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2020

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni

Mourkas, E., Taylor, A. J., Méric, G., Bayliss, S. C., Pascoe, B., Mageiros, L., Calland, J. K., Hitchings, M. D., Ridley, A., Vidal, A., Forbes, K. J., Strachan, N. J. C., Parker, C. T., Parkhill, J., Jolley, K. A., Cody, A. J., Maiden, M. C. J., Kelly, D. J. & Sheppard, S. K., 4 May 2020, In : Proceedings of the National Academy of Sciences.

Research output: Contribution to journalArticle

Open Access

High-resolution sweep metagenomics using fast probabilistic inference

Mäklin, T., Kallonen, T., David, S., Boinett, C. J., Pascoe, B., Méric, G., Aanensen, D. M., Feil, E. J., Baker, S., Parkhill, J., Sheppard, S. K., Corander, J. & Honkela, A., 30 Jan 2020, In : Wellcome Open Research. 5, p. 14

Research output: Contribution to journalArticle

Open Access

The emergence of plasmid-borne cfr-mediated linezolid resistant-staphylococci in Vietnam

Nguyen, L. T. T., Nguyen, K. N. T., Le, P. N. T. A., Cafini, F., Pascoe, B., Sheppard, S. K., Nguyen, T. B., Hoang, T. P. N., Nguyen, T. V., Pham, T. T. K., Morikawa, K., Nguyen, D. Q. & Duong, H. X., 27 Apr 2020, In : Journal of Global Antimicrobial Resistance.

Research output: Contribution to journalArticle

Open Access
2019

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, S. K., Pascoe, B. & Patchanee, P., 2 Sep 2019, In : International Journal of Food Microbiology. 304, p. 68-74 7 p.

Research output: Contribution to journalArticle

Open Access
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Domestication of Campylobacter jejuni NCTC 11168

Pascoe, B., Williams, L. K., Calland, J. K., Meric, G., Hitchings, M. D., Dyer, M., Ryder, J., Shaw, S., Lopes, B. S., Chintoan-Uta, C., Allan, E., Vidal, A., Fearnley, C., Everest, P., Pachebat, J. A., Cogan, T. A., Stevens, M. P., Humphrey, T. J., Wilkinson, T. S., Cody, A. J. & 12 others, Colles, F. M., Jolley, K. A., Maiden, M. C. J., Strachan, N., Pearson, B. M., Linton, D., Wren, B. W., Parkhill, J., Kelly, D. J., van Vliet, A. H. M., Forbes, K. J. & Sheppard, S. K., 1 Jul 2019, In : Microbial Genomics. 5, 7, 000279.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

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

Mourkas, E., Florez-Cuadrado, D., Pascoe, B., Calland, J. K., Bayliss, S. C., Mageiros, L., Méric, G., Hitchings, M. D., Quesada, A., Porrero, C., Ugarte-Ruiz, M., Gutiérrez-Fernández, J., Domínguez, L. & Sheppard, S. K., 5 Aug 2019, In : Environmental Microbiology. p. 1-17 17 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Genetic diversity of composite enterotoxigenic Staphylococcus epidermidis pathogenicity islands

Banaszkiewicz, S., Calland, J., Mourkas, E., Sheppard, S., Pascoe, B. & Bania, J., 1 Dec 2019, In : Genome biology and evolution. 11, 12, p. 3498-3509 evz259.

Research output: Contribution to journalArticle

Open Access

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, M. D., Sheppard, S. K. & Williams, N. J., 1 Jan 2019, In : Veterinary Record Open. 6, 1, e000307.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)
2018

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, J. M., Engstrand, L., Enroth, H., Burette, A., Megraud, F., Varon, C., Atherton, J. C., Smith, S., Wilkinson, T. S., Hitchings, M. D., Falush, D. & Sheppard, S. K., 2 Aug 2018, In : BMC Biology. 16, p. 1-11 11 p., 84.

Research output: Contribution to journalArticle

Open Access
10 Citations (Scopus)

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

Marques Rossi, G. A., Silva, H. O., Gamero Aguilar, C. E., Rochetti, A. L., Pascoe, B., Méric, G., Mourkas, E., Hitchings, M. D., Mathias, L. A., De Azevedo Ruiz, V. L., Fukumasu, H., Sheppard, S. K. & Centola Vidal, A. M., 1 Feb 2018, In : FEMS Microbiology Letters. 365, 3, p. 1 - 9 9 p., fnx283.

Research output: Contribution to journalArticle

Open Access
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2 Citations (Scopus)
38 Downloads (Pure)

Convergent amino acid signatures in polyphyletic Campylobacter jejuni sub-populations suggest human niche tropism

Méric, G., McNally, A., Pessia, A., Mourkas, E., Pascoe, B., Mageiros, L., Vehkala, M., Corander, J. & Sheppard, S. K., 1 Mar 2018, In : Genome biology and evolution. 10, 3, p. 763-774 12 p.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

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, J. E., Morgenstern, M., Jolley, K. A., Maiden, M. C. J., Feil, E. J., Didelot, X., Miragaia, M., de Lencastre, H., Moriarty, T. F. & 5 others, Rohde, H., Massey, R., Mack, D., Corander, J. & Sheppard, S. K., 1 Dec 2018, In : Nature Communications. 9, 1, p. 1-11 11 p., 5034.

Research output: Contribution to journalArticle

Open Access
13 Citations (Scopus)

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, A. J., Murray, E., Williams, P., Lubben, A., Reeksting, S., Meric, G., Pascoe, B., Sheppard, S. K., Recker, M., Hurst, L. D. & Massey, R. C., 18 Jul 2018, In : Genome Biology. 19, 1, p. 1-12 12 p., 94.

Research output: Contribution to journalArticle

Open Access
8 Citations (Scopus)

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

Dunn, S. J., Pascoe, B., Turton, J., Fleming, V., Diggle, M., Sheppard, S. K., McNally, A. & Manning, G., 11 Oct 2018, In : Microbial Genomics. 4, 10, p. 1-8 8 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

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

Bayliss, S. C., Verner-Jeffreys, D. W., Ryder, D., Suarez, R., Ramirez, R., Romero, J., Pascoe, B., Sheppard, S. K., Godoy, M. & Feil, E. J., 1 Sep 2018, In : Microbial Genomics. 4, 9, 12 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

High resolution whole genome multilocus sequence typing (wgMLST) schemes for Salmonella enterica Weltevreden epidemiologic investigations

Tadee, P., Tadee, P., Hitchings, M. D., Pascoe, B., Sheppard, S. & Patchanee, P., 1 Jun 2018, In : Microbiology and Biotechnology Letters. 46, 2, p. 162-170 9 p.

Research output: Contribution to journalArticle

Open Access

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, D. J., Mourkas, E., Lamble, S., Bowden, R., Jolley, K. A., Raymond, B. & Sheppard, S. K., 1 Apr 2018, In : Molecular Ecology. 27, 7, p. 1524-1540 17 p.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

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

Kirk, K. F., Méric, G., Nielsen, H. L., Pascoe, B., Sheppard, S. K., Thorlacius-Ussing, O. & Nielsen, H., 30 Jan 2018, In : Scientific Reports. 8, 1, 1902.

Research output: Contribution to journalArticle

Open Access
12 Citations (Scopus)

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, S. K., Olsen, B., Järhult, J. D. & Ellström, P., 29 Mar 2018, In : Frontiers in Microbiology. 9, p. 1-12 12 p., 591.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)
2017

A comparative genomics study of Staphylococcus epidermidis from orthopedic device-related infections correlated with patient outcome

Post, V., Harris, L. G., Morgenstern, M., Mageiros, L., Hitchings, M. D., Méric, G., Pascoe, B., Sheppard, S. K., Richards, R. G. & Moriarty, T. F., 1 Oct 2017, In : Journal of Clinical Microbiology. 55, 10, p. 3089-3103 00881-17.

Research output: Contribution to journalArticle

Open Access
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22 Citations (Scopus)
112 Downloads (Pure)

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, M. C., Pascoe, B., Sáez-Llorente, J. L., Orozco, G. L., Domínguez, L. & Sheppard, S. K., 2017, In : Frontiers in Microbiology. 8, 8 p., 2240.

Research output: Contribution to journalArticle

Open Access
14 Citations (Scopus)

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

Yahara, K., Méric, G., Taylor, A. J., de Vries, S. P. W., Murray, S., Pascoe, B., Mageiros, L., Torralbo, A., Vidal, A., Ridley, A., Komukai, S., Wimalarathna, H., Cody, A. J., Colles, F. M., McCarthy, N., Harris, D., Bray, J. E., Jolley, K. A., Maiden, M. C. J., Bentley, S. D. & 7 others, Parkhill, J., Bayliss, C. D., Grant, A., Maskell, D., Didelot, X., Kelly, D. J. & Sheppard, S. K., 25 Jan 2017, In : Environmental Microbiology. 19, 1, p. 361-380

Research output: Contribution to journalArticle

Open Access
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32 Citations (Scopus)
145 Downloads (Pure)

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, S. K., Apr 2017, In : Applied and Environmental Microbiology. 83, 7, e03085-16.

Research output: Contribution to journalArticle

Open Access
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27 Citations (Scopus)
131 Downloads (Pure)

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

Vale, F. F., Nunes, A., Oleastro, M., Gomes, J. P., Sampaio, D. A., Rocha, R., Vítor, J. M. B., Engstrand, L., Pascoe, B., Berthenet, E., Sheppard, S. K., Hitchings, M. D., Mégraud, F., Vadivelu, J. & Lehours, P., 16 Feb 2017, In : Scientific Reports. 7, p. 42471

Research output: Contribution to journalArticle

Open Access
15 Citations (Scopus)

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, M. D., Sproston, E. L., Carrillo, C. D., Taboada, E. N., Cooper, K. K., Huynh, S., Cody, A. J., Jolley, K. A., Maiden, M. C. J., McCarthy, N. D., Didelot, X., Parker, C. T. & Sheppard, S. K., 24 Aug 2017, In : Molecular Ecology. 26, 17, p. 4497–4508

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)
130 Downloads (Pure)

Recombination-mediated host-adaptation by avian Staphylococcus aureus

Murray, S., Pascoe, B., Méric, G., Mageiros, L., Yahara, K., Hitchings, M. D., Friedmann, Y., Wilkinson, T. S., Gormley, F. J., Mack, D., Bray, J. E., Lamble, S., Bowden, R., Jolley, K. A., Maiden, M. C. J., Wendlandt, S., Schwarz, S., Corander, J., Ross Fitzgerald, J. & Sheppard, S. K., 1 Apr 2017, In : Genome biology and evolution. 9, 4, p. 830-842

Research output: Contribution to journalArticle

Open Access
11 Citations (Scopus)
2016

Bayesian identification of bacterial strains from sequencing data

Sankar, A., Malone, B., Bayliss, S., Pascoe, B., Méric, G., Hitchings, M. D., Sheppard, S. K., Feil, E. J., Corander, J. & Honkela, A., 1 Aug 2016, In : Microbial Genomics. 2, 8, p. e000075 9 p.

Research output: Contribution to journalArticle

Open Access
File
4 Citations (Scopus)
122 Downloads (Pure)

Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples

Harris, L. G., Murray, S., Pascoe, B., Bray, J., Meric, G., Magerios, L., Wilkinson, T. S., Jeeves, R., Rohde, H., Schwarz, S., de Lencastre, H., Miragaia, M., Rolo, J., Bowden, R., Jolley, K. A., Maiden, M. C. J., Mack, D. & Sheppard, S. K., 15 Mar 2016, In : PLoS ONE. 11, 3, p. e0151240

Research output: Contribution to journalArticle

Open Access
22 Citations (Scopus)

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, M. B., Ashour, A., Avram, O., Pupko, T., Dobrindt, U., Literak, I., Guenther, S., Schaufler, K., Wieler, L. H., Zhiyong, Z., Sheppard, S. K., McInerney, J. O. & 1 others, Corander, J., 12 Sep 2016, In : Plos Genetics. 12, 9, p. e1006280

Research output: Contribution to journalArticle

Open Access
63 Citations (Scopus)

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

Harris, L. G., Murray, S., Pascoe, B., Bray, J. E., Meric, G., Mageiros, L., Wilkinson, T. S., Jeeves, R., Rohde, H., Schwarz, S., de Lencastre, H., Miragaia, M., Rolo, J., Bowden, R., Jolley, K. A., Maiden, M. C. J., Mack, D. & Sheppard, S. K., 21 Apr 2016, In : PLoS ONE. 11, 4, e0154510.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)

Draft genome sequence of an Enterobacter species associated with illnesses and powdered infant formula

Jackson, E. E., Ogrodzki, P., Pascoe, B., Sheppard, S. K. & Forsythe, S. J., 14 Jan 2016, In : Genome announcements. 4, 1, p. e01479-15

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

From Escherich to the Escherichia coli genome

Méric, G., Hitchings, M. D., Pascoe, B. & Sheppard, S. K., Jun 2016, In : The Lancet Infectious Diseases. 16, 6, p. 634-636 3 p.

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)
152 Downloads (Pure)

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, M. A., Tao, X., Ni, M., Hu, Y., Li, Z., Grundmann, H., Murray, S., Pascoe, B., Sheppard, S. K., Bo, X., Dijl, J. M. V., Du, P., Zhang, M., You, Y., Yu, X., Meng, F., Wang, S. & Zhang, J., Dec 2016, In : International Journal of Medical Microbiology. 306, 8, p. 722–729

Research output: Contribution to journalArticle

Open Access
File
11 Citations (Scopus)
152 Downloads (Pure)

Large sequence diversity within biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides

Culebro, A., Revez, J., Pascoe, B., Friedmann, Y., Hitchings, M. D., Stupak, J., Sheppard, S. K., Li, J. & Rossi, M., Oct 2016, In : Journal of Bacteriology. 198, 20, p. 2829-2840

Research output: Contribution to journalArticle

3 Citations (Scopus)

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections

Dearlove, B. L., Cody, A. J., Pascoe, B., Meric, G., Wilson, D. J. & Sheppard, S. K., 1 Mar 2016, In : ISME Journal. 10, 3, p. 721-729 9 p.

Research output: Contribution to journalArticle

Open Access
47 Citations (Scopus)
2015

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, L. G., Wilkinson, T. S., Rolo, J., Lamble, S., Bray, J. E., Jolley, K. A., Hanage, W. P., Bowden, R., Maiden, M. C. J., Mack, D., de Lencastre, H., Feil, E. J., Corander, J. & 1 others, Sheppard, S. K., May 2015, In : Genome biology and evolution. 7, 5, p. 1313-1328 16 p.

Research output: Contribution to journalArticle

Open Access
54 Citations (Scopus)

Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni

Pascoe, B., Méric, G., Murray, S., Yahara, K., Mageiros, L., Bowen, R., Jones, N. H., Jeeves, R. E., Lappin-Scott, H. M., Asakura, H. & Sheppard, S. K., Nov 2015, In : Environmental Microbiology. 17, 11, p. 4779-4789 11 p.

Research output: Contribution to journalArticle

Open Access
35 Citations (Scopus)

Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species

Baily, J. L., Méric, G., Bayliss, S., Foster, G., Moss, S. E., Watson, E., Pascoe, B., Mikhail, J., Pizzi, R., Goldstone, R. J., Smith, D. G. E., Willoughby, K., Hall, A. J., Sheppard, S. K. & Dagleish, M. P., 6 Jan 2015, In : Molecular Ecology. 24, 1, p. 208-221 14 p.

Research output: Contribution to journalArticle

Open Access
File
9 Citations (Scopus)
107 Downloads (Pure)

Persistent Staphylococcus aureus isolates from two independent cases of bacteremia display increased bacterial fitness and novel immune evasion phenotypes

Richards, R. L., Haigh, R. D., Pascoe, B., Sheppard, S. K., Price, F., Jenkins, D., Rajakumar, K. & Morrissey, J. A., Aug 2015, In : Infection and immunity. 83, 8, p. 3311-3324 14 p.

Research output: Contribution to journalArticle

Open Access
11 Citations (Scopus)
2014

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, M. C. J., Jolley, K. A. & Sheppard, S. K., 27 Mar 2014, In : PLoS ONE. 9, 3, p. e92798

Research output: Contribution to journalArticle

Open Access
60 Citations (Scopus)

Dormant cells of Staphylococcus aureus are resuscitated by spent culture supernatant

Pascoe, B., Dams, L., Wilkinson, T. S., Harris, L. G., Bodger, O., Mack, D. & Davies, A. P., Feb 2014, In : PLoS ONE. 9, 2, p. e85998

Research output: Contribution to journalArticle

Open Access
14 Citations (Scopus)
2013

Progressive genome-wide introgression in agricultural Campylobacter coli

Sheppard, S. K., Didelot, X., Jolley, K. A., Darling, A. E., Pascoe, B., Meric, G., Kelly, D. J., Cody, A., Colles, F. M., Strachan, N. J. C., Ogden, I. D., Forbes, K., French, N. P., Carter, P., Miller, W. G., McCarthy, N. D., Owen, R., Litrup, E., Egholm, M., Affourtit, J. P. & 4 others, Bentley, S. D., Parkhill, J., Maiden, M. C. J. & Falush, D., Feb 2013, In : Molecular Ecology. 22, 4, p. 1051-1064 14 p.

Research output: Contribution to journalArticle

Open Access
72 Citations (Scopus)
2011

Mechanisms of staphylococcus epidermidis biofilm formation in different types of biomaterial-related infections

Mack, D., Harris, L. G., Jeeves, R., Pascoe, B., Davis, A. P. & Wilkinson, T. S., 1 Jul 2011, In : European Cells and Materials. 21, 2, p. 21 1 p.

Research output: Contribution to journalArticle

2010

The zinc-responsive regulator Zur controls expression of the coelibactin gene cluster in Streptomyces coelicolor

Kallifidas, D., Pascoe, B., Owen, G. A., Strain-Damerell, C. M., Hong, H-J. & Paget, M. S. B., Jan 2010, In : Journal of Bacteriology. 192, 2, p. 608-611 4 p.

Research output: Contribution to journalArticle

44 Citations (Scopus)
2007

Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and σR▿

Owen, G. A., Pascoe, B., Kallifidas, D. & Paget, M. S. B., Jun 2007, In : Journal of Bacteriology. 189, 11, p. 4078-4086 9 p.

Research output: Contribution to journalArticle

55 Citations (Scopus)