Table 1.
Overview and classical typing data of S. Typhimurium and S. 1,4,[5],12:i:- isolates in the study.
Fig 1.
Schematic representation of the tested SNP-based subtyping workflows.
Left: data analysis steps of a SNP-based subtyping workflow; Right: details of variant calling and SNP matrix construction steps of the tested SNP-based subtyping workflows. AF: allele frequency, COV: coverage, GQ: genotype quality, MQ: mapping quality, Rel. COV: relative coverage.
Fig 2.
Phylogenetic tree generated with the tested SNP-based subtyping workflows.
The workflows were run using the original dataset and LT2 as a reference genome. (A) CSI-based workflow, (B) PHEnix-based workflow, (C) CFSAN-based workflow. Isolates are coloured according to the MLVA-profile. The minimal and maximal SNP distances observed between the five outbreak isolates and the three isolates obtained from the same patient are indicated near the clusters. The two stably recurring groups of isolates mentioned in the text consist of (1) 12–3582, 12–3583, 12–2998, 12–2984, 12–3558, 12–3067 (yellow) and (2) 12–2314, 12–2460, 12–2599, 12–2455, 12–2379, 12–1558 (green and red). The trees are drawn to scale, with branch lengths measured in the number of substitutions per site. The scale axis is provided below each tree. BS: bootstrap values.
Table 2.
Performance metrics of the tested SNP-based subtyping workflows.
Fig 3.
SNP distance matrices generated with the tested SNP-based subtyping workflows.
The workflows were run using the original dataset and LT2 as a reference genome. (A) CSI Phylogeny-based workflow, (B) PHEnix-based workflow, (C) CFSAN-based workflow. Colours indicate pairwise SNP distances between isolates. Outbreak isolates are shown in bold and isolates obtained from the same patient are underlined.