title: Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database.
abstract: BACKGROUND
  Bacillus anthracis is known to have low genetic variability. In spite of this lack of diversity, multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) and single nucleotide polymorphisms (SNPs) including the canonical SNPs assay (canSNP) have proved to be highly effective to differentiate strains. Five different MLVA schemes based on a collection of 31 VNTR loci (MLVA8, MLVA15, MLVA20, MLVA25 and MLVA31) with increased resolving power have been described.
  
  
  RESULTS
  MLVA31 was applied to characterize the French National Reference Laboratory collection. The total collection of 130 strains is resolved in 35 genotypes. The 119 veterinary and environmental strains collection in France were resolved into 26 genotypes belonging to three canSNP lineages and four MLVA clonal complexes (CCs) with particular geographical clustering. A subset of seven loci (MLVA7) is proposed to constitute a first line assay. The loci are compatible with moderate resolution equipment such as agarose gel electrophoresis and show a good congruence value with MLVA31. The associated MLVA and SNP data was imported together with published genotyping data by taking advantage of major enhancements to the MLVAbank software and web site.
  
  
  CONCLUSIONS
  The present report provides a wide coverage of the genetic diversity of naturally occurring B. anthracis strains in France as can be revealed by MLVA. The data obtained suggests that once such coverage is achieved, it becomes possible to devise optimized first-line MLVA assays comprising a sufficiently low number of loci to be typed either in one multiplex PCR or on agarose gels. Such a selection of seven loci is proposed here, and future similar investigations in additional countries will indicate to which extend the same selection can be used worldwide as a common minimum set. It is hoped that this approach will contribute to an efficient and low-cost routine surveillance of important pathogens for biosecurity such as B. anthracis.
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Thierry
authors.affiliation: Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France; CNRS, Orsay, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Tourterel
authors.affiliation: Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France; CNRS, Orsay, France; Division of Analytical Microbiology, DGA CBRN Defence, Vert le Petit, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Le Flèche
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Sylviane
authors.initials: S
authors.lastname: Derzelle
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Neira
authors.initials: N
authors.lastname: Dekhil
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Christiane
authors.initials: C
authors.lastname: Mendy
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Colaneri
authors.affiliation: Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France; CNRS, Orsay, France; DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Vergnaud
authors.affiliation: University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France.
authors.forename: Nora
authors.initials: N
authors.lastname: Madani
mesh_terms: D000881:Anthrax / Q000453:epidemiology / Q000382:microbiology; D001408:Bacillus anthracis / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D005602:France; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D020407:Internet; D018598:Minisatellite Repeats; D058885:Multilocus Sequence Typing; D020641:Polymorphism, Single Nucleotide; D019371:Topography, Medical
chemical_list: D005819:Genetic Markers