Phylogeny of the 13 STEC O104:H4 isolates under investigation and of ten more STEC O104:H4 strains based on selected SNPs in their published genome sequences assignes the two German sporadic isolates 11–06681 and 11–07153 to a clade clearly separate from the one containing the 2011 outbreak strain isolates.

<p>The tree was calculated using the MrBayes tool from the GENEIOUS software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.ref026" target="_blank">26</a>] and routed to the German historical isolate 01–09591 which served as outgroup. The sequences for EL-2071 and EL-2050, two sporadic isolates from cases in Georgia in 2009 and C-3493, an isolate obtained in the USA from a person with travelling history to Germany in May 2011 were published by Ahmed et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.ref021" target="_blank">21</a>]. The sequences for Ec04-8351 and Ec09-7901, two historical strains from France and the sequences of Ec11-9450, Ec11-9941, Ec11-9990, Ec12-0456, Ec12-0466, five more recent sporadic isolates from France were published by Grad et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.ref022" target="_blank">22</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.ref023" target="_blank">23</a>]. The selected SNPs used for tree calculation are given in supplementary files <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.s001" target="_blank">S1 Dataset</a> (SNP positions) and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122074#pone.0122074.s002" target="_blank">S2 Dataset</a> (sequences).