메뉴 건너뛰기




Volumn 9, Issue 8, 2014, Pages

The complete genome sequence of escherichia coli EC958: A high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone

Author keywords

[No Author keywords available]

Indexed keywords

ADHESIN; FIMBRIA PROTEIN; QUINOLINE DERIVED ANTIINFECTIVE AGENT; ANTIINFECTIVE AGENT;

EID: 84925470770     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104400     Document Type: Article
Times cited : (103)

References (52)
  • 2
    • 40749102940 scopus 로고    scopus 로고
    • Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing
    • Lau SH, Reddy S, Cheesbrough J, Bolton FJ, Willshaw G, et al. (2008) Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing. J Clin Microbiol 46: 1076-1080.
    • (2008) J Clin Microbiol , vol.46 , pp. 1076-1080
    • Lau, S.H.1    Reddy, S.2    Cheesbrough, J.3    Bolton, F.J.4    Willshaw, G.5
  • 5
    • 76749123412 scopus 로고    scopus 로고
    • Molecular epidemiology of Escherichia coli producing CTX-M beta-lactamases: The worldwide emergence of clone ST131 O25:H4
    • Peirano G, Pitout JD (2010) Molecular epidemiology of Escherichia coli producing CTX-M beta-lactamases: the worldwide emergence of clone ST131 O25:H4. Int J Antimicrob Agents 35: 316-321.
    • (2010) Int J Antimicrob Agents , vol.35 , pp. 316-321
    • Peirano, G.1    Pitout, J.D.2
  • 6
    • 84891591168 scopus 로고    scopus 로고
    • The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx
    • Price LB, Johnson JR, Aziz M, Clabots C, Johnston B, et al. (2013) The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio 4: e00377-00313.
    • (2013) MBio , vol.4
    • Price, L.B.1    Johnson, J.R.2    Aziz, M.3    Clabots, C.4    Johnston, B.5
  • 7
    • 80055045142 scopus 로고    scopus 로고
    • Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: Genome analysis and virulence mechanisms
    • Totsika M, Beatson SA, Sarkar S, Phan M-D, Petty NK, et al. (2011) Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms. PloS one 6: e26578.
    • (2011) PloS One , vol.6
    • Totsika, M.1    Beatson, S.A.2    Sarkar, S.3    Phan, M.-D.4    Petty, N.K.5
  • 8
    • 56649108214 scopus 로고    scopus 로고
    • UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone
    • Lau SH, Kaufmann ME, Livermore DM, Woodford N, Willshaw GA, et al. (2008) UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone. J Antimicrob Chemother 62: 1241-1244.
    • (2008) J Antimicrob Chemother , vol.62 , pp. 1241-1244
    • Lau, S.H.1    Kaufmann, M.E.2    Livermore, D.M.3    Woodford, N.4    Willshaw, G.A.5
  • 9
    • 84883237676 scopus 로고    scopus 로고
    • A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug-resistant uropathogenic Escherichia coli ST131
    • Totsika M, Kostakioti M, Hannan TJ, Upton M, Beatson SA, et al. (2013) A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug-resistant uropathogenic Escherichia coli ST131. The Journal of infectious diseases 208: 921-928.
    • (2013) The Journal of Infectious Diseases , vol.208 , pp. 921-928
    • Totsika, M.1    Kostakioti, M.2    Hannan, T.J.3    Upton, M.4    Beatson, S.A.5
  • 10
    • 84867730641 scopus 로고    scopus 로고
    • Escherichia coli-mediated impairment of ureteric contractility is uropathogenic E. Coli specific
    • Floyd RV, Upton M, Hultgren SJ, Wray S, Burdyga TV, et al. (2012) Escherichia coli-mediated impairment of ureteric contractility is uropathogenic E. coli specific. J Infect Dis 206: 1589-1596.
    • (2012) J Infect Dis , vol.206 , pp. 1589-1596
    • Floyd, R.V.1    Upton, M.2    Hultgren, S.J.3    Wray, S.4    Burdyga, T.V.5
  • 11
    • 84887314032 scopus 로고    scopus 로고
    • The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone
    • Phan M-D, Peters KM, Sarkar S, Lukowski SW, Allsopp LP, et al. (2013) The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone. PLoS genetics 9: e1003834.
    • (2013) PLoS Genetics , vol.9
    • Phan, M.-D.1    Peters, K.M.2    Sarkar, S.3    Lukowski, S.W.4    Allsopp, L.P.5
  • 12
    • 84857893016 scopus 로고    scopus 로고
    • GAGE: A critical evaluation of genome assemblies and assembly algorithms
    • Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
    • (2012) Genome Res , vol.22 , pp. 557-567
    • Salzberg, S.L.1    Phillippy, A.M.2    Zimin, A.3    Puiu, D.4    Magoc, T.5
  • 13
    • 77950814686 scopus 로고    scopus 로고
    • Finishing genomes with limited resources: Lessons from an ensemble of microbial genomes
    • Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, et al. (2010) Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC genomics 11: 242.
    • (2010) BMC Genomics , vol.11 , pp. 242
    • Nagarajan, N.1    Cook, C.2    Di Bonaventura, M.3    Ge, H.4    Richards, A.5
  • 14
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford C, Schatz MC, Pop M (2010) Assembly complexity of prokaryotic genomes using short reads. BMC bioinformatics 11: 21.
    • (2010) BMC Bioinformatics , vol.11 , pp. 21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 15
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: Finding the elusive mis-assembly
    • Phillippy AM, Schatz MC, Pop M (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome biology 9: R55.
    • (2008) Genome Biology , vol.9
    • Phillippy, A.M.1    Schatz, M.C.2    Pop, M.3
  • 16
    • 84865363124 scopus 로고    scopus 로고
    • The limitations of draft assemblies for understanding prokaryotic adaptation and evolution
    • Ricker N, Qian H, Fulthorpe RR (2012) The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics 100: 167-175.
    • (2012) Genomics , vol.100 , pp. 167-175
    • Ricker, N.1    Qian, H.2    Fulthorpe, R.R.3
  • 18
    • 75749094779 scopus 로고    scopus 로고
    • Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2
    • Toh H, Oshima K, Toyoda A, Ogura Y, Ooka T, et al. (2010) Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. Journal of bacteriology 192: 1165-1166.
    • (2010) Journal of Bacteriology , vol.192 , pp. 1165-1166
    • Toh, H.1    Oshima, K.2    Toyoda, A.3    Ogura, Y.4    Ooka, T.5
  • 19
    • 79961163061 scopus 로고    scopus 로고
    • Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India
    • Avasthi TS, Kumar N, Baddam R, Hussain A, Nandanwar N, et al. (2011) Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. Journal of bacteriology 193: 4272-4273.
    • (2011) Journal of Bacteriology , vol.193 , pp. 4272-4273
    • Avasthi, T.S.1    Kumar, N.2    Baddam, R.3    Hussain, A.4    Nandanwar, N.5
  • 20
    • 84999723822 scopus 로고    scopus 로고
    • Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M- 15-Producing H30-Rx Subclone of Escherichia coli ST131
    • Andersen PS, Stegger M, Aziz M, Contente-Cuomo T, Gibbons HS, et al. (2013) Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M- 15-Producing H30-Rx Subclone of Escherichia coli ST131. Genome announcements 1.
    • (2013) Genome Announcements , vol.1
    • Andersen, P.S.1    Stegger, M.2    Aziz, M.3    Contente-Cuomo, T.4    Gibbons, H.S.5
  • 22
    • 84872125886 scopus 로고    scopus 로고
    • Role of homologous recombination in adaptive diversification of extraintestinal Escherichia coli
    • Paul S, Linardopoulou EV, Billig M, Tchesnokova V, Price LB, et al. (2013) Role of homologous recombination in adaptive diversification of extraintestinal Escherichia coli. J Bacteriol 195: 231-242.
    • (2013) J Bacteriol , vol.195 , pp. 231-242
    • Paul, S.1    Linardopoulou, E.V.2    Billig, M.3    Tchesnokova, V.4    Price, L.B.5
  • 23
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods 10: 563-569.
    • (2013) Nature Methods , vol.10 , pp. 563-569
    • Chin, C.-S.1    Alexander, D.H.2    Marks, P.3    Klammer, A.A.4    Drake, J.5
  • 24
    • 77956193448 scopus 로고    scopus 로고
    • progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 5: e11147.
    • (2010) PloS One , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 28
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS genetics 5: e1000344.
    • (2009) PLoS Genetics , vol.5
    • Touchon, M.1    Hoede, C.2    Tenaillon, O.3    Barbe, V.4    Baeriswyl, S.5
  • 31
    • 79961109150 scopus 로고    scopus 로고
    • BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons
    • Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12: 402.
    • (2011) BMC Genomics , vol.12 , pp. 402
    • Alikhan, N.F.1    Petty, N.K.2    Ben Zakour, N.L.3    Beatson, S.A.4
  • 34
    • 53849104729 scopus 로고    scopus 로고
    • The pangenome structure of Escherichia coli: Comparative genomic analysis of E. Coli commensal and pathogenic isolates
    • Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, et al. (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of bacteriology 190: 6881-6893.
    • (2008) Journal of Bacteriology , vol.190 , pp. 6881-6893
    • Rasko, D.A.1    Rosovitz, M.J.2    Myers, G.S.A.3    Mongodin, E.F.4    Fricke, W.F.5
  • 40
    • 67549090009 scopus 로고    scopus 로고
    • Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12
    • Ferenci T, Zhou Z, Betteridge T, Ren Y, Liu Y, et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. Journal of bacteriology 191: 4025-4029.
    • (2009) Journal of Bacteriology , vol.191 , pp. 4025-4029
    • Ferenci, T.1    Zhou, Z.2    Betteridge, T.3    Ren, Y.4    Liu, Y.5
  • 41
    • 0036841680 scopus 로고    scopus 로고
    • Genetic structure and distribution of four pathogenicity islands (PAI I536 to PAI IV536) of uropathogenic Escherichia coli strain 536
    • DOI 10.1128/IAI.70.11.6365-6372.2002
    • Dobrindt U, Blum-Oehler G, Nagy G, Schneider G, Johann A, et al. (2002) Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536. Infection and immunity 70: 6365-6372. (Pubitemid 35192729)
    • (2002) Infection and Immunity , vol.70 , Issue.11 , pp. 6365-6372
    • Dobrindt, U.1    Blum-Oehler, G.2    Nagy, G.3    Schneider, G.4    Johann, A.5    Gottschalk, G.6    Hacker, J.7
  • 43
    • 84891935788 scopus 로고    scopus 로고
    • When whole-genome alignments just won't work: KSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes
    • Gardner SN, Hall BG (2013) When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One 8: e81760.
    • (2013) PLoS One , vol.8
    • Gardner, S.N.1    Hall, B.G.2
  • 44
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5
  • 45
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • DOI 10.1101/gr.074492.107
    • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research 18: 821-829. (Pubitemid 351645072)
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 46
    • 0028338908 scopus 로고
    • Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres
    • Sandmeier H (1994) Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Molecular microbiology 12: 343-350.
    • (1994) Molecular Microbiology , vol.12 , pp. 343-350
    • Sandmeier, H.1
  • 47
    • 65449175727 scopus 로고    scopus 로고
    • Genetics and virulence association of the Shigella flexneri sit iron transport system
    • Fisher CR, Davies NMLL, Wyckoff EE, Feng Z, Oaks EV, et al. (2009) Genetics and virulence association of the Shigella flexneri sit iron transport system. Infection and immunity 77: 1992-1999.
    • (2009) Infection and Immunity , vol.77 , pp. 1992-1999
    • Fisher, C.R.1    Davies, N.M.L.L.2    Wyckoff, E.E.3    Feng, Z.4    Oaks, E.V.5
  • 48
    • 34247601641 scopus 로고    scopus 로고
    • Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli
    • DOI 10.1128/JB.01744-06
    • Lloyd AL, Rasko DA, Mobley HLT (2007) Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli. Journal of bacteriology 189: 3532-3546. (Pubitemid 46668818)
    • (2007) Journal of Bacteriology , vol.189 , Issue.9 , pp. 3532-3546
    • Lloyd, A.L.1    Rasko, D.A.2    Mobley, H.L.T.3
  • 49
    • 84893435615 scopus 로고    scopus 로고
    • Control of directionality in Streptomyces phage phiBT1 integrase-mediated site-specific recombination
    • Zhang L, Zhu B, Dai R, Zhao G, Ding X (2013) Control of directionality in Streptomyces phage phiBT1 integrase-mediated site-specific recombination. PLoS One 8: e80434.
    • (2013) PLoS One , vol.8
    • Zhang, L.1    Zhu, B.2    Dai, R.3    Zhao, G.4    Ding, X.5
  • 50
    • 0023376605 scopus 로고
    • Role of the central dinucleotide at the crossover sites for the selection of quasi sites in DNA inversion mediated by the site-specific Cin recombinase of phage P1
    • Iida S, Hiestand-Nauer R (1987) Role of the central dinucleotide at the crossover sites for the selection of quasi sites in DNA inversion mediated by the site-specific Cin recombinase of phage P1. Mol Gen Genet 208: 464-468.
    • (1987) Mol Gen Genet , vol.208 , pp. 464-468
    • Iida, S.1    Hiestand-Nauer, R.2
  • 51
    • 0022482112 scopus 로고
    • Localized conversion at the crossover sequences in the site-specific DNA inversion system of bacteriophage P1
    • Iida S, Hiestand-Nauer R (1986) Localized conversion at the crossover sequences in the site-specific DNA inversion system of bacteriophage P1. Cell 45: 71-79. (Pubitemid 16046628)
    • (1986) Cell , vol.45 , Issue.1 , pp. 71-79
    • Iida, S.1    Hiestand-Nauer, R.2
  • 52
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012) Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7: e47768.
    • (2012) PLoS One , vol.7
    • English, A.C.1    Richards, S.2    Han, Y.3    Wang, M.4    Vee, V.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.