Fig. 4: T cells and antigen-specific responses in the BAL and blood post-BCG infection.

A BAL (upper panels) and whole blood (lower panels) cells (baseline, D2, D7, D14, D28, D56), Panel 2 staining. T cells (live singlets, CD19-, CD14-, CD3+ ); % Leucocytes (singlets, CD19-). (i) Total T cells; (ii) CD4 + T cells; (iii) CD8+ T cells; (iv) CD4-CD8- T cells (double negative, DN); (v) CD4+ CD8+ T cells (double positive, DP). (i) Total T cells: BAL BCG D2 v D7 p < 0.0001, after correction p = 0.0003; Blood baseline to D2 p = 0.003, after correction p = 0.03. (ii) CD4 + T cells: BAL BCG D2 v D7 p = 0.0016, after correction p = 0.003. (iii) CD8+ T cells: BAL D7 control v BCG p = 0.02, after correction p = 0.03; BCG D2 v D7 p = 0.02. (iv) DN T cells: BAL D7 control v BCG p = 0.04. (iv) CD4+ CD8+ cells: BAL D2 control v BCG p = 0.01; D7 control v BCG p = 0.009 after correction p = 0.02. BCG D2 v D7 p = 0.002, after correction p = 0.01. B BAL, Panel 2 or 4 staining. Antigen (BCG)-specific IFN-γ+ T-cells in (i) Total T cells; (ii) CD4+; (iii) CD8+; (iv) DN; or (v) CD4+ CD8+ T cells. Shown as % parent. (i+ii) Total and CD4 + T cells: BCG D2 v D7 p = 0.02 with correction p = 0.03. (v) CD4+ CD8+ T cells: D7 control v BCG p = 0.02, BCG D2 v D7 p = 0.03. C, D BCG-stimulated whole blood cells. Panel 2 or 4 staining. C Antigen (BCG)-specific IFN-γ+ (i), TNF-α+ (ii) or IL-2+ (iii) CD4+ T cells or CD8+ T cells. Shown as % parent. C (i) IFN-γ+ CD4+ T cells: D7 p = 0.03, D28 p = 0.03. IFN-γ+ CD8+ T cells: D28 p = 0.03. (iii) IL2+ CD4+ T cells: D28 p = 0.03, D56 p = 0.0002. IL2+ CD8+ T cells: D2 p = 0.03. D TNF-α+ BCG-reactive monocytes. D7 p = 0.004, D14 p = 0.02, D56 p = 0.003. E Antigen (PPD)-specific IFN-γ ELISpot responses in fresh PBMCs. SFC = spot-forming cells. Different timepoints after BCG: Wilcoxon paired test, D7 p < 0.0001, D14 p = 0.0003, D28 p = 0.01, D56 p = 0.04; after correction, D7 p = 0.0008, D14 p = 0.003. BCG v control: Mann-Whitney, D2 p = 0.049, D7 p = 0.0006, D14 p = 0.04, D56 p = 0.01; after correction, D7 p = 0.001, D56 p = 0.04. Statistically significant differences are presented in the figure. BAL: Two-sided Mann-Whitney; blood: two-sided paired Wilcoxon against baseline. Red asterix indicates significant differences after correction (Dunns). *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. See Supplementary Note 2 and source data (provided as a Source Data file) for sample sizes. BAL: Black dots BCG, grey squares saline control. Blood: Solid dots Group 1 (D2 bronchoscopy), circles Group 2 (D7 bronchoscopy). Box and whisker plots show median, IQR and min/max, crosses show mean.