DOI: 10.5061/dryad.rc6m9
title: Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

description: Background: Single nucleotide polymorphisms (SNPs) are ideal signatures
 for subtyping monomorphic pathogens such as Bacillus anthracis. Here we
 report the use of next-generation sequencing technology to investigate the
 historical, geographic and genetic diversity of Bacillus anthracis in
 France. 122 strains isolated over a 50-years period throughout the country
 were whole-genome sequenced and comparative analyses were carried out with
 a focus on SNPs discovery to discriminate regional sub-groups of
 strains.Results: A total of 1581 chromosomal SNPs precisely establish the
 phylogenetic relationships existing between the French strains.
 Phylogeography patterns within the three canSNP sub-lineages present in
 France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One
 of the more remarkable findings was the identification of a variety of
 genotypes within the A.Br.011/009 sub-group that are persisting in the
 different regions of France. The 560 SNPs defining the A.Br.011/009-
 affiliated French strains split the Trans-Eurasian sub-group into six
 distinct branches without any intermediate nodes. Distinct sub-branches,
 with some geographic clustering, were resolved. The 345 SNPs defining the
 major B.Br CNEVA sub-lineage clustered three main phylogeographic clades,
 the Alps, the Pyrenees, and the Massif Central, with a small
 Saône-et-Loire sub-cluster nested within the latter group. The French
 strains affiliated to the minor A.Br.001/002 group were characterized by
 226 SNPs. All recent isolates collected from the Doubs department were
 closely related. Identification of SNPs from whole-genome sequences
 facilitates high-resolution strain tracking and provides the level of
 discrimination required for outbreak investigations. Eight diagnostic
 SNPs, representative of the main French-specific phylogeographic clusters,
 were therefore selected and developed into high-resolution melting SNP
 discriminative assays. Conclusions: This work has established one of the
 most accurate phylogenetic reconstruction of B. anthracis population
 structure in a country. An extensive next-generation sequencing (NGS)
 dataset of 122 French strains have been created that allowed the
 identification of novel diagnostic SNPs useful to rapidly determine the
 geographic origin of any strain found in France.
description: Figure 1: Phylogeny of
 126 B. anthracis strains based on whole-genome SNP
 analysisPhylogeny of 126 B.
 anthracis strains based on whole-genome SNP analysis. A. Minimum spanning
 tree based on 3987 chromosomal SNPs (obtained with BioNumerics 6.6 from
 Applied Maths). The 3 canSNP groups present in France are color-coded:
 B.Br CNEVA in light blue, A.Br 011/009 in purple and A.Br 001/002 in
 green. The African lineage A.Br 005/006 is indicated in red. Positions of
 the B. anthracis Sterne (in green), Ames ancestor (in yellow) and A1055
 (in black) strains are also marked. Each circle represents a unique SNP
 genotype. The diameter of each circle varies according to the number of
 isolates having the same genotype. The length of each branch is
 proportional (logarithmic scale) to the number of SNPs identified between
 strains. Indicated in red are the position and name of the new identified
 French canSNPs. The star marks the approximate branching point of the B.
 anthracis lineage within the B. cereus group. Based on a parsimony
 approach, the tree size is 4018, i.e. it contains approximately 0.77% of
 homoplasia. B. Linear phylogenetic tree rooted with the B. cereus AH820
 strain as outgroup. This figure illustrates the relationship between
 French and globally diverse B. anthracis strains.Figure1.tifFigure 2: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineageMinimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 345 chromosomal SNPs (A), 14 pXO1 SNPs (B) and 15 pXO2 SNPs (C). The geographic clustering of the French strains is color-coded: Alps in green (34 strains), Pyrenees in purple (9 strains), Massif Central in red (18 strains) and Saône et Loire department in yellow (6 strains). The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of four French canSNPs described in this study. Based on a parsimony approach, the tree size is 352, i.e. it contains approximately 1.98% of homoplasia. Concerning the plasmids, the tree sizes are 14 and 15 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.Figure2.TIFFigure 3: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroupMinimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 560 chromosomal SNPs (A), 20 pXO1 SNPs (B) and 18 pXO2 SNPs (C). The six resolved branches are color-coded. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the positions and names for two canSNPs described in this study. NE: North-East, SW: South-West, SE: South-East. Based on a parsimony approach, the tree size is 561, i.e. it contains approximately 0.18% of homoplasia. Concerning the plasmids, the tree sizes are 20 and 18 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.Figure3.TIF