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Items: 1 to 50 of 113

1.

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.

Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ.

Gigascience. 2019 Oct 1;8(10). pii: giz119. doi: 10.1093/gigascience/giz119.

PMID:
31598686
2.

Phage Predation Shapes the Population Structure of Shiga-Toxigenic Escherichia coli O157:H7 in the UK: An Evolutionary Perspective.

Cowley LA, Dallman TJ, Jenkins C, Sheppard SK.

Front Genet. 2019 Aug 30;10:763. doi: 10.3389/fgene.2019.00763. eCollection 2019.

3.

Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages.

Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M.

Front Microbiol. 2019 Aug 27;10:1971. doi: 10.3389/fmicb.2019.01971. eCollection 2019.

4.

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.

Mourkas E, Florez-Cuadrado D, Pascoe B, Calland JK, Bayliss SC, Mageiros L, Méric G, Hitchings MD, Quesada A, Porrero C, Ugarte-Ruiz M, Gutiérrez-Fernández J, Domínguez L, Sheppard SK.

Environ Microbiol. 2019 Aug 5. doi: 10.1111/1462-2920.14760. [Epub ahead of print]

PMID:
31385413
5.

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.

6.

Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain.

Prasertsee T, Chuammitri P, Deeudom M, Chokesajjawatee N, Santiyanont P, Tadee P, Nuangmek A, Tadee P, Sheppard SK, Pascoe B, Patchanee P.

Int J Food Microbiol. 2019 Sep 2;304:68-74. doi: 10.1016/j.ijfoodmicro.2019.05.022. Epub 2019 May 28.

PMID:
31174037
7.

Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates.

Berthenet E, Thépault A, Chemaly M, Rivoal K, Ducournau A, Buissonnière A, Bénéjat L, Bessède E, Mégraud F, Sheppard SK, Lehours P.

Sci Rep. 2019 May 30;9(1):8098. doi: 10.1038/s41598-019-44454-2.

8.

Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials.

Colclough A, Corander J, Sheppard SK, Bayliss SC, Vos M.

Evol Appl. 2019 Jan 28;12(5):878-887. doi: 10.1111/eva.12762. eCollection 2019 Jun.

9.

Prevalence of faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in veterinary hospital staff and students.

Royden A, Ormandy E, Pinchbeck G, Pascoe B, Hitchings MD, Sheppard SK, Williams NJ.

Vet Rec Open. 2019 Jan 7;6(1):e000307. doi: 10.1136/vetreco-2018-000307. eCollection 2019.

10.

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.

11.

PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter.

Aidley J, Wanford JJ, Green LR, Sheppard SK, Bayliss CD.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000228. Epub 2018 Oct 23.

12.

Genomic epidemiology of clinical Campylobacter spp. at a single health trust site.

Dunn SJ, Pascoe B, Turton J, Fleming V, Diggle M, Sheppard SK, McNally A, Manning G.

Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000227. Epub 2018 Oct 11.

13.

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk.

Berthenet E, Yahara K, Thorell K, Pascoe B, Meric G, Mikhail JM, Engstrand L, Enroth H, Burette A, Megraud F, Varon C, Atherton JC, Smith S, Wilkinson TS, Hitchings MD, Falush D, Sheppard SK.

BMC Biol. 2018 Aug 2;16(1):84. doi: 10.1186/s12915-018-0550-3.

14.

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry.

Bayliss SC, Verner-Jeffreys DW, Ryder D, Suarez R, Ramirez R, Romero J, Pascoe B, Sheppard SK, Godoy M, Feil EJ.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000201. Epub 2018 Jul 24.

15.

Trends in fluoroquinolone resistance in Campylobacter.

Sproston EL, Wimalarathna HML, Sheppard SK.

Microb Genom. 2018 Jan;4(8). doi: 10.1099/mgen.0.000198. Epub 2018 Jul 19.

16.

Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA.

Yokoyama M, Stevens E, Laabei M, Bacon L, Heesom K, Bayliss S, Ooi N, O'Neill AJ, Murray E, Williams P, Lubben A, Reeksting S, Meric G, Pascoe B, Sheppard SK, Recker M, Hurst LD, Massey RC.

Genome Biol. 2018 Jul 18;19(1):94. doi: 10.1186/s13059-018-1469-2.

17.

Population genomics of bacterial host adaptation.

Sheppard SK, Guttman DS, Fitzgerald JR.

Nat Rev Genet. 2018 Sep;19(9):549-565. doi: 10.1038/s41576-018-0032-z. Review.

PMID:
29973680
18.

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015.

Thépault A, Rose V, Quesne S, Poezevara T, Béven V, Hirchaud E, Touzain F, Lucas P, Méric G, Mageiros L, Sheppard SK, Chemaly M, Rivoal K.

Sci Rep. 2018 Jun 18;8(1):9305. doi: 10.1038/s41598-018-27558-z.

19.

The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species.

Atterby C, Mourkas E, Méric G, Pascoe B, Wang H, Waldenström J, Sheppard SK, Olsen B, Järhult JD, Ellström P.

Front Microbiol. 2018 Mar 29;9:591. doi: 10.3389/fmicb.2018.00591. eCollection 2018.

20.

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria.

Thorpe HA, Bayliss SC, Sheppard SK, Feil EJ.

Gigascience. 2018 Apr 1;7(4):1-11. doi: 10.1093/gigascience/giy015.

21.

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.

22.

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism.

Méric G, McNally A, Pessia A, Mourkas E, Pascoe B, Mageiros L, Vehkala M, Corander J, Sheppard SK.

Genome Biol Evol. 2018 Mar 1;10(3):763-774. doi: 10.1093/gbe/evy026.

23.

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil.

Rossi GAM, Silva HO, Aguilar CEG, Rochetti AL, Pascoe B, Méric G, Mourkas E, Hitchings MD, Mathias LA, de Azevedo Ruiz VL, Fukumasu H, Sheppard SK, Vidal AMC.

FEMS Microbiol Lett. 2018 Feb 1;365(3). doi: 10.1093/femsle/fnx283.

PMID:
29390131
24.

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.

Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK, Thorlacius-Ussing O, Nielsen H.

Sci Rep. 2018 Jan 30;8(1):1902. doi: 10.1038/s41598-018-20135-4.

25.

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP.

Genetics. 2018 Mar;208(3):1247-1260. doi: 10.1534/genetics.117.300662. Epub 2018 Jan 12.

26.

Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes.

Florez-Cuadrado D, Ugarte-Ruiz M, Meric G, Quesada A, Porrero MC, Pascoe B, Sáez-Llorente JL, Orozco GL, Domínguez L, Sheppard SK.

Front Microbiol. 2017 Nov 15;8:2240. doi: 10.3389/fmicb.2017.02240. eCollection 2017.

27.

Corrigendum: Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry.

Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM.

Front Cell Infect Microbiol. 2017 Nov 14;7:480. doi: 10.3389/fcimb.2017.00480. eCollection 2017.

28.

Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter.

Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK.

Sci Rep. 2017 Aug 29;7(1):9650. doi: 10.1038/s41598-017-09483-9.

29.

Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry.

Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM.

Front Cell Infect Microbiol. 2017 Aug 11;7:354. doi: 10.3389/fcimb.2017.00354. eCollection 2017. Erratum in: Front Cell Infect Microbiol. 2017 Nov 14;7:480.

30.

Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome.

Post V, Harris LG, Morgenstern M, Mageiros L, Hitchings MD, Méric G, Pascoe B, Sheppard SK, Richards RG, Moriarty TF.

J Clin Microbiol. 2017 Oct;55(10):3089-3103. doi: 10.1128/JCM.00881-17. Epub 2017 Aug 9.

31.

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

Connor TR, Loman NJ, Thompson S, Smith A, Southgate J, Poplawski R, Bull MJ, Richardson E, Ismail M, Thompson SE, Kitchen C, Guest M, Bakke M, Sheppard SK, Pallen MJ.

Microb Genom. 2016 Sep 20;2(9):e000086. doi: 10.1099/mgen.0.000086. eCollection 2016 Sep.

32.

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.

33.

Correction: Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D.

PLoS Genet. 2017 Apr 14;13(4):e1006730. doi: 10.1371/journal.pgen.1006730. eCollection 2017 Apr.

34.

Bayesian identification of bacterial strains from sequencing data.

Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A.

Microb Genom. 2016 Aug 25;2(8):e000075. doi: 10.1099/mgen.0.000075. eCollection 2016 Aug.

35.

Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens.

Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK.

Microb Genom. 2016 Oct 21;2(10):e000089. doi: 10.1099/mgen.0.000089. eCollection 2016 Oct.

36.

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.

37.

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D.

PLoS Genet. 2017 Feb 23;13(2):e1006546. doi: 10.1371/journal.pgen.1006546. eCollection 2017 Feb. Erratum in: PLoS Genet. 2017 Apr 14;13(4):e1006730.

38.

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ.

Front Microbiol. 2017 Feb 3;8:121. doi: 10.3389/fmicb.2017.00121. eCollection 2017. Review.

39.

Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins.

Vale FF, Nunes A, Oleastro M, Gomes JP, Sampaio DA, Rocha R, Vítor JM, Engstrand L, Pascoe B, Berthenet E, Sheppard SK, Hitchings MD, Mégraud F, Vadivelu J, Lehours P.

Sci Rep. 2017 Feb 16;7:42471. doi: 10.1038/srep42471.

40.

Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.

Esson D, Gupta S, Bailey D, Wigley P, Wedley A, Mather AE, Méric G, Mastroeni P, Sheppard SK, Thomson NR, Parkhill J, Maskell DJ, Christie G, Grant AJ.

Microb Pathog. 2017 Mar;104:202-211. doi: 10.1016/j.micpath.2017.01.042. Epub 2017 Jan 25.

41.

Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni.

Thépault A, Méric G, Rivoal K, Pascoe B, Mageiros L, Touzain F, Rose V, Béven V, Chemaly M, Sheppard SK.

Appl Environ Microbiol. 2017 Mar 17;83(7). pii: e03085-16. doi: 10.1128/AEM.03085-16. Print 2017 Apr 1.

42.

Characterization of nasal methicillin-resistant Staphylococcus aureus isolated from international human and veterinary surgeons.

Post V, Harris LG, Morgenstern M, Geoff Richards R, Sheppard SK, Fintan Moriarty T.

J Med Microbiol. 2017 Mar;66(3):360-370. doi: 10.1099/jmm.0.000415. Epub 2017 Mar 20.

PMID:
28005521
43.

Genomic variations leading to alterations in cell morphology of Campylobacter spp.

Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell DJ, Grant AJ.

Sci Rep. 2016 Dec 2;6:38303. doi: 10.1038/srep38303.

44.

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.

45.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J.

PLoS Genet. 2016 Sep 12;12(9):e1006280. doi: 10.1371/journal.pgen.1006280. eCollection 2016 Sep.

47.

Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance.

Yan X, Li Z, Chlebowicz MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, van Dijl JM, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J.

Int J Med Microbiol. 2016 Dec;306(8):722-729. doi: 10.1016/j.ijmm.2016.08.001. Epub 2016 Aug 10.

PMID:
27528592
48.

Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides.

Culebro A, Revez J, Pascoe B, Friedmann Y, Hitchings MD, Stupak J, Sheppard SK, Li J, Rossi M.

J Bacteriol. 2016 Sep 22;198(20):2829-40. doi: 10.1128/JB.00347-16. Print 2016 Oct 15.

49.

Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.

Gilbert MJ, Miller WG, Yee E, Zomer AL, van der Graaf-van Bloois L, Fitzgerald C, Forbes KJ, Méric G, Sheppard SK, Wagenaar JA, Duim B.

Genome Biol Evol. 2016 Jul 2;8(6):2006-19. doi: 10.1093/gbe/evw146.

50.

From Escherich to the Escherichia coli genome.

Méric G, Hitchings MD, Pascoe B, Sheppard SK.

Lancet Infect Dis. 2016 Jun;16(6):634-636. doi: 10.1016/S1473-3099(16)30066-4. No abstract available.

PMID:
27301915

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