Phylogeny of the major groups of <i>B. anthracis</i> after Pearson et al. (2004) and VanErt et al. (2007).

<p>The new branch, “A.Br.011,” is flanked by branches A.Br.008 and A.Br.009. Thus, the group A.Br.008/009 is now subdivided into two groups: A.Br.008/011 and A.Br.011/009. The canSNP signature and assay that defines this new branch is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone-0028274-t003" target="_blank">Table 3</a>.</p

Dendrogram of MLVA-8 analysis of <i>B. anthracis</i> isolates collected from the 1976 California, 2006 New York, 2007 Connecticut anthrax cases, and 2009 New Hampshire case.

<p>All other genotypes are reference genotypes from Keim et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone.0028274-Keim1" target="_blank">[8]</a>. For the California case, the clinical isolates were GT 76 (n = 4), while environmental isolates were GT 71 (n = 2), GT 72 (n = 2), GT 92 (n = 1), and GT 105 (n = 1). All clinical and environmental isolates from the New York (one clinical, 35 environmental) and Connecticut cases (one clinical specimen, 15 environmental isolates) were GT 1. All clinical (n = 2) and environmental (n = 9) isolates from the NH case were GT 149. Scale bar indicates amount of evolutionary change <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone.0028274-McDonald1" target="_blank">[12]</a>.</p

MLVA-8 results of clinical and environmental <i>B. anthracis</i> isolates associated with the California, New York, Connecticut, and New Hampshire anthrax cases.

<p>—, plasmid loci not detected.</p><p>NA, not applicable.</p><p>*, new allele size not previously described by Keim et al.</p

Novel <i>B. anthracis</i> canSNP assays developed in this report.

a<p>Using ‘Ames ancestor’ genome (GenBank ref: AE017334).</p>b<p>Underlined nucleotides indicate the position of the SNP; bolded nucleotides indicate an introduced GC clamp that increases the melt temperature of the primer, thus enhancing allelic discrimination <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone.0028274-Germer1" target="_blank">[13]</a>; small-case nucleotides represent deliberate mismatches incorporated into the allele-specific primers.</p>c<p>All assays were optimized on an Applied Biosystems ABI PRISM 7900HT Sequence Detection System using default thermocycling parameters, with the addition of the dissociation curve <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone.0028274-Germer1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028274#pone.0028274-Germer2" target="_blank">[14]</a>.</p