Data Sheet 1_Distinct time-dependent S. Typhi-specific CD8+ T cell programs are associated with clinical outcome following Ty21a immunization and wild-type S. Typhi challenge in humans.docx

Some participants developed typhoid disease (TD) and some did not (NoTD), allowing us to assess the immune program of CD8⁺ T_M subsets involved in the prevention of typhoid disease using mass cytometry, CyTOF. </p>Results and discussion<p>Our high-dimensional profiling data showed that TD and NoTD participants followed divergent memory CD8⁺ T cell trajectories. We observed that CD8⁺ T clusters from NoTD participants are enriched for early multifunctional, protection-associated programs while TD participants exhibited a distinct clustering associated with susceptibility states.

Specifically, using unsupervised dimensionality reduction and clustering analysis, T-REX, and feature-ranking analyses, we identified memory CD8⁺ T cell subsets including effector/memory (T_EM), T central/memory (T_CM) and CD45RA+ T_EM (T_EMRA) associated with clinical outcomes. CD8⁺ T_EM from NoTD participants were generally characterized by stronger effector-associated signatures such as CXCR3, IL-17A, TNFα, and MIP1b.

In contrast, CD8⁺ T_EM from TD participants showed CCR6- and integrin α4β7-biased immune profiles. Detailed analysis revealed that CD8⁺ T_CM and T_EMRA subsets also contained distinct outcome-associated states. These patterns were confirmed by conventional supervised gating that validated both protection-associated and susceptibility-associated marker combinations across CD8⁺ T_EM, T_CM and T_EMRA subsets.

These data suggest that: 1. Protection and susceptibility are not restricted to one CD8⁺ T cell subset but rather are distributed across the broader CD8⁺ T memory landscape and, 2. Typhoid clinical outcome is associated with qualitatively distinct CD8⁺ T memory programs rather than differences only in the magnitude of the overall anti-S. Typhi immune response. </p>