메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Analysis of whole genome sequencing for the Escherichia coli O157: H7 typing phages

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; VIRUS DNA;

EID: 84938986913     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1470-z     Document Type: Article
Times cited : (22)

References (41)
  • 1
    • 0036895178 scopus 로고    scopus 로고
    • Trends in indigenous foodborne disease and deaths, England and Wales: 1992 to 2000
    • Adak GK, Long SM, O'Brien SJ. Trends in indigenous foodborne disease and deaths, England and Wales: 1992 to 2000. Gut. 2002;51:832-41.
    • (2002) Gut , vol.51 , pp. 832-841
    • Adak, G.K.1    Long, S.M.2    O'Brien, S.J.3
  • 3
    • 84871702878 scopus 로고    scopus 로고
    • Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak
    • Underwood AP, Dallman T, Thomson NR, Williams M, Harker K, Perry N, et al. Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. JClinMicrobiol. 2013;51:232-7. doi:JCM.01696-12; 10.1128/JCM.01696-12.
    • (2013) JClinMicrobiol , vol.51 , pp. 232-237
    • Underwood, A.P.1    Dallman, T.2    Thomson, N.R.3    Williams, M.4    Harker, K.5    Perry, N.6
  • 4
    • 84884976663 scopus 로고    scopus 로고
    • Application of multilocus variable number tandem repeat analysis to monitor Verocytotoxin-producing Escherichia coli O157 phage type 8 in England and Wales: emergence of a profile associated with a national outbreak
    • 115:1052-1058
    • Perry N, Cheasty T, Dallman T, Launders N, Willshaw G. Application of multilocus variable number tandem repeat analysis to monitor Verocytotoxin-producing Escherichia coli O157 phage type 8 in England and Wales: emergence of a profile associated with a national outbreak. JApplMicrobiol. 2013;115:1052-8. doi:115:1052-1058; 10.1111/jam.12303.
    • (2013) JApplMicrobiol , vol.115 , pp. 1052-1058
    • Perry, N.1    Cheasty, T.2    Dallman, T.3    Launders, N.4    Willshaw, G.5
  • 5
    • 84863938676 scopus 로고    scopus 로고
    • Large outbreak of verocytotoxin-producing Escherichia coli O157 infection in visitors to a petting farm in South East England, 2009
    • Ihekweazu C, Carroll K, Adak B, Smith G, Pritchard GC, Gillespie IA, et al. Large outbreak of verocytotoxin-producing Escherichia coli O157 infection in visitors to a petting farm in South East England, 2009. EpidemiolInfect. 2012;140:1400-13. doi:S0950268811002111;10.1017/S0950268811002111.
    • (2012) EpidemiolInfect , vol.140 , pp. 1400-1413
    • Ihekweazu, C.1    Carroll, K.2    Adak, B.3    Smith, G.4    Pritchard, G.C.5    Gillespie, I.A.6
  • 6
    • 84898662179 scopus 로고    scopus 로고
    • Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England
    • PONE-D-13-31410
    • Byrne L, Elson R, Dallman TJ, Perry N, Ashton P, Wain J, et al. Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England. PLoSOne. 2014;9:e85901. doi:10.1371/journal.pone.0085901; PONE-D-13-31410.
    • (2014) PLoSOne , vol.9
    • Byrne, L.1    Elson, R.2    Dallman, T.J.3    Perry, N.4    Ashton, P.5    Wain, J.6
  • 7
    • 84878201439 scopus 로고    scopus 로고
    • Experimental coevolution of species interactions
    • Brockhurst MA, Koskella B. Experimental coevolution of species interactions. Trends EcolEvol. 2013;28:367-75. doi:S0169-5347 (13) 00061-X;10.1016/j.tree.2013.02.009.
    • (2013) Trends EcolEvol , vol.28 , pp. 367-375
    • Brockhurst, M.A.1    Koskella, B.2
  • 8
    • 0036169156 scopus 로고    scopus 로고
    • Expression of receptors for verotoxin 1 from Escherichia coli O157 on bovine intestinal epithelium
    • Hoey DE, Currie C, Else RW, Nutikka A, Lingwood CA, Gally DL, et al. Expression of receptors for verotoxin 1 from Escherichia coli O157 on bovine intestinal epithelium. J Med Microbiol. 2002;51:143-9.
    • (2002) J Med Microbiol , vol.51 , pp. 143-149
    • Hoey, D.E.1    Currie, C.2    Else, R.W.3    Nutikka, A.4    Lingwood, C.A.5    Gally, D.L.6
  • 9
    • 0035477452 scopus 로고    scopus 로고
    • Diversification of Escherichia coli genomes: are bacteriophages the major contributors?
    • Ohnishi M, Kurokawa K, Hayashi T. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 2001;9:481-5. doi:S0966-842X (01) 02173-4.
    • (2001) Trends Microbiol , vol.9 , pp. 481-485
    • Ohnishi, M.1    Kurokawa, K.2    Hayashi, T.3
  • 10
    • 0035120334 scopus 로고    scopus 로고
    • Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli
    • Scholl D, Rogers S, Adhya S, Merril CR. Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli. JVirol. 2001;75:2509-15. doi:10.1128/JVI.75.6.2509-2515.2001.
    • (2001) JVirol , vol.75 , pp. 2509-2515
    • Scholl, D.1    Rogers, S.2    Adhya, S.3    Merril, C.R.4
  • 11
    • 0023140319 scopus 로고
    • Phage-typing scheme for Escherichia coli O157:H7
    • Ahmed R, Bopp C, Borczyk A, Kasatiya S. Phage-typing scheme for Escherichia coli O157:H7. J Infect Dis. 1987;155:806-9.
    • (1987) J Infect Dis , vol.155 , pp. 806-809
    • Ahmed, R.1    Bopp, C.2    Borczyk, A.3    Kasatiya, S.4
  • 15
  • 16
    • 84874527551 scopus 로고    scopus 로고
    • The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5
    • 1743-422X-10-76
    • Kropinski AM, Waddell T, Meng J, Franklin K, Ackermann HW, Ahmed R, et al. The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5. VirolJ. 2013;10:76. doi:1743-422X-10-76;10.1186/1743-422X-10-76.
    • (2013) VirolJ , vol.10 , pp. 76
    • Kropinski, A.M.1    Waddell, T.2    Meng, J.3    Franklin, K.4    Ackermann, H.W.5    Ahmed, R.6
  • 17
    • 60349118910 scopus 로고    scopus 로고
    • Sequence analysis of Escherichia coli O157:H7 bacteriophage PhiV10 and identification of a phage-encoded immunity protein that modifies the O157 antigen
    • FML1511
    • Perry LL, SanMiguel P, Minocha U, Terekhov AI, Shroyer ML, Farris LA, et al. Sequence analysis of Escherichia coli O157:H7 bacteriophage PhiV10 and identification of a phage-encoded immunity protein that modifies the O157 antigen. FEMS MicrobiolLett. 2009;292:182-6. doi:FML1511;10.1111/j.1574-6968.2009.01511.x.
    • (2009) FEMS MicrobiolLett , vol.292 , pp. 182-186
    • Perry, L.L.1    SanMiguel, P.2    Minocha, U.3    Terekhov, A.I.4    Shroyer, M.L.5    Farris, L.A.6
  • 18
    • 0026045287 scopus 로고
    • An improved method for the small scale preparation of bacteriophage DNA based on phage precipitation by zinc chloride
    • Santos MA. An improved method for the small scale preparation of bacteriophage DNA based on phage precipitation by zinc chloride. Nucleic Acids Res. 1991;19:5442.
    • (1991) Nucleic Acids Res , vol.19 , pp. 5442
    • Santos, M.A.1
  • 19
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • gr.074492.107
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-9. doi:gr.074492.107;10.1101/gr.074492.107.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 20
    • 84901417347 scopus 로고    scopus 로고
    • Prokka: rapid prokaryotic genome annotation
    • published online: March 18, 2014.
    • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014. doi:10.1093/bioinformatics/btu153First published online: March 18, 2014.
    • (2014) Bioinformatics
    • Seemann, T.1
  • 21
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. JComputBiol. 2012;19:455-77. doi:10.1089/cmb.2012.0021.
    • (2012) JComputBiol , vol.19 , pp. 455-477
    • Bankevich, A.1    Nurk, S.2    Antipov, D.3    Gurevich, A.A.4    Dvorkin, M.5    Kulikov, A.S.6
  • 23
    • 77952696795 scopus 로고    scopus 로고
    • An efficient algortihm for optimizing bipartite modularity in bipartite networks
    • Liu X, Murata T. An efficient algortihm for optimizing bipartite modularity in bipartite networks. JACIII. 2010;14:408-15.
    • (2010) JACIII , vol.14 , pp. 408-415
    • Liu, X.1    Murata, T.2
  • 24
    • 85019263504 scopus 로고    scopus 로고
    • A weighted modularity algorithm for bipartite networks
    • Beckett, SJ. A weighted modularity algorithm for bipartite networks. figshare. 2014. http://dx.doi.org/10.6084/m9.figshare.999114 .
    • (2014) figshare
    • Beckett, S.J.1
  • 25
    • 84923250410 scopus 로고    scopus 로고
    • FALCON: a software package for analysis of nestedness in bipartite networks
    • Beckett SJ, Boulton CA, Williams HT. FALCON: a software package for analysis of nestedness in bipartite networks. F1000Res. 2014;3:185. doi:10.12688/f1000research.4831.1.
    • (2014) F1000Res , vol.3 , pp. 185
    • Beckett, S.J.1    Boulton, C.A.2    Williams, H.T.3
  • 26
    • 49249087447 scopus 로고    scopus 로고
    • A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement
    • Almeida-Neto M, Guimaraes P, Guimaraes Jr PR, Loyola RD, Ulrich W. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos. 2008;117:1227-39.
    • (2008) Oikos , vol.117 , pp. 1227-1239
    • Almeida-Neto, M.1    Guimaraes, P.2    Guimaraes, P.R.3    Loyola, R.D.4    Ulrich, W.5
  • 27
    • 0027331799 scopus 로고
    • The measure of order and disorder in the distribution of species in fragmented habitat
    • Atmar W, Patterson BD. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia. 1993;96:373-82.
    • (1993) Oecologia , vol.96 , pp. 373-382
    • Atmar, W.1    Patterson, B.D.2
  • 29
    • 0032938427 scopus 로고    scopus 로고
    • Nested species subsets, gaps, and discrepancy
    • Brualdi RA, Sanderson JG. Nested species subsets, gaps, and discrepancy. Oecologia. 1999;119:256-64.
    • (1999) Oecologia , vol.119 , pp. 256-264
    • Brualdi, R.A.1    Sanderson, J.G.2
  • 30
    • 0042424615 scopus 로고
    • The nested assembly of plant-animal mutualistic networks
    • 9383-0387
    • Bascompte J, Patterson BD. The nested assembly of plant-animal mutualistic networks. Proc Natl Acad Sci U S A. 1993;100:9383-0387.
    • (1993) Proc Natl Acad Sci U S A , vol.100
    • Bascompte, J.1    Patterson, B.D.2
  • 31
    • 79961109150 scopus 로고    scopus 로고
    • BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
    • 1471-2164-12-402
    • Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMCGenomics. 2011;12:402. doi:1471-2164-12-402;10.1186/1471-2164-12-402.
    • (2011) BMCGenomics , vol.12 , pp. 402
    • Alikhan, N.F.1    Petty, N.K.2    Ben Zakour, N.L.3    Beatson, S.A.4
  • 32
    • 79953306448 scopus 로고    scopus 로고
    • Easyfig: a genome comparison visualizer
    • btr039
    • Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009-10. doi:btr039;10.1093/bioinformatics/btr039.
    • (2011) Bioinformatics , vol.27 , pp. 1009-1010
    • Sullivan, M.J.1    Petty, N.K.2    Beatson, S.A.3
  • 33
    • 84885047100 scopus 로고    scopus 로고
    • Predicting the public health benefit of vaccinating cattle against Escherichia coli O157
    • 1304978110
    • Matthews L, Reeve R, Gally DL, Low JC, Woolhouse ME, McAteer SP, et al. Predicting the public health benefit of vaccinating cattle against Escherichia coli O157. Proc Natl Acad Sci U S A. 2013;110:16265-70. doi:1304978110;10.1073/pnas.1304978110.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 16265-16270
    • Matthews, L.1    Reeve, R.2    Gally, D.L.3    Low, J.C.4    Woolhouse, M.E.5    McAteer, S.P.6
  • 34
    • 34447620875 scopus 로고    scopus 로고
    • The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities
    • Leiman PG, Battisti AJ, Bowman VD, Stummeyer K, Muhlenhoff M, Gerardy-Schahn R, et al. The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. JMolBiol. 2007;371:836-49. doi:S0022-2836 (07) 00756-5;10.1016/j.jmb.2007.05.083.
    • (2007) JMolBiol , vol.371 , pp. 836-849
    • Leiman, P.G.1    Battisti, A.J.2    Bowman, V.D.3    Stummeyer, K.4    Muhlenhoff, M.5    Gerardy-Schahn, R.6
  • 35
    • 78651138418 scopus 로고
    • Host-induced modification of t-even phages due to defective glucosylation of their DNA
    • Hattman S, Fukasawa T. Host-induced modification of t-even phages due to defective glucosylation of their DNA. Proc Natl Acad Sci U S A. 1963;50:297-300.
    • (1963) Proc Natl Acad Sci U S A , vol.50 , pp. 297-300
    • Hattman, S.1    Fukasawa, T.2
  • 36
    • 25144479277 scopus 로고    scopus 로고
    • Gene order constrains adaptation in bacteriophage T7
    • Springman R, Badgett MR, Molineux IJ, Bull JJ. Gene order constrains adaptation in bacteriophage T7. Virology. 2005;341:141-52. doi:S0042-6822 (05) 00418-6;10.1016/j.virol.2005.07.008.
    • (2005) Virology , vol.341 , pp. 141-152
    • Springman, R.1    Badgett, M.R.2    Molineux, I.J.3    Bull, J.J.4
  • 37
    • 84886712023 scopus 로고    scopus 로고
    • Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks
    • rsfs20130033
    • Beckett SJ, Williams HT. Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks. Interface Focus. 2013;3:20130033. doi:10.1098/rsfs.2013.0033; rsfs20130033.
    • (2013) Interface Focus , vol.3 , pp. 20130033
    • Beckett, S.J.1    Williams, H.T.2
  • 40
    • 4644274269 scopus 로고    scopus 로고
    • Phage types and genotypes of shiga toxin-producing Escherichia coli O157:H7 isolates from humans and animals in spain: identification and characterization of two predominating phage types (PT2 and PT8)
    • 42/9/4007
    • Mora A, Blanco M, Blanco JE, Alonso MP, Dhabi G, Thomson-Carter F, et al. Phage types and genotypes of shiga toxin-producing Escherichia coli O157:H7 isolates from humans and animals in spain: identification and characterization of two predominating phage types (PT2 and PT8). JClinMicrobiol. 2004;42:4007-15. doi:10.1128/JCM.42.9.4007-4015.2004;42/9/4007.
    • (2004) JClinMicrobiol , vol.42 , pp. 4007-4015
    • Mora, A.1    Blanco, M.2    Blanco, J.E.3    Alonso, M.P.4    Dhabi, G.5    Thomson-Carter, F.6
  • 41
    • 77952501214 scopus 로고    scopus 로고
    • Phage typing of Salmonella Typhimurium - is it still a useful tool for surveillance and outbreak investigation?
    • Baggesen DL, Sorensen G, Nielsen EM, Wegener HC. Phage typing of Salmonella Typhimurium - is it still a useful tool for surveillance and outbreak investigation? Euro Surveill. 2010;15:19471.
    • (2010) Euro Surveill , vol.15 , pp. 19471
    • Baggesen, D.L.1    Sorensen, G.2    Nielsen, E.M.3    Wegener, H.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.