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Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages.

Wang H, Yang C, Sun Z, Zheng W, Zhang W, Yu H, Wu Y, Didelot X, Yang R, Pan J, Cui Y.

PLoS Negl Trop Dis. 2020 Feb 18;14(2):e0008046. doi: 10.1371/journal.pntd.0008046. eCollection 2020 Feb.


Identification of hidden population structure in time-scaled phylogenies.

Volz EM, Wiuf C, Grad YH, Frost SDW, Dennis AM, Didelot X.

Syst Biol. 2020 Feb 12. pii: syaa009. doi: 10.1093/sysbio/syaa009. [Epub ahead of print]


Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics.

Whittles LK, White PJ, Didelot X.

Clin Infect Dis. 2020 Jan 6. pii: ciz1241. doi: 10.1093/cid/ciz1241. [Epub ahead of print]


Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12.

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.

Microb Genom. 2019 Oct 4. doi: 10.1099/mgen.0.000287. [Epub ahead of print] No abstract available.


The speciation and hybridization history of the genus Salmonella.

Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D, Brisse S.

Microb Genom. 2019 Aug;5(8). doi: 10.1099/mgen.0.000284. Epub 2019 Jul 26.


Machine-learning-assisted selection of antibiotic prescription.

Didelot X, Pouwels KB.

Nat Med. 2019 Jul;25(7):1033-1034. doi: 10.1038/s41591-019-0517-0. No abstract available.


The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages.

Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR.

Genome Biol Evol. 2019 Jul 1;11(1):1780-1796. doi: 10.1093/gbe/evz119.


Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps.

Ailloud F, Didelot X, Woltemate S, Pfaffinger G, Overmann J, Bader RC, Schulz C, Malfertheiner P, Suerbaum S.

Nat Commun. 2019 May 22;10(1):2273. doi: 10.1038/s41467-019-10050-1.


Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves.

Moniri A, Rodriguez-Manzano J, Malpartida-Cardenas K, Yu LS, Didelot X, Holmes A, Georgiou P.

Anal Chem. 2019 Jun 4;91(11):7426-7434. doi: 10.1021/acs.analchem.9b01466. Epub 2019 May 14.


Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage.

Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TEA, Walker AS, Wilcox MH, Dingle KE.

EBioMedicine. 2019 May;43:347-355. doi: 10.1016/j.ebiom.2019.04.038. Epub 2019 Apr 27.


Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains.

van Dorp 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.

Microb Genom. 2019 Apr;5(4). doi: 10.1099/mgen.0.000263. Epub 2019 Apr 2.


A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078.

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.

mBio. 2019 Mar 12;10(2). pii: e02790-18. doi: 10.1128/mBio.02790-18.


A dynamic power-law sexual network model of gonorrhoea outbreaks.

Whittles LK, White PJ, Didelot X.

PLoS Comput Biol. 2019 Mar 8;15(3):e1006748. doi: 10.1371/journal.pcbi.1006748. eCollection 2019 Mar.


Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

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, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK.

Nat Commun. 2018 Nov 28;9(1):5034. doi: 10.1038/s41467-018-07368-7.


Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection.

Pandey A, Cleary DW, Laver JR, Gorringe A, Deasy AM, Dale AP, Morris PD, Didelot X, Maiden MCJ, Read RC.

Nat Commun. 2018 Nov 12;9(1):4753. doi: 10.1038/s41467-018-07235-5.


outbreaker2: a modular platform for outbreak reconstruction.

Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart T.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):363. doi: 10.1186/s12859-018-2330-z.


Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages.

Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000215. No abstract available.


Bayesian inference of ancestral dates on bacterial phylogenetic trees.

Didelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ.

Nucleic Acids Res. 2018 Dec 14;46(22):e134. doi: 10.1093/nar/gky783.


Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages.

Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M.

Microb Genom. 2018 Aug;4(8). doi: 10.1099/mgen.0.000205. Epub 2018 Jul 31. Erratum in: Microb Genom. 2018 Sep;4(9):.


Epidemiological Trends of Antibiotic Resistant Gonorrhoea in the United Kingdom.

Whittles LK, White PJ, Paul J, Didelot X.

Antibiotics (Basel). 2018 Jul 13;7(3). pii: E60. doi: 10.3390/antibiotics7030060. Review.


Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States.

Séraphin MN, Didelot X, Nolan DJ, May JR, Khan MSR, Murray ER, Salemi M, Morris JG, Lauzardo M.

Am J Trop Med Hyg. 2018 Oct;99(4):867-874. doi: 10.4269/ajtmh.17-0700.


Testing for gonorrhoea should routinely include the pharynx.

Whittles LK, Didelot X, Grad YH, White PJ.

Lancet Infect Dis. 2018 Jul;18(7):716-717. doi: 10.1016/S1473-3099(18)30341-4. No abstract available.


The global distribution and spread of the mobilized colistin resistance gene mcr-1.

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.

Nat Commun. 2018 Mar 21;9(1):1179. doi: 10.1038/s41467-018-03205-z.


Correction to: Neisseria lactamica Y92-1009 complete genome sequence.

Pandey AK, Cleary DW, Laver JR, Maiden MCJ, Didelot X, Gorringe A, Read RC.

Stand Genomic Sci. 2018 Feb 16;13:4. doi: 10.1186/s40793-017-0288-5. eCollection 2018.


A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.

Collins C, Didelot X.

PLoS Comput Biol. 2018 Feb 5;14(2):e1005958. doi: 10.1371/journal.pcbi.1005958. eCollection 2018 Feb.


Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus.

Challagundla L, Luo X, Tickler IA, Didelot X, Coleman DC, Shore AC, Coombs GW, Sordelli DO, Brown EL, Skov R, Larsen AR, Reyes J, Robledo IE, Vazquez GJ, Rivera R, Fey PD, Stevenson K, Wang SH, Kreiswirth BN, Mediavilla JR, Arias CA, Planet PJ, Nolan RL, Tenover FC, Goering RV, Robinson DA.

mBio. 2018 Jan 2;9(1). pii: e02016-17. doi: 10.1128/mBio.02016-17.


Estimating the fitness cost and benefit of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy: A modelling study.

Whittles LK, White PJ, Didelot X.

PLoS Med. 2017 Oct 31;14(10):e1002416. doi: 10.1371/journal.pmed.1002416. eCollection 2017 Oct.


Whole genome sequencing of Neisseria gonorrhoeae reveals transmission clusters involving patients of mixed HIV serostatus.

Peters J, Cresswell F, Amor L, Cole K, Dean G, Didelot X, De Silva D, Eyre DW, Paul J.

Sex Transm Infect. 2018 Mar;94(2):138-143. doi: 10.1136/sextrans-2017-053198. Epub 2017 Oct 11.


Neisseria lactamica Y92-1009 complete genome sequence.

Pandey AK, Cleary DW, Laver JR, Maiden MCJ, Didelot X, Gorringe A, Read RC.

Stand Genomic Sci. 2017 Jul 24;12:41. doi: 10.1186/s40793-017-0250-6. eCollection 2017. Erratum in: Stand Genomic Sci. 2018 Feb 16;13:4.


A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011-2014.

Rosner BM, Schielke A, Didelot X, Kops F, Breidenbach J, Willrich N, Gölz G, Alter T, Stingl K, Josenhans C, Suerbaum S, Stark K.

Sci Rep. 2017 Jul 11;7(1):5139. doi: 10.1038/s41598-017-05227-x.


Model-based analysis of an outbreak of bubonic plague in Cairo in 1801.

Didelot X, Whittles LK, Hall I.

J R Soc Interface. 2017 Jun;14(131). pii: 20170160. doi: 10.1098/rsif.2017.0160.


Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C.

Mol Biol Evol. 2017 Oct 1;34(10):2537-2554. doi: 10.1093/molbev/msx173.


Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

Klinkenberg D, Backer JA, Didelot X, Colijn C, Wallinga J.

PLoS Comput Biol. 2017 May 18;13(5):e1005495. doi: 10.1371/journal.pcbi.1005495. eCollection 2017 May.


Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations.

Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker CT, Sheppard SK.

Mol Ecol. 2017 Sep;26(17):4497-4508. doi: 10.1111/mec.14176. Epub 2017 Jun 19.


Clostridium difficile in England: can we stop washing our hands? - Authors' reply.

Eyre DW, Dingle KE, Didelot X, Quan TP, Peto TEA, Wilcox MH, Walker AS, Crook DW.

Lancet Infect Dis. 2017 May;17(5):478-479. doi: 10.1016/S1473-3099(17)30185-8. No abstract available.


Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography.

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.

Clin Infect Dis. 2017 Apr 1;64(7):894-901. doi: 10.1093/cid/ciw876.


Declaring a tuberculosis outbreak over with genomic epidemiology.

Hatherell HA, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, Colijn C, Gardy JL.

Microb Genom. 2016 May 31;2(5):e000060. doi: 10.1099/mgen.0.000060. eCollection 2016 May.


Effects of control interventions on Clostridium difficile infection in England: an observational study.

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; Modernising Medical Microbiology Informatics Group.

Lancet Infect Dis. 2017 Apr;17(4):411-421. doi: 10.1016/S1473-3099(16)30514-X. Epub 2017 Jan 25.


Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus.

Ledda A, Price JR, Cole K, Llewelyn MJ, Kearns AM, Crook DW, Paul J, Didelot X.

J Antimicrob Chemother. 2017 May 1;72(5):1285-1288. doi: 10.1093/jac/dkw570.


Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.

Didelot X, Fraser C, Gardy J, Colijn C.

Mol Biol Evol. 2017 Apr 1;34(4):997-1007. doi: 10.1093/molbev/msw275.


Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.


Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes.

Collins C, Didelot X.

Methods Mol Biol. 2017;1535:109-137.


Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

Yahara K, Méric G, Taylor AJ, de Vries SP, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley A, Komukai S, Wimalarathna H, Cody AJ, Colles FM, McCarthy N, Harris D, Bray JE, Jolley KA, Maiden MC, Bentley SD, Parkhill J, Bayliss CD, Grant A, Maskell D, Didelot X, Kelly DJ, Sheppard SK.

Environ Microbiol. 2017 Jan;19(1):361-380. doi: 10.1111/1462-2920.13628.


Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study.

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 TE, Walker AS, Paul J, Eyre DW.

Lancet Infect Dis. 2016 Nov;16(11):1295-1303. doi: 10.1016/S1473-3099(16)30157-8. Epub 2016 Jul 12.


SimBac: simulation of whole bacterial genomes with homologous recombination.

Brown T, Didelot X, Wilson DJ, Maio N.

Microb Genom. 2016 Jan 19;2(1). doi: 10.1099/mgen.0.000044.


Dynamics of genome change among Legionella species.

Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D.

Sci Rep. 2016 Sep 16;6:33442. doi: 10.1038/srep33442.


Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen.

Joseph SJ, Marti H, Didelot X, Read TD, Dean D.

Genome Biol Evol. 2016 Sep 2;8(8):2613-23. doi: 10.1093/gbe/evw182.


Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis.

Eldholm V, Rieux A, Monteserin J, Lopez JM, Palmero D, Lopez B, Ritacco V, Didelot X, Balloux F.

Elife. 2016 Aug 9;5. pii: e16644. doi: 10.7554/eLife.16644.


Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree.

Ansari MA, Didelot X.

Genetics. 2016 Sep;204(1):89-98. doi: 10.1534/genetics.116.190496. Epub 2016 Jul 13.

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