Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing

Infection, Genetics and Evolution

Volumn 11, Issue 7, 2011, Pages 1761-1768

  Hayford, Alice E ^a   Mammel, Mark K ^a   Lacher, David W ^a   Brown, Eric W ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

Phylogenetics; Pyrosequencing; Shigella; Single nucleotide polymorphisms

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CONTROLLED STUDY; DNA SEQUENCE; GAPA GENE; GENE LOCATION; GENETIC IDENTIFICATION; GENETIC LINE; GENETIC SELECTION; GENOTYPE; HOUSEKEEPING GENE; LPXC GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; SANA GENE; SEQUENCE ANALYSIS; SHIGELLA BOYDII; SHIGELLA DYSENTERIAE; SHIGELLA FLEXNERI; SHIGELLA SONNEI; SINGLE NUCLEOTIDE POLYMORPHISM; STRAIN DIFFERENCE; THRB GENE; YAAH GENE; YBAP GENE; YGAZ GENE; YHBO GENE; YNHA GENE;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA, BACTERIAL; DYSENTERY, BACILLARY; FOOD MICROBIOLOGY; GENOME, BACTERIAL; HUMANS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEROTYPING; SHIGELLA;

SHIGELLA;

EID: 80053561448     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.07.015     Document Type: Article

References (43)

1. 2006. Preliminary FoodNet data on the incidence of infection with pathogens transmitted commonly through food - 10 States, United States, 2005. MMWR Morb. Mortal. Wkly. Rep. 55, pp. 392-395.
2. 2008. Preliminary FoodNet data on the incidence of infection with pathogens transmitted commonly through food - 10 states, 2007. MMWR Morb. Mortal. Wkly. Rep. 57, pp. 366-370.
3. Bando S.Y., do Valle G.R., Martinez M.B., Trabulsi L.R., Moreira-Filho C.A. Characterization of enteroinvasive Escherichia coli and Shigella strains by RAPD analysis. FEMS Microbiol. Lett. 1998, 165:159-165.
4. Bryant D., Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004, 21:255-265.
5. Budowle B., Schutzer S.E., Einseln A., Kelley L.C., Walsh A.C., Smith J.A., Marrone B.L., Robertson J., Campos J. Public health. Building microbial forensics as a response to bioterrorism. Science 2003, 301:1852-1853.
6. Cebula T.A., Brown E.W., Jackson S.A., Mammel M.K., Mukherjee A., Leclerc J.E. Molecular applications for identifying microbial pathogens in the post-9/11 era. Expert. Rev. Mol. Diagn. 2005, 5:431-445.
7. Centers for Disease Control and Prevention, 2008. Shigella Surveillance: Annual Summary, 2006, pp. 1-30.
8. Dodd C.E.R., Jones D. A numerical taxonomic study of the genus Shigella. J. Gen. Microbiol. 1982, 128:1933-1957.
9. Ekdahl K., Andersson Y. The epidemiology of travel-associated shigellosis - regional risks, seasonality and serogroups. J. Infect. 2005, 51:222-229.
10. Harris S.R., Feil E.J., Holden M.T.G., Quail M.A., Nickerson E.K., Chantratita N., Gardete S., Tavares A., Day N., Lindsay J.A., Edgeworth J.D., de Lencastre H.n., Parkhill J., Peacock S.J., Bentley S.D. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
11. Hommais F., Pereira S., Acquaviva C., Escobar-Paramo P., Denamur E. Single-nucleotide polymorphism phylotyping of Escherichia coli. Appl. Environ. Microbiol. 2005, 71:4784-4792.
12. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
13. Jiang Y., Yang F., Zhang X., Yang J., Chen L., Yan Y., Nie H., Xiong Z., Wang J., Dong J., Xue Y., Xu X., Zhu Y., Chen S., Jin Q. The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei. Plasmid 2005, 54:149-159.
14. Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002, 30:4432-4441.
15. Kingombe C.I., Cerqueira-Campos M.L., Farber J.M. Molecular strategies for the detection, identification, and differentiation between enteroinvasive Escherichia coli and Shigella spp. J. Food Protect. 2005, 68:239-245.
16. Kolavic S., Kimura A., Simons S., Slutsker L., Barth S., Haley C. An outbreak of Shigella dysenteriae type 2 among laboratory workers due to intentional food contamination. JAMA 1997, 278:396-398.
17. Kotloff K.L., Winickoff J.P., Ivanoff B., Clemens J.D., Swerdlow D.L., Sansonetti P.J., Adak G.K., Levine M.M. Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull. World Health Organ. 1999, 77:651-666.
18. Kumar S., Tamura K., Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 2004, 5:150-163.
19. Lampel K., Sandlin R., Formal S. Shigella. Encyclopedia of Food Microbiology 1999, 2015-2020. Academic Press Ltd., London. R. Robinson, C. Batt, P. Patel (Eds.).
20. Lan R., Reeves P.R. Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect. 2002, 4:1125-1132.
21. Li B., Brown E.W., D'Agostino C., Leclerc J.E., Cebula T.A. Structure and distribution of the phosphoprotein phosphatase genes, prpA and prpB, among Shigella subgroups. Microbiology 2005, 151:2671-2683.
22. Li Y., Cao B., Liu B., Liu D., Gao Q., Peng X., Wu J., Bastin D.A., Feng L., Wang L. Molecular detection of all 34 distinct O-antigen forms of Shigella. J. Med. Microbiol. 2009, 58:69-81.
23. Li Y., Liu D., Cao B., Han W., Liu Y., Liu F., Guo X., Bastin D.A., Feng L., Wang L. Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J. Clin. Microbiol. 2006, 44:4376-4383.
24. Liang S.Y., Watanabe H., Terajima J., Li C.C., Liao J.C., Tung S.K., Chiou C.S. Multilocus variable-number tandem repeat analysis for molecular typing of Shigella sonnei. J. Clin. Microbiol. 2007, 45:3574-3580.
25. Lienau E.K., Strain E., Wang C., Zheng J., Ottesen A.R., Keys C.E., Hammack T.S., Musser S.M., Brown E.W., Allard M.W., Cao G., Meng J., Stones R. Identification of a salmonellosis outbreak by means of molecular sequencing. N. Engl. J. Med. 2011, 364:981-982.
26. Lin C.S., Wang T.K., Tsai J.L., Ho S.I., Lee C.L., Lu C.H. Molecular subtyping of Shigella flexneri 3a isolates by plasmid profile analysis and pulsed-field gel electrophoresis. J. Microbiol. Immunol. Infect. 2001, 34:103-108.
27. Liu B., Knirel Y.A., Feng L., Perepelov A.V., Senchenkova S.N., Wang Q., Reeves P.R., Wang L. Structure and genetics of Shigella O antigens. FEMS Microbiol. Rev. 2008, 32:627-653.
28. Melito P.L., Woodward D.L., Munro J., Walsh J., Foster R., Tilley P., Paccagnella A., Isaac-Renton J., Ismail J., Ng L.K. A novel Shigella dysenteriae serovar isolated in Canada. J. Clin. Microbiol. 2005, 43:740-744.
29. Moorhead S.M., Dykes G.A., Cursons R.T. An SNP-based PCR assay to differentiate between Listeria monocytogenes lineages derived from phylogenetic analysis of the sigB gene. J. Microbiol. Methods 2003, 55:425-432.
30. Petrovskaya V., Khomenko N. Proposal for improving the classification of members of the genus Shigella. Int. J. Syst. Bacteriol. 1979, 29:400-402.
31. Pupo G.M., Lan R., Reeves P.R. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl Acad. Sci. USA 2000, 97:10567-10572.
32. Reuter M., Kupper Y., Schmitz A., Breuer J.P., Wend U., Hennig J. Detection of new single nucleotide polymorphisms by means of real time PCR. J. Genet. 2005, 84:341-345.
33. Rolland K., Lambert-Zechovsky N., Picard B., Denamur E. Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli. Microbiology 1998, 144(Pt 9):2667-2672.
34. Ronaghi M., Elahi E. Pyrosequencing for microbial typing. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2002, 782:67-72.
35. Strockbine N.A., Maurelli A.T. Genus xxxv. Shigella. Bergey's Manual of Systematic Bacteriology 2005, 811-823. Springer Science and Business, New York. second ed. D.J. Brenner, N.R. Krieg, J.T. Staley (Eds.).
36. Talukder K.A., Islam Z., Islam M.A., Dutta D.K., Safa A., Ansaruzzaman M., Faruque A.S., Shahed S.N., Nair G.B., Sack D.A. Phenotypic and genotypic characterization of provisional serotype Shigella flexneri 1c and clonal relationships with 1a and 1b strains isolated in Bangladesh. J. Clin. Microbiol. 2003, 41:110-117.
37. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
38. Van Ert M.N., Easterday W.R., Simonson T.S., U'ren J.M., Pearson T., Kenefic L.J., Busch J.D., Huynh L.Y., Dukerich M., Trim C.B., Beaudry J., Welty-Bernard A., Read T., Fraser C.M., Ravel J., Keim P. Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. J. Clin. Microbiol. 2007, 45:47-53.
39. Wang Y.W., Watanabe H., Phung D., Tung S., Lee Y.S., Terajima J., Liang S.Y., Chiou C.S. Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri. BMC Microbiol. 2009, 9:278.
40. Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G., Mayhew G.F., Plunkett G., Rose D.J., Darling A., Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 2003, 71:2775-2786.
41. Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J., Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J., Xu J., Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J., Jin Q. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 2005, 33:6445-6458.
42. Yang J., Nie H., Chen L., Zhang X., Yang F., Xu X., Zhu Y., Yu J., Jin Q. Revisiting the molecular evolutionary history of Shigella spp. J. Mol. Evol. 2007, 64:71-79.
43. Yang J., Wang J., Chen L., Yu J., Dong J., Yao Z.J., Shen Y., Jin Q., Chen R. Identification and characterization of simple sequence repeats in the genomes of Shigella species. Gene 2003, 322:85-92.