Lung mucosal and systemic responses at single-cell resolution in an aerosolized Mycobacterium bovis BCG human challenge model.

Tuberculosis (TB) vaccine development is hindered by limited understanding of human immune responses to Mycobacterium tuberculosis. Using an aerosolized Mycobacterium bovis BCG human challenge model, we perform single-cell and bulk immune profiling of bronchoalveolar lavage and blood samples to define the temporal immune dynamics in BCG-naive individuals. Rapid changes in cellular composition and gene expression occur in both compartments, with TB-associated gene signatures evident on days 2 and 7 post-challenge. T cell receptor clones that expand in blood at day 7 persist in the lung mucosa until day 56 and are often detectable in blood before challenge. Pre-existing expanded clones are more enriched for activated CD4+ T cells and preferentially localize to the lung mucosa than newly expanded clones. Public expanded clones in the lung mucosa are validated as mycobacterial antigen-reactive using reporter T cells. These findings provide insights into mucosal and systemic immunity post-mycobacterial infection, informing TB vaccine design.