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Domestication of Campylobacter jejuni NCTC 11168.

Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD, Dyer M, Ryder J, Shaw S, Lopes BS, Chintoan-Uta C, Allan E, Vidal A, Fearnley C, Everest P, Pachebat JA, Cogan TA, Stevens MP, Humphrey TJ, Wilkinson TS, Cody AJ, Colles FM, Jolley KA, Maiden MCJ, Strachan N, Pearson BM, Linton D, Wren BW, Parkhill J, Kelly DJ, van Vliet AHM, Forbes KJ, Sheppard SK.

Microb Genom. 2019 Jul 16. doi: 10.1099/mgen.0.000279. [Epub ahead of print]


Detection of OXA-48-like-producing Enterobacterales in Irish recreational water.

Mahon BM, Brehony C, Cahill N, McGrath E, O'Connor L, Varley A, Cormican M, Ryan S, Hickey P, Keane S, Mulligan M, Ruane B, Jolley KA, Maiden MC, Brisse S, Morris D.

Sci Total Environ. 2019 Jun 30;690:1-6. doi: 10.1016/j.scitotenv.2019.06.480. [Epub ahead of print]


Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes.

Weiser R, Green AE, Bull MJ, Cunningham-Oakes E, Jolley KA, Maiden MCJ, Hall AJ, Winstanley C, Weightman AJ, Donoghue D, Amezquita A, Connor TR, Mahenthiralingam E.

Microb Genom. 2019 Jun 6. doi: 10.1099/mgen.0.000276. [Epub ahead of print]


cgMLST characterisation of invasive Neisseria meningitidis serogroup C and W strains associated with increasing disease incidence in the Republic of Ireland.

Mulhall RM, Bennett DE, Bratcher HB, Jolley KA, Bray JE, O'Lorcain PP, Cotter SM, Maiden MCJ, Cunney RJ.

PLoS One. 2019 May 29;14(5):e0216771. doi: 10.1371/journal.pone.0216771. eCollection 2019.


Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens.

Colles FM, Preston SG, Barfod KK, Flammer PG, Maiden MCJ, Smith AL.

Sci Rep. 2019 Apr 17;9(1):6204. doi: 10.1038/s41598-019-42207-9.


Hospital effluent: A reservoir for carbapenemase-producing Enterobacterales?

Cahill N, O'Connor L, Mahon B, Varley Á, McGrath E, Ryan P, Cormican M, Brehony C, Jolley KA, Maiden MC, Brisse S, Morris D.

Sci Total Environ. 2019 Jul 1;672:618-624. doi: 10.1016/j.scitotenv.2019.03.428. Epub 2019 Apr 3.


Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens.

Rodrigues CMC, Chan H, Vipond C, Jolley K, Harrison OB, Wheeler J, Whiting G, Feavers IM, Maiden MCJ.

Version 2. Wellcome Open Res. 2019 Mar 19 [revised 2019 Jan 1];3:151. doi: 10.12688/wellcomeopenres.14859.2. eCollection 2018.


A proposed core genome scheme for analyses of the Salmonella genus.

Pearce ME, Chattaway MA, Grant K, Maiden MCJ.

Genomics. 2019 Mar 21. pii: S0888-7543(18)30698-0. doi: 10.1016/j.ygeno.2019.02.016. [Epub ahead of print]


Genome Sequencing and Interrogation of Genome Databases: A Guide to Neisseria meningitidis Genomics.

Bratcher HB, Harrison OB, Maiden MCJ.

Methods Mol Biol. 2019;1969:51-82. doi: 10.1007/978-1-4939-9202-7_4.


Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

van Tonder AJ, Bray JE, Jolley KA, Jansen van Rensburg M, Quirk SJ, Haraldsson G, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB.

Front Microbiol. 2019 Feb 25;10:317. doi: 10.3389/fmicb.2019.00317. eCollection 2019.


Risk factors for acquisition of meningococcal carriage in the African meningitis belt.

Cooper LV, Robson A, Trotter CL, Aseffa A, Collard JM, Daugla DM, Diallo A, Hodgson A, Jusot JF, Omotara B, Sow S, Hassan-King M, Manigart O, Nascimento M, Woukeu A, Chandramohan D, Borrow R, Maiden MCJ, Greenwood B, Stuart JM; MenAfriCar Consortium.

Trop Med Int Health. 2019 Apr;24(4):392-400. doi: 10.1111/tmi.13203. Epub 2019 Feb 6.


The Impact of Nucleotide Sequence Analysis on Meningococcal Vaccine Development and Assessment.

Maiden MCJ.

Front Immunol. 2019 Jan 15;9:3151. doi: 10.3389/fimmu.2018.03151. eCollection 2018. Review.


Characterization of meningococcal carriage isolates from Greece by whole genome sequencing: Implications for 4CMenB vaccine implementation.

Kesanopoulos K, Bratcher HB, Hong E, Xirogianni A, Papandreou A, Taha MK, Maiden MCJ, Tzanakaki G.

PLoS One. 2018 Dec 28;13(12):e0209919. doi: 10.1371/journal.pone.0209919. eCollection 2018.


Development of a PCR algorithm to detect and characterize Neisseria meningitidis carriage isolates in the African meningitis belt.

Diallo K, Coulibaly MD, Rebbetts LS, Harrison OB, Lucidarme J, Gamougam K, Tekletsion YK, Bugri A, Toure A, Issaka B, Dieng M, Trotter C, Collard JM, Sow SO, Wang X, Mayer LW, Borrow R, Greenwood BM, Maiden MCJ, Manigart O; MenAfriCar Consortium.

PLoS One. 2018 Dec 5;13(12):e0206453. doi: 10.1371/journal.pone.0206453. eCollection 2018.


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.


Narrative review of methods and findings of recent studies on the carriage of meningococci and other Neisseria species in the African Meningitis Belt.

Greenwood BM, Aseffa A, Caugant DA, Diallo K, Kristiansen PA, Maiden MCJ, Stuart JM, Trotter CL.

Trop Med Int Health. 2019 Feb;24(2):143-154. doi: 10.1111/tmi.13185. Epub 2018 Dec 6. Review.


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.


Open-access bacterial population genomics: BIGSdb software, the website and their applications.

Jolley KA, Bray JE, Maiden MCJ.

Wellcome Open Res. 2018 Sep 24;3:124. doi: 10.12688/wellcomeopenres.14826.1. eCollection 2018.


A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis.

Alfsnes K, Frye SA, Eriksson J, Eldholm V, Brynildsrud OB, Bohlin J, Harrison OB, Hood DW, Maiden MCJ, Tønjum T, Ambur OH.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000222. Epub 2018 Sep 25.


Author Correction: Invasive meningococcal disease in Shanghai, China from 1950 to 2016: implications for serogroup B vaccine implementation.

Chen M, Rodrigues CMC, Harrison OB, Zhang C, Tan T, Chen J, Zhang X, Chen M, Maiden MCJ.

Sci Rep. 2018 Sep 4;8(1):13484. doi: 10.1038/s41598-018-31649-2.


Potential Coverage of the 4CMenB Vaccine against Invasive Serogroup B Neisseria meningitidis Isolated from 2009 to 2013 in the Republic of Ireland.

Mulhall RM, Bennett D, Cunney R, Borrow R, Lucidarme J, Findlow J, Jolley KA, Bray J, Maiden MCJ, Moschioni M, Serino L, Stella M, Medini D.

mSphere. 2018 Aug 22;3(4). pii: e00196-18. doi: 10.1128/mSphere.00196-18.


Invasive meningococcal disease in Shanghai, China from 1950 to 2016: implications for serogroup B vaccine implementation.

Chen M, Rodrigues CMC, Harrison OB, Zhang C, Tan T, Chen J, Zhang X, Chen M, Maiden MCJ.

Sci Rep. 2018 Aug 17;8(1):12334. doi: 10.1038/s41598-018-30048-x. Erratum in: Sci Rep. 2018 Sep 4;8(1):13484.


Characterization of capsule genes in non-pathogenic Neisseria species.

Clemence MEA, Maiden MCJ, Harrison OB.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000208. Epub 2018 Aug 3.


B Part of It protocol: a cluster randomised controlled trial to assess the impact of 4CMenB vaccine on pharyngeal carriage of Neisseria meningitidis in adolescents.

Marshall HS, McMillan M, Koehler A, Lawrence A, MacLennan JM, Maiden MCJ, Ramsay M, Ladhani SN, Trotter C, Borrow R, Finn A, Sullivan T, Richmond P, Kahler CM, Whelan J, Vadivelu K.

BMJ Open. 2018 Jul 10;8(7):e020988. doi: 10.1136/bmjopen-2017-020988.


Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year.

Bratcher HB, Brehony C, Heuberger S, Pieridou-Bagatzouni D, Křížová P, Hoffmann S, Toropainen M, Taha MK, Claus H, Tzanakaki G, Erdôsi T, Galajeva J, van der Ende A, Skoczyńska A, Pana M, Vaculíková A, Paragi M, Maiden MC, Caugant DA.

Euro Surveill. 2018 May;23(20). doi: 10.2807/1560-7917.ES.2018.23.20.17-00474.


Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya.

Cehovin A, Harrison OB, Lewis SB, Ward PN, Ngetsa C, Graham SM, Sanders EJ, Maiden MCJ, Tang CM.

J Infect Dis. 2018 Jul 24;218(5):801-808. doi: 10.1093/infdis/jiy240.


A world without bacterial meningitis: how genomic epidemiology can inform vaccination strategy.

Rodrigues CMC, Maiden MCJ.

F1000Res. 2018 Mar 27;7:401. doi: 10.12688/f1000research.13793.1. eCollection 2018. Review.


The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.

Blanchard AM, Jolley KA, Maiden MCJ, Coffey TJ, Maboni G, Staley CE, Bollard NJ, Warry A, Emes RD, Davies PL, Tötemeyer S.

Front Microbiol. 2018 Mar 23;9:551. doi: 10.3389/fmicb.2018.00551. eCollection 2018.


Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.

Pearce ME, Alikhan NF, Dallman TJ, Zhou Z, Grant K, Maiden MCJ.

Int J Food Microbiol. 2018 Jun 2;274:1-11. doi: 10.1016/j.ijfoodmicro.2018.02.023. Epub 2018 Feb 28.


Genomic Surveillance of 4CMenB Vaccine Antigenic Variants among Disease-Causing Neisseria meningitidis Isolates, United Kingdom, 2010-2016.

Rodrigues CMC, Lucidarme J, Borrow R, Smith A, Cameron JC, Moxon ER, Maiden MCJ.

Emerg Infect Dis. 2018 Apr;24(4):673-682. doi: 10.3201/eid2404.171480.


Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain.

Sütterlin S, Téllez-Castillo CJ, Anselem L, Yin H, Bray JE, Maiden MCJ.

Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e00209-18. doi: 10.1128/AAC.00209-18. Print 2018 May.


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.


Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease.

Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB.

BMC Genomics. 2018 Feb 9;19(1):130. doi: 10.1186/s12864-018-4522-3.


A RESTful application programming interface for the PubMLST molecular typing and genome databases.

Jolley KA, Bray JE, Maiden MCJ.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax060.


Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein.

Lourenço J, Watkins ER, Obolski U, Peacock SJ, Morris C, Maiden MCJ, Gupta S.

Sci Rep. 2017 Aug 22;7(1):9023. doi: 10.1038/s41598-017-08990-z.


Investigation of correlates of protection against pharyngeal carriage of Neisseria meningitidis genogroups W and Y in the African meningitis belt.

Cooper LV, Boukary RM, Aseffa A, Mihret W, Collard JM, Daugla D, Hodgson A, Sokhna C, Omotara B, Sow S, Quaye SL, Diallo K, Manigart O, Maiden MCJ, Findlow H, Borrow R, Stuart JM, Greenwood BM, Trotter CL.

PLoS One. 2017 Aug 10;12(8):e0182575. doi: 10.1371/journal.pone.0182575. eCollection 2017.


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.


Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models.

Sharp C, Bray J, Housden NG, Maiden MCJ, Kleanthous C.

PLoS Comput Biol. 2017 Jul 17;13(7):e1005652. doi: 10.1371/journal.pcbi.1005652. eCollection 2017 Jul.


Neisseria genomics: current status and future perspectives.

Harrison OB, Schoen C, Retchless AC, Wang X, Jolley KA, Bray JE, Maiden MCJ.

Pathog Dis. 2017 Aug 31;75(6). doi: 10.1093/femspd/ftx060. Review.


Frequent capsule switching in 'ultra-virulent' meningococci - Are we ready for a serogroup B ST-11 complex outbreak?

Lucidarme J, Lekshmi A, Parikh SR, Bray JE, Hill DM, Bratcher HB, Gray SJ, Carr AD, Jolley KA, Findlow J, Campbell H, Ladhani SN, Ramsay ME, Maiden MCJ, Borrow R.

J Infect. 2017 Aug;75(2):95-103. doi: 10.1016/j.jinf.2017.05.015. Epub 2017 Jun 1.


Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad.

Diallo K, Gamougam K, Daugla DM, Harrison OB, Bray JE, Caugant DA, Lucidarme J, Trotter CL, Hassan-King M, Stuart JM, Manigart O, Greenwood BM, Maiden MCJ.

BMC Genomics. 2017 May 22;18(1):398. doi: 10.1186/s12864-017-3789-0.


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.


Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.

Cody AJ, Bray JE, Jolley KA, McCarthy ND, Maiden MCJ.

J Clin Microbiol. 2017 Jul;55(7):2086-2097. doi: 10.1128/JCM.00080-17. Epub 2017 Apr 26.


Recent Progress in the Prevention of Serogroup B Meningococcal Disease.

Feavers IM, Maiden MCJ.

Clin Vaccine Immunol. 2017 May 5;24(5). pii: e00566-16. doi: 10.1128/CVI.00566-16. Print 2017 May. Review.


Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.

Murray S, Pascoe B, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Wilkinson TS, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK.

Genome Biol Evol. 2017 Apr 1;9(4):830-842. doi: 10.1093/gbe/evx037.


Acquisition of the capsule locus by horizontal gene transfer in Neisseria meningitidis is often accompanied by the loss of UDP-GalNAc synthesis.

Bartley SN, Mowlaboccus S, Mullally CA, Stubbs KA, Vrielink A, Maiden MC, Harrison OB, Perkins TT, Kahler CM.

Sci Rep. 2017 Mar 14;7:44442. doi: 10.1038/srep44442.


Molecular characterization of invasive capsule null Neisseria meningitidis in South Africa.

Ganesh K, Allam M, Wolter N, Bratcher HB, Harrison OB, Lucidarme J, Borrow R, de Gouveia L, Meiring S, Birkhead M, Maiden MC, von Gottberg A, du Plessis M.

BMC Microbiol. 2017 Feb 21;17(1):40. doi: 10.1186/s12866-017-0942-5.


Genomic analysis of urogenital and rectal Neisseria meningitidis isolates reveals encapsulated hyperinvasive meningococci and coincident multidrug-resistant gonococci.

Harrison OB, Cole K, Peters J, Cresswell F, Dean G, Eyre DW, Paul J, Maiden MC.

Sex Transm Infect. 2017 Sep;93(6):445-451. doi: 10.1136/sextrans-2016-052781. Epub 2017 Jan 30.


Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes.

van Tonder AJ, Bray JE, Quirk SJ, Haraldsson G, Jolley KA, Maiden MCJ, Hoffmann S, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB.

Microb Genom. 2016 Oct 1;2(10):000090. doi: 10.1099/mgen.0.000090.


Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages.

Watkins ER, Maiden MC.

Sci Rep. 2017 Jan 23;7:41126. doi: 10.1038/srep41126.

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