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Items: 45

1.

Influenza Classification from Short Reads with VAPOR Facilitates Robust Mapping Pipelines and Zoonotic Strain Detection for Routine Surveillance Applications.

Southgate JA, Bull MJ, Brown CM, Watkins J, Corden S, Southgate B, Moore C, Connor TR.

Bioinformatics. 2019 Nov 6. pii: btz814. doi: 10.1093/bioinformatics/btz814. [Epub ahead of print]

PMID:
31693070
2.

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Webster G, Mullins AJ, Bettridge AS, Jones C, Cunningham-Oakes E, Connor TR, Parkhill J, Mahenthiralingam E.

Microbiol Resour Announc. 2019 Aug 22;8(34). pii: e00778-19. doi: 10.1128/MRA.00778-19.

3.

Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes.

Weiser R, Green AE, Bull MJ, Cunningham-Oakes E, Jolley KA, Maiden MCJ, Hall AJ, Winstanley C, Weightman AJ, Donoghue D, Amezquita A, Connor TR, Mahenthiralingam E.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000276. Epub 2019 Jun 6.

4.

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.

Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C, Webster G, Green AE, Neill DR, Connor TR, Parkhill J, Challis GL, Mahenthiralingam E.

Nat Microbiol. 2019 Jun;4(6):996-1005. doi: 10.1038/s41564-019-0383-z. Epub 2019 Mar 4.

5.

The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation.

Green AE, Amézquita A, Le Marc Y, Bull MJ, Connor TR, Mahenthiralingam E.

FEMS Microbiol Lett. 2018 May 1;365(9). doi: 10.1093/femsle/fny062.

6.

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01384-17. doi: 10.1128/JCM.01384-17. Print 2018 Mar.

7.

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.

8.

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

Baker KS, Campos J, Pichel M, Della Gaspera A, Duarte-Martínez F, Campos-Chacón E, Bolaños-Acuña HM, Guzmán-Verri C, Mather AE, Diaz Velasco S, Zamudio Rojas ML, Forbester JL, Connor TR, Keddy KH, Smith AM, López de Delgado EA, Angiolillo G, Cuaical N, Fernández J, Aguayo C, Morales Aguilar M, Valenzuela C, Morales Medrano AJ, Sirok A, Weiler Gustafson N, Diaz Guevara PL, Montaño LA, Perez E, Thomson NR.

Clin Microbiol Infect. 2017 Nov;23(11):845-853. doi: 10.1016/j.cmi.2017.03.021. Epub 2017 Apr 4.

9.

The Type III Secretion System Effector SeoC of Salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis.

Pollard DJ, Young JC, Covarelli V, Herrera-León S, Connor TR, Fookes M, Walker D, Echeita A, Thomson NR, Berger CN, Frankel G.

Infect Immun. 2016 Nov 18;84(12):3618-3628. Print 2016 Dec.

10.

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE; International Typhoid Consortium.

Nat Commun. 2016 Oct 5;7:12827. doi: 10.1038/ncomms12827.

11.

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.

12.

Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities.

Baker KS, Dallman TJ, Behar A, Weill FX, Gouali M, Sobel J, Fookes M, Valinsky L, Gal-Mor O, Connor TR, Nissan I, Bertrand S, Parkhill J, Jenkins C, Cohen D, Thomson NR.

Emerg Infect Dis. 2016 Sep;22(9):1545-53. doi: 10.3201/eid2209.151953.

13.

Engineering of Isogenic Cells Deficient for MR1 with a CRISPR/Cas9 Lentiviral System: Tools To Study Microbial Antigen Processing and Presentation to Human MR1-Restricted T Cells.

Laugel B, Lloyd A, Meermeier EW, Crowther MD, Connor TR, Dolton G, Miles JJ, Burrows SR, Gold MC, Lewinsohn DM, Sewell AK.

J Immunol. 2016 Aug 1;197(3):971-82. doi: 10.4049/jimmunol.1501402. Epub 2016 Jun 15.

14.

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.

15.

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3574-81. doi: 10.1073/pnas.1501049112. Epub 2015 Jun 22.

16.

Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA.

PLoS Negl Trop Dis. 2015 Jun 15;9(6):e0003848. doi: 10.1371/journal.pntd.0003848. eCollection 2015 Jun. No abstract available.

17.

Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.

Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G, Crook PD, Gilbart VL, Zittermann S, Allen VG, Howden BP, Tomita T, Valcanis M, Harris SR, Connor TR, Sintchenko V, Howard P, Brown JD, Petty NK, Gouali M, Thanh DP, Keddy KH, Smith AM, Talukder KA, Faruque SM, Parkhill J, Baker S, Weill FX, Jenkins C, Thomson NR.

Lancet Infect Dis. 2015 Aug;15(8):913-21. doi: 10.1016/S1473-3099(15)00002-X. Epub 2015 Apr 27.

PMID:
25936611
18.

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA.

PLoS Negl Trop Dis. 2015 Mar 24;9(3):e0003611. doi: 10.1371/journal.pntd.0003611. eCollection 2015 Mar. Erratum in: PLoS Negl Trop Dis. 2015 Jun;9(6):e0003848. PLoS Negl Trop Dis. 2015 Aug;9(8):e0003970.

19.

Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.

Vehkala M, Shubin M, Connor TR, Thomson NR, Corander J.

PLoS One. 2015 Mar 18;10(3):e0118392. doi: 10.1371/journal.pone.0118392. eCollection 2015.

20.

Patterns of genome evolution that have accompanied host adaptation in Salmonella.

Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, Wigley P, Peters SE, Maskell DJ, Corander J, Chabalgoity JA, Barrow P, Parkhill J, Dougan G, Thomson NR.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):863-8. doi: 10.1073/pnas.1416707112. Epub 2014 Dec 22.

21.

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.

22.

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.

23.

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.

24.

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
25.

Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J, Kingsley RA, Connor TR, Sie A, Hodgson A, Dougan G, Parkhill J, Bentley SD, Pluschke G.

MBio. 2014 Oct 21;5(5):e01974-14. doi: 10.1128/mBio.01974-14.

26.

Parallel independent evolution of pathogenicity within the genus Yersinia.

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6768-73. doi: 10.1073/pnas.1317161111. Epub 2014 Apr 21.

27.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J.

Mol Ecol. 2014 May;23(10):2442-51. doi: 10.1111/mec.12742. Epub 2014 Apr 25.

28.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR.

Science. 2013 Sep 27;341(6153):1514-7. doi: 10.1126/science.1240578. Epub 2013 Sep 12.

29.

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.

30.

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

McDonnell J, Dallman T, Atkin S, Turbitt DA, Connor TR, Grant KA, Thomson NR, Jenkins C.

Epidemiol Infect. 2013 Dec;141(12):2568-75. doi: 10.1017/S0950268813000137. Epub 2013 Feb 21.

PMID:
23425681
31.

Hierarchical and spatially explicit clustering of DNA sequences with BAPS software.

Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J.

Mol Biol Evol. 2013 May;30(5):1224-8. doi: 10.1093/molbev/mst028. Epub 2013 Feb 13.

32.

Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms.

Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G, Langridge GC, Eckert S, Chaudhuri RR, Ewers C, Mellata M, Mukhopadhyay S, Curtiss R 3rd, Dougan G, Wieler LH, Thomson NR, Pickard DJ, Stevens MP.

Infect Immun. 2013 Mar;81(3):838-49. doi: 10.1128/IAI.00585-12. Epub 2012 Dec 28.

33.

Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D'Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD.

Nat Genet. 2013 Jan;45(1):109-13. doi: 10.1038/ng.2478. Epub 2012 Dec 9.

34.

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.

Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J, Dougan G.

PLoS Pathog. 2012;8(10):e1002995. doi: 10.1371/journal.ppat.1002995. Epub 2012 Oct 25.

35.

Population subdivision and the detection of recombination in non-typable Haemophilus influenzae.

Connor TR, Corander J, Hanage WP.

Microbiology. 2012 Dec;158(Pt 12):2958-64. doi: 10.1099/mic.0.063073-0. Epub 2012 Oct 4.

36.

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E, Wain J, Heyderman RS, Obaro S, Alonso PL, Mandomando I, MacLennan CA, Tapia MD, Levine MM, Tennant SM, Parkhill J, Dougan G.

Nat Genet. 2012 Nov;44(11):1215-21. doi: 10.1038/ng.2423. Epub 2012 Sep 30.

37.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y.

BMC Genomics. 2012 Jul 24;13:341. doi: 10.1186/1471-2164-13-341.

38.

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, Becq J, Bignell GR, Cheetham RK, Cheng W, Connor TR, Cox AJ, Feng ZP, Gu Y, Grocock RJ, Harris SR, Khrebtukova I, Kingsbury Z, Kowarsky M, Kreiss A, Luo S, Marshall J, McBride DJ, Murray L, Pearse AM, Raine K, Rasolonjatovo I, Shaw R, Tedder P, Tregidgo C, Vilella AJ, Wedge DC, Woods GM, Gormley N, Humphray S, Schroth G, Smith G, Hall K, Searle SM, Carter NP, Papenfuss AT, Futreal PA, Campbell PJ, Yang F, Bentley DR, Evers DJ, Stratton MR.

Cell. 2012 Feb 17;148(4):780-91. doi: 10.1016/j.cell.2011.11.065.

39.

Population structure in the Neisseria, and the biological significance of fuzzy species.

Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP.

J R Soc Interface. 2012 Jun 7;9(71):1208-15. doi: 10.1098/rsif.2011.0601. Epub 2011 Nov 9.

40.

Detection of recombination events in bacterial genomes from large population samples.

Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J.

Nucleic Acids Res. 2012 Jan;40(1):e6. doi: 10.1093/nar/gkr928. Epub 2011 Nov 7.

41.

Salmonella bongori provides insights into the evolution of the Salmonellae.

Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, Bäumler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G, Thomson NR.

PLoS Pathog. 2011 Aug;7(8):e1002191. doi: 10.1371/journal.ppat.1002191. Epub 2011 Aug 18.

42.

Evidence for several waves of global transmission in the seventh cholera pandemic.

Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M, Niyogi SK, Kim EJ, Ramamurthy T, Chun J, Wood JL, Clemens JD, Czerkinsky C, Nair GB, Holmgren J, Parkhill J, Dougan G.

Nature. 2011 Aug 24;477(7365):462-5. doi: 10.1038/nature10392.

43.

Bayesian semi-supervised classification of bacterial samples using MLST databases.

Cheng L, Connor TR, Aanensen DM, Spratt BG, Corander J.

BMC Bioinformatics. 2011 Jul 26;12:302. doi: 10.1186/1471-2105-12-302.

44.

Hyper-recombination, diversity, and antibiotic resistance in pneumococcus.

Hanage WP, Fraser C, Tang J, Connor TR, Corander J.

Science. 2009 Jun 12;324(5933):1454-7. doi: 10.1126/science.1171908.

45.

Assessing the reliability of eBURST using simulated populations with known ancestry.

Turner KM, Hanage WP, Fraser C, Connor TR, Spratt BG.

BMC Microbiol. 2007 Apr 12;7:30.

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