We have also replicated the recent linkage findings of Cooke et al. [8], thus providing the first replication report of the newly published TB candidate genes, CTSZ and MC3R. By examining distinct phenotypes that represent different stages of the natural history of Mtb infection, we demonstrate that these different stages (i.e. exposure, infection, disease) have distinct genetic influences that underlie the likely different biological mechanisms involved in resistance to infection vs. controlling latent infection vs. progression to active pulmonary TB. Here, CTSZ is linked to pulmonary tuberculosis.