Fig. 4: Infection is initiated by related populations of C. rodentium in the cecum and colon.

a–e C. rodentium populations in whole organ homogenates from 5 cohoused (intra-cage) C57BL/6 J mice 5 days post inoculation with 4 × 10⁸ CFU of STAMP-CR253. Within a mouse (intra-mouse) the C. rodentium populations at the primary sites of colonization (cecum, proximal colon, distal colon, feces) share founders (number, identity, and frequency of barcodes). a, b Lines connect intra-mouse samples. c Clustering of barcode populations by principal component analysis (PCA). d, e Relatedness determined by comparing the barcode frequencies by genetic distance (arithmetic means) with zero indicating no difference between populations (identical). e Two-tailed t test with p-value 5.8 × 10⁻⁴⁸. p proximal, m mid, d distal, SI small intestine. Heatmap depicting genetic distance relationships of all intra-cage populations in Supplemental Fig. 3. Source data are provided as a Source Data file. f, g To determine when/where C. rodentium establishes a replicative niche, C57BL/6 J mice were orally gavaged with between 3 × 10⁹ and 6 × 10⁹ CFU STAMP-CR253. Following dissection, the cecum and colon were flushed to separate organ adherent (f) and luminal (g) bacteria. Burden and founders display geometric means and standard deviations. Bacteria not detected (ND) counted as 0.5. Relatedness of populations was determined by comparing the barcode frequencies of colon and cecal populations from within the same animal (intra-mouse) by genetic distance (arithmetic mean and standard deviation). 22 animals. Source data are provided as a Source Data file. h Model depicting how related C. rodentium populations could initiate infection in both the cecum and colon: (1) the inoculum minorly constricts passing through the stomach and SI to deposit diverse populations in the cecum and colon, (2) the populations in the cecum and colon contract separately over the first 24–48 h becoming dissimilar, and then (3) expansion occurs in either the cecum or colon moving to both locations. We depict the movement from cecum to colon as we judge this to be more likely, but the opposite is possible.