title: Molecular diversity of Bacillus anthracis in the Netherlands: investigating the relationship to the worldwide population using whole-genome SNP discovery.
abstract: Bacillus anthracis, the causative agent of anthrax, has been widely described as a clonal species. Here we report the use of both canonical SNP analysis and whole-genome sequencing to characterize the phylogenetic lineages of B. anthracis from the Netherlands. Eleven strains isolated over a 25-years period (1968-1993) were paired-end sequenced using parallel sequencing technology. Five canSNP groups or lineages, i.e. A.Br.001/002 (n=6), A.Br.Aust94 (n=2), A.Br.008/011 (n=1), A.Br.011/009 (n=1) and A.Br.Vollum (n=1) were identified. Comparative analyses, with a focus on SNPs discovery, were carried out using a total of 52 B. anthracis genomes. A phylogeographic "Dutch" cluster within the dominant A.Br.001/002 group was discovered, involving isolates from a single outbreak. Diagnostic SNPs specific to the newly identified sub-groups were developed into high-resolution melting SNP discriminative assays for the purpose of rapid molecular epidemiology. Phylogenetic relationships with strains from other parts of the world are discussed.
authors.affiliation: University Paris-Est, Anses, 14 rue Pierre et Marie Curie, 94701 Maisons Alfort, France. Electronic address: sderzelle@dbmail.com.
authors.forename: Sylviane
authors.initials: S
authors.lastname: Derzelle
authors.affiliation: University Paris-Est, Anses, 14 rue Pierre et Marie Curie, 94701 Maisons Alfort, France. Electronic address: guillaume.girault@anses.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Girault
authors.affiliation: Central Veterinary Institute of Wageningen University and Research Centre, Edelhertweg 15, 8219PH Lelystad, Netherlands. Electronic address: hendrikjan.roest@wur.nl.
authors.forename: Hendrik Ido Jan
authors.initials: HI
authors.lastname: Roest
authors.affiliation: Central Veterinary Institute of Wageningen University and Research Centre, Edelhertweg 15, 8219PH Lelystad, Netherlands. Electronic address: miriam.koene@wur.nl.
authors.forename: Miriam
authors.initials: M
authors.lastname: Koene
mesh_terms: D000818:Animals; D000881:Anthrax / Q000453:epidemiology*; D001408:Bacillus anthracis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000235:genetics; D056726:Genetic Association Studies; D016680:Genome, Bacterial; D005838:Genotype; D060005:Genotyping Techniques; D017720:Molecular Epidemiology; D009426:Netherlands / Q000453:epidemiology; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial
keywords: Bacillus anthracis; Comparative genomics; High resolution melting (HRM); Molecular typing; Single nucleotide polymorphism; Whole genome sequencing