Single-cell analysis reveals a weak macrophage subpopulation response to Mycobacterium tuberculosis infection

Mycobacterium tuberculosis (Mtb) infection remains one of society’s greatest human health challenges. Macrophages integrate multiple signals derived from ontogeny, infection, and the environment. This integration proceeds heterogeneously during infection. Some macrophages are infected, while others are not; therefore, bulk approaches mask the subpopulation dynamics. We establish a modular, targeted, single-cell protein analysis framework to study the immune response to Mtb. We demonstrate that during Mtb infection, only a small fraction of resting macrophages produce tumor necrosis factor (TNF) protein. We demonstrate that Mtb infection results in muted phosphorylation of p38 and JNK, regulators of inflammation, and leverage our single-cell methods to distinguish between pathogen-mediated interference in host signaling and weak activation of host pathways. We demonstrate that the inflammatory signal magnitude is decoupled from the ability to control Mtb growth. These data underscore the importance of developing pathogen-specific models of signaling and highlight barriers to activation of pathways that control inflammation. [Display omitted] •Single-cell analysis shows dynamics of Mtb responses in primary human cells•A small population of Mtb-infected human macrophages produces TNF•Dynamic profiling shows poor activation of p38 and JNK following Mtb infection•Single-cell assay enables novel strategy to study Mtb-mediated inhibition of host Solomon and Bryson develop a single-cell strategy to dissect the earliest signaling dynamics in human macrophages following Mtb infection, revealing unique responses in directly infected versus bystander cells and a strategy to dissect pathogen-mediated inhibition of host pathways in cis or trans.