Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung

J Exp Med. 2021 Sep 6;218(9):e20210615. doi: 10.1084/jem.20210615. Epub 2021 Jul 22.


In this study, we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression, and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis-infected alveolar (AMs) and interstitial macrophages (IMs) in vivo. We identify clusters of pro-inflammatory AMs associated with stressed bacteria, in addition to three different populations of IMs with heterogeneous bacterial phenotypes. Finally, we show that the main macrophage populations in the lung are epigenetically constrained in their response to infection, while inter-species comparison reveals that most AMs subsets are conserved between mice and humans. This conceptual approach is readily transferable to other infectious disease agents with the potential for an increased understanding of the roles that different host cell populations play during the course of an infection.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antitubercular Agents / pharmacology
  • Bronchoalveolar Lavage Fluid / microbiology
  • CD11 Antigens / immunology
  • CD11 Antigens / metabolism
  • Epigenesis, Genetic
  • Gene Expression Regulation, Bacterial
  • Heme / metabolism
  • Host-Pathogen Interactions
  • Humans
  • Lung / microbiology
  • Lung / pathology
  • Macrophages, Alveolar / immunology
  • Macrophages, Alveolar / microbiology*
  • Macrophages, Alveolar / pathology
  • Mice
  • Mice, Inbred C57BL
  • Microorganisms, Genetically-Modified
  • Mycobacterium tuberculosis / drug effects*
  • Mycobacterium tuberculosis / genetics*
  • Mycobacterium tuberculosis / immunology
  • Mycobacterium tuberculosis / pathogenicity
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Tuberculosis, Pulmonary / genetics
  • Tuberculosis, Pulmonary / microbiology
  • Tuberculosis, Pulmonary / pathology*


  • Antitubercular Agents
  • CD11 Antigens
  • Itgax protein, mouse
  • Heme