Extended Data Fig. 1: Broad alterations of peripheral immune cell distributions in LTBI.

PBMCs from 14 latently infected and 14 uninfected participants of a South African adolescent cohort were characterized using CyTOF with antibody panel 1 (Supplementary Table 2), followed by Citrus analysis and clustering. This unsupervised hierarchical clustering analysis produced a branching structure (dendrogram) that allowed the grouping of total live cells into known immune cell compartments (contoured). Cell clusters are represented as nodes (circles) in this Citrus-derived circular dendrogram, which delineates lineage relationships that were identified from the data. Cluster granularity (that is, cell subset specificity) increases from the centre of the diagram to the periphery. a, Annotation of cluster hierarchy plots based on surface marker expression. The expression intensity of each marker used for cell population characterization is overlaid per cluster on the Citrus circular dendrogram and is indicated, independently for each marker, by the coloured gradient for which the range corresponds to the arcsinh-transformed expression of the median marker expression measured across all Citrus clusters. For each marker, we also provide a dot plot graph demonstrating the marker labelling in the manually gated indicated population. b, Citrus plots showing, based on cell-surface protein expression, clusters (in red, designated A–F) that exhibit significantly different abundances (SAM analysis with FDR < 1%) between the uninfected and latently infected individuals. Individual cell clusters are mapped to well-established, gross-cell types: B cells (CD19⁺), CD8⁺ αβ T cells (CD3⁺TCRβ⁺CD8⁺), CD4⁺ αβ T cells (CD3⁺TCRβ⁺CD4⁺), γδ T cells (CD3⁺TCRδ⁺), monocytes (CD3⁻CD19⁻CD33⁺CD14⁺HLA-DR⁺), NK cells (CD3⁻CD19⁻CD14⁻HLA-DR⁻CD16⁺CD56^bright/dim), identifiable by annotated shaded background groupings. c, The phenotype and the composition of cells in each of the stratifying cell subsets (A–F), identified by Citrus analysis. d, Percentages of NK cells and B cells determined by manual gating of 20 additional samples using CyTOF antibody panel 2 (left; Supplementary Table 2) and 32 samples using flow cytometry (right). e, Percentages of CD4⁺ αβ T cells, CD8⁺ αβ T cells and γδ T cells in uninfected controls and latently infected individuals, analysed by CyTOF (n = 24 per group; top) and flow cytometry (n = 16 per group; bottom). Throughout, P values were derived using a Mann–Whitney U-test. Mean and error bars representing the 95% confidence intervals are shown for each comparison.