Comparative analysis of BCG vaccination routes in mice reveals preferential reprogramming of pulmonary macrophages upon mucosal administration.

Bacille Calmette-Guerin (BCG) is the only licensed vaccine against tuberculosis (TB) but provides inconsistent protection against disease. Studies in non-human primates show that intravenous BCG confers superior protection compared to intradermal vaccination, yet how different vaccination routes reprogram lung immunity in mice - the primary model for mechanistic studies - remains incompletely defined at single cell or spatial resolution. Moreover, while lung macrophages are key effectors during Mycobacterium tuberculosis infection, most studies have focused on alveolar macrophages, leaving interstitial macrophage responses to vaccination largely unexplored. Here, we define the cellular and spatial immune landscape shaped by three BCG vaccination routes in mice using flow cytometry, single-cell RNA sequencing, and spatial transcriptomics. Comparing intratracheal (IT), intravenous (IV), and subcutaneous (SC) vaccination, we demonstrate that mucosal IT delivery uniquely reprograms interstitial macrophages, establishes spatially organized immune hubs with CD4 T cells, and provides superior protection against infectious challenge. These findings identify IM as key mediators of mucosal vaccine-induced protection and provide a framework for the rational optimization of vaccines against respiratory pathogens.