Distinct <i>Salmonella</i> subpopulations arise in systemic and intestinal tissues during chronic infection.

<p>Mice were oral gavaged with 10⁸<i>S.</i> Typhimurium consisting of an equal mixture of 8 WITS strains. WITS profiles in various tissues were determined by qPCR. Data shown represent 3 independent experiments (n = 19). A) Spleen, liver, gallbladder (gb), PP (pp), small intestine (si), cecum, colon, and fecal samples were collected after 35 days of infection. Bars depict the relative abundance of each WITS strain in different tissue compartments, each box contains the WITS profile for an individual mouse (1–19). Systemic tissues are highlighted in gray. <i>Inset:</i> composition of the WITS inoculum. B) Bray-Curtis dissimilarity values of WITS relative abundances in organ A versus organ B. Each circle represents an individual mouse (n = 19), lines represent medians. The lowest median dissimilarity in the depicted comparisons was observed between the colon and cecum (black circles). Intergroup differences were evaluated by paired t-tests. ** p = 0.0024, *** p = 0.0002, **** p<0.0001.