Geographic distribution of 93 Malagasy <i>Y</i>. <i>pestis</i> clinical samples from 2007.

<p>Light gray shaded polygons indicate Madagascar districts where <i>Y</i>. <i>pestis</i> samples used in this study were obtained (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.s001" target="_blank">S1 Table</a>, column E,F). Circles represent the locations of the communes where samples were collected. Colors within the mapped circles correspond to the MLVA subclade color designations in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.g001" target="_blank">Fig 1</a>. Divisions within circles indicate that multiple MLVA subclades were found at that location. Numbers within MLVA subclade I.A (red) and I.B (orange) circles and pie chart slices indicate the node within lineages s and q, respectively, of the SNP phylogeny in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.g001" target="_blank">Fig 1</a> that the mapped samples belong to. Where the SNP genotype could not be definitively determined for any of the subclade I.A or I.B samples from a particular location, no number is shown. Unaffiliated Group I and II samples (i.e., subclades I.NONE and II.NONE) are indicated by a “*” and a “+,” respectively.</p

MLVA (A), SNP (B), and CRISPR (C) based phylogenies of 93 <i>Y</i>. <i>pestis</i> clinical samples from Madagascar in 2007.

<p>MLVA subclades were named as in reference [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref012" target="_blank">12</a>] for the 8 of 15 previously described subclades identified here, except for subclade II.A, which was subdivided into subclades II.A.1 and II.A.2 in this analysis. Two new subclades described here, including II.A.2, are bolded and marked with stars. One Group I sample and one Group II sample did not fall into any recognized MLVA subclade and so were classified as I.NONE and II.NONE, respectively (A). SNP phylogeny nodes were named as in references [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref011" target="_blank">11</a>–<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref013" target="_blank">13</a>] and include 13 of the 31 nodes described there. Previously described nodes that were not represented in this study are indicated by gray circles and arrows in the SNP phylogeny (B). The numbers of samples in each MLVA subclade and SNP phylogeny node with >1 sample as well as the total number of samples in each CRISPR genotype are indicated. Asterisks indicate 7 samples with incomplete SNP data that were assigned to a SNP phylogeny lineage or node based upon MLVA data (B). Color shading in each phylogeny is based upon the identified MLVA subclade and corresponds to the MLVA subclade colors in reference [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref012" target="_blank">12</a>] for the 8 previously described MLVA subclades. Bootstrap values ≥50 supporting MLVA phylogeny branches (A) and specific CRISPR mutations marking CRISPR phylogeny branches (C) are also indicated. Note that CRISPR genotypes I.1 and II.1 are identical and consist of the following CRISPR pattern: a1-a2-a3-a4-a5-a6-a7-a8 b1-b2-b3-b4-b5 c1-c2-c3 (C). An updated CRISPR dictionary is available in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.s002" target="_blank">S2 Table</a>.</p