Fig. 3: BCG-specific immune responses.

tSNE analysis of the total cytokine-expressing lymphocytes observed after BCG restimulation of whole blood collected at day 70 in participants from all study arms (n = 76) (a). Mean proportions of each lymphocyte subset among the total cytokine-expressing cells are indicated by the horizontal bars. Error bars represent the 95% CI and colors correspond to those in the tSNE plot. Two cell populations were not identifiable with the flow cytometry antibody panel. b The same tSNE plot, disaggregated by cytokine and vaccine arm (placebo, blue, n = 23; H4:IC31, red n = 26; and BCG, green, n = 27). c Frequencies of lymphocytes in two BCG-reactive cytokine-expressing cell clusters that were found to be differentially abundant (FDR < 0.1) between day 0 and day 70 in BCG recipients (n = 27) by CITRUS Significance Analysis of Microarrays (SAM) analysis (Supplementary Fig. 7a). d Identity of CITRUS clusters shown in c was confirmed by manual gating in FlowJo as BCG-reactive Th1 and IL-22-producing CD4 T cells. Bars denote medians; p values were computed by comparing frequencies between day 0 and day 70 by Wilcoxon signed-rank test. e Frequencies of lymphocytes in four BCG-reactive cytokine-expressing cell clusters that were found to be differentially abundant (FDR < 0.1) between placebo (blue) and BCG (green) recipients at day 70 by CITRUS SAM analysis (Supplementary Fig. 7b). f Identity of CITRUS cluster A and B shown in e was confirmed by manual gating in FlowJo as BCG-reactive Th1 and IL-22-producing CD4 T cells. Bars denote medians and inter-quartile ranges; p values were computed by comparing frequencies between placebo and BCG recipients by Mann–Whitney U test.