Granulomas that drove bacterial control were characterized by cellular ecosystems enriched for type 1-type 17, stem-like, and cytotoxic T cells engaged in pro-inflammatory signaling networks involving diverse cell populations. Bacterial persistence occurred in granulomas enriched for mast, endothelial, fibroblast, and plasma cells, signaling amongst themselves via type 2 immunity and wound-healing pathways. We identified correlates of bacterial control in cynomolgus macaque lung granulomas by co-registering longitudinal positron emission tomography and computed tomography imaging, single-cell RNA sequencing, and measures of bacterial clearance. In some granulomas, immune activity promotes bacterial clearance, but in others, bacteria persist and grow. Mycobacterium tuberculosis lung infection results in a complex multicellular structure: the granuloma. Christopher Love, 4, 17, 18 Philana Ling Lin, 2, 19 Alasdair Leslie, 10, 20, 21 Samuel M. Scanga, 1, 2 Jose Ordovas-Montanes, 4, 5 Bonnie Berger, 12 Joshua T. Rosenberg, 4, 8, 13 Angela Shih, 13 Michael Chao, 4, 8 Edwin Klein, 14 Charles A. Cochran, 1 Samira Ibrahim, 3, 4, 5 Jaime A. Jacob Borish, 1 Pauline Maiello, 1 Alexander G. Grant, 1 Kievershen Nargan, 10 Jia Yao Phuah, 1 H. Hopkins, 4, 8 Jun-Rong Wei, 4, 8 Conner Kummerlowe, 9 Nicole L. Wadsworth, II, 3, 4, 5, 6 Ang Andy Tu, 7 Todd M.
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