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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;5(7). doi: 10.1099/mgen.0.000279. Epub 2019 Jul 16.


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 Nov 10;690:1-6. doi: 10.1016/j.scitotenv.2019.06.480. Epub 2019 Jun 30.


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 Jul;5(7). doi: 10.1099/mgen.0.000276. Epub 2019 Jun 6.


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.


Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes.

Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M, Jolley KA, Brisse S, Sassera D, Zarrilli R.

Front Microbiol. 2019 May 3;10:930. doi: 10.3389/fmicb.2019.00930. eCollection 2019.


High diversity of invasive Haemophilus influenzae isolates in France and the emergence of resistance to third generation cephalosporins by alteration of ftsI gene.

Deghmane AE, Hong E, Chehboub S, Terrade A, Falguières M, Sort M, Harrison O, Jolley KA, Taha MK.

J Infect. 2019 Jul;79(1):7-14. doi: 10.1016/j.jinf.2019.05.007. Epub 2019 May 14.


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.


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.


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.


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.


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.


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.


Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.

Méric G, Mageiros L, Pascoe B, Woodcock DJ, Mourkas E, Lamble S, Bowden R, Jolley KA, Raymond B, Sheppard SK.

Mol Ecol. 2018 Apr;27(7):1524-1540. doi: 10.1111/mec.14546. Epub 2018 Apr 2.


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.


Clonal Expansion of New Penicillin-Resistant Clade of Neisseria meningitidis Serogroup W Clonal Complex 11, Australia.

Mowlaboccus S, Jolley KA, Bray JE, Pang S, Lee YT, Bew JD, Speers DJ, Keil AD, Coombs GW, Kahler CM.

Emerg Infect Dis. 2017 Aug;23(8):1364-1367. doi: 10.3201/eid2308.170259. Epub 2017 Aug 15.


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.


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.


Database for the ampC alleles in Acinetobacter baumannii.

Karah N, Jolley KA, Hall RM, Uhlin BE.

PLoS One. 2017 May 1;12(5):e0176695. doi: 10.1371/journal.pone.0176695. eCollection 2017.


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.


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.


Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.

Gonzalez-Escalona N, Jolley KA, Reed E, Martinez-Urtaza J.

J Clin Microbiol. 2017 Jun;55(6):1682-1697. doi: 10.1128/JCM.00227-17. Epub 2017 Mar 22.


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.


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.


Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer.

Mulhall RM, Brehony C, O'Connor L, Meyler K, Jolley KA, Bray J, Bennett D, Maiden MC, Cunney R.

J Clin Microbiol. 2016 Dec;54(12):2891-2899. Epub 2016 Sep 14.


Correction for van Tonder et al., Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci.

van Tonder AJ, Bray JE, Roalfe L, White R, Zancolli M, Quirk SJ, Haraldsson G, Jolley KA, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Goldblatt D, Brueggemann AB.

J Clin Microbiol. 2016 Jun;54(6):1670. doi: 10.1128/JCM.00619-16. No abstract available.


Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes.

Chalker VJ, Smith A, Al-Shahib A, Botchway S, Macdonald E, Daniel R, Phillips S, Platt S, Doumith M, Tewolde R, Coelho J, Jolley KA, Underwood A, McCarthy ND.

Emerg Infect Dis. 2016 Jun;22(6):973-80. doi: 10.3201/eid2206.142050.


Correction: Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.

Harris LG, Murray S, Pascoe B, Bray J, Meric G, Mageiros L, Wilkinson TS, Jeeves R, Rohde H, Schwarz S, de Lencastre H, Miragaia M, Rolo J, Bowden R, Jolley KA, Maiden MC, Mack D, Sheppard SK.

PLoS One. 2016 Apr 21;11(4):e0154510. doi: 10.1371/journal.pone.0154510. eCollection 2016. No abstract available.


Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.

Harris LG, Murray S, Pascoe B, Bray J, Meric G, Mageiros L, Wilkinson TS, Jeeves R, Rohde H, Schwarz S, de Lencastre H, Miragaia M, Rolo J, Bowden R, Jolley KA, Maiden MC, Mack D, Sheppard SK.

PLoS One. 2016 Mar 15;11(3):e0151240. doi: 10.1371/journal.pone.0151240. eCollection 2016. Erratum in: PLoS One. 2016;11(4):e0154510. Magerios, Leonardos [corrected to Mageiros, Leonardos].


Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013.

du Plessis M, Allam M, Tempia S, Wolter N, de Gouveia L, von Mollendorf C, Jolley KA, Mbelle N, Wadula J, Cornick JE, Everett DB, McGee L, Breiman RF, Gladstone RA, Bentley SD, Klugman KP, von Gottberg A.

J Clin Microbiol. 2016 May;54(5):1326-34. doi: 10.1128/JCM.00055-16. Epub 2016 Mar 9.


The Landscape of Realized Homologous Recombination in Pathogenic Bacteria.

Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MC, Sheppard SK, Falush D.

Mol Biol Evol. 2016 Feb;33(2):456-71. doi: 10.1093/molbev/msv237. Epub 2015 Oct 29.


Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.

Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MC.

Lancet Infect Dis. 2015 Dec;15(12):1420-8. doi: 10.1016/S1473-3099(15)00267-4. Epub 2015 Oct 27. Erratum in: Lancet Infect Dis. 2016 Jan;16(1):16. Lancet Infect Dis. 2016 Jan;16(1):16.


Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage.

Lucidarme J, Hill DM, Bratcher HB, Gray SJ, du Plessis M, Tsang RS, Vazquez JA, Taha MK, Ceyhan M, Efron AM, Gorla MC, Findlow J, Jolley KA, Maiden MC, Borrow R.

J Infect. 2015 Nov;71(5):544-52. doi: 10.1016/j.jinf.2015.07.007. Epub 2015 Jul 28.

35. new home for the Borrelia MLSA database.

Margos G, Binder K, Dzaferovic E, Hizo-Teufel C, Sing A, Wildner M, Fingerle V, Jolley KA.

Ticks Tick Borne Dis. 2015 Sep;6(6):869-71. doi: 10.1016/j.ttbdis.2015.06.007. Epub 2015 Jun 17. No abstract available.


Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci.

van Tonder AJ, Bray JE, Roalfe L, White R, Zancolli M, Quirk SJ, Haraldsson G, Jolley KA, Maiden MC, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Goldblatt D, Brueggemann AB.

J Clin Microbiol. 2015 Jul;53(7):2271-85. doi: 10.1128/JCM.00744-15. Epub 2015 May 13. Erratum in: J Clin Microbiol. 2016 Jun;54(6):1670.


Genome-Based Characterization of Emergent Invasive Neisseria meningitidis Serogroup Y Isolates in Sweden from 1995 to 2012.

Törös B, Hedberg ST, Unemo M, Jacobsson S, Hill DM, Olcén P, Fredlund H, Bratcher HB, Jolley KA, Maiden MC, Mölling P.

J Clin Microbiol. 2015 Jul;53(7):2154-62. doi: 10.1128/JCM.03524-14. Epub 2015 Apr 29.


Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.

Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK.

Genome Biol Evol. 2015 Apr 16;7(5):1313-28. doi: 10.1093/gbe/evv066.


TypOn: the microbial typing ontology.

Vaz C, Francisco AP, Silva M, Jolley KA, Bray JE, Pouseele H, Rothganger J, Ramirez M, Carriço JA.

J Biomed Semantics. 2014 Oct 18;5(1):43. doi: 10.1186/2041-1480-5-43. eCollection 2014.


A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC.

BMC Genomics. 2014 Dec 18;15:1138. doi: 10.1186/1471-2164-15-1138.


Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis.

Forsythe SJ, Dickins B, Jolley KA.

BMC Genomics. 2014 Dec 16;15:1121. doi: 10.1186/1471-2164-15-1121.


The domestication of the probiotic bacterium Lactobacillus acidophilus.

Bull MJ, Jolley KA, Bray JE, Aerts M, Vandamme P, Maiden MC, Marchesi JR, Mahenthiralingam E.

Sci Rep. 2014 Nov 26;4:7202. doi: 10.1038/srep07202.


Defining the estimated core genome of bacterial populations using a Bayesian decision model.

van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J, Jolley KA, Maiden MC, Brueggemann AB.

PLoS Comput Biol. 2014 Aug 21;10(8):e1003788. doi: 10.1371/journal.pcbi.1003788. eCollection 2014 Aug.


Using multilocus sequence typing to study bacterial variation: prospects in the genomic era.

Jolley KA, Maiden MC.

Future Microbiol. 2014;9(5):623-30. doi: 10.2217/fmb.14.24.


Neisseria adhesin A variation and revised nomenclature scheme.

Bambini S, De Chiara M, Muzzi A, Mora M, Lucidarme J, Brehony C, Borrow R, Masignani V, Comanducci M, Maiden MC, Rappuoli R, Pizza M, Jolley KA.

Clin Vaccine Immunol. 2014 Jul;21(7):966-71. doi: 10.1128/CVI.00825-13. Epub 2014 May 7.


Implications of differential age distribution of disease-associated meningococcal lineages for vaccine development.

Brehony C, Trotter CL, Ramsay ME, Chandra M, Jolley KA, van der Ende A, Carion F, Berthelsen L, Hoffmann S, Harðardóttir H, Vazquez JA, Murphy K, Toropainen M, Caniça M, Ferreira E, Diggle M, Edwards GF, Taha MK, Stefanelli P, Kriz P, Gray SJ, Fox AJ, Jacobsson S, Claus H, Vogel U, Tzanakaki G, Heuberger S, Caugant DA, Frosch M, Maiden MC.

Clin Vaccine Immunol. 2014 Jun;21(6):847-53. doi: 10.1128/CVI.00133-14. Epub 2014 Apr 2.


Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences.

Wörmann ME, Horien CL, Bennett JS, Jolley KA, Maiden MC, Tang CM, Aho EL, Exley RM.

BMC Genomics. 2014 Apr 1;15:253. doi: 10.1186/1471-2164-15-253.


Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J.

Mol Ecol. 2014 May;23(10):2442-51. doi: 10.1111/mec.12742. Epub 2014 Apr 25.


A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.

Méric G, Yahara K, Mageiros L, Pascoe B, Maiden MC, Jolley KA, Sheppard SK.

PLoS One. 2014 Mar 27;9(3):e92798. doi: 10.1371/journal.pone.0092798. eCollection 2014.


Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene.

Bennett JS, Watkins ER, Jolley KA, Harrison OB, Maiden MC.

J Clin Microbiol. 2014 May;52(5):1375-81. doi: 10.1128/JCM.03529-13. Epub 2014 Feb 12.

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