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 167 <i>B</i>. <i>anthracis</i> strains based on whole-genome SNP analysis.

<p>Data are based on 6690 chromosomal SNPs. Geographic origin is reflected by a color code shown on the figure. Each circle represents a unique SNP genotype, the diameter 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 devoid of length value indication have a length of one SNP. The name of the published genomes included in this study is indicated next to their node in the tree. Five colored stars mark major splits in the <i>B</i>. <i>anthracis</i> phylogeny. CanSNPs are indicated in colored disks next to the branch where they occur in the tree.</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

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

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

(a) Minimum spanning tree of MLVA31 data from 119 animal and environmental <i>B. anthracis</i> strains.

<p>Each circle represents a unique genotype. The diameter of each circle corresponds to the number of isolates with the same genotype. Genotypes connected by a shaded background differ by a maximum of 3 of the 31 VNTR markers and could be considered as a “clonal complex”. Thick connecting lines represent one locus differences; regular connecting lines represent two loci differences. The length of each branch is proportional to the number of differences. Each epidemiological situation is represented by a specific color as defined in part b.(<b>b</b>). Localization of the 119 animal and environmental <i>B. anthracis</i> strains.</p

Electrophoresis gel of the MLVA7 panel on four strains.

<p>Well 1: Sterne strain, wells 2 to 4: French bovine strains. Migration on 3% standard agarose gel at 110 V during 4 hours. A 100 bp ladder was used running from 100 bp up to 1000 bp, the 500 bp and 1000 bp bands are more intense.</p

Genotyping of French <i>Bacillus anthracis</i> Strains Based on 31-Loci Multi Locus VNTR Analysis: Epidemiology, Marker Evaluation, and Update of the Internet Genotype Database

<div><p>Background</p><p><i>Bacillus anthracis</i> 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.</p><p>Results</p><p>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.</p><p>Conclusions</p><p>The present report provides a wide coverage of the genetic diversity of naturally occurring <i>B. anthracis</i> 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 <i>B. anthracis</i>.</p></div

Discriminatory power and linkage disequilibrium analysis results for 5 sets of VNTR markers: the newly proposed MLVA7 and MLVA8, MLVA15, MLVA25, MLVA31.

<p>*Values as calculated from MLVA31 data published by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095131#pone.0095131-Beyer1" target="_blank">[16]</a>.</p

Congruence analysis of 5 sets of VNTR markers: MLVA7, MLVA8, MLVA15, MLVA25 and MLVA31.

<p>a congruence analysis in the “France” dataset (this study); b congruence analysis in the “Namibia” dataset <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095131#pone.0095131-Beyer1" target="_blank">[16]</a>.</p