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Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

Merla C, Rodrigues C, Passet V, Corbella M, Thorpe HA, Kallonen TVS, Zong Z, Marone P, Bandi C, Sassera D, Corander J, Feil EJ, Brisse S.

Front Microbiol. 2019 Oct 25;10:2360. doi: 10.3389/fmicb.2019.02360. eCollection 2019.


Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae.

Comandatore F, Sassera D, Bayliss SC, Scaltriti E, Gaiarsa S, Cao X, Gales AC, Saito R, Pongolini S, Brisse S, Feil EJ, Bandi C.

Genome Biol Evol. 2019 Nov 1;11(11):3240-3251. doi: 10.1093/gbe/evz236.


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.


Corrigendum: Phylogeny of Vibrio vulnificus From the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.

Roig FJ, González-Candelas F, Sanjuán E, Fouz B, Feil EJ, Llorens C, Baker-Austin C, Oliver JD, Danin-Poleg Y, Gibas CJ, Kashi Y, Gulig PA, Morrison SS, Amaro C.

Front Microbiol. 2019 Aug 21;10:1904. doi: 10.3389/fmicb.2019.01904. eCollection 2019.


Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

David S, Reuter S, Harris SR, Glasner C, Feltwell T, Argimon S, Abudahab K, Goater R, Giani T, Errico G, Aspbury M, Sjunnebo S; EuSCAPE Working Group; ESGEM Study Group, Feil EJ, Rossolini GM, Aanensen DM, Grundmann H.

Nat Microbiol. 2019 Nov;4(11):1919-1929. doi: 10.1038/s41564-019-0492-8. Epub 2019 Jul 29.


WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.

Pinholt M, Bayliss SC, Gumpert H, Worning P, Jensen VVS, Pedersen M, Feil EJ, Westh H.

J Antimicrob Chemother. 2019 Jul 1;74(7):1776-1785. doi: 10.1093/jac/dkz118.


Real time monitoring of Aeromonas salmonicida evolution in response to successive antibiotic therapies in a commercial fish farm.

Du X, Bayliss SC, Feil EJ, Liu Y, Wang C, Zhang G, Zhou D, Wei D, Tang N, Leclercq SO, Feng J.

Environ Microbiol. 2019 Mar;21(3):1113-1123. doi: 10.1111/1462-2920.14531. Epub 2019 Feb 22.


Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens.

Hernandez RJ, Hesse E, Dowling AJ, Coyle NM, Feil EJ, Gaze WH, Vos M.

PeerJ. 2019 Jan 4;6:e6150. doi: 10.7717/peerj.6150. eCollection 2019.


Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK.

Nat Commun. 2018 Nov 28;9(1):5034. doi: 10.1038/s41467-018-07368-7.


Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation.

Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JO, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O'Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V.

Sci Adv. 2018 Oct 17;4(10):eaat5869. doi: 10.1126/sciadv.aat5869. eCollection 2018 Oct.


Multi-locus sequence typing of Ixodes ricinus and its symbiont Candidatus Midichloria mitochondrii across Europe reveals evidence of local co-cladogenesis in Scotland.

Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, Dinnis RE, Margos G, Medlock JM, Feil EJ, Darby AC, McGarry JW, Gilbert L, Plantard O, Sassera D, Makepeace BL.

Ticks Tick Borne Dis. 2019 Jan;10(1):52-62. doi: 10.1016/j.ttbdis.2018.08.016. Epub 2018 Aug 31.


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.


Gene exchange drives the ecological success of a multi-host bacterial pathogen.

Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR.

Nat Ecol Evol. 2018 Sep;2(9):1468-1478. doi: 10.1038/s41559-018-0617-0. Epub 2018 Jul 23.


Evidence for an effect of landscape connectivity on Borrelia burgdorferi sensu stricto dispersion in a zone of range expansion.

Mechai S, Margos G, Feil EJ, Lindsay LR, Michel P, Kotchi SO, Ogden NH.

Ticks Tick Borne Dis. 2018 Sep;9(6):1407-1415. doi: 10.1016/j.ttbdis.2018.07.001. Epub 2018 Jul 2.


Whole genome sequencing and phylogenetic analysis of strains of the agent of Lyme disease Borrelia burgdorferi from Canadian emergence zones.

Tyler S, Tyson S, Dibernardo A, Drebot M, Feil EJ, Graham M, Knox NC, Lindsay LR, Margos G, Mechai S, Van Domselaar G, Thorpe HA, Ogden NH.

Sci Rep. 2018 Jul 12;8(1):10552. doi: 10.1038/s41598-018-28908-7.


Enantioselective fractionation of fluoroquinolones in the aqueous environment using chiral liquid chromatography coupled with tandem mass spectrometry.

Castrignanò E, Kannan AM, Feil EJ, Kasprzyk-Hordern B.

Chemosphere. 2018 Sep;206:376-386. doi: 10.1016/j.chemosphere.2018.05.005. Epub 2018 May 4.


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.


Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.

Roig FJ, González-Candelas F, Sanjuán E, Fouz B, Feil EJ, Llorens C, Baker-Austin C, Oliver JD, Danin-Poleg Y, Gibas CJ, Kashi Y, Gulig PA, Morrison SS, Amaro C.

Front Microbiol. 2018 Jan 5;8:2613. doi: 10.3389/fmicb.2017.02613. eCollection 2017. Erratum in: Front Microbiol. 2019 Aug 21;10:1904.


Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.

Donker T, Reuter S, Scriberras J, Reynolds R, Brown NM, Török ME, James R, Network EOEMR, Aanensen DM, Bentley SD, Holden MTG, Parkhill J, Spratt BG, Peacock SJ, Feil EJ, Grundmann H.

Microb Genom. 2017 Jul 4;3(7):e000113. doi: 10.1099/mgen.0.000113. eCollection 2017 Jul.


Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

Reuter S, Török ME, Holden MTG, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, Feil EJ, Spratt BG, Parkhill J, Peacock SJ.

Genome Res. 2017 Sep;27(9):1622. doi: 10.1101/gr.228155.117. No abstract available.


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.


Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum.

Brynildsrud O, Gulla S, Feil EJ, Nørstebø SF, Rhodes LD.

Microb Genom. 2016 Apr 29;2(4):e000055. doi: 10.1099/mgen.0.000055. eCollection 2016 Apr.


Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM.

Microb Genom. 2016 Nov 30;2(11):e000093. doi: 10.1099/mgen.0.000093. eCollection 2016 Nov.


The use of Oxford Nanopore native barcoding for complete genome assembly.

Bayliss SC, Hunt VL, Yokoyama M, Thorpe HA, Feil EJ.

Gigascience. 2017 Mar 1;6(3):1-6. doi: 10.1093/gigascience/gix001.


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.


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.


Enterobacteriaceae: joining the dots with pan-European epidemiology.

Feil EJ.

Lancet Infect Dis. 2017 Feb;17(2):118-119. doi: 10.1016/S1473-3099(16)30333-4. Epub 2016 Nov 18. No abstract available.


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.


Correction: The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos.

Phetsouvanh R, Sonthayanon P, Pukrittayakamee S, Paris DH, Newton PN, Feil EJ, Day NP.

PLoS Negl Trop Dis. 2016 May 17;10(5):e0004742. doi: 10.1371/journal.pntd.0004742. eCollection 2016 May.


Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Aanensen DM, Feil EJ, Holden MT, Dordel J, Yeats CA, Fedosejev A, Goater R, Castillo-Ramírez S, Corander J, Colijn C, Chlebowicz MA, Schouls L, Heck M, Pluister G, Ruimy R, Kahlmeter G, Åhman J, Matuschek E, Friedrich AW, Parkhill J, Bentley SD, Spratt BG, Grundmann H; European SRL Working Group.

mBio. 2016 May 5;7(3). pii: e00444-16. doi: 10.1128/mBio.00444-16.


The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.

J Theor Biol. 2016 May 7;396:53-62. doi: 10.1016/j.jtbi.2016.02.019. Epub 2016 Feb 23.


Evidence for Host-Genotype Associations of Borrelia burgdorferi Sensu Stricto.

Mechai S, Margos G, Feil EJ, Barairo N, Lindsay LR, Michel P, Ogden NH.

PLoS One. 2016 Feb 22;11(2):e0149345. doi: 10.1371/journal.pone.0149345. eCollection 2016.


Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus.

Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M.

Genome Med. 2016 Feb 13;8(1):18. doi: 10.1186/s13073-016-0274-3.


The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus.

Senn L, Clerc O, Zanetti G, Basset P, Prod'hom G, Gordon NC, Sheppard AE, Crook DW, James R, Thorpe HA, Feil EJ, Blanc DS.

mBio. 2016 Jan 19;7(1):e02039-15. doi: 10.1128/mBio.02039-15.


Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

Reuter S, Török ME, Holden MT, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, Feil EJ, Spratt BG, Parkhill J, Peacock SJ.

Genome Res. 2016 Feb;26(2):263-70. doi: 10.1101/gr.196709.115. Epub 2015 Dec 15. Erratum in: Genome Res. 2017 Sep;27(9):1622.


Toward a synthesis of genotypic typing and phenotypic inference in the genomics era.

Feil EJ.

Future Microbiol. 2015;10(12):1897-9. doi: 10.2217/fmb.15.113. Epub 2015 Nov 19. No abstract available.


The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos.

Phetsouvanh R, Sonthayanon P, Pukrittayakamee S, Paris DH, Newton PN, Feil EJ, Day NP.

PLoS Negl Trop Dis. 2015 Aug 28;9(8):e0004024. doi: 10.1371/journal.pntd.0004024. eCollection 2015. Erratum in: PLoS Negl Trop Dis. 2016 May;10(5):e0004742.


Evolutionary aspects of emerging Lyme disease in Canada.

Ogden NH, Feil EJ, Leighton PA, Lindsay LR, Margos G, Mechai S, Michel P, Moriarty TJ.

Appl Environ Microbiol. 2015 Nov;81(21):7350-9. doi: 10.1128/AEM.01671-15. Epub 2015 Aug 21. Review.


Alternative Splice in Alternative Lice.

Tovar-Corona JM, Castillo-Morales A, Chen L, Olds BP, Clark JM, Reynolds SE, Pittendrigh BR, Feil EJ, Urrutia AO.

Mol Biol Evol. 2015 Oct;32(10):2749-59. doi: 10.1093/molbev/msv151. Epub 2015 Jul 13.


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.


Complex population structure of Borrelia burgdorferi in southeastern and south central Canada as revealed by phylogeographic analysis.

Mechai S, Margos G, Feil EJ, Lindsay LR, Ogden NH.

Appl Environ Microbiol. 2015 Feb;81(4):1309-18.


Predicting the virulence of MRSA from its genome sequence.

Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, Williams P, Endres JL, Bayles KW, Fey PD, Yajjala VK, Widhelm T, Hawkins E, Lewis K, Parfett S, Scowen L, Peacock SJ, Holden M, Wilson D, Read TD, van den Elsen J, Priest NK, Feil EJ, Hurst LD, Josefsson E, Massey RC.

Genome Res. 2014 May;24(5):839-49. doi: 10.1101/gr.165415.113. Epub 2014 Apr 9.


Molecular epidemiology and population structure of the honey bee brood pathogen Melissococcus plutonius.

Budge GE, Shirley MD, Jones B, Quill E, Tomkies V, Feil EJ, Brown MA, Haynes EG.

ISME J. 2014 Aug;8(8):1588-97. doi: 10.1038/ismej.2014.20. Epub 2014 Mar 6.


Multilocus sequence typing using mitochondrial genes (mtMLST) reveals geographic population structure of Ixodes ricinus ticks.

Dinnis RE, Seelig F, Bormane A, Donaghy M, Vollmer SA, Feil EJ, Kurtenbach K, Margos G.

Ticks Tick Borne Dis. 2014 Mar;5(2):152-60. doi: 10.1016/j.ttbdis.2013.10.001. Epub 2013 Dec 19.


Multilocus variable-number tandem-repeat genotyping of Renibacterium salmoninarum, a bacterium causing bacterial kidney disease in salmonid fish.

Matejusova I, Bain N, Colquhoun DJ, Feil EJ, McCarthy U, McLennan D, Snow M, Verner-Jeffreys D, Wallace IS, Weir SJ, Hall M.

BMC Microbiol. 2013 Dec 6;13:285. doi: 10.1186/1471-2180-13-285.


Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements.

Brynildsrud O, Feil EJ, Bohlin J, Castillo-Ramirez S, Colquhoun D, McCarthy U, Matejusova IM, Rhodes LD, Wiens GD, Verner-Jeffreys DW.

ISME J. 2014 Apr;8(4):746-56. doi: 10.1038/ismej.2013.186. Epub 2013 Oct 31.


Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset.

Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP.

PLoS One. 2013 May 7;8(5):e62369. doi: 10.1371/journal.pone.0062369. Print 2013.


Genetic relationships of Vibrio parahaemolyticus isolates from clinical, human carrier, and environmental sources in Thailand, determined by multilocus sequence analysis.

Theethakaew C, Feil EJ, Castillo-Ramírez S, Aanensen DM, Suthienkul O, Neil DM, Davies RL.

Appl Environ Microbiol. 2013 Apr;79(7):2358-70. doi: 10.1128/AEM.03067-12. Epub 2013 Feb 1.

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