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Volume 11, Number 8—August 2005
Letter

Yersinia pestis Genotyping

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Thumbnail of A) sequence-to-code correspondence (1 letter per 16-bp repeat unit). Differences from repeat unit "e" are shown. B) Tandem repeat arrays were coded accordingly. All sequences were obtained from Genbank (Ypseu: Yersinia pseudotuberculosis IP32953; Microtus: "Y. microtus" Chinese strain #91001).

Figure. . . A) sequence-to-code correspondence (1 letter per 16-bp repeat unit). Differences from repeat unit "e" are shown. B) Tandem repeat arrays were coded accordingly. All sequences were obtained from Genbank...

To the Editor: Drancourt et al. (1) report the development of an original genotyping system for Yersinia pestis based on intergenic spacer sequencing. However, the approach appears to rely upon the characterization of polymorphisms due to tandem repeat variation. Eight spacers are used in the report, 7 of which contain tandem repeats, and the sequence variability used to produce the typing data and the strain clustering result from variation in the number of tandem repeats (and incorrect data analysis produces a dendrogram with 34 branches from only 19 different isolate types). Three of the spacers and associated polymorphisms were previously reported. Spacers YP3 and YP5 are, respectively, ms38 and ms56 (2); spacer YP10 is M61 (3). YP3 is later used to investigate ancient DNA samples, and 3 amplification products are described in detail. The sequences are compared to modern sequences by BLAST analysis, which is not relevant for tandem repeats. Instead, the Figure shows how internal variation within the array can be coded to facilitate interpretation. In this collection, Orientalis strains are "abcdeeef," whereas Antiqua strains from Africa are "abcdeef." All these different codes can be deduced one from the other by simple duplication and deletion events, with no need to invoke point mutations. The codes for all 3 ancient samples are identical to the Orientalis code "abcdeeef."

In conclusion, the data presented by Drancourt et al. do not appear to support their claim. They did not invent a new genotyping method but used the well-known multiple locus variable analysis (MLVA) number of tandem repeats approach. The finding that the "genotype Orientalis was involved in all three pandemics" is not valid since the Orientalis type is defined by a biochemical assay, resulting in all known Orientalis strains from a 93-bp glycerol-3-phosphate dehydrogenase microdeletion (4,5), which was not investigated here.

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Gilles Vergnaud*Comments to Author 

Author affiliation: *Centre d'Etudes du Bouchet, Vert le Petit, France

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References

  1. Drancourt  M, Roux  V, Dang  LV, Tran-Hung  L, Castex  D, Chenal-Francisque  V, Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerg Infect Dis. 2004;10:158592.PubMed
  2. Le Flèche  P, Hauck  Y, Onteniente  L, Prieur  A, Denoeud  F, Ramisse  V, A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol. 2001;1:2. DOIPubMed
  3. Klevytska  AM, Price  LB, Schupp  JM, Worsham  PL, Wong  J, Keim  P. Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. J Clin Microbiol. 2001;39:317985. DOIPubMed
  4. Motin  VL, Georgescu  AM, Elliott  JM, Hu  P, Worsham  PL, Ott  LL, Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD). J Bacteriol. 2002;184:101927. DOIPubMed
  5. Pourcel  C, Andre-Mazeaud  F, Neubauer  H, Ramisse  F, Vergnaud  G. Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol. 2004;4:22. DOIPubMed

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Cite This Article

DOI: 10.3201/eid1108.040942

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Table of Contents – Volume 11, Number 8—August 2005

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Please use the form below to submit correspondence to the authors or contact them at the following address:

Gilles Vergnaud, Department of Analytical Microbiology, Centre d'Etudes du Bouchet 91710, Vert le Petit, France; fax: 33-1-69-15-66-78

Didier Raoult, Unité des Rickettsies, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France; fax: 33-4-91-38-77-72

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Page created: April 23, 2012
Page updated: April 23, 2012
Page reviewed: April 23, 2012
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