High-resolution intravital microscopy has transformed the study of dynamic cellular behavior within intact tissues by enabling direct visualization of cell migration, vascular interactions, and immune surveillance at single-cell resolution1,2,3,4. While these approaches are widely used in cancer research3,5, their application to pulmonary infections has been limited by respiratory motion, tissue fragility, and biosafety constraints. Recent advances in thoracic imaging platforms, including vacuum-stabilized and permanently implanted optical windows, have addressed many of these technical challenges by providing stable, motion-free imaging of the pulmonary microenvironment over extended periods6,7,8,9,10. Permanently implantable windows, in particular, are powerful tools as they enable repeated visualization of vascular flow, immune cell dynamics, and single-cell behavior over hours to weeks, and have been instrumental in defining mechanisms of cancer metastasis, vascular permeability, and immune surveillance11,12.
Despite these advances, intravital imaging has not previously been applied to Mycobacterium tuberculosis (Mtb) infection in the in vivo mammalian lung at single-cell resolution. The closest precedents come from intravital imaging of mycobacterial infections in other settings. Real-time imaging of Mycobacterium marinum infection in zebrafish embryos13 revealed early macrophage interactions and granuloma initiation, while two-photon imaging of BCG-induced granulomas in the mouse liver14,15 revealed macrophage and T cell dynamics during granuloma development and demonstrated limited antigen presentation and T cell effector function within granulomatous lesions. These studies established foundational insights into mycobacterial host-pathogen interactions but did not access the intact mammalian lung8,16.
Intravital imaging approaches have also been applied to the lung in other infectious and biological contexts, including general pulmonary imaging8, studies revealing that patrolling alveolar macrophages can conceal bacteria from the immune system17 and characterizing the immediate myeloid response to SARS-CoV-2 infection in the human lung16. Intravital imaging has similarly been applied to influenza-infected lungs, enabling direct visualization of dynamic immune-cell behavior within infected lung tissue18,19.
Whole-body optical imaging approaches using fiber-optic microendoscopic excitation20 and reporter enzyme fluorescence technology21,22 have enabled sensitive detection of Mtb in mouse lungs, but cannot detect individual or small clusters of bacilli, track bacterial aggregation dynamics, or visualize direct interactions between mycobacteria and host cells within intact lung tissue. High-containment intravital imaging approaches have been implemented for infected lungs in BSL-3 settings, including SARS-CoV-2 infection23 and Mtb-focused24 multiphoton imaging platforms. These studies demonstrate the feasibility of imaging infected lungs under containment, but such setups remain technically demanding and are not widely accessible. Work with virulent Mtb requires BSL-3 containment, posing significant engineering and biosafety challenges for intravital imaging23,24. As a result, most studies of early Mtb infection rely on static endpoint assays that cannot capture the spatial and temporal dynamics of bacterial behavior within the lung.
The development of genetically defined, BSL-2-approved triple-auxotrophic Mtb strains provides a unique opportunity to overcome these limitations. The mc27902 strain, a pantothenate-leucine-arginine Mtb auxotroph derivative of H37Rv, is fully attenuated, fails to replicate in immunocompromised mice, retains classical acid-fast staining, exhibits normal phage susceptibility, and can be safely handled outside of BSL-3 facilities25. These properties make mc27902 an ideal surrogate for establishing intravital imaging approaches and probing early host-pathogen interactions under reduced biosafety containment.
Here, we apply the Window for High-Resolution Imaging of the Lung (WHRIL) with mc28471, a fluorescent tdTomato-expressing derivative of the triple-auxotrophic Mtb strain mc27902, to visualize early Mtb infection in the intact murine lung. Experiments were performed in immunocompromised Rag2-/- mice26 crossed with MacBlue mice27, in which the Csf1r promoter drives expression of enhanced cyan fluorescent protein (ECFP) in monocytes, microglia, and subsets of dendritic cells and macrophages. The MacBlue transgene enables clear visualization of mononuclear phagocyte populations during early Mtb infection. We chose to utilize Rag2-deficient mice to focus the system on the earliest innate host-pathogen interactions and to avoid the added complexity of adaptive immune responses during the short imaging window examined here. Importantly, this technique is not restricted to Rag2-deficient mice and can also be performed in immunocompetent animals.
By combining a permanent lung window with a BSL-2-compatible fluorescent attenuated Mtb strain, this platform enables serial intravital imaging of bacilli-host cell interactions in the same lung microenvironment at single-cell resolution over multiple days. Although demonstrated here for early infection, the platform itself is not inherently restricted to early time points and could, in principle, be applied to later stages depending on the experimental model and study design. Since the successful application of this imaging platform depends on the use of the specific fluorescent bacillary preparation described here, we included the essential steps required to generate and prepare that reagent as part of the complete protocol. This platform provides direct, real-time imaging of Mtb behavior in vivo and establishes a foundation for future mechanistic studies of bacterial physiology, host recognition, and immune-mediated clearance.