Virulence genes in the STEC/ETEC genomes.

<p>Virulence genes in the STEC/ETEC genomes.</p

Phylogenetic placement of STEC/ETEC chromosomes using restriction-based and <i>in silico</i> whole genome maps.

<p>STEC/ETEC chromosomal maps (red boxes) were compared to other <i>E</i>. <i>coli</i> and <i>Shigella</i> spp. chromosomal maps. Similarities were calculated using UPGMA algorithm.</p

Whole genome map comparison of STEC/ETEC strains.

<p>Areas in blue are common between two maps, areas in white are unique to the map in which they are contained, and areas in red are matching more than once. (A) Comparison between IH53473 and IH57218, (B) comparison between IH53473 and FE95160, and (C) comparison between IH57218 and FE95160.</p

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>].</p

The Univariate and multivariate results for individual risk factors and the generalized additive model risk ratios with the spatial term of a waterborne outbreak in Vuorela, July 2012.

<p>The Univariate and multivariate results for individual risk factors and the generalized additive model risk ratios with the spatial term of a waterborne outbreak in Vuorela, July 2012.</p

Categorized distance and proportion of cases within those groups in a waterborne outbreak in Vuorela, July 2012.

<p>Categorized distance and proportion of cases within those groups in a waterborne outbreak in Vuorela, July 2012.</p

Epidemic curve of a waterborne outbreak in Vuorela, July 2012 based on the reported onset date of illness of the cases, and <i>E. coli</i> bacteria counts and chlorine levels in the point 7 (See Fig. 1) of the water distribution network.

<p>Epidemic curve of a waterborne outbreak in Vuorela, July 2012 based on the reported onset date of illness of the cases, and <i>E. coli</i> bacteria counts and chlorine levels in the point 7 (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104713#pone-0104713-g001" target="_blank">Fig. 1</a>) of the water distribution network.</p

Microbiological results of faecal samples from symptomatic patients of a waterborne outbreak in Vuorela, July 2012.

<p>Methods used were cultivation¹, PCR/RT-PCR² (polymerase chain reaction/reverse transcripition-PCR), EM³ (electron microscopy) and/or EIA⁴ (Enzyme Immunoassay). ⁵<i>Campylobacter jejuni</i> and ⁶EHEC O157:H7 (from one sample) and ⁷sapovirus GII.P3 were isolated from the samples.</p

Phylogenetic relationships among OTUs (•) of the genus <i>Arcobacter</i> in a waterborne outbreak in Vuorela, July 2012.

<p>The tree was inferred from a maximum likelihood analysis of aligned 16S rRNA gene sequence (≈255 bp) and nodes with a bootstrap value ≥50% of 1 000 replicates are identified. <i>Sulfurospirillum deleyianum</i> (NR_074378) and <i>Campylobacter fetus</i> (L04314) were used as outgroup. Number in bracket represents the total amount of DNA/RNA reads identified in samples from A) the upper storage reservoir before cleaning, B) tap water during contamination and C) the upper storage reservoir after cleaning. *<i>A. butzleri</i>, <i>A. cryaerophilus</i> and <i>A. skirrowii</i> have been associated with gastrointestinal diseases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104713#pone.0104713-Collado1" target="_blank">[76]</a>.</p