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Volume 154, Issue 8

Phylogenetic analysis of type A by multi-locus sequence typing Free

Abstract

The genus comprises a heterogeneous group of organisms for which the phylogeny and evolutionary relationships are poorly understood. The elucidation of these evolutionary relationships necessitates the use of experimental methods that can distinguish lineages that are time and cost effective, and can be accurately and reproducibly employed in different laboratories. Multi-locus sequence typing (MLST) has been successfully used as a reproducible and discriminating system in the study of eukaryotic and prokaryotic evolutionary biology, and for strain typing of various bacteria. In this study, MLST was applied to evaluate the evolutionary lineages in the serotype A group of . . type A has recently been shown to produce multiple subtypes, suggesting that it is not monophyletic as previously reported, but comprises distinct lineages. For MLST analysis, we initially evaluated 14 housekeeping genes (, , , , , , , , , , , , and ) for amplification and sequence analysis. In the first phase of the analysis, 30 type A strains producing botulinum neurotoxin subtypes A1–A4 were examined. Results of this pilot study suggested that seven of the genes (, , , , , and ) could be used for elucidation of evolutionary lineages and strain typing. These seven housekeeping genes were successfully applied for the elucidation of lineages for 73 type A strains, which resulted in 24 distinct sequence types. This strategy should be applicable to phylogenetic studies and typing of other serotypes and species.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): BoNT, botulinum neurotoxin , HA, haemagglutinin , MLST, multi-locus sequence typing , NJ, neighbour-joining and ST, sequence type
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2008-08-01
2024-04-18
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References

  1. Arndt J. W., Jacobson M. J., Abola E. E., Forsyth C. M., Tepp W. H., Marks J. D., Johnson E. A., Stevens R. C. 2006; A structural perspective of the sequence variability within botulinum neurotoxin subtypes A1–A4. J Mol Biol 362:733–742
     [Google Scholar]
  2. Arnon S. S., Schechter R., Inglesby T. V., Henderson D. A., Bartlett J. G., Ascher M. S., Eitzen E., Fine A. D., Hauer J. other authors 2001; Botulinum toxin as a biological weapon: medical and public health management. JAMA 285:1059–1070
     [Google Scholar]
  3. Bruen T. C., Philippe H., Bryant D. 2006; A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665–2681
     [Google Scholar]
  4. Bryant D., Moulton V. 2004; Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255–265
     [Google Scholar]
  5. Collins M. D., Lawson P. A. 1994; The phylogeny of the genus Clostridum: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44:812–826
     [Google Scholar]
  6. DasGupta B. R. 2006; Botulinum neurotoxins: perspective on their existence and as polyproteins harboring viral proteases. J Gen Appl Microbiol 52:1–8
     [Google Scholar]
  7. Dineen S. S., Bradshaw M., Johnson E. A. 2003; Neurotoxin gene clusters in Clostridium botulinum type A strains: sequence comparison and evolutionary implications. Curr Microbiol 46:345–352
     [Google Scholar]
  8. Gatei W., Das P., Dutta P., Sen A., Cama V., Lal A. A., Xiao L. 2007; Multilocus sequence typing and genetic structure of Cryptosporidium hominis from children in Kolkata, India. Infect Genet Evol 7:197–205
     [Google Scholar]
  9. Gimenez D. F., Gimenez J. A. 1995; The typing of botulinal neurotoxins. Int J Food Microbiol 27:1–9
     [Google Scholar]
  10. Hatheway C. L., Johnson E. A. 1998; Clostridium: the spore-bearing anaerobes. In Topley & Wilson's Microbiology and Infections , 9th edn. vol 2 pp 731–782 Systematic Bacteriology Edited by Collier L., Balows A., Sussman M. London: Arnold;
     [Google Scholar]
  11. Hill K. K., Smith T. J., Helma C. H., Ticknor L. O., Foley B. T., Svensson R. T., Brown J. L., Johnson E. A., Smith L. A. & other authors; 2007; Genetic diversity among botulinum neurotoxin-producing clostridial strains. J Bacteriol 189:818–832
     [Google Scholar]
  12. Huson D. H., Bryant D. 2006; Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267
     [Google Scholar]
  13. Jacobson M. J., Lin G., Raphael B., Andreadis J., Johnson E. A. 2008; Analysis of neurotoxin cluster genes in Clostridium botulinum strains producing botulinum neurotoxin serotype A subtypes. Appl Environ Microbiol 74:2778–2786
     [Google Scholar]
  14. Johnson E. A., Bradshaw M. 2001; Clostridium botulinum and its neurotoxins: a metabolic and cellular perspective. Toxicon 39:1703–1722
     [Google Scholar]
  15. Johnson E. A., Tepp W. H., Bradshaw M., Gilbert R. J., Cook P. E., McIntosh E. D. 2005; Characterization of Clostridium botulinum strains associated with an infant botulism case in the United Kingdom. J Clin Microbiol 43:2602–2607
     [Google Scholar]
  16. Jolley K. A., Feil E. J., Chan M. S., Maiden M. C. 2001; Sequence type analysis and recombinational tests (START). Bioinformatics 17:1230–1231
     [Google Scholar]
  17. Jolley K. A., Chan M. S., Maiden M. C. 2004; mlstdbNet – distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5:86
     [Google Scholar]
  18. Jost B. H., Trinh H. T., Songer J. G. 2006; Clonal relationships among Clostridium perfringens of porcine origin as determined by multilocus sequence typing. Vet Microbiol 116:158–165
     [Google Scholar]
  19. Kozaki S., Nakaue S., Kamata Y. 1995; Immunological characterization of the neurotoxin produced by Clostridium botulinum type A associated with infant botulism in Japan. Microbiol Immunol 39:767–774
     [Google Scholar]
  20. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150–163
     [Google Scholar]
  21. Lacher D. W., Steinsland H., Blank T. E., Donnenberg M. S., Whittam T. S. 2007; Molecular evolution of typical enteropathogenic Escherichia coli: clonal analysis by multilocus sequence typing and virulence gene allelic profiling. J Bacteriol 189:342–350
     [Google Scholar]
  22. Lindstrom M., Korkeala H. 2006; Laboratory diagnostics of botulinum. Clin Microbiol Rev 19:298–314
     [Google Scholar]
  23. Maiden M. C. 2006; Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588
     [Google Scholar]
  24. Maiden M. C., Bygraves J. A., Feil E., Morelli G., Russell J. E., Urwin R., Zhang Q., Zhou J., Zurth K. other authors 1998; Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145
     [Google Scholar]
  25. Noller A. C., McEllistrem M. C., Pacheco A. G., Boxrud D. J., Harrison L. H. 2003; Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157 : H7 isolates. J Clin Microbiol 41:5389–5397
     [Google Scholar]
  26. Pond S. L., Frost S. D. 2005; Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533
     [Google Scholar]
  27. Rozen S., Skaletsky H. 2000; Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
     [Google Scholar]
  28. Sebaihia M., Peck M. W., Minton N. P., Thomson N. R., Holden M. T., Mitchell W. J., Carter A. T., Bentley S. D., Mason D. R. other authors 2007; Genome sequence of a proteolytic (group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res 17:1082–1092
     [Google Scholar]
  29. Smith G. R., Moryson C. J. 1977; A comparison of the distribution of Clostridium botulinum in soil and in lake mud. J Hyg (Lond 78:39–41
     [Google Scholar]
  30. Smith L. D. S., Sugiyama H. 1988 Botulism. The Organism, its Toxin, the Disease Springfield, IL: Charles C. Thomas;
     [Google Scholar]
  31. Smith T. J., Lou J., Geren I. N., Forsyth C. M., Tsai R., Laporte S. L., Tepp W. H., Bradshaw M., Johnson E. A. other authors 2005; Sequence variation within botulinum neurotoxin serotypes impacts antibody binding and neutralization. Infect Immun 73:5450–5457
     [Google Scholar]
  32. Urwin R., Maiden M. C. 2003; Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479–487
     [Google Scholar]
  33. Vassileva M., Torii K., Oshimoto M., Okamoto A., Agata N., Yamada K., Hasegawa T., Ohta M. 2006; Phylogenetic analysis of Bacillus cereus isolates from severe systemic infections using multilocus sequence typing scheme. Microbiol Immunol 50:743–749
     [Google Scholar]
  34. Woodruff B. A., Griffin P. M., McCroskey L. M., Smart J. F., Wainwright R. B., Bryant R. G., Hutwagner L. C., Hatheway C. L. 1992; Clinical and laboratory comparison of botulism from toxin types A, B, and E in the United States, 1975–1988. J Infect Dis 166:1281–1286
     [Google Scholar]
  35. Zadoks R. N., Schukken Y. H., Wiedmann M. 2005; Multilocus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA . J Clin Microbiol 43:2407–2417
     [Google Scholar]
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Phylogenetic analysis of Clostridium botulinum type A by multi-locus sequence typing
Microbiology 154, 2408 (2008); https://doi.org/10.1099/mic.0.2008/016915-0
/content/journal/micro/10.1099/mic.0.2008/016915-0
/content/journal/micro/10.1099/mic.0.2008/016915-0
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