Phylogenetic placement of STEC/ETEC strains using core genome MLST and sequence alignment.

<p>UPGMA tree based on aligned sequences of the defined <i>E</i>. <i>coli</i> core genome genes (n = 1341) showing the phylogenetic relationship of the three STEC/ETEC genomes and 73 additional <i>E</i>. <i>coli</i> and <i>Shigella</i> spp. strains. The different pathogroups, STEC, ETEC, EPEC, EIEC, EAEC, AIEC (adherent/invasive <i>E</i>. <i>coli</i>), APEC (avian pathogenic <i>E</i>. <i>coli</i>), UPEC (uropathogenic <i>E</i>. <i>coli</i>), ExPEC (extraintestinal pathogenic <i>E</i>. <i>coli</i>), MNEC (meningitis causing <i>E</i>. <i>coli</i>), commensal, and environmental <i>E</i>. <i>coli</i> are marked by colors. The reference genomes STEC O139:H1 S1191, ETEC UMNF18, STEC O2:H25 7v, STEC O8:H19 MHI813, and STEC O73:H18 C165-02 were previously characterized as STEC/ETEC hybrids [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135936#pone.0135936.ref014" target="_blank">14</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135936#pone.0135936.ref037" target="_blank">37</a>]. The reference genomes ETEC O6 E8, ETEC O6 E66, ETEC O78 E36, ETEC O25 E135, ETEC O115 E21, ETEC ON3 E562, ETEC O169 E344, ETEC O148 E222, ETEC O27 E220, ETEC O114 E934, ETEC O159 E159, ETEC O15 E330, ETEC O112ab E399, and ETEC ON5 E620 represent the phylogenetic lineages L1-L14 of the ETEC pathogroup, respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135936#pone.0135936.ref017" target="_blank">17</a>].