Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei

Vartul Sangal; K.E. Holt; J Yuan; D.J. Brown; I. Filliol-Toutain; François-Xavier  Weill; D.W. Kim; W.D. da Silveira; D. Pickard; N.R. Thomson; J. Parkhill; Jun Yu

doi:10.1128/JCM.02238-12

Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei

Vartul Sangal, K.E. Holt, J Yuan, D.J. Brown, I. Filliol-Toutain, François-Xavier Weill, D.W. Kim, W.D. da Silveira , D. Pickard, N.R. Thomson , J. Parkhill, Jun Yu

Strathclyde Institute Of Pharmacy And Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

17 Citations (Scopus)

Abstract

The current Shigella sonnei pandemic involves geographically associated, multidrug resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited SNPs. By typing 6 informative SNPs using high-resolution melting (HRM) assay major S. sonnei lineages/sublineages can be identified as defined from whole-genome variation.

Original language	English
Journal	Journal of Clinical Microbiology
Early online date	31 Oct 2012
DOIs	https://doi.org/10.1128/JCM.02238-12
Publication status	Published - 1 Jan 2013

Keywords

global phylogeny
shigella sonnei
single nucleotide polymorphisms
snp-typing scheme
strain identification
high resolution
melting analysis

Access to Document

10.1128/JCM.02238-12

Fingerprint

Dive into the research topics of 'Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei'. Together they form a unique fingerprint.

Genotyping epidemic Shigella sonnei
Yu, J. (Principal Investigator)
Medical Research Council
11/11/08 → 10/11/11
Project: Research

Rapid genotyping of Shigella sonnei using multiplex high resolution melting
Mazi, W., Sangal, V., Saeed, A., Sandstom, G., Weill , F.-X. & Yu, J., 1 Jul 2015, In: Journal of Clinical Microbiology. 53, 7, p. 1-2 2 p., JCM.00874-15.
Research output: Contribution to journal › Article › peer-review
9 Link opens in a new tab Citations (Scopus)
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
Holt, K., Baker, S., Weill, F.-X., Holmes, E. C., Kitchen, A., Yu, J., Sangal, V., Brown, D. J., Coia, J. E., Kim, D. W., Choi, S. Y., Kim, S. H., da Silveira, W. D., Pickard, D. J., Farrar, J. J., Parkhill, J., Dougan, G. & Thomson, N. R., Sept 2012, In: Nature Genetics. 44, 9, p. 1056–1059 4 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
240 Link opens in a new tab Citations (Scopus)

93 Downloads (Pure)

Cite this

Sangal, V., Holt, K. E., Yuan, J., Brown, D. J., Filliol-Toutain, I., Weill, F.-X., Kim, D. W., da Silveira , W. D., Pickard, D., Thomson , N. R., Parkhill, J., & Yu, J. (2013). Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei. Journal of Clinical Microbiology. https://doi.org/10.1128/JCM.02238-12

@article{1f03877f60d44f62a61cb1fd7a5f105f,

title = "Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei",

abstract = "The current Shigella sonnei pandemic involves geographically associated, multidrug resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited SNPs. By typing 6 informative SNPs using high-resolution melting (HRM) assay major S. sonnei lineages/sublineages can be identified as defined from whole-genome variation.",

keywords = "global phylogeny , shigella sonnei , single nucleotide polymorphisms , snp-typing scheme, strain identification, high resolution , melting analysis",

author = "Vartul Sangal and K.E. Holt and J Yuan and D.J. Brown and I. Filliol-Toutain and Fran{\c c}ois-Xavier Weill and D.W. Kim and \{da Silveira\}, W.D. and D. Pickard and N.R. Thomson and J. Parkhill and Jun Yu",

year = "2013",

month = jan,

day = "1",

doi = "10.1128/JCM.02238-12",

language = "English",

journal = "Journal of Clinical Microbiology",

issn = "0095-1137",

publisher = "American Society for Microbiology",

}

Sangal, V, Holt, KE, Yuan, J, Brown, DJ, Filliol-Toutain, I, Weill, F-X, Kim, DW, da Silveira , WD, Pickard, D, Thomson , NR, Parkhill, J & Yu, J 2013, 'Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei', Journal of Clinical Microbiology. https://doi.org/10.1128/JCM.02238-12

Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei. / Sangal, Vartul; Holt, K.E.; Yuan, J et al.
In: Journal of Clinical Microbiology, 01.01.2013.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting

T2 - rapid SNP-typing S. sonnei

AU - Sangal, Vartul

AU - Holt, K.E.

AU - Yuan, J

AU - Brown, D.J.

AU - Filliol-Toutain, I.

AU - Weill, François-Xavier

AU - Kim, D.W.

AU - da Silveira , W.D.

AU - Pickard, D.

AU - Thomson , N.R.

AU - Parkhill, J.

AU - Yu, Jun

PY - 2013/1/1

Y1 - 2013/1/1

N2 - The current Shigella sonnei pandemic involves geographically associated, multidrug resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited SNPs. By typing 6 informative SNPs using high-resolution melting (HRM) assay major S. sonnei lineages/sublineages can be identified as defined from whole-genome variation.

AB - The current Shigella sonnei pandemic involves geographically associated, multidrug resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited SNPs. By typing 6 informative SNPs using high-resolution melting (HRM) assay major S. sonnei lineages/sublineages can be identified as defined from whole-genome variation.

KW - global phylogeny

KW - shigella sonnei

KW - single nucleotide polymorphisms

KW - snp-typing scheme

KW - strain identification

KW - high resolution

KW - melting analysis

UR - http://www.scopus.com/inward/record.url?scp=84871699295&partnerID=8YFLogxK

U2 - 10.1128/JCM.02238-12

DO - 10.1128/JCM.02238-12

M3 - Article

SN - 0095-1137

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

ER -

Sangal V, Holt KE, Yuan J, Brown DJ, Filliol-Toutain I, Weill FX et al. Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei. Journal of Clinical Microbiology. 2013 Jan 1. Epub 2012 Oct 31. doi: 10.1128/JCM.02238-12

Global phylogeny of Shigella sonnei from limited single nucleotide polymorphisms and development of a rapid and cost-effective SNP-typing scheme for strain identification by high resolution melting: rapid SNP-typing S. sonnei

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Projects

Genotyping epidemic Shigella sonnei

Research output

Rapid genotyping of Shigella sonnei using multiplex high resolution melting

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Cite this