Figure 2: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage

Minimum 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

S1 Fig. Evolutionary analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs.

S1 Fig. Evolutionary analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs. Phylogenetic relationships were inferred using the Maximum Likelihood method (A), the Maximum Parsimony method (B), the Neighbor-Joining method (C) and the UPGMA method (D). Bootstrap values (100 iterations) higher than 70% are shown next to the branches. All evolutionary analyses were conducted in MEGA6 [28]. The maximum likelihood tree with the highest log likelihood (0.000) is shown in A. Tree #1 out of 2 most parsimonious trees (length = 7469, consistency index = 0.815, retention index = 0.947) is shown in B. The optimal neighbour-joining tree with the sum of branch length = 0.251 is shown in C. The optimal UPGMA tree with the sum of branch length = 0.239 is shown in D. The later tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree

Figure 3: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup

Minimum 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

Whole-sequenced strains and canSNP typing.

<p>* Genome coverage are based on the Ames Ancestor genome size (5227419 bp).</p><p>The whole genome sequences of the Danish strains are available at: <a href="http://www.ebi.ac.uk/ena/data/view/PRJEB9705" target="_blank">http://www.ebi.ac.uk/ena/data/view/PRJEB9705</a></p

Specific canSNPs and primer sequences used for HRM analysis.

<p>* localisation on the Ames Ancestor chromosome (GenBank accession no. AE017334.2).</p><p>Specific canSNPs and primer sequences used for HRM analysis.</p

Whole-genome sequences from public database used in this study.

<p>Whole-genome sequences from public database used in this study.</p

Minimum spanning tree of 28 <i>B</i>. <i>anthracis</i> strains belonging to the A.Br.001/002 polytomy.

<p>The tree is based upon 1669 chromosomal SNPs. The diameter of each circle varies according to the number of isolates sharing the same genotype. The length of each branch is proportional (logarithmic scale) to the indicated number of SNPs. Branches with no indication of length value have a length of one SNP. The red star indicates the position of the root, as defined by using the Australia_94 strain genome as an outgroup. The red arrow indicates the approximate position of the timing of the introduction of the Ames lineage to the USA according to [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146216#pone.0146216.ref014" target="_blank">14</a>].</p

Correction: Comparison of French and Worldwide <i>Bacillus anthracis</i> Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade

Correction: Comparison of French and Worldwide <i>Bacillus anthracis</i> Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clad

Minimum spanning tree of 38 <i>B</i>. <i>anthracis</i> strains belonging to the A.Br.011/009 polytomy.

<p>Tree drawing is based upon 1934 chromosomal SNPs. The six branches constituting the polytomy are numbered as previously reported [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146216#pone.0146216.ref017" target="_blank">17</a>]. 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 indicated number of SNPs. Branches with no indication of length value have a length of one SNP. A tentative dating of the initial outbreak represented by the red star is indicated, based on the assumption that (1) the split towards WNA-Senegal-Gambia occurred within 1550–1650 (2) the average expansion rate of lineage 2 which remained in the same ecosystem (within France) did not vary from the founder outbreak event until the end of the nineteenth century. Under these hypotheses, the outbreak most likely occurred during the hundred years war between France and England, 1350–1450.</p

Comparison of French and Worldwide <i>Bacillus anthracis</i> Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade

<div><p>Background</p><p><i>Bacillus anthracis</i>, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French <i>B</i>. <i>anthracis</i> lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins.</p><p>Results</p><p>A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant <i>B</i>. <i>anthracis</i> lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France.</p><p>Conclusions/Significance</p><p>The present work extends the range of observed substitution rate heterogeneity within <i>B</i>. <i>anthracis</i>, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.</p></div