BCG vaccination induces different mechanisms of mycobacterial growth control compared to natural protection

Abstract Bacillus Calmette-Guèrin (BCG) vaccination induces considerable protection in infants and young children against not only severe forms of tuberculosis (TB), but also all-cause mortality and heterologous infections. These effects are mediated through a combination of specific adaptive immune memory and sustained innate immune activation (also called trained immunity). To delineate factors influencing mycobacterial growth control, we investigated the effects of BCG vaccination in healthy Dutch adults. About a quarter of individuals already controlled BCG outgrowth prior to vaccination, whereas a quarter of vaccinees acquired the capacity to control 3 months upon BCG vaccination. This leaves a considerable percentage of the population (54% of total) incapable to control BCG outgrowth even after vaccination. Detailed characterization of biological samples, including single cell RNA sequencing (scRNAseq), identified multiple processes associated with mycobacterial growth control. Differential gene expression was abundant in all cell types of individuals with natural control, compared to those who did not control mycobacterial growth. In contrast, BCG-induced acquired control was mostly characterized by differential gene expression in monocytes. Control prior to BCG vaccination was associated with increased oxidative phosphorylation, whereas control acquired upon BCG vaccination was associated with glycolysis. Moreover, samples with natural control expressed genes linked to the type I IFN pathway, whereas samples with acquired control expressed genes associated with the Th1 pathway. These data suggest that natural control and control induced upon BCG vaccination employ different mechanisms to control BCG outgrowth, and that a substantial proportion of individuals (≈50%) fail to develop measurable growth control even following BCG vaccination.