TCR sequencing identifies clonotypes linked to recognition of infected macrophages. (A and B) Bar graphs of the top 50 TCR clonotypes and their frequencies from representatives of (A) eight LTBI and (B) six non-LTBI participants. TCR clonotypes are displayed as CDR3α_CDR3β; some TCRs contained two CDR3α or CDR3β chains. Blue font highlights a CDR3β motif previously annotated as specific for EspA_301-315. (C and D) Summary box plots of median (with IQR and range) (C) Shannon and (D) Inverse Simpson index scores for eight LTBI and six non-LTBI participants. Each symbol represents individual participant TCR repertoires. (E) Summary box plots of median (with IQR and range) percentage of TCR clonotypes present in ≥2, 3, or 4 copies with fold differences listed above each graph. Statistical significance was determined by unpaired Welch’s t test. (F and G) Pie charts showing percentage (and number) of unique (left) and total (right) TCRβ sequences linked to (F) responses to infected macrophages (green) or after adding MTB300 (blue), and (G) responses to infected macrophages (green) or after adding lysate (yellow), combined from seven to eight individuals.