Phylogenetic relationships resulting from <i>E</i>. <i>coli</i> core gene SNP analysis of spiked STEC genomes, metagenomic samples, and other <i>E</i>. <i>coli</i> strains.

<p>This neighbor-joining tree was constructed using a <i>p</i> distance matrix and 500 bootstrap replications. Metagenomic samples are color-coded as follows: green, spiked STEC only <i>E</i>. <i>coli</i> detected in sample; blue, indigenous <i>E</i>. <i>coli</i> present but clusters with spiked strain; and red, indigenous <i>E</i>. <i>coli</i> present and does not cluster with spiked strain. Closed genome strains are labeled with their strain name and GenBank accession number. Phylogroups are indicated by the square brackets. Bootstrap values >80% are given at the internal nodes.