Article Figures & Data
Figures
- FIG 1
Deleted region around mutS in the isolates used in this study. Closed arrows indicate the presence of the gene, and open arrows indicate the absence of the gene. The genes where the junction is located are highlighted in black. The number represents the nucleotide position in the reference strain Sakai.
- FIG 2
Phylogenetic tree of all strains used in this study. The tree was constructed by the maximum likelihood method with 1,000 bootstrap replicates (42) using a concatenated SNP alignment after removal of recombinant regions. The color of the branch and of the first ring indicates the MLVA group. The color of the second ring indicates the locus variant (LV) in each MLVA group: SLV, single locus variants; DLV, double locus variants; and TLV, triple locus variants.
- FIG 3
Histogram of pairwise SNP distances between the epi-linked isolates.
- FIG 4
Box plots of pairwise SNPs stratified by MLVA allele difference. From the pairwise data matrix of all the isolates, two distance values (cgSNP and MLVA allele difference) were generated. This figure illustrates the relationship of the values. The x axis represents the number of MLVA allele differences. In each value, the number of pairwise cgSNP loci was shown as a box plot (y axis). Circles and crosses represent outliers and means, respectively. The first and third quartile and the maximum and minimum values without outliers are shown. Prop., proportion.
- FIG 5
Histogram showing the relationship between the number of SNP loci and interval of isolation date. This figure was generated using cgSNP results of the isolate pairs that have zero or one MLVA allele difference.
- FIG 6
Box plots of pairwise difference of cgMLST allele stratified by MLVA allele difference. From the pairwise data matrix of all the isolates, two distance values (cgMLST and MLVA allele difference) were generated. This figure illustrates the relationship of the values. The x axis represents the number of MLVA allele differences. In each value, the number of cgMLST allele differences was shown as a box plot (y axis). Circles and crosses represent outliers and means, respectively. The first and third quartile and the maximum and minimum values without outliers are shown. Prop., proportion.
- FIG 7
Histogram of pairwise cgMLST allele differences between epi-linked isolates.
- FIG 8
Schematic view of EHEC O157 surveillance workflow using MLVA and WGS analyses. The colored ellipses represent EHEC O157 isolates of different MLVA types. The maximum time required for the analysis is shown on the right.
Tables
- TABLE 1
Number of isolates of each MLVA group
MLVA group Index MLVA type ID No. of isolates ofa: Index SLV DLV TLV G1 13m0551 56 10 1 7 G2 15m0278 39 9 0 2 G3 16m0110 26 2 0 0 G4 17m0121 41 6 24 2 G5 13m0157 18 11 6 10 G6 13m0694 36 18 19 6 G7 14m0004 5 9 4 2 ↵a Index, index MLVA type; SLV, single locus variant; DLV, double locus variant; TLV, triple locus variant.
Supplemental material
- Supplemental file 1 -
Fig. S1 to S7
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- Supplemental file 2 -
Table S1
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- Supplemental file 3 -
Table S2
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- Supplemental file 1 -
