Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs

Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes(MNPs) with astounding ability to evade elimination. ESX-1, a type VII secretion system, acts asa virulence determinant that contributes to MTB’s ability to survive within MNPs, but its effect onMNP recruitment and/or differentiation remains unknown. Here, using single-cell RNAsequencing, we studied the role of ESX-1 in MNP heterogeneity and response in mice andmurine bone marrow-derived macrophages (BMDM). We found that ESX-1 is required for MTB to recruit diverse MNP subsets with high MTB burden. Further, MTB induces an antiinflammatory signature in MNPs and BMDM in an ESX-1 dependent manner. Similarly, spatialtranscriptomics revealed an upregulation of anti-inflammatory signals in MTB lesions, wheremonocyte-derived macrophages concentrate near MTB-infected cells. Together, our findings suggest that MTB ESX-1 mediates the recruitment and differentiation of anti-inflammatoryMNPs, which MTB can infect and manipulate for survival.