Extended Data Fig. 6: Additional characterization of T cell responses after RLD Mtb challenge.

a,b, Ex vivo enumeration of CD3⁺ T cells per ml recovered BAL in relation to total BAL cellular yield (a), and individual Boolean-gated CD4⁺ T cell cytokine-producing subsets in response to PPD stimulation (b), eight weeks after the first Mtb inoculation. c–f, Percentage of cytokine-producing T cells in PPD-stimulated CD4⁺ and CD8⁺ PBMCs (c) and ESAT-CFP10-stimulated CD4⁺ (e) and CD8⁺ PBMCs (f). Samples from three animals (one from the BCG group, two from the BCG.muc group) were not acquired due to a technical error. The ‘+’ symbol indicates either PPD- (c,d) or ESAT6–CFP10-stimulated samples (e,f); the ‘−’ symbol indicates unstimulated culture medium-incubated samples as controls. g–j, Further characterization of mucosal response signatures. g, Breakdown of mucosal (from left to right) IFNγ, TNFα, IL2, and IL17A-producing CD4⁺ T cells in BAL per treatment group into CD28⁺CD95⁺ central memory phenotype. h, PD-1 expression of the cytokine-producing CD4⁺ T cells in BAL samples from the BCG.muc group after stimulation with PPD. i, Ex vivo CD69 expression on CD4⁺ T cells from BAL. j, Percentage of granzyme B-expressing CD8⁺ T cells in BAL. a, Box-whisker plot indicating the 95% CI (box) and range (whiskers), with the line within the box indicating the median value. b–j, The horizontal lines indicate the group medians. For all graphs n = 8 animals per group, unless otherwise indicated. The significance of group differences was determined with a two-sided Mann–Whitney U-test adjusted for multiple comparisons. Šidák-Holm-adjusted P values are shown. The color coding per individual is consistent throughout (see also Supplementary Table 1).