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Outputs

Papers

2019

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition.
Svolos V, Hansen R, Nichols B, Quince C, Ijaz UZ, Papadopoulou RT, Edwards CA, Watson D, Alghamdi A, Brejnrod A, Ansalone C, Duncan H, Gervais L, Tayler R, Salmond J, Bolognini D, Klopfleisch R, Gaya DR, Milling S, Russell RK, Gerasimidis K.
Gastroenterology. 2019 Apr;156(5):1354-1367.e6. doi: 10.1053/j.gastro.2018.12.002. Epub 2018 Dec 11.
PMID: 30550821

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG.
Genome Biol. 2019 Jan 8;20(1):8. doi: 10.1186/s13059-018-1618-7.
PMID: 30621750

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N.
Cell. 2019 Jan 24;176(3):649-662.e20. doi: 10.1016/j.cell.2019.01.001. Epub 2019 Jan 17.
PMID: 30661755

Reply to ‘Errors in long-read assemblies can critically affect protein prediction’.
Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2019 Feb;37(2):127-128. doi: 10.1038/s41587-018-0005-y. No abstract available.
PMID: 30670797

Prevalence of faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coliin 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.
PMID: 30687506

Riding the wave of genomics to investigate aquatic coliphage diversity and activity.
Michniewski S, Redgwell T, Grigonyte A, Rihtman B, Aguilo-Ferretjans M, Christie-Oleza J, Jameson E, Scanlan DJ, Millard AD.
Environ Microbiol. 2019 Mar 18. doi: 10.1111/1462-2920.14590. [Epub ahead of print]
PMID: 30884081

 

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

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells.
Heidrich ES, Dolfing J, Wade MJ, Sloan WT, Quince C, Curtis TP.
Bioelectrochemistry. 2018 Feb;119:43-50. doi: 10.1016/j.bioelechem.2017.07.006. Epub 2017 Jul 22.
PMID: 28910698

Towards a genomics-informed, real-time, global pathogen surveillance system.
Gardy JL, Loman NJ.
Nat Rev Genet. 2018 Jan;19(1):9-20. doi: 10.1038/nrg.2017.88. Epub 2017 Nov 13. Review.
PMID: 29129921

Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O’Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.
Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13.
PMID: 29255284

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.
PMID: 29382867

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

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O’Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.
PMID: 29431738

Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.
Azevedo Antunes C, Richardson EJ, Quick J, Fuentes-Utrilla P, Isom GL, Goodall EC, Möller J, Hoskisson PA, Mattos-Guaraldi AL, Cunningham AF, Loman NJ, Sangal V, Burkovski A, Henderson IR.
Genome Announc. 2018 Feb 1;6(5). pii: e01566-17. doi: 10.1128/genomeA.01566-17.
PMID: 29437107

RADpainter and fineRADstructure: Population Inference from RADseq Data.
Malinsky M, Trucchi E, Lawson DJ, Falush D.
Mol Biol Evol. 2018 May 1;35(5):1284-1290. doi: 10.1093/molbev/msy023.
PMID: 29474601

Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015.
Pini A, Zomahoun D, Duraffour S, Derrough T, Charles M, Quick J, Loman N, Cowley L, Leno M, Ouedraogo N, Thiam O, Hernández-Romieu A, Iko A, Keita H, Konate D, Soumah AA, Bouchouar E, Ileka-Priouzeau S, Keita S, Diallo B, Cisse F, Jansa J, Carroll M, Günther S, Severi E, Formenty P.
Euro Surveill. 2018 Mar;23(12). doi: 10.2807/1560-7917.ES.2018.23.12.17-00140.
PMID: 29589579

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.
Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O’Flaherty V, Abram F.
Front Microbiol. 2018 Mar 21;9:540. doi: 10.3389/fmicb.2018.00540. eCollection 2018.
PMID: 29619022

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.
Nat Microbiol. 2018 Jul;3(7):804-813. doi: 10.1038/s41564-018-0176-9. Epub 2018 Jun 11. Erratum in: Nat Microbiol. 2018 Aug;3(8):963.
PMID: 29891866

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.
PMID: 30021593

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.
PMID: 30024366

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.
PMID: 30307843

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.
Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M.
Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19.
PMID: 30033331

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.
PMID: 30040063

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.
PMID: 30071832

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots.
Lawson DJ, van Dorp L, Falush D.
Nat Commun. 2018 Aug 14;9(1):3258. doi: 10.1038/s41467-018-05257-7.
PMID: 30108219

Genomic and epidemiological monitoring of yellow fever virus transmission potential.
Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG.
Science. 2018 Aug 31;361(6405):894-899. doi: 10.1126/science.aat7115. Epub 2018 Aug 23.
PMID: 30139911

Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.
Ring N, Abrahams JS, Jain M, Olsen H, Preston A, Bagby S.
Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000234. Epub 2018 Nov 21.
PMID: 30461375

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.
PMID: 30487573

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

Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child.
Sissoko D, Keïta M, Diallo B, Aliabadi N, Fitter DL, Dahl BA, Akoi Bore J, Raymond Koundouno F, Singethan K, Meisel S, Enkirch T, Mazzarelli A, Amburgey V, Faye O, Alpha Sall A, Magassouba N, Carroll MW, Anglaret X, Malvy D, Formenty P, Bruce Aylward R, Keïta S, Harouna Djingarey M, Loman NJ, Günther S, Duraffour S.
Clin Infect Dis. 2017 Feb 15;64(4):513-516. doi: 10.1093/cid/ciw793.
PMID: 27940938

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.
Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.
PMID: 28967888

Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.
Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.
PMID: 28405027

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

First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador.
Márquez S, Carrera J, Pullan ST, Lewandowski K, Paz V, Loman N, Quick J, Bonsall D, Powell R, Thézé J, Pybus OG, Klenerman P, Eisenberg J, Coloma J, Carroll MW, Trueba G, Logue CH.
Genome Announc. 2017 Feb 23;5(8). pii: e01673-16. doi: 10.1128/genomeA.01673-16.
PMID: 28232448

 

2016

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections.
Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK.ISME J. 2016 Mar;10(3):721-9. doi: 10.1038/ismej.2015.149. Epub 2015 Aug 25.
PMID: 26305157

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.
PMID: 26516092

Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq.
Rashid SR, Clokie MR, Millard AD.
Genome Announc. 2016 Feb 25;4(1). pii: e00033-16. doi: 10.1128/genomeA.00033-16.
PMID: 26950326

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes.
Rihtman B, Meaden S, Clokie MR, Koskella B, Millard AD.
PeerJ. 2016 Jun 1;4:e2055. doi: 10.7717/peerj.2055. eCollection 2016.
PMID: 27280068

Mobile real-time surveillance of Zika virus in Brazil.
Faria NR, Sabino EC, Nunes MR, Alcantara LC, Loman NJ, Pybus OG.
Genome Med. 2016 Sep 29;8(1):97.
PMID: 27683027

Seqenv: linking sequences to environments through text mining.
Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E.
PeerJ. 2016 Dec 20;4:e2690. doi: 10.7717/peerj.2690. eCollection 2016.
PMID: 28028456

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.
PMID: 28493321

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.
PMID: 27910897

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.
Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.
Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.
PMID: 28538723

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.
Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.
PMID: 28538727

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ.
Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24.
PMID: 28538739

Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.
Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N, Henderson IR.
Microb Genom. 2017 Mar 23;3(3):mgen000106. doi: 10.1099/mgen.0.000106. eCollection 2017 Mar.
PMID: 28663823

Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach.
Fonseca VG, Sinniger F, Gaspar JM, Quince C, Creer S, Power DM, Peck LS, Clark MS.
Sci Rep. 2017 Jul 21;7(1):6094. doi: 10.1038/s41598-017-06687-x.
PMID: 28733608

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing.
McMurray CL, Hardy KJ, Calus ST, Loman NJ, Hawkey PM.
Microbiome. 2016 Dec 2;4(1):63.
PMID: 27912796

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.
PMID: 28851932

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.
PMID: 28348830

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.
PMID: 27618184

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

What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.
Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, Herrera S, Gilmour M, Cloeckaert A, Achtman M, Parkhill J, Wain J, De Pinna E, Weill FX, Peters T, Thomson N.
MBio. 2016 Aug 23;7(4). pii: e00527-16. doi: 10.1128/mBio.00527-16.
PMID: 27555304

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.

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.
PMID: 27481928

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.
PMID: 28348870

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.
PMID: 27333878

Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle.
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.
Sci Rep. 2016 May 25;6:26589. doi: 10.1038/srep26589.
PMID: 27220895

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.
Ray JL, Althammer J, Skaar KS, Simonelli P, Larsen A, Stoecker D, Sazhin A, Ijaz UZ, Quince C, Nejstgaard JC, Frischer M, Pohnert G, Troedsson C.
Mol Ecol. 2016 Nov;25(21):5585-5602. doi: 10.1111/mec.13844. Epub 2016 Oct 20.
PMID: 27662431

Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days.
Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S.
Clin Infect Dis. 2016 Nov 15;63(10):1353-1356. Epub 2016 Sep 1.
PMID: 27585800

Draft Genome Sequence of the Bacteriophage vB_Eco_slurp01.
Sazinas P, Smith C, Suhaimi A, Hobman JL, Dodd CE, Millard AD.
Genome Announc. 2016 Nov 17;4(6). pii: e01111-16. doi: 10.1128/genomeA.01111-16.
PMID: 27856574

VSEARCH: a versatile open source tool for metagenomics.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F.
PeerJ. 2016 Oct 18;4:e2584. eCollection 2016.
PMID: 27781170

The effect of DNA extraction methodology on gut microbiota research applications.
Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, Calus S, Loman N, Ijaz UZ.
BMC Res Notes. 2016 Jul 26;9:365. doi: 10.1186/s13104-016-2171-7.
PMID: 27456340

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.
Senghore M, Bayliss SC, Kwambana-Adams BA, Foster-Nyarko E, Manneh J, Dione M, Badji H, Ebruke C, Doughty EL, Thorpe HA, Jasinska AJ, Schmitt CA, Cramer JD, Turner TR, Weinstock G, Freimer NB, Pallen MJ, Feil EJ, Antonio M.
Appl Environ Microbiol. 2016 Sep 16;82(19):5910-7. doi: 10.1128/AEM.01496-16. Print 2016 Oct 1.
PMID: 27474712

Challenges in microbial ecology: building predictive understanding of community function and dynamics.
Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.
ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.
PMID: 27022995

Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015.
Keita M, Duraffour S, Loman NJ, Rambaut A, Diallo B, Magassouba N, Carroll MW, Quick J, Sall AA, Glynn JR, Formenty P, Subissi L, Faye O.
Emerg Infect Dis. 2016 Dec;22(12):2149-2152. doi: 10.3201/eid2212.160847.
PMID: 27869596

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.
Schirmer M, D’Amore R, Ijaz UZ, Hall N, Quince C.
BMC Bioinformatics. 2016 Mar 11;17:125. doi: 10.1186/s12859-016-0976-y.
PMID: 26968756

Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters.
Haig SJ, Gauchotte-Lindsay C, Collins G, Quince C.
Environ Sci Technol. 2016 Mar 15;50(6):3101-10. doi: 10.1021/acs.est.5b05027. Epub 2016 Mar 3.
PMID: 26895622

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.
Torondel B, Ensink JH, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C.
Microb Biotechnol. 2016 Mar;9(2):209-23. doi: 10.1111/1751-7915.12334. Epub 2016 Feb 15.
PMID: 26875588

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].
PMID: 26978068

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.

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.
PMID: 28785418

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.
PMID: 28794175

Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface.
Abrahams KA, Cox JAG, Fütterer K, Rullas J, Ortega-Muro F, Loman NJ, Moynihan PJ, Pérez-Herrán E, Jiménez E, Esquivias J, Barros D, Ballell L, Alemparte C, Besra GS.
Sci Rep. 2017 Aug 25;7(1):9430. doi: 10.1038/s41598-017-09642-y.
PMID: 28842600

Real-time, portable genome sequencing for Ebola surveillance.
Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sanchez A, Carter LL, Doerrbecker J, Enkirch T, Dorival IGG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallash E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Trina R, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner D, Pollakis G, Hiscox JA, Matthews DA, O’Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Woelfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keita S, Rambaut A, Formenty P, Gunther S, Carroll MW.
Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3.
PMID: 26840485

 

2015

Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target.
Gurcha SS, Usha V, Cox JA, Fütterer K, Abrahams KA, Bhatt A, Alderwick LJ, Reynolds RC, Loman NJ, Nataraj V, Alemparte C, Barros D, Lloyd AJ, Ballell L, Hobrath JV, Besra GS.
PLoS One. 2014 Nov 19;9(11):e113568. doi: 10.1371/journal.pone.0113568. eCollection 2014.
PMID: 25409504

Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011.
Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM, Browne HP, Harris D, Lipman L, Keessen EC, Corver J, Kuijper EJ, Lawley TD.
Euro Surveill. 2014 Nov 13;19(45):20954.
PMID: 25411691

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR.
Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20.
PMID: 25414349

Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan.
Jones LS, Carvalho MJ, Toleman MA, White PL, Connor TR, Mushtaq A, Weeks JL, Kumarasamy KK, Raven KE, Török ME, Peacock SJ, Howe RA, Walsh TR.
Antimicrob Agents Chemother. 2015 Feb;59(2):923-9. doi: 10.1128/AAC.03242-14. Epub 2014 Nov 24.
PMID: 25421466

Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.
Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G.
Appl Environ Microbiol. 2015 Jun;81(11):3641-7. doi: 10.1128/AEM.00546-15. Epub 2015 Mar 20.
PMID: 25795671

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.
PMID: 25888688

Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.
Facey PD, Méric G, Hitchings MD, Pachebat JA, Hegarty MJ, Chen X, Morgan LV, Hoeppner JE, Whitten MM, Kirk WD, Dyson PJ, Sheppard SK, Del Sol R.
Genome Biol Evol. 2015 Jul 15;7(8):2188-202. doi: 10.1093/gbe/evv136.
PMID: 26185096

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.
Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR.
Elife. 2015 Aug 4;4:e07335. doi: 10.7554/eLife.07335.
PMID: 26238191

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 NH, Jeeves RE, Lappin-Scott HM, Asakura H, Sheppard SK.
Environ Microbiol. 2015 Nov;17(11):4779-89. doi: 10.1111/1462-2920.13051. Epub 2015 Oct 14.
PMID: 26373338

Twenty years of bacterial genome sequencing.
Loman NJ, Pallen MJ.
Nat Rev Microbiol. 2015 Dec;13(12):787-94. doi: 10.1038/nrmicro3565. Epub 2015 Nov 9. Review.
PMID: 26548914

Draft Genome Sequences of 14 Escherichia coli Phages Isolated from Cattle Slurry.
Smith R, O’Hara M, Hobman JL, Millard AD.
Genome Announc. 2015 Dec 31;3(6). pii: e01364-15. doi: 10.1128/genomeA.01364-15.
PMID: 26722010

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

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
D’Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.
BMC Genomics. 2016 Jan 14;17:55. doi: 10.1186/s12864-015-2194-9.
PMID: 26763898

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition.
Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K.
Am J Gastroenterol. 2015 Dec;110(12):1718-29; quiz 1730. doi: 10.1038/ajg.2015.357. Epub 2015 Nov 3.
PMID: 26526081

The relationship between microbial community evenness and function in slow sand filters.
Haig SJ, Quince C, Davies RL, Dorea CC, Collins G.
MBio. 2015 Oct 13;6(5):e00729-15. doi: 10.1128/mBio.00729-15.
PMID: 26463159

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.
Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C.
ISME J. 2016 Jan;10(1):85-96. doi: 10.1038/ismej.2015.101. Epub 2015 Jul 3.
PMID: 26140533

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.

2014

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW.
BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z.
PMID: 25387460

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.
Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M.
Genome Med. 2014 Nov 15;6(11):101. doi: 10.1186/s13073-014-0101-7. eCollection 2014.
PMID: 25484920

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.
von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A, Thomson NR, Rasko DA, Joffre E, Corander J, Pickard D, Wiklund G, Svennerholm AM, Sjöling Å, Dougan G.
Nat Genet. 2014 Dec;46(12):1321-6. doi: 10.1038/ng.3145. Epub 2014 Nov 10.
PMID: 25383970

Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.
Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, Loman NJ.
BMJ Open. 2014 Nov 4;4(11):e006278. doi: 10.1136/bmjopen-2014-006278.
PMID: 25371418

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