Summary of mutations detected in evolved clones isolated from mice infected with wild-type <i>S</i>.

Typhimurium at day 47–70 p.i. For all clones (n = 22; 11 where SipC was detected, and 11 without detectable SipC expression; taken from mice in Fig 1A–1D), the SipC phenotype from our colony protein blot assay [29,50] (as a proxy for TTSS-1 expression) is indicated by a symbol and by the color-code of the column; + and the blue color code indicate positive detection of a SipC signal; +/- and the yellow color code indicate intermediate SipC expression (for the purposes of this study, we considered these SipC expressing clones);—and the red color code indicate the lack of detectable SipC expression. The table shows non-synonymous mutations that are absent from the ancestral strain (S6 Table). The position in the SL1344 reference chromosome (NCBI accession FQ312003.1) is indicated along with the allele change. If blank, the region of the genome contains no mutations. If more than 1 mutation is observed in that gene, we simply show the number of variants present in that gene. Percentages indicate the fraction of isolates, which show a particular mutation. Mutations that occur only in clones with a mutS mutation (mutator strains) are listed in a separate sub-table labeled “Mutator-specific mutations.” (XLSX)