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Outputs

Papers

2018

Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group
Guillaume Méric Leonardos Mageiros  Ben Pascoe  Dan J. Woodcock  Evangelos Mourkas Sarah Lamble  Rory Bowden  Keith A. Jolley  Ben Raymond  Samuel K. Sheppard
Mol Ecol. 2018 Apr;27(7):1524-1540.
doi: 10.1111/mec.14546.
PMID: 29509989

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans
C. W. Knetsch, N. Kumar, S. C. Forster, T. R. Connor, H. P. Browne, C. Harmanus, I. M. Sanders, S. R. Harris, L. Turner, T. Morris, M. Perry, F. Miyajima, P. Roberts, M. Pirmohamed, J. G. Songer, J. S. Weese, A. Indra, J. Corver, M. Rupnik, B. W. Wren, T.V., Riley, E. J. Kuijper and T. D. Lawley
J. Clin. Microbiol. March 2018 vol. 56 no. 3 e01384-17.
doi: 10.1128/JCM.01384-1
PMID: 29237792

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, SK
Genome Biol Evol. 2018 Mar 1;10(3):763-774.
doi: 10.1093/gbe/evy026
PMID: 29452359

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria
Harry A Thorpe, Sion C Bayliss, Samuel K Sheppard, Edward J Feil
Gigascience. 2018 Apr 1;7(4):1-11
doi: 10.1093/gigascience/giy015
PMID: 29635296

2017

Bacterial Flagellins: Does Size Matter?
Thomson NM, Rossmann FM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ.
Trends Microbiol. 2017 Dec 16. pii: S0966-842X(17)30259-7. doi:10.1016/j.tim.2017.11.010. Review.
PMID:29258714

Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.
Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M.
PLoS One. 2017 Sep 19;12(9):e0184510.
doi: 10.1371/journal.pone.0184510. eCollection 2017.
PMID:28926571

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.
Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, Woodward MJ, Anjum MF.
MBio. 2017 Jul 18;8(4). pii: e00777-17.
doi: 10.1128/mBio.00777-17.
PMID:28720731

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?
Pallen MJ, Quraishi MN.
Dig Dis. 2017;35(4):377-383. doi: 10.1159/000456590. Epub 2017 May 3. Review.
PMID:28468018

Identification of the anti-mycobacterial functional properties of piperidinol derivatives.
Guy CS, Tichauer E, Kay GL, Phillips DJ, Bailey TL, Harrison J, Furze CM, Millard AD, Gibson MI, Pallen MJ, Fullam E.
Br J Pharmacol. 2017 Jul;174(14):2183-2193. doi: 10.1111/bph.13744. Epub 2017 Mar 23.
PMID:28195652

The Enigmatic Esx Proteins: Looking Beyond Mycobacteria.
Unnikrishnan M, Constantinidou C, Palmer T, Pallen MJ.
Trends Microbiol. 2017 Mar;25(3):192-204. doi: 10.1016/j.tim.2016.11.004. Epub 2016 Nov 25. Review.
PMID: 27894646

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.
PMID: 28338786

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.
PMID: 28205536

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.
PMID: 28231283

Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027, Originally Isolated from an Outer Ear Infection.
Jayal A, Johns BE, Purdy KJ, Maddocks SE.
Genome Announc. 2017 Nov 30;5(48). pii: e01397-17. doi: 10.1128/genomeA.01397-17.
PMID: 29192089

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR.
Microb Genom. 2017 Sep 4;3(10):e000131. doi: 10.1099/mgen.0.000131. eCollection 2017 Oct.
PMID: 29177089

Comparison of classical multi-locus sequence typing software for next-generation sequencing data.
Page AJ, Alikhan NF, Carleton HA, Seemann T, Keane JA, Katz LS.
Microb Genom. 2017 Jul 4;3(8):e000124. doi: 10.1099/mgen.0.000124. eCollection 2017 Aug. Review.
PMID: 29026660

Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species.
Thorpe HA, Bayliss SC, Hurst LD, Feil EJ.
Genetics. 2017 May;206(1):363-376. doi: 10.1534/genetics.116.195784. Epub 2017 Mar 9.
PMID: 28280056

Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors
Connelly, Stephanie, Shin, Seung G., Dillon, Robert J., Ijaz, Umer Z., Quince, Christopher, Sloan, William T. and Collins, Gavin
Front Microbiol. 2017 May 1;8:664. doi:10.3389/fmicb.2017.00664
PMID: 28507535

DESMAN: a new tool for de novo extraction of strains from metagenomes
Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G. and Eren, A. M.
Genome Biol. 2017 Sep 21;18(1):181. doi:10.1186/s13059-017-1309-9
PMID:28934976

Shotgun metagenomics, from sampling to analysis
Quince, C, Walker, AW, Simpson, JT, Loman, NJ & Segata, N
Nat Biotechnol. 2017 Sep 12;35(9):833-844 . doi: 10.1038/nbt.3935
PMID: 28898207

Comparative Genomics of Bacteriophage of the Genus Seuratvirus
Pavelas Sazinas Tamsin Redgwell Branko Rihtman Aurelija Grigonyte Slawomir Michniewski David J Scanlan Jon Hobman Andrew Millard
Genome Biol Evol. 2018 Jan 1;10(1):72-76. doi: 10.1093/gbe/evx275
PMID: 29272407

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred
Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nick Loman, Szymon T. Calus, Martin Bertz, Christine A. Edwards, Daniel R. Gaya, Richard Hansen, Paraic McGrogan, Richard K. Russell, Konstantinos Gerasimidis
PLoS One. 2017 Feb 21;12(2):e0172605. doi: 10.1371/journal.pone.0172605
PMID: 28222161

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 and Sheppard SK
Front Microbiol. 2017 Nov 15;8:2240. doi: 10.3389/fmicb.2017.02240
PMID: 29187841

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
Koji Yahara, Guillaume Méric, Aidan J. Taylor, Stefan P. W. de Vries, Susan Murray, Ben Pascoe, Leonardos Mageiros, Alicia Torralbo, Ana Vidal, Anne Ridley, Sho Komukai, Helen Wimalarathna, Alison J. Cody, Frances M. Colles, Noel McCarthy, David Harris, James E. Bray, Keith A. Jolley, Martin C. J. Maiden, Stephen D. Bentley, Julian Parkhill, Christopher D. Bayliss, Andrew Grant, Duncan Maskell, Xavier Didelot, David J. Kelly, Samuel K. Sheppard
Environ Microbiol. 2017 Jan;19(1):361-380. doi: 10.1111/1462-2920.13628
PMID: 27883255

Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape
Diane Esson, Srishti Gupta, David Bailey, Paul Wigley, Amy Wedley, Alison E. Mather, Guillaume Méric, Pietro Mastroeni, Samuel K. Sheppard, Nicholas R. Thomson, Julian Parkhill, Duncan J. Maskell, Graham Christie, Andrew J. Grant
Microb Pathog. 2017 Mar;104:202-211. doi: 10.1016/j.micpath.2017.01.042
PMID: 28131954

Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex
Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW, Khan Z, Neilson L, Tomeva M, Adams SE, Wood AC, Rodriguez-Martin D, Pinel I, Parkhill J, Mahenthiralingam E, Crosby J.
J Bacteriol. 2017 Jun 13;199(13). doi: 10.1128/JB.00125-17.
PMID: 28439036

Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1
Owen SV, Wenner N, Canals R, Makumi A, Hammarlöf DL, Gordon MA, Aertsen A, Feasey NA and Hinton JCD
Front Microbiol. 2017 Feb 23;8:235. doi: 10.3389/fmicb.2017.00235.
PMID: 28280485

Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
Amandine Thépault Guillaume Méric, Katell Rivoal, Ben Pascoe, Leonardos Mageiros, Fabrice Touzain, Valérie Rose, Véronique Béven, Marianne Chemaly, and Samuel K. Sheppard
Appl Environ Microbiol. 2017 Mar 17;83(7). pii: e03085-16. doi: 10.1128/AEM.03085-16.
PMID: 28115376

Draft Genome Sequence of Bacteriophage vB_Eco_swan01
Michniewski S, Redgwell T, Scanlan DJ, Millard AD
Send to
Genome Announc. 2017 Jul 13;5(28). pii: e00501-17. doi: 10.1128/genomeA.00501-17.
PMID: 28705961

Genomic variation and evolution of Vibrio parahaemolyticus ST36 over the course of a transcontinental epidemic expansion
Martinez-Urtaza J, van Aerle R, Abanto M, Haendiges J, Myers RA, Trinanes J, Baker-Austin C, Gonzalez-Escalona N
MBio. 2017 Nov 14;8(6). pii: e01425-17. doi: 10.1128/mBio.01425-17.
PMID: 29138301

 

2016

Lucas Sinclair, Umer Z Ijaz, Lars Juhl Jensen, Marco JL Coolen, Cecile Gubry-Rangin, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis 2016. Seqenv: linking sequences to environments through text mining. PeerJ 4: e2690.

Pascoe B, Meric G, Yahara K, Wimaralathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MC, McCarthy ND, Didelot X, Parker C, Sheppard SK. (2016) Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations. PeerJ Preprints 4:e2638v1

Esson D, Mather AE, Scanlan E, Gupta S, de Vries SPW, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell D, Grant AJ. (2016) Genomic variations leading to alterations in cell morphology of Campylobacter spp. Scientific Reports 6:38303. 

Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK. (2016) Genomic plasticity and rapid host switching promote the evolution of generalism in the zoonotic pathogen Campylobacter. bioRxiv 080077; doi:10.1101/

Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK. (2016) Population-genomic insights into emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens. Microbial Genomics 2(10): doi:10.1099/mgen.0.000089

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. (2016) Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations. PLoS Genetics 12(9): e1006280. doi: 10.1371/journal.pgen.1006280

Yana X, Li Z, Chlebowiczc MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, Maarten van Dijl J, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J. (2016) Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance. International Journal of Medical Microbiology 306(8):722–729

Thorell K, Yahara K, Berthenet E, Lawson DJ, Kato I, Tenorio Mendez A, Canzian F, Mercedes Bravo M, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D. (2016) Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Culebro A, Revez J, Pascoe B, Friedmann Y, Hitchings MD, Stupak J, Sheppard SK, Li J, Rossi M. (2016) Large sequence diversity within biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides. Journal of Bacteriology 198(20):2829-40

Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A. (2016) Bayesian identification of bacterial strains from sequencing data. Microbial Genomics 2(8): doi:10.1099/mgen.0.000075

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. (2016) Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. Genome Biology and Evolution. 2;8(6):2006-19.

Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BM, Gally DL. Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle. Scientific Reports. 25(6):26589.

Jessica L Ray, Julia Althammer, Katrine S Skaar, Paolo Simonelli, Aud Larsen, Diane Stoecker, Andrey Sazhin, Umer Z Ijaz, Christopher Quince, Jens C Nejstgaard, Marc Frischer, Georg Pohnert, Christofer Troedsson. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities 2016. Molecular ecology 25 (21): 5585-5602.

Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé. VSEARCH: a versatile open source tool for metagenomics 2016. PeerJ 4: e2584.

Konstantinos Gerasimidis, Martin Bertz, Christopher Quince, Katja Brunner, Alanna Bruce, Emilie Combet, Szymon Calus, Nick Loman, Umer Zeeshan Ijaz 2016. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes 9 (1): 365.

Stefanie Widder, Rosalind J Allen, Thomas Pfeiffer, Thomas P Curtis, Carsten Wiuf, William T Sloan, Otto X Cordero, Sam P Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J Flint, Andreas F Haas, Béatrice Laroche, Jan-Ulrich Kreft, Paul B Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R van der Meer, Tobias Groβkopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F Smets, Harris Wang, Orkun S Soyer 2016. Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME journal 10(11):2557-2568.

Melanie Schirmer, Rosalinda D’Amore, Umer Z Ijaz, Neil Hall, Christopher Quince 2016. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC bioinformatics 17 (1): 1

Sarah-Jane Haig, Caroline Gauchotte-Lindsay, Gavin Collins, Christopher Quince 2016. Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters. Environmental science & technology 50 (6): 3101-3110

Belen Torondel, Jeroen HJ Ensink, Ozan Gundogdu, Umer Zeeshan Ijaz, Julian Parkhill, Faraji Abdelahi, Viet‐Anh Nguyen, Steven Sudgen, Walter Gibson, Alan W Walker, Christopher Quince 2016. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial biotechnology 9 (2): 209-223.

Eduard Vico Oton, Christopher Quince, Graeme W Nicol, James I Prosser, Cécile Gubry-Rangin 2016. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota 2016. The ISME journal 10(1): 85-96.

Connor, T.R et al. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics. Aug 2016 doi: 10.1099/mgen.0.000086

Quick J, Loman NJ et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 11;530(7589):228-32. doi: 10.1038/nature16996. Epub 2016 Feb 3.

 

2015

Connor, T.R et al. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 2015;4:e07335

Gesing S, Connor TR and Ian Taylor.  Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility. 2015 Nov. arXiv:1511.02689

D’Amore, R., U. Z. Ijaz, M. Schirmer, J. Kenny, R. Gregory, A. C. Darby, M. Shakya, M. Podar, C. Quince, and N. Hall 2015. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. Accepted BMC Genomics.

Quince, C., U. Z. Ijaz, N. Loman, A. M. Eren, D. Saulnier, J. Russell, S. J. Haig, S. T. Calus, J. Quick, A. Barclay, M. Bertz, M. Blaut, R. Hansen, P. McGrogan, R. K. Russell, C. A. Edwards, and K. Gerasimidis 2015. Extensive modulation of the fecal metagenome in children with Crohn’s disease during exclusive enteral nutrition. American Journal of Gastroenterolgy doi: 10.1038/ajg.2015.357.

Haig, S. J., C. Quince, R.L. Davies, C.C. Dorea, and G. Collins, 2015. The relationship between microbial community evenness and function in slow sand filters. mBio 6, e00729-15.

Oton, E.V., C. Quince, G. W. Nicol, J. I. Prosser, and C. Gubry-Rangin 2015. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal doi:10.1038/ismej.2015.101.

Harris, K., T.L. Parsons, U.Z. Ijaz, L. Lahti, I. Holmes, and C. Quince, 2015. Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE: doi: 10.1109/JPROC.2015.2428213.

 

Talks

Microbiomes and metagenomes: window on the past, promises for the future   Midlands Molecular Microbiology meeting     Nottingham    September 2015

Genomics and metagenomics in medical microbiology: opportunities and challenges  BMFZ meeting   Düsseldorf     November 2015

Implementing a nationwide cyber infrastructure for microbiology: CLIMB    UCISA Infrastructure Group Meeting  Oxford October 2015

Bioinformatics showcase  Applied Bioinformatics and Public Health Microbiology Cambridge  May 2015

CLIMB  Balti and Bioinformatics     Birmingham  May   2014

 

 

Training

For a list of past training events please follow see our training page