Highlights d Live, but not killed, Mtb induces type I IFN-mediated metabolic changes in macrophages d IFNb restrains glycolysis and drives mitochondrial stress in activated macrophages d Type I IFN signaling in vivo limits pulmonary macrophage metabolic responses to Mtb d STING signaling is upstream of mitochondrial damage during mycobacterial infection

Progress in tuberculosis vaccine development is hampered by an incomplete understanding of the immune mechanisms that protect against infection with Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. Although the M72/ASOE1 trial yielded encouraging results (54% efficacy in subjects with prior exposure to Mtb), a highly effective vaccine against adult tuberculosis remains elusive. We show that in a mouse model, establishment of a contained and persistent yet non-pathogenic infection with Mtb ("contained Mtb infection", CMTB) rapidly and durably reduces tuberculosis disease burden after re-exposure through aerosol challenge. Protection is associated with elevated activation of alveolar macrophages, the first cells that respond to inhaled Mtb, and accelerated recruitment of Mtbspecific T cells to the lung parenchyma. Systems approaches, as well as ex vivo functional assays and in vivo infection experiments, demonstrate that CMTB reconfigures tissue resident alveolar macrophages via low grade interferon-γ exposure. These studies demonstrate that under certain circumstances, the continuous interaction of the immune system with Mtb is beneficial to the host by maintaining elevated innate immune responses.

As innate sentinels in the lung, alveolar macrophages (AMs) play a critical role during Mycobacterium tuberculosis (Mtb) infection as the first cells to encounter bacteria. We previously showed that AMs initially respond to Mtb infection in vivo by mounting a cell-protective, rather than pro-inflammatory response, yet whether the AM response could be modified by environmental factors was unknown. Here, we characterize how previous exposure to mycobacteria, either through subcutaneous vaccination with Mycobacterium bovis (scBCG) or through a contained Mtb infection (coMtb), impacts the initial response by AMs and early innate response in the lung. We find that both scBCG and coMtb accelerate early innate cell activation and recruitment and generate a stronger pro-inflammatory AM response to Mtb in vivo. AMs from scBCG vaccinated mice mount a robust interferon response, while AMs from coMtb mice produce a broader and more diverse inflammatory response. Using single-cell RNA-sequencing, we identify exposure-induced changes to airway-resident cells, with scBCG and coMtb enriching for different AM subpopulations. Ex vivo stimulation assays reveal that AMs from scBCG and coMtb mice switch on an interferon-dependent response, which is absent in AMs from unexposed mice. Overall, our studies reveal significant, durable, and cell-intrinsic modifications to AMs following exposure to mycobacterium, and comparison of scBCG and coMtb models reveals that AMs can be reprogrammed into more than one state. These findings highlight the plasticity of innate responses in the airway and underscore the unexplored potential of targeting AMs through vaccination or host-directed therapy to augment host responses.

An efficacious vaccine against adult tuberculosis (TB) remains elusive. Progress is hampered by an incomplete understanding of the immune mechanisms that protect against infection with Mycobacterium tuberculosis (Mtb), the causative agent of TB 1 . Over 90% of people who become infected with Mtb mount an immune response that contains the bacteria indefinitely, leading to a state known as "latent TB infection" (LTBI) 2 . A significant body of epidemiologic evidence indicates that LTBI protects against active TB after re-exposure, offering an intriguing avenue to identifying protective mechanisms 3,4 . We show that in a mouse model, LTBI is highly protective against infection with Mtb for up to 100 days following aerosol challenge. LTBI mice are also protected against heterologous bacterial challenge (Listeria monocytogenes) and disseminated melanoma suggesting that protection is in part mediated by alterations in the activation state of the innate immune system. Protection is associated with elevated activation of alveolar macrophages (AM), the first cells that respond to inhaled Mtb, and accelerated recruitment of Mtb-specific T cells to the lung parenchyma upon aerosol challenge. Systems approaches, including transcriptome analysis of both naïve and infected AMs, as well as ex vivo functional assays, demonstrate that LTBI reconfigures the response of tissue resident AMs.. Furthermore, we demonstrate that both LTBI mice and latently infected humans show similar alterations in the relative proportions of circulating innate immune cells, suggesting that the same cellular changes observed in the LTBI mouse model are also occurring in humans. Therefore, we argue that under certain circumstances, LTBI could be beneficial to the host by providing protection against subsequent Mtb exposure. * * CD11b PerCPCy5.5

Previous studies have identified whole-blood transcriptional risk and disease signatures for Tuberculosis (TB); however, several lines of evidence suggest that these signatures primarily reflect bacterial burden, which increases prior to symptomatic disease. We found that the peripheral blood transcriptome of mice with contained Mycobacterium tuberculosis infection (CMTB) has striking similarities to that of humans with active TB and that a signature derived from these mice predicts human disease with comparable accuracy to signatures derived directly from humans. A set of genes associated with immune defense are upregulated in CMTB mice but not in humans with active TB suggesting that their upregulation is associated with bacterial containment. A signature comprised of these genes predicts both protection from TB disease and successful treatment at early time points where current signatures are not predictive. These results suggest that detailed study of the CMTB mouse model may enable identification of biomarkers for human TB.