<i>L</i>. <i>monocytogenes</i> CC8 genome sequences used in the present study.

<p><i>L</i>. <i>monocytogenes</i> CC8 genome sequences used in the present study.</p

Phylogeny for the <i>L</i>. <i>monocytogenes</i> CC8 isolates based on whole-genome SNP analysis.

<p>Maximum Parsimony tree based on 872 non-homoplasic chromosomal SNPs. The tree was rooted on <i>L</i>. <i>monocytogenes</i> IZSAM_Lm_14–16064. Bootstrap support is shown for nodes with <100% bootstrap support. Branch lengths are in the units of the number of changes over the whole sequence (except for the branch for IZSAM_Lm_14–16064 which has been shortened for clarity), and the number of contributing SNPs is indicated below each branch (numbers in pink). For details on the identity of the indicated SNPs differentiating the strains, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151117#pone.0151117.s001" target="_blank">S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151117#pone.0151117.s002" target="_blank">S2</a> Tables. The ST8 lineage is indicated by a box with dashed line, for the other strains the ST is indicated in parenthesis after strain names. The origin of strains is indicated by the colour of the strain name: Blue; salmon processing facility, green; poultry processing facility or meat, orange; cheese, pink; human clinical strain. Superscripts after strain names indicate the variant of the <i>hsdRMS</i> locus found in each strain (see text, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151117#pone.0151117.g002" target="_blank">Fig 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151117#pone.0151117.t003" target="_blank">Table 3</a> for details). The year of isolation (when known) is noted below the name of each isolate.</p

Non-SNP differences between the <i>L</i>. <i>monocytogenes</i> ST8 genomes.

<p>Non-SNP differences between the <i>L</i>. <i>monocytogenes</i> ST8 genomes.</p

Comparison of prophages present in the <i>L</i>. <i>monocytogenes</i> ST8 genomes.

<p>Predicted ORFs are represented by blue arrows. Highly conserved segments, determined by pairwise BLASTn comparisons, are indicated by grey shaded regions with the color intensity indicating the nucleotide identity levels (from 66% to 100%). Similarities with E values lower than 0.001 were plotted. The prophages are denoted by names indicating the locus where they are inserted into the genome, followed by the host strain name(s) in parenthesis. For the prophages denoted by R479a, almost identical prophages were also identified in isolates MF4245, MF3949, MF4077, MF5369, MF5377 and SHL004, and in the case of the <i>comK</i> prophage, also in strain Lm21045.</p

Comparison of <i>L</i>. <i>monocytogenes</i> plasmids.

<p>Predicted ORFs are represented by arrows, with the <i>repA</i> replication initiation gene in red, the <i>cadAC</i> cadmium resistance transposon Tn<i>5422</i> in orange, the <i>pemI</i>-<i>pemK</i> toxin-antitoxin module in green, and a predicted arsenic resistance operon in blue. Highly conserved segments, determined by pairwise BLASTn comparisons, are indicated by grey shaded regions with the color intensity indicating the nucleotide identity levels (from 93% to 100%). Similarities with E values lower than 0.001 and a minimum length of 1000 bp were plotted.</p