Figure 6.

Patients with slow microbiological culture conversion show decreased cytotoxic CD8⁺ and γδ enriched CD4⁺ naïve T-cell subsets before treatment initiation and after two months of treatment compared to fast converters. Fast converters (n = 18) were defined as patients with permanently negative M. tuberculosis culture after two months of treatment (T1), whereas slow converters (n = 4) were defined as patients with persistently positive cultures at T1. The abundance of all FlowSOM clusters at baseline was compared between fast and slow converters. CD4⁺ clusters were represented in red, CD8⁺ clusters in blue, and γδ T-cell clusters in green. Clusters which were significantly decreased (A, C) or enriched (B, D) at T1 in slow converters compared to fast converters were compared to the reference UMAP (E). Normalized, arcsinh-transformed mean marker expression levels were visualized (F). Each row represents one cluster. Scales indicate normalized mass signal intensity. Boxplot data represent medians + interquartile range. Statistical analysis: Only clusters within which differences passing a threshold of p<0.035 (Mann-Whitney U test) were represented. Exact, unadjusted p-values are indicated on the figures. Benjamini-Hochberg corrections for multiple comparisons were performed as an indication and were not used for cluster selection for phenotype analyses. Adjusted p-values did not reach significance. All adjusted p-values and complete test statistics are available in Supplementary Table 8 .