Macrophages are central to host defense against microbes, but intracellular pathogens have evolved to evade their antimicrobial functions. Mycobacterium tuberculosis (MTB) has successfully exploited macrophages as its primary niche in vivo, but the bacterial genome-wide requirements that promote its intracellular survival remain undefined. Here we comprehensively identify the MTB genes required for survival by screening for transposon mutants that fail to grow within primary macrophages. We identify mutants showing decreased growth in macrophage environments that model stages of the host immune response. By systematically analyzing several biologically relevant data sets, we have been able to identify putative pathways that could not be predicted by genome organization alone. In one example, phosphate transport, requiring physically unlinked genes, was found to be critical for MTB growth in macrophages and important for establishing persistent infection in lungs. Remarkably, the majority of MTB genes found by this analysis to be required for survival are constitutively expressed rather than regulated by macrophages, revealing the host-adapted lifestyle of an evolutionarily selected intracellular pathogen. mutagenesis U p to one-third of humans world-wide harbor Mycobacterium tuberculosis (MTB) in a latent asymptomatic state and are thus at risk for tuberculosis when immune-compromised (1). Macrophages are critical both for permitting the survival of MTB and in linking innate and adaptive immunity in the host (2). They promote T cell activation and recruitment, crucial for containing MTB within granulomas in the lung. Virulent MTB can replicate within the hostile environment of macrophages, sequestered in poorly acidified phagosomes that fail to fuse with lysosomes (3-5). Although phagocytosis by IFN-â„-activated murine macrophages results in some bacterial killing, in part via nitric oxide-dependent mechanisms (6), MTB can evade macrophage bactericidal function by inhibiting IFN-â„-mediated signaling (7). MTB is also reported to interfere with antigen presentation, multiple signaling pathways, and transcriptional responses within the macrophage (2). However, the mycobacterial genes involved are largely unknown.We sought to systematically identify the MTB genes required for growth in macrophages. We used transposon site hybridization (TraSH) (8), a microarray-based technique that comprehensively identifies genes from large pools of transposon mutants that are essential for growth under different conditions (described in Fig. 1a). We devised screens to identify MTB mutants that fail to survive prolonged infection of primary murine macrophages and are thus attenuated for growth. We have identified 126 genes as necessary for survival in macrophages under conditions that model the immune response. Comparative analyses with biologically relevant data sets allow association of genes into functional groups, provide insights into gene regulation in mycobacteria, and highlight key gene products for further detailed study. W...