An unrooted tree showing the inferred relationship between the nine <i>S</i>. Typhimurium clinical isolates.

The S. Typhimurium strain LT2 was used as the reference genome sequence for read mapping. More than 95% of the reference genome was included in the core genome derived for this set of isolates. The core genome contained 1,979 sites that varied in one or more of the clinical isolates. The tree was inferred using Fast Tree and the greatest pairwise distance between isolates is 1,017 SNPs between isolates 36A and 34A.