-018-03205-z.
Whittles LK, Didelot X, Grad YH, White PJ (2018).“Testing for Gonorrhoea Should Routinely Include the Pharynx.”Lancet Infectious Diseases, 18(7), 716–717.doi:10.1016/S1473-3099(18)30341-4.
Whittles LK, White PJ, Paul J, Didelot X (2018).“Epidemiological Trends of Antibiotic Resistant Gonorrhea in the United Kingdom.”Antibiotics, 7(3), 60.doi:10.3390/antibiotics7030060.
Séraphin MN, Didelot X, Nolan DJ, May JR, Khan MSR, Murray ER, Salemi M, Morris JG, Lauzardo M (2018).“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.doi:10.4269/ajtmh.17-0700.
Yahara K, Nakayama S, Shimuta K, Lee K, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M (2018).“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.doi:10.1099/mgen.0.000205.
Campbell F, Didelot X, Fitzjohn R, Ferguson NM, Cori A, Jombart T (2018).“Outbreaker2: A Modular Platform for Outbreak Reconstruction.”BMC Bioinformatics, 19, 363.doi:10.1186/s12859-018-2330-z.
Pandey A, Cleary DW, Laver JR, Gorringe A, Deasy AM, Dale AP, Morris PD, Didelot X, Maiden MCJ, Read RC (2018).“Microevolution of Neisseria Lactamica during Nasopharyngeal Colonisation Induced by Controlled Human Infection.”Nature Communications, 9(1), 4753.doi:10.1038/s41467-018-07235-5.
Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, deLencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK (2018).“Disease-Associated Genotypes of the Commensal Skin Bacterium Staphylococcus Epidermidis.”Nature Communications, 9(1), 5034.doi:10.1038/s41467-018-07368-7.
Didelot X, Fraser C, Gardy J, Colijn C (2017).“Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.”Molecular Biology and Evolution, 34, 997–1007.doi:10.1093/molbev/msw275.
Didelot X, Whittles LK, Hall I (2017).“Model-Based Analysis of an Outbreak of Bubonic Plague in Cairo in 1801.”Journal of The Royal Society Interface, 14(131), 20170160.doi:10.1098/rsif.2017.0160.
Ledda A, Price JR, Cole K, Llewelyn MJ, Kearns AM, Crook DW, Paul J, Didelot X (2017).“Re-Emergence of Methicillin Susceptibility in a Resistant Lineage of Staphylococcus Aureus.”Journal Of Antimicrobial Chemotherapy, 72, 1285–1288.doi:10.1093/jac/dkw570.
Collins C, Didelot X (2017).“Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes.”In Bacterial Pathogenesis: Methods and Protocols, volume 1535, 109–137.Springer, Clifton, N.J..doi:10.1007/978-1-4939-6673-8_8, 27914076.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain M, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon A, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C, on behalf of the PANGEA-HIV consortium (2017).“Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.”Molecular Biology and Evolution, 34, 185–203.doi:10.1093/molbev/msw217.
Yahara K, Méric G, Taylor AJ, deVries SP, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley AM, Komukai S, Wimalarathna H, Cody AJ, Colles FM, McCarthy ND, Harris D, Bray JE, Jolley KA, Maiden MC, Bentley SD, Parkhill J, Bayliss CD, Grant AJ, Maskell D, Didelot X, Kelly DJ, Sheppard SK (2017).“Genome-Wide Association of Functional Traits Linked with Campylobacter Jejuni Survival from Farm to Fork.”Environmental Microbiology, 19, 361–380.doi:10.7287/PEERJ.PREPRINTS.2300V1.
Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Golubchik T, Harding RM, Wilson DJ, Griffiths D, Vaughan A, Finney JM, Wyllie DH, Oakley SJ, Fawley WN, Freeman J, Morris K, Martin J, Howard P, Gorbach S, Goldstein EJC, Citron DM, Hopkins S, Hope R, Johnson AP, Wilcox MH, Peto TEA, Walker AS, Crook DW, Del Ojo Elias C, Crichton C, Kostiou V, Giess A, Davies J (2017).“Effects of Control Interventions on Clostridium Difficile Infection in England: An Observational Study.”Lancet Infectious Diseases, 17(4), 411–421.doi:10.1016/S1473-3099(16)30514-X.
Yang S, Hemarajata P, Hindler J, Li F, Adisetiyo H, Aldrovandi G, Sebra R, Kasarskis A, MacCannell D, Didelot X, Russell D, Rubin Z, Humphries R (2017).“Evolution and Transmission of Carbapenem-Resistant Klebsiella Pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography.”Clinical Infectious Diseases, 64, 894–901.doi:10.1093/cid/ciw876.
Eyre DW, Dingle KE, Didelot X, Quan TP, Peto TEA, Wilcox MH, Walker AS, Crook DW (2017).“Clostridium Difficile in England: Can We Stop Washing Our Hands? – Authors’ Reply.”Lancet Infectious Diseases, 17(5), 478–479.doi:10.1016/S1473-3099(17)30185-8.
Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MDM, Sproston ELE, Carrillo CDC, Taboada EEN, Cooper KKK, Huynh S, Cody AAJ, Jolley KAK, Maiden MMC, McCarthy NND, Didelot X, Parker CC, Sheppard SKS, Meric G, Yahara K, Wimaralathna H, Murray S, Hitchings MDM, Sproston ELE, Carrillo CDC, Taboada EEN, Cooper KKK, Huynh S, Cody AAJ, Jolley KAK, Maiden MMC, McCarthy NND, Didelot X, Parker CC, Sheppard SKS (2017).“Local Genes for Local Bacteria: Evidence of Allopatry in the Genomes of Transatlantic Campylobacter Populations.”Molecular Ecology, 26(17), 4497–4508.doi:10.1111/mec.14176.
Klinkenberg D, Backer JA, Didelot X, Colijn C, Wallinga J (2017).“Simultaneous Inference of Phylogenetic and Transmission Trees in Infectious Disease Outbreaks.”PLoS Computational Biology, 13(5), e1005495.doi:10.1371/journal.pcbi.1005495.
Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C (2017).“Pneumococcal Capsule Synthesis Locus Cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.”Molecular Biology and Evolution, 34(10), 2537–2554.doi:10.1093/molbev/msx173.
Rosner BM, Schielke A, Didelot X, Kops F, Breidenbach J, Willrich N, Gölz G, Alter T, Stingl K, Josenhans C, Suerbaum S, Stark K (2017).“A Combined Case-Control and Molecular Source Attribution Study of Human Campylobacter Infections in Germany, 2011–2014.”Scientific Reports, 7(1), 5139.doi:10.1038/s41598-017-05227-x.
Peacock S, Barnes E, Breuer J, Carroll M, Crook D, Didelot X, Fife M, Fox A, Greatorex J, Goodfellow I, Kellam P, Kind D, Parkhill J, Walker TM (2017).“Pathogen Genomics.”In Chief Medical Officier Annual Report, 134–153.Department of Health and Social Care.
Pandey AAK, Cleary DWD, Laver JJR, Maiden MCJM, Didelot X, Gorringe A, Read RCR (2017).“Neisseria Lactamica Y92-1009 Complete Genome Sequence.”Standards in Genomic Sciences, 12(1), 41.doi:10.1186/s40793-017-0250-6.
Whittles LK, White PJ, Didelot X (2017).“Estimating the Fitness Benefit and Cost of Cefixime Resistance in Neisseria Gonorrhoeae to Inform Prescription Policy: A Modelling Study.”PLoS Medicine, 14(10), e1002416.doi:10.1371/journal.pmed.1002416.
Didelot X, Walker AS, Peto TE, Crook DW, Wilson DJ (2016).“Within-Host Evolution of Bacterial Pathogens.”Nature Reviews Microbiology, 14, 150–162.doi:10.1038/nrmicro.2015.13.
Didelot X, Dordel J, Whittles LK, Collins C, Bilek N, Bishop CJ, White PJ, Aanensen DM, Parkhill J, Bentley SD, Spratt BG, Harris SR (2016).“Genomic Analysis and Comparison of Two Gonorrhea Outbreaks.”mBio, 7(3), e00525-16.doi:10.1128/mBio.00525-16.
Whittles LK, Didelot X (2016).“Epidemiological Analysis of the Eyam Plague Outbreak of 1665-1666.”Proceedings of the Royal Society B, 283, 20160618.doi:10.1098/rspb.2016.0618.
Bubendorfer S, Krebes J, Yang I, Hage E, Schulz TF, Bahlawane C, Didelot X, Suerbaum S (2016).“Genome-Wide Analysis of Chromosomal Import Patterns after Natural Transformation of Helicobacter Pylori.”Nature Communications, 7, 11995.doi:10.1038/ncomms11995.
Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MCJ, Sheppard SK, Falush D (2016).“The Landscape of Realized Homologous Recombination in Pathogenic Bacteria.”Molecular Biology and Evolution, 33, 456–471.doi:10.1093/molbev/msv237.
Brown T, Didelot X, Wilson DJ, De Maio N (2016).“SimBac: Simulation of Whole Bacterial Genomes with Homologous Recombination.”Microbial Genomics, 2, 10.1099/mgen.0.000044.doi:10.1099/mgen.0.000044.
Stoesser N, Sheppard A, Pankhurst L, deMaio N, Moore CE, Sebra R, Turner P, Anson LW, Kasarskis A, Batty EM, Kos V, Wilson DJ, Phetsouvanh R, Wyllie D, Sokurenko E, Manges AR, Johnson TJ, Price LB, Peto TEA, Johnson JR, Didelot X, Walker AS, Crook DW (2016).“Evolutionary History of the Global Emergence of the Escherichia Coli Epidemic Clone ST131.”mBio, 7(2), e02162-15.doi:10.1128/mBio.02162-15.Invited.
Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ, Vos M (2016).“A Barrier to Homologous Recombination between Sympatric Strains of the Cooperative Soil Bacterium Myxococcus Xanthus.”ISME Journal, 10, 2468–2477.doi:10.1038/ismej.2016.34.
Hatherell H, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, Colijn C, Gardy J (2016).“Declaring a Tuberculosis Outbreak over with Genomic Epidemiology.”Microbial Genomics, 1, 10.1099/mgen.0.000060.doi:10.1099/mgen.0.000060.v1.
De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas DR, Foster K, Waldram A, Wilson DJ, Didelot X, Grad YH, Crook DW, Peto TEA, Walker AS, Paul J, Eyre DW (2016).“Whole-Genome Sequencing to Determine Transmission of Neisseria Gonorrhoeae: An Observational Study.”Lancet Infectious Diseases, 16(11), 1295–1303.doi:10.1016/S1473-3099(16)30157-8.
Ansari MA, Didelot X (2016).“Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree.”Genetics, 204(1), 89–98.doi:10.1534/genetics.116.190496.
Eldholm V, Rieux A, Monteserin J, Lopez JM, Palmero D, Lopez B, Ritacco V, Didelot X, Balloux F (2016).“Impact of HIV Co-Infection on the Evolution and Transmission of Multidrug-Resistant Tuberculosis.”eLife, 5, e16644.doi:10.7554/eLife.16644.
Joseph SJ, Marti H, Didelot X, Read TD, Dean D (2016).“Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia Suis: A Recently Identified Zoonotic Pathogen.”Genome Biology and Evolution, 8, 2613–2623.doi:10.1093/gbe/evw182.
Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D (2016).“Dynamics of Genome Change among Legionella Species.”Scientific Reports, 6, 33442.doi:10.1038/srep33442.
Didelot X (2016).“Heroic Sacrifice or Tragic Mistake? Revisiting the Eyam Plague, 350 Years On.”Significance, 13(5), 20–25.doi:10.1111/j.1740-9713.2016.00961.x.
Didelot X, Wilson DJ (2015).“ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes.”PLoS Computational Biology, 11(2), e1004041.doi:10.1371/journal.pcbi.1004041.
Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B (2015).“The Role of China in the Global Spread of the Current Cholera Pandemic.”PLoS Genetics, 11, e1005072.doi:10.1371/journal.pgen.1005072.
Biek R, Pybus OG, Lloyd-Smith JO, Didelot X (2015).“Measurably Evolving Pathogens in the Genomic Era.”Trends in Ecology & Evolution, 30, 306–313.doi:10.1016/j.tree.2015.03.009.
Croucher NJ, Didelot X (2015).“The Application of Genomics to Tracing Bacterial Pathogen Transmission.”Current Opinion in Microbiology, 23, 62–67.doi:10.1016/j.mib.2014.11.004.
Cao Q, Didelot X, Wu Z, Li ZZ, He L, Li Y, Ni M, You Y, Lin X, Li ZZ, Gong Y, Zheng M, Zhang M, Liu J, Wang W, Bo X, Falush D, Wang S, Zhang J (2015).“Progressive Genomic Convergence of Two Helicobacter Pylori Strains during Mixed Infection of a Patient with Chronic Gastritis.”Gut, 64, 554–61.doi:10.1136/gutjnl-2014-307345, 25007814.
Nandi T, Holden M, Didelot X, Mehershahi K, a. Boddey J, Beacham I, Peak I, Harting J, Baybayan P, Guo Y, Wang S, Lee CH, Sim B, Essex-Lopresti A, Sarkar-Tyson M, Nelson M, Smither S, Ong C, Aw LT, Chua HH, Michell S, Studholme DJ, Titball RW, Chen SL, Parkhill J, Tan P (2015).“Burkholderia Pseudomallei Sequencing Identifies Genomic Clades with Distinct Recombination, Accessory and Epigenetic Profiles.”Genome Research, 25, 129–141.doi:10.1101/gr.177543.114.
Cui Y, Yang X, Didelot X, Guo C, Li D, Yan Y, Zhang Y, Yuan Y, Yang H, Wang J, Wang J, Song Y, Zhou D, Falush D, Yang R (2015).“Epidemic Clones, Oceanic Gene Pools and Eco-LD in the Free Living Marine Pathogen Vibrio Parahaemolyticus.”Molecular Biology and Evolution, 32, 1396–1410.doi:10.1093/molbev/msv009.
Ezewudo MN, Joseph S, Castillo-Ramirez S, Dean D, Rio CD, Didelot X, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD (2015).“Population Structure of Neisseria Gonorrhoeae Based on Whole Genome Data and Its Relationship with Antibiotic Resistance.”PeerJ, 3, e806.doi:10.7717/peerj.806.
Montano V, Didelot X, Foll M, Linz B, Reinhardt R, Suerbaum S, Moodley Y, Jensen JD (2015).“Worldwide Population Structure, Long Term Demography, and Local Adaptation of Helicobacter Pylori.”Genetics, 200, 947–963.doi:10.1534/genetics.115.176404.
Achtman M, Zhou Z, Didelot X (2015).“Formal Comment to Pettengill.”PLoS One, 10(8), e0134435.doi:10.1371/journal.pone.0134435.
Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook DW, Sifri CD (2015).“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.doi:10.1128/AAC.04292-14, 25561339.
Joseph SJ, Marti H, Didelot X, Castillo-Ramirez S, Read TD, Dean D (2015).“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.doi:10.1093/gbe/evv201.
Didelot X, Gardy J, Colijn C (2014).“Bayesian Inference of Infectious Disease Transmission from Whole Genome Sequence Data.”Molecular Biology and Evolution, 31, 1869–1879.doi:10.1093/molbev/msu121.
Ansari MA, Didelot X (2014).“Inference of the Properties of the Recombination Process from Whole Bacterial Genomes.”Genetics, 196, 253–265.doi:10.1534/genetics.113.157172, 24172133.
Dingle KE, Elliott B, Robinson E, Griffiths D, Eyre DW, Stoesser N, Vaughan A, Golubchik T, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Riley TV, Crook DW, Didelot X (2014).“Evolutionary History of the Clostridium Difficile Pathogenicity Locus.”Genome Biology and Evolution, 6, 36–52.doi:10.1093/gbe/evt204.
Haase JK, Didelot X, Lecuit M, Korkeala H, Achtman M (2014).“The Ubiquitous Nature of Listeria Monocytogenes Clones: A Large Scale MultiLocus Sequence Typing Study.”Environmental Microbiology, 16, 405–416.doi:10.1111/1462-2920.12342, 24274459.
Miller R, Price J, Batty E, Didelot X, Wyllie D, Golubchik T, Crook DW, Paul J, Peto TEA, Wilson DJ, Cule M, Ip C, Day N, Moore C, Bowden R, Llewelyn M (2014).“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.doi:10.1016/j.jhin.2013.11.007.
Krause DJ, Didelot X, Cadillo-Quiroz H, Whitaker RJ (2014).“Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain.”Genome Biology and Evolution, 6, 170–178.doi:10.1093/gbe/evu003, 24391154.
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N (2014).“Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data.”PLoS Computational Biology, 10, e1003457.doi:10.1371/journal.pcbi.1003457.
Yahara K, Didelot X, Ansari MA, Sheppard SK, Falush D (2014).“Efficient Inference of Recombination Hot Regions in Bacterial Genomes.”Molecular Biology and Evolution, 31, 1593–605.doi:10.1093/molbev/msu082, 24586045.
O’Brien J, Didelot X, Iqbal Z, Amenga-Etego L, Ahiska B, Falush D (2014).“A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data.”Genetics, 197, 925–937.doi:10.1534/genetics.114.161299.
Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, a. Suchard M, Wallinga J, Ypma R, Ferguson N (2014).“OutbreakTools: A New Platform for Disease Outbreak Analysis Using the R Software.”Epidemics, 7, 28–34.doi:10.1016/j.epidem.2014.04.003.
Everitt RG, Didelot X, Batty EM, Miller RR, Knox K, Young BC, Bowden R, Auton A, Votintseva A, Larner-Svensson H, Charlesworth J, Golubchik T, Ip CLC, Godwin H, Fung R, Peto TEA, Walker AS, Crook DW, Wilson DJ (2014).“Mobile Elements Drive Recombination Hotspots in the Core Genome of Staphylococcus Aureus.”Nature communications, 5, 3956.doi:10.1038/ncomms4956.
Krebes J, Didelot X, Kennemann L, Suerbaum S (2014).“Bidirectional Genomic Exchange between Helicobacter Pylori Strains from a Family in Coventry, United Kingdom.”International Journal of Medical Microbiology, 304, 1135–1146.doi:10.1016/j.ijmm.2014.08.007.
Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TEA, Crook DW, Donnelly P, Thorson S, Amatya P, Joshi S (2014).“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.doi:10.1128/AAC.03900-14, 25267672.
Elliott B, Dingle KE, Didelot X, Crook DW, Riley TV (2014).“The Complexity and Diversity of the Pathogenicity Locus in Clostridium Difficile Clade 5.”Genome Biology and Evolution, 6, 3159–3170.doi:10.1093/gbe/evu248.
Didelot X, Nell S, Yang I, Woltemate S, vanderMerwe S, Suerbaum S (2013).“Genomic Evolution and Transmission of Helicobacter Pylori in Two South African Families.”Proc Natl Acad Sci USA, 110(34), 13880–13885.doi:10.1073/pnas.1304681110.
Didelot X (2013).“Genomic Analysis to Improve the Management of Outbreaks of Bacterial Infection.”Expert Review of Anti-infective Therapy, 11(4), 335–337.doi:10.1586/eri.13.15.
Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MCJ, Parkhill J, Falush D (2013).“Genome-Wide Association Study Identifies Vitamin B5 Biosynthesis as a Host Specificity Factor in Campylobacter.”Proc Natl Acad Sci USA, 110(29), 11923–7.doi:10.5061/dryad.28n35..
Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O’Connor L, Ip CLC, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TEA, Walker AS (2013).“Diverse Sources of C. Difficile Infection Identified on Whole-Genome Sequencing.”New England Journal of Medicine, 369(13), 1195–1205.doi:10.1056/NEJMoa1216064, 24066741.
Price JR, Didelot X, Crook DW, Llewelyn MJ, Paul J (2013).“Whole Genome Sequencing in the Prevention and Control of Staphylococcus Aureus Infection.”Journal of Hospital Infection, 83, 14–21.doi:10.1016/j.jhin.2012.10.003.
Dingle KE, Didelot X, Ansari MA, Eyre DW, Vaughan A, Griffiths D, Ip CLC, Batty EM, Golubchik T, Bowden R, Jolley KA, Hood DW, Fawley WN, Walker AS, Peto TEA, Wilcox MH, Crook DW (2013).“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.doi:10.1093/infdis/jis734.
Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJC, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MCJ, Falush D (2013).“Progressive Genome-Wide Introgression in Agricultural Campylobacter Coli.”Molecular Ecology, 22, 1051–1064.doi:10.1111/mec.12162.
deMuinck EJ, Lagesen K, Afset JE, Didelot X, Rønningen KS, Rudi K, Stenseth NC, Trosvik P (2013).“Comparisons of Infant Escherichia Coli Isolates Link Genomic Profiles with Adaptation to the Ecological Niche.”BMC Genomics, 14, 81.doi:10.1186/1471-2164-14-81, 23384204.
Read TD, Joseph SJ, Didelot X, Liang B, Patel L, Dean D (2013).“Comparative Analysis of Chlamydia Psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range.”mBio, 4(2), e00604-12.doi:10.1128/mBio.00604-12, 23532978.
Golubchik T, Batty EM, Miller RR, Farr H, Young BC, Larner-Svensson H, Fung R, Godwin H, Knox K, Votintseva A, Everitt RG, Street T, Cule M, Ip CLC, Didelot X, aPeto TE, Harding RM, Wilson DJ, Crook DW, Bowden R (2013).“Within-Host Evolution of Staphylococcus Aureus during Asymptomatic Carriage.”PLoS One, 8(5), e61319.doi:10.1371/journal.pone.0061319.
Behrens W, Schweinitzer T, Bal J, Dorsch M, Bleich A, Kops F, Brenneke B, Didelot X, Suerbaum S, Josenhans C (2013).“Role of Energy Sensor TlpD of Helicobacter Pylori in Gerbil Colonization and Genome Analyses after Adaptation in the Gerbil.”Infection and Immunity, 81(10), 3534–3551.doi:10.1128/IAI.00750-13.
Didelot X, Méric G, Falush D, Darling AE (2012).“Impact of Homologous and Non-Homologous Recombination in the Genomic Evolution of Escherichia Coli.”BMC Genomics, 13(1), 256.doi:10.1186/1471-2164-13-256.
Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW (2012).“Transforming Clinical Microbiology with Bacterial Genome Sequencing.”Nature Reviews Genetics, 13, 601–612.doi:10.1038/nrg3226.
Didelot X, Eyre DW, Cule M, Ip CLC, Ansari MA, Griffiths D, Vaughan A, O’Connor L, Golubchik T, Batty EM, Piazza P, Wilson DJ, Bowden R, Donnelly PJ, Dingle KE, Wilcox M, Walker AS, Crook DW, Peto TE, Harding RM (2012).“Microevolutionary Analysis of Clostridium Difficile Genomes to Investigate Transmission.”Genome Biology, 13, R118.doi:10.1186/gb-2012-13-12-r118.
Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling AE, Reno ML, Krause DJ, Whitaker RJ (2012).“Patterns of Gene Flow Define Species of Thermophilic Archaea.”PLoS Biology, 10(2), e1001265.doi:10.1371/journal.pbio.1001265.
Moccia C, Krebes J, Kulick S, Didelot X, Kraft C, Bahlawane C, Suerbaum S (2012).“The Nucleotide Excision Repair (NER) System of Helicobacter Pylori: Role in Mutation Prevention and Chromosomal Import Patterns after Natural Transformation.”BMC Microbiology, 12, 67.doi:10.1186/1471-2180-12-67, 22559785.
Namouchi A, Didelot X, Scho U, Gicquel B, Rocha EPC (2012).“After the Bottleneck: Genome-wide Diversification of the Mycobacterium Tuberculosis Complex by Mutation, Recombination, and Natural Selection.”Genome Research, 22, 721–34.doi:10.1101/gr.129544.111.2002.
Young BC, Golubchik T, Batty EM, Fung R, Larner-Svensson H, Votintseva AA, Miller RR, Godwin H, Knox K, Everitt RG, Iqbal Z, Rimmer AJ, Cule M, Ip CLC, Didelot X, Harding RM, Donnelly PJ, Peto TEA, Crook DW, Bowden R, Wilson DJ (2012).“Evolutionary Dynamics of Staphylococcus Aureus during Progression from Carriage to Disease.”Proc Natl Acad Sci USA, 109, 4550–4555.doi:10.1073/pnas.1113219109.
Zwick ME, Joseph SJ, Didelot X, Chen PE, aBishop-Lilly K, Stewart AC, Willner K, Lentz S, Nolan N, Thomason MK, Sozhamannan S, Mateczun AJ, Du L, Read TD (2012).“Genomic Characterization of the Bacillus Cereus Sensu Lato Species: Backdrop to the Evolution of Bacillus Anthracis.”Genome Research, 22(8), 1512–24.doi:10.1101/gr.134437.111, 22645259.
Eyre DW, Golubchik T, Gordon NC, Bowden R, Piazza P, Batty EM, Ip CLC, Wilson DJ, Didelot X, O’Connor L, Lay R, Buck D, Kearns AM, Shaw A, Paul J, Wilcox MH, Donnelly PJ, Peto TEA, Walker AS, Crook DW (2012).“A Pilot Study of Rapid Benchtop Sequencing of Staphylococcus Aureus and Clostridium Difficile for Outbreak Detection and Surveillance.”BMJ Open, 2, e001124.doi:10.1136/bmjopen-2012-001124.
Achtman M, Wain J, Weill F, Nair S, Zhou Z, Sangal V, Krauland MG, Hale J, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S, S.entericaMLSTstudygroup T (2012).“Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella Enterica.”PLoS Pathogens, 8(6), e1002776.doi:10.1371/journal.ppat.1002776.
Joseph SJ, Didelot X, Rothschild J, deVries HJC, Morré SA, Read TD, Dean D (2012).“Population Genomics of Chlamydia Trachomatis: Insights on Drift, Selection, Recombination and Population Structure.”Molecular Biology and Evolution, 29, 3933–46.doi:10.1093/molbev/mss198, 22891032.
Zhang L, Thomas JC, Didelot X, Robinson DA (2012).“Molecular Signatures Identify a Candidate Target of Balancing Selection in an arcD-Like Gene of Staphylococcus Epidermidis.”Journal Molecular Evolution, 75, 43–54.doi:10.1007/s00239-012-9520-5, 23053194.
Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly PJ (2011).“Recombination and Population Structure in Salmonella Enterica.”PLoS Genetics, 7(7), e1002191.doi:10.1371/journal.pgen.1002191.
Didelot X, Everitt RG, Johansen AM, Lawson DJ (2011).“Likelihood-Free Estimation of Model Evidence.”Bayesian Analysis, 6, 48–76.doi:10.1214/11-BA602.
Dingle KE, Griffiths D, Didelot X, Evans J, Vaughan A, Kachrimanidou M, Stoesser N, Jolley KA, Golubchik T, Harding RM, Peto TEA, Fawley W, Walker AS, Wilcox M, Crook DW (2011).“Clinical Clostridium Difficile: Clonality and Pathogenicity Locus Diversity.”PLoS One, 6(5), e19993.doi:10.1371/journal.pone.0019993.
Gripp E, Hlahla D, Didelot X, Kops F, Maurischat S, Tedin K, Alter T, Ellerbroek L, Schreiber K, Schomburg D, Janssen T, Bartholomäus P, Hofreuter D, Woltemate S, Uhr M, Brenneke B, Grüning P, Gerlach G, Wieler L, Suerbaum S, Josenhans C (2011).“Closely Related Campylobacter Jejuni Strains from Different Sources Reveal a Generalist Rather than a Specialist Lifestyle.”BMC Genomics, 12(1), 584.doi:10.1186/1471-2164-12-584, 22122991.
Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD (2011).“Interplay of Recombination and Selection in the Genomes of Chlamydia Trachomatis.”Biology Direct, 6, 28.doi:10.1186/1745-6150-6-28.
Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B, Droege M, Reinhardt R, Correa P, Meyer TF, Josenhans C, Falush D, Suerbaum S (2011).“Helicobacter Pylori Genome Evolution during Human Infection.”Proc Natl Acad Sci USA, 108(12), 5033–5038.doi:10.1073/pnas.1018444108, 21383187.
Laukkanen-Ninios R, Didelot X, Jolley KA, Morelli G, Sangal V, Kristo P, Brehony C, Imori PFM, Fukushima H, Siitonen A, Tseneva G, Voskressenskaya E, Falcao JP, Korkeala H, Maiden MCJ, Mazzoni CJ, Carniel E, Skurnik M, Achtman M (2011).“Population Structure of the Yersinia Pseudotuberculosis Complex According to Multilocus Sequence Typing.”Environmental Microbiology, 13(12), 3114–3127.doi:10.1111/j.1462-2920.2011.02588.x.
Didelot X, Lawson DJ, Darling AE, Falush D (2010).“Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences.”Genetics, 186(4), 1435–49.doi:10.1534/genetics.110.120121, 20923983.
Didelot X (2010).“Sequence-Based Analysis of Bacterial Population Structures.”In Robinson D, Falush D, Feil EJ (eds.), Bacterial Population Genetics in Infectious Disease, 37–60.John Wiley & Sons, Inc..doi:10.1002/9780470600122.ch3.
Didelot X, Maiden MCJ (2010).“Impact of Recombination on Bacterial Evolution.”Trends in Microbiology, 18(7), 315–322.doi:10.1016/j.tim.2010.04.002, 20452218.
Morelli G, Didelot X, Kusecek B, Schwarz S, Bahlawane C, Falush D, Suerbaum S, Achtman M (2010).“Microevolution of Helicobacter Pylori during Prolonged Infection of Single Hosts and within Families.”PLoS Genetics, 6(7), e1001036.doi:10.1371/journal.pgen.1001036.
Sangal V, Harbottle H, Mazzoni CJ, Helmuth R, Guerra B, Didelot X, Paglietti B, Rabsch W, Brisse S, Weill F, Roumagnac P, Achtman M (2010).“Evolution and Population Structure of Salmonella Enterica Serovar Newport.”Journal of Bacteriology, 192(24), 6465–76.doi:10.1128/JB.00969-10, 20935094.
Didelot X, Darling A, Falush D (2008).“Inferring Genomic Flux in Bacteria.”Genome Research, 19(2), 306–317.doi:10.1101/gr.082263.108.
Didelot X, Barker M, Falush D, Priest FG (2009).“Evolution of Pathogenicity in the Bacillus Cereus Group.”Systematic and Applied Microbiology, 32(2), 81–90.doi:10.1016/j.syapm.2009.01.001, 19200684.
Didelot X, Lawson DJ, Falush D (2009).“SimMLST: Simulation of Multi-Locus Sequence Typing Data under a Neutral Model.”Bioinformatics, 25(11), 1442–4.doi:10.1093/bioinformatics/btp145, 19286834.
Didelot X, Urwin R, Maiden MCJ, Falush D (2009).“Genealogical Typing of Neisseria Meningitidis.”Microbiology, 155, 3176–86.doi:10.1099/mic.0.031534-0.
Vos M, Didelot X (2009).“A Comparison of Homologous Recombination Rates in Bacteria and Archaea.”ISME Journal, 3(2), 199–208.doi:10.1038/ismej.2008.93, 18830278.
Zhang J, Zhang F, Didelot X, Bruce KD, Cagampang FR, Vatish M, Hanson M, Lehnert H, Ceriello A, Byrne CD (2009).“Maternal High Fat Diet during Pregnancy and Lactation Alters Hepatic Expression of Insulin like Growth Factor-2 and Key microRNAs in the Adult Offspring.”BMC Genomics, 10, 478.doi:10.1186/1471-2164-10-478, 19835573.
Didelot X, Falush D (2008).“Bacterial Recombination in Vivo.”In Hensel M, Schmidt H (eds.), Horizontal Gene Transfer in the Evolution of Pathogenesis, 23–46.Cambridge University Press.doi:10.1017/CBO9780511541520.003.
Didelot X, Taylor JE, Watkins JC (2008).“A Duality Identity between a Model of Bacterial Recombination and the Wright-Fisher Diffusion.”Markov Processes and Related Topics, 4, 315–324.doi:10.1214/074921708000000453.
denBakker HC, Didelot X, Fortes ED, Nightingale KK, Wiedmann M (2008).“Lineage Specific Recombination Rates and Microevolution in Listeria Monocytogenes.”BMC Evolutionary Biology, 8, 277.doi:10.1186/1471-2148-8-277.
Kulick S, Moccia C, Didelot X, Falush D, Kraft C, Suerbaum S (2008).“Mosaic DNA Imports with Interspersions of Recipient Sequence after Natural Transformation of Helicobacter Pylori.”PLoS One, 3(11), e3797.doi:10.1371/journal.pone.0003797.
Didelot X, Achtman M, Parkhill J, Thomson N, Falush D (2007).“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.doi:10.1101/gr.5512906.1.
Didelot X, Falush D (2007).“Inference of Bacterial Microevolution Using Multilocus Sequence Data.”Genetics, 175(3), 1251–66.doi:10.1534/genetics.106.063305.
Falush D, Torpdahl M, Didelot X, Conrad DF, Wilson DJ, Achtman M (2006).“Mismatch Induced Speciation in Salmonella: Model and Data.”Philosophical Transactions of the Royal Society B: Biological Sciences, 361(1475), 2045–53.doi:10.1098/rstb.2006.1925.