Fig. 3

Co-ordinated expression of the non-LEE-encoded effector repertoire in vivo. a Expression dynamics of the NLE repertoire in vivo compared to in vitro growth in DMEM. The line plots illustrate fold-change in expression at each site and time point during infection. A selection of NLEs (espS, espI^nleA, espO, espM3 and espK) displaying the highest fold changes in expression are labelled and colour coded while remaining NLE genes are illustrated in grey. Gene expression data represents the mean of three replicates in all cases and full expression heatmaps are found in Supplementary Figure 4a. b Venn diagrams illustrating the overlap in NLEs differentially expressed throughout infection (P ≤ 0.05; EDGE test). NLEs that were significantly differentially expressed in all in vivo samples are colour coded as in panel 3a. c Enumeration of colonic epithelial cell crypt length (µm) from mice (groups of n = 10; ± SEM) infected with either wild type C. rodentium, ∆espS or uninfected controls. Sampling was carried out at peak infection (day eight PI). Representative images of H&E-stained colon sections from wild type or ∆espS-infected mice are presented additionally. d Percentage measurement of epithelial proliferation in response to wild type or ∆espS infection by Ki-67 staining (±SEM). Representative images of stained colon sections from wild type or ∆espS-infected mice are presented. Markers used stained for C. rodentium (anti-Int280β; Cy3 red), Ki-67 (alexa-488 green) and host cells (DAPI blue). For all quantification, *** denotes P ≤ 0.0001 (one-way ANOVA with Bonferroni multiple correction test). Error bars represent standard error of the mean