title: Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis.
abstract: BACKGROUND
  Yersinia pestis, the agent of plague, is a young and highly monomorphic species. Three biovars, each one thought to be associated with the last three Y. pestis pandemics, have been defined based on biochemical assays. More recently, DNA based assays, including DNA sequencing, IS typing, DNA arrays, have significantly improved current knowledge on the origin and phylogenetic evolution of Y. pestis. However, these methods suffer either from a lack of resolution or from the difficulty to compare data. Variable number of tandem repeats (VNTRs) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses in a growing number of pathogens and have given promising results for Y. pestis as well.
  
  
  RESULTS
  In this study we have genotyped 180 Y. pestis isolates by multiple locus VNTR analysis (MLVA) using 25 markers. Sixty-one different genotypes were observed. The three biovars were distributed into three main branches, with some exceptions. In particular, the Medievalis phenotype is clearly heterogeneous, resulting from different mutation events in the napA gene. Antiqua strains from Asia appear to hold a central position compared to Antiqua strains from Africa. A subset of 7 markers is proposed for the quick comparison of a new strain with the collection typed here. This can be easily achieved using a Web-based facility, specifically set-up for running such identifications.
  
  
  CONCLUSIONS
  Tandem-repeat typing may prove to be a powerful complement to the existing phylogenetic tools for Y. pestis. Typing can be achieved quickly at a low cost in terms of consumables, technical expertise and equipment. The resulting data can be easily compared between different laboratories. The number and selection of markers will eventually depend upon the type and aim of investigations.
authors.affiliation: Génome, Polymorphisme et Minisatellites (GPMS), Institut de Génétique et Microbiologie, Bat, 400, UMR CNRS 8621, Université Paris XI, 91405 Orsay cedex, France. Gilles. christine.pourcel@igmors.u-psud.fr
authors.forename: C
authors.initials: C
authors.lastname: Pourcel
authors.forename: F
authors.initials: F
authors.lastname: André-Mazeaud
authors.forename: H
authors.initials: H
authors.lastname: Neubauer
authors.forename: F
authors.initials: F
authors.lastname: Ramisse
authors.forename: G
authors.initials: G
authors.lastname: Vergnaud
mesh_terms: D000349:Africa / Q000453:epidemiology; D001208:Asia / Q000453:epidemiology; D015373:Bacterial Typing Techniques / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics*; D004196:Disease Outbreaks; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D018598:Minisatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D015010:Yersinia pestis / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers