Fig. 1

Dominant Salmonella clones emerge during chronic infections. Five mice were infected I.P. with 10⁴  S. Typhimurium consisting of an equal mixture of eight WITS strains (the inoculum). WITS distribution in indicated samples was determined by a PCR/sequencing strategy. Fecal samples were collected after 4 to 6 weeks of infection, as indicated. All systemic samples were collected after 6 weeks, except for samples from mice 5B and 5D which were euthanized after 4 weeks. Pie charts depict the relative abundance of each WITS strain in different samples. Each pie chart contains the WITS profile of the indicated sample. Above pie charts, the mouse IDs from which the sample was collected are indicated. To the left of pie charts, the respective samples are denoted. The number to the bottom right of each pie chart denotes the number of individual clones analyzed