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Volumn 11, Issue 1, 2016, Pages

The salmonella in silico typing resource (SISTR): An open web-accessible tool for rapidly typing and subtyping draft salmonella genome assemblies

Author keywords

[No Author keywords available]

Indexed keywords

ADOPTION; BIOINFORMATICS; DATA BASE; GENOME; MOLECULAR EPIDEMIOLOGY; PREDICTION; PUBLIC HEALTH; SALMONELLA; SEROTYPE; SEROTYPING; BACTERIAL GENOME; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; INTERNET; PHYLOGENY; VALIDATION STUDY;

EID: 84958212710     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0147101     Document Type: Article
Times cited : (365)

References (44)
  • 1
    • 0035057454 scopus 로고    scopus 로고
    • Diverse virulence traits underlying different clinical outcomes of Salmonella infection
    • 11285291
    • Fierer J, Guiney DG. Diverse virulence traits underlying different clinical outcomes of Salmonella infection. J Clin Invest. 2001; 107: 775-780. PMID: 11285291
    • (2001) J Clin Invest. , vol.107 , pp. 775-780
    • Fierer, J.1    Guiney, D.G.2
  • 2
    • 38449104523 scopus 로고    scopus 로고
    • A study of invasiveness of different Salmonella serovars based on analysis of the Enter-net database
    • Wollin R. A study of invasiveness of different Salmonella serovars based on analysis of the Enter-net database. Euro Surveill Bull Eur Sur Mal Transm Eur Commun Dis Bull. 2007; 12: E070927.3.
    • (2007) Euro Surveill Bull Eur sur Mal Transm Eur Commun Dis Bull. , vol.12 , pp. E0709273
    • Wollin, R.1
  • 3
    • 57449095929 scopus 로고    scopus 로고
    • 9th ed [Internet]. WHO Collaborating Centre for Reference and Research on Salmonella. Institut Pasteur, Paris, France. Available: http://www. pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089
    • Grimont PAD, Weill F-X. Antigenic formulae of the Salmonella serovars, 9th ed [Internet]. WHO Collaborating Centre for Reference and Research on Salmonella. Institut Pasteur, Paris, France. http://www.pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089; 2007. Available: http://www.pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089
    • (2007) Antigenic Formulae of the Salmonella Serovars
    • Grimont, P.A.D.1    Weill, F.-X.2
  • 4
    • 77950468839 scopus 로고    scopus 로고
    • Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes
    • 20164272
    • Ben-Darif E, Jury F, De Pinna E, Threlfall EJ, Bolton FJ, Fox AJ, et al. Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes. J Clin Microbiol. 2010; 48: 1055-1060. doi: 10.1128/JCM.01566-09 PMID: 20164272
    • (2010) J Clin Microbiol. , vol.48 , pp. 1055-1060
    • Ben-Darif, E.1    Jury, F.2    De Pinna, E.3    Threlfall, E.J.4    Bolton, F.J.5    Fox, A.J.6
  • 5
    • 35348839697 scopus 로고    scopus 로고
    • Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups
    • 17634307
    • Fitzgerald C, Collins M, van Duyne S, Mikoleit M, Brown T, Fields P. Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. J Clin Microbiol. 2007; 45: 3323-3334. doi: 10.1128/JCM.00025-07 PMID: 17634307
    • (2007) J Clin Microbiol. , vol.45 , pp. 3323-3334
    • Fitzgerald, C.1    Collins, M.2    Van Duyne, S.3    Mikoleit, M.4    Brown, T.5    Fields, P.6
  • 7
    • 79951486830 scopus 로고    scopus 로고
    • Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array
    • 21159932
    • McQuiston JR, Waters RJ, Dinsmore BA, Mikoleit ML, Fields PI. Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array. J Clin Microbiol. 2011; 49: 565-573. doi: 10.1128/JCM.01323-10 PMID: 21159932
    • (2011) J Clin Microbiol. , vol.49 , pp. 565-573
    • McQuiston, J.R.1    Waters, R.J.2    Dinsmore, B.A.3    Mikoleit, M.L.4    Fields, P.I.5
  • 10
    • 42649092544 scopus 로고    scopus 로고
    • Evaluation of the Premi1Test Salmonella, a commercial low-density DNA microarray system intended for routine identification and typing of Salmonella enterica
    • 18258323
    • Wattiau P, Weijers T, Andreoli P, Schliker C, Veken HV, Maas HME, et al. Evaluation of the Premi1Test Salmonella, a commercial low-density DNA microarray system intended for routine identification and typing of Salmonella enterica. Int J Food Microbiol. 2008; 123: 293-298. doi: 10.1016/j.ijfoodmicro. 2008.01.006 PMID: 18258323
    • (2008) Int J Food Microbiol. , vol.123 , pp. 293-298
    • Wattiau, P.1    Weijers, T.2    Andreoli, P.3    Schliker, C.4    Veken, H.V.5    Maas, H.M.E.6
  • 11
    • 34547579220 scopus 로고    scopus 로고
    • Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes
    • 17555834
    • Yoshida C, Franklin K, Konczy P, McQuiston JR, Fields PI, Nash JH, et al. Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes. J Microbiol Methods. 2007; 70: 261-271. doi: 10.1016/j.mimet.2007.04.018 PMID: 17555834
    • (2007) J Microbiol Methods. , vol.70 , pp. 261-271
    • Yoshida, C.1    Franklin, K.2    Konczy, P.3    McQuiston, J.R.4    Fields, P.I.5    Nash, J.H.6
  • 12
    • 77649103376 scopus 로고    scopus 로고
    • Development and evaluation of a multiplex real-time polymerase chain reaction procedure to clinically type prevalent Salmonella enterica serovars
    • 20110454
    • Muñoz N, Diaz-Osorio M, Moreno J, Sánchez-Jiménez M, Cardona-Castro N. Development and evaluation of a multiplex real-time polymerase chain reaction procedure to clinically type prevalent Salmonella enterica serovars. J Mol Diagn JMD. 2010; 12: 220-225. doi: 10.2353/jmoldx.2010.090036 PMID: 20110454
    • (2010) J Mol Diagn JMD. , vol.12 , pp. 220-225
    • Muñoz, N.1    Diaz-Osorio, M.2    Moreno, J.3    Sánchez-Jiménez, M.4    Cardona-Castro, N.5
  • 13
    • 79960946552 scopus 로고    scopus 로고
    • Rapid genoserotyping tool for classification of Salmonella serovars
    • 21697324
    • Franklin K, Lingohr EJ, Yoshida C, Anjum M, Bodrossy L, Clark CG, et al. Rapid genoserotyping tool for classification of Salmonella serovars. J Clin Microbiol. 2011; 49: 2954-2965. doi: 10.1128/JCM.02347-10 PMID: 21697324
    • (2011) J Clin Microbiol. , vol.49 , pp. 2954-2965
    • Franklin, K.1    Lingohr, E.J.2    Yoshida, C.3    Anjum, M.4    Bodrossy, L.5    Clark, C.G.6
  • 14
    • 84927557501 scopus 로고    scopus 로고
    • Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars
    • 25219780
    • Yoshida C, Lingohr EJ, Trognitz F, MacLaren N, Rosano A, Murphy SA, et al. Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars. Diagn Microbiol Infect Dis. 2014; 80: 185-190. doi: 10.1016/j.diagmicrobio.2014.08.006 PMID: 25219780
    • (2014) Diagn Microbiol Infect Dis. , vol.80 , pp. 185-190
    • Yoshida, C.1    Lingohr, E.J.2    Trognitz, F.3    MacLaren, N.4    Rosano, A.5    Murphy, S.A.6
  • 15
    • 33847043072 scopus 로고    scopus 로고
    • Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray
    • 17108073
    • Ballmer K, Korczak BM, Kuhnert P, Slickers P, Ehricht R, Hächler H. Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray. J Clin Microbiol. 2007; 45: 370-379. doi: 10.1128/ JCM.01361-06 PMID: 17108073
    • (2007) J Clin Microbiol. , vol.45 , pp. 370-379
    • Ballmer, K.1    Korczak, B.M.2    Kuhnert, P.3    Slickers, P.4    Ehricht, R.5    Hächler, H.6
  • 16
    • 2442596132 scopus 로고    scopus 로고
    • Sequencing and Comparative Analysis of Flagellin Genes fliC, fljB, and flpA from Salmonella
    • 15131150
    • McQuiston JR, Parrenas R, Ortiz-Rivera M, Gheesling L, Brenner F, Fields PI. Sequencing and Comparative Analysis of Flagellin Genes fliC, fljB, and flpA from Salmonella. J Clin Microbiol. 2004; 42: 1923-1932. doi: 10.1128/JCM.42.5.1923-1932.2004 PMID: 15131150
    • (2004) J Clin Microbiol. , vol.42 , pp. 1923-1932
    • McQuiston, J.R.1    Parrenas, R.2    Ortiz-Rivera, M.3    Gheesling, L.4    Brenner, F.5    Fields, P.I.6
  • 18
    • 84876061050 scopus 로고    scopus 로고
    • Public health genomics and the new molecular epidemiology of bacterial pathogens
    • 23548714
    • Gilmour MW, Graham M, Reimer A, Van Domselaar G. Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics. 2013; 16: 25-30. doi: 10.1159/ 000342709 PMID: 23548714
    • (2013) Public Health Genomics. , vol.16 , pp. 25-30
    • Gilmour, M.W.1    Graham, M.2    Reimer, A.3    Van Domselaar, G.4
  • 20
    • 84866148001 scopus 로고    scopus 로고
    • Routine use of microbial whole genome sequencing in diagnostic and public health microbiology
    • 22876174
    • Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012; 8: e1002824. doi: 10.1371/journal.ppat.1002824 PMID: 22876174
    • (2012) PLoS Pathog. , vol.8
    • Köser, C.U.1    Ellington, M.J.2    Cartwright, E.J.P.3    Gillespie, S.H.4    Brown, N.M.5    Farrington, M.6
  • 21
    • 84873847270 scopus 로고    scopus 로고
    • From molecular to genomic epidemiology: Transforming surveillance and control of infectious diseases
    • 23369387
    • Struelens MJ, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Eurosurveillance. 2013; 18: 20386. PMID: 23369387
    • (2013) Eurosurveillance. , vol.18 , pp. 20386
    • Struelens, M.J.1    Brisse, S.2
  • 22
    • 80052522056 scopus 로고    scopus 로고
    • Everything at once: Comparative analysis of the genomes of bacterial pathogens
    • 21764529
    • Laing CR, Zhang Y, Thomas JE, Gannon VPJ. Everything at once: Comparative analysis of the genomes of bacterial pathogens. Vet Microbiol. 2011; 153: 13-26. doi: 10.1016/j.vetmic.2011.06.014 PMID: 21764529
    • (2011) Vet Microbiol. , vol.153 , pp. 13-26
    • Laing, C.R.1    Zhang, Y.2    Thomas, J.E.3    Gannon, V.P.J.4
  • 23
    • 84863322057 scopus 로고    scopus 로고
    • A gene-by-gene approach to bacterial population genomics: Whole genome MLST of campylobacter
    • 24704917
    • Sheppard SK, Jolley KA, Maiden MCJ. A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter. Genes. 2012; 3: 261-277. doi: 10.3390/genes3020261 PMID: 24704917
    • (2012) Genes. , vol.3 , pp. 261-277
    • Sheppard, S.K.1    Jolley, K.A.2    Maiden, M.C.J.3
  • 25
    • 84905843066 scopus 로고    scopus 로고
    • Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
    • Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms. PLoS ONE. 2014; 9. doi: 10.1371/journal. pone.0104984
    • (2014) PLoS ONE. , vol.9
    • Kaas, R.S.1    Leekitcharoenphon, P.2    Aarestrup, F.M.3    Lund, O.4
  • 26
    • 84928040686 scopus 로고    scopus 로고
    • SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
    • 25422674
    • Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014; 6: 90. doi: 10.1186/ s13073-014-0090-6 PMID: 25422674
    • (2014) Genome Med. , vol.6 , pp. 90
    • Inouye, M.1    Dashnow, H.2    Raven, L.-A.3    Schultz, M.B.4    Pope, B.J.5    Tomita, T.6
  • 27
    • 0035351051 scopus 로고    scopus 로고
    • PulseNet: The molecular subtyping network for foodborne bacterial disease surveillance, United States
    • 11384513
    • Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis. 2001; 7: 382-389. PMID: 11384513
    • (2001) Emerg Infect Dis. , vol.7 , pp. 382-389
    • Swaminathan, B.1    Barrett, T.J.2    Hunter, S.B.3    Tauxe, R.V.4
  • 28
    • 13244267001 scopus 로고    scopus 로고
    • MlstdbNet-distributed multi-locus sequence typing (MLST) databases
    • 15230973
    • Jolley KA, Chan M-S, Maiden MC. mlstdbNet-distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics. 2004; 5: 86. doi: 10.1186/1471-2105-5-86 PMID: 15230973
    • (2004) BMC Bioinformatics. , vol.5 , pp. 86
    • Jolley, K.A.1    Chan, M.-S.2    Maiden, M.C.3
  • 29
    • 13144252236 scopus 로고    scopus 로고
    • Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
    • 9501229
    • Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998; 95: 3140-3145. PMID: 9501229
    • (1998) Proc Natl Acad Sci U S A. , vol.95 , pp. 3140-3145
    • Maiden, M.C.J.1    Bygraves, J.A.2    Feil, E.3    Morelli, G.4    Russell, J.E.5    Urwin, R.6
  • 30
    • 84859151133 scopus 로고    scopus 로고
    • Ribosomal multilocus sequence typing: Universal characterization of bacteria from domain to strain
    • Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol Read Engl. 2012; 158: 1005-1015. doi: 10.1099/mic.0.055459-0
    • (2012) Microbiol Read Engl. , vol.158 , pp. 1005-1015
    • Jolley, K.A.1    Bliss, C.M.2    Bennett, J.S.3    Bratcher, H.B.4    Brehony, C.5    Colles, F.M.6
  • 33
    • 84864059917 scopus 로고    scopus 로고
    • Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
    • 22737074
    • Achtman M, Wain J, Weill F-X, Nair S, Zhou Z, Sangal V, et al. Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica. PLoS Pathog. 2012; 8: e1002776. doi: 10.1371/ journal.ppat.1002776 PMID: 22737074
    • (2012) PLoS Pathog. , vol.8
    • Achtman, M.1    Wain, J.2    Weill, F.-X.3    Nair, S.4    Zhou, Z.5    Sangal, V.6
  • 34
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • 20211023
    • Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11: 119. doi: 10.1186/1471-2105-11-119 PMID: 20211023
    • (2010) BMC Bioinformatics. , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.-L.2    LoCascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 35
    • 33745634395 scopus 로고    scopus 로고
    • CD-HIT: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinforma Oxf Engl. 2006; 22: 1658-1659. doi: 10.1093/bioinformatics/btl158
    • (2006) Bioinforma Oxf Engl. , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 36
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: Accelerated for clustering the next-generation sequencing data
    • 23060610
    • Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28: 3150-3152. doi: 10.1093/bioinformatics/bts565 PMID: 23060610
    • (2012) Bioinformatics. , vol.28 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 38
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • 23329690
    • Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013; 30: 772-780. doi: 10.1093/molbev/mst010 PMID: 23329690
    • (2013) Mol Biol Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 39
    • 84878460994 scopus 로고    scopus 로고
    • Fastcluster: Fast hierarchical, agglomerative clustering routines for r and python
    • Available
    • Müllner D. fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python. J Stat Softw. 2013; 53. Available: http://www.jstatsoft.org/v53/i09
    • (2013) J Stat Softw. , vol.53
    • Müllner, D.1
  • 41
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinforma Oxf Engl. 2013; 29: 1072-1075. doi: 10.1093/bioinformatics/btt086
    • (2013) Bioinforma Oxf Engl. , vol.29 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 44
    • 84928034064 scopus 로고    scopus 로고
    • Salmonella serotype determination utilizing high-throughput genome sequencing data
    • 25762776
    • Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, et al. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 2015; 53: 1685-1692. doi: 10.1128/JCM.00323-15 PMID: 25762776
    • (2015) J Clin Microbiol. , vol.53 , pp. 1685-1692
    • Zhang, S.1    Yin, Y.2    Jones, M.B.3    Zhang, Z.4    Deatherage Kaiser, B.L.5    Dinsmore, B.A.6


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