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Mycobacterium tuberculosis (Mtb) remains a pathogen of significant importance with respect to global health. Although approximately one third of the world is infected with TB, only 5-10% develop clinical manifestations of active TB within 2 years post exposure. Infection with Mtb can cause active tuberculosis (ATB), inactive latent infection (LTBI) and be reactivated. The immune response is contained within the formation of a collection of immune cells, a granuloma, in the infected individualâ€™s lungs, which is seen in all disease states. The granuloma functions both as an immune response to contain the bacterium from surrounding lung parenchyma as well as a site for the bacterium to remain in the individual; therefore, providing an environment in which the bacterium maintains the ability to reactivate. We currently lack a complete understanding of the physiology and the metabolic state of Mtb in this granulomatous environment during different states of infection. Leveraging a novel technique known as mesodisection, we microdissect TB granulomas from various infective stages as well as from different sections of the granuloma from non-human primate (NHP) derived formalin fixed paraffin embedded (FFPE) lung tissue. From these extracted tissue sections, RNA is extracted, amplified and subsequent microarray and nCounter analysis is performed; consequently, allowing us to uncover the Mtb specific transcriptomic profiles. First, our findings reveal statistically significant Mtb genes induced in ATB and LTBI in various granuloma types. Of the genes induced, many belong to the following categories: PE/ PPE, sigma factors, toxin-antitoxin complexes and the DosR regulon. In addition, our findings reveal a core group of genes commonly identified in both ATB and LTBI induced in ATB and LTBI in various granuloma types. Of the genes induced, many belong to the following categories: PE/ PPE, sigma factors, toxin-antitoxin complexes and the DosR regulon. In addition, our findings reveal a core group of genes commonly identified in both ATB and LTBI in all lesion types. Further, we propose that these findings improve our understanding of the physiology of the pathogen as well as its virulence which in turn can be used for the development of improved therapeutics, diagnostics and vaccines.