CoMtb alters the immune landscape following Mtb infection. (A and B) d35 after ULD infection, n = 8. (A) PCoA analysis of ROI transcriptomes, colored by lesion type (necrotic versus non-necrotic, 3 ROIs per point) or location (uninvolved, 1 ROI per point). (B) GSEA analysis showing enriched pathways per lesion type. (C–E) Multiple time points after CD infection. (C) UMAP depicting cell types identified by scRNAseq analysis of lung parenchymal cells, heatmap showing cellular abundance, numbers reflect the median number of cells per thousand. (D) Proportions of selected cell populations over time, scRNAseq. (E) Numbers of selected cell populations over time, flow cytometry. (F) UMAP depicting clusters within activated CD4⁺ cell cluster from C, heatmap showing the top 10 discriminatory genes. (G) Pseudotime analysis showing neutrophils across time points. (H) UMAP depicting clusters within d34 neutrophils from C, as well as heatmap showing the top 10 discriminatory genes. Points represent individual lesions (A, 3 ROIs samples per lesion, 1 per uninvolved area) and individual mice (D–F). False discovery rate–adjusted P values determined using the R fgsea package. Single-group comparisons by t test. Data are representative of one (A–D and F–H) or two (E) independent experiments with at least four mice per group. See also Fig. S2. UMAP, uniform manifold approximation and projection.