which is the author's version after external peer review and before publication in the Journal, is available under a CC BY license at PMC6955640.

Pathogenetic processes that facilitate the entry, replication, and persistence of Mycobacterium tuberculosis (MTB) in the mammalian host likely include the regulated expression of specific sets of genes at different stages of infection. Identification of genes that are differentially expressed in vivo would provide insights into host-pathogen interactions in tuberculosis (TB); this approach might be particularly valuable for the study of human TB, where experimental opportunities are limited. In this study, the levels of selected MTB mRNAs were quantified in vitro in axenic culture, in vivo in the lungs of mice, and in lung specimens obtained from TB patients with active disease. We report the differential expression of MTB mRNAs associated with iron limitation, alternative carbon metabolism, and cellular hypoxia, conditions that are thought to exist within the granulomatous lesions of TB, in the lungs of wild-type C57BL͞6 mice as compared with bacteria grown in vitro. Analysis of the same set of mRNAs in lung specimens obtained from TB patients revealed differences in MTB gene expression in humans as compared with mice.T he clinical course of tuberculosis (TB) comprises a sequence of different stages (1). Airborne bacilli that implant in the lung alveoli are phagocytosed by alveolar macrophages (2). Intracellular replication of Mycobacterium tuberculosis (MTB) results in a primary lesion, followed by lymphohematogenous dissemination and secondary lesions in the lungs and other organs. In most individuals, disease progression is arrested at this stage by the acquired immune response, and a clinically latent state ensues. Postprimary disease arises from the subsequent reactivation of dormant tuberculous foci (3, 4). For the nearly 2 billion individuals worldwide who have been infected with MTB, the lifetime risk of developing TB is Ϸ10% (5). In the absence of effective treatment, TB case fatality rates can exceed 50%, as evidenced by longitudinal clinical studies in the preantimicrobial era (6).Despite the global importance of TB as a leading cause of morbidity and mortality, little is known about the host-pathogen interactions at each stage of infection in humans. This information has been difficult to obtain because medical ethics demand that anti-TB therapy be initiated immediately on diagnosis. The uninterrupted course of disease can be studied in TB patients who are unresponsive to therapy, typically due to multidrugresistant MTB. In such cases, palliative resection of diseased tissue is sometimes undertaken (7). Resected human tissues, which would otherwise be discarded, can be used to analyze host-pathogen interactions in situ (8, 9).Adaptation of MTB to environmental changes in the course of infection is likely mediated by differential gene expression. An important role for transcriptional regulation in the life cycle of MTB is suggested by genes encoding 13 RNA polymerase -factors and Ͼ100 putative regulatory proteins in the genome (10). Although the cellular processes controlled by these transcription f...