Mycobacterium tuberculosis (Mtb) is an obligate human pathogen whose growth, replication and transmission have been shaped by two important selective pressures imposed by humans; a potent immune system, which most of the times controls bacterial survival and replication, and human demography, which influences the number of susceptible hosts available for infection. The long lasting co-existence of Mtb with humans has created a relationship of dual nature between the immune system and Mtb, in which the immune cells and structures necessary for the host to contain the infection (i.e. macrophages and granulomas) are under subverted by the bacteria for replication and transmission to new hosts. The complicated nature of this relationship is not fully understood and has hampered the development of efficient vaccines. In the last 20 to 30 years the epidemics of HIV fueled the epidemics of tuberculosis. The presentation of tuberculosis is different in HIV+ and HIV- patients, mostly due to the fact that HIV infection depletes CD4+ T-cells that are essential for macrophage activation and granuloma formation, which in turn influence cavitation and consequently transmission of Mtb. Hence, the immune selection acting on Mtb in HIV+ and HIV- patients is likely to differ both within the host (due to CD4+depletion) and between host (due to differences in cavitation with downstream effects on transmissibility). Consequently, different bacterial genes and pathways may be affected in HIV+ and HIV- patients. The epidemics of HIV/TB co-infection represent a new selective environment to which Mtb is adapting. The genetic characterization of this adaptation process is a powerful tool for revealing genes and pathways involved in the interaction between Mtb and the host immune system. Within this framework, we propose that studying the genetic trajectories of Mtb in HIV+and HIV- patients will bring important insights into the interactions between the human immune system and Mtb. Specifically, we hypothesize that immune-induced selection on Mtb in HIV+and HIV- patients differs, and that signatures of this selection can be detected in the genomes of Mtb. We will test this hypothesis by studying genomic alterations in Mtb isolates using next-generation sequencing and addressing the following three specific aims:
1) Characterize genetically the evolutionary trajectories of Mtb evolved within patients (relapse cases) in both HIV+ and HIV- patients;
2) Pinpoint metabolic pathways, genes, and mutations involved in the interaction between Mtb and the human immune system;
3) Identify possible bacterial factors that could contribute to the relapse of TB and their association with patient immune characteristics such as CD4+ cell number and previous BCG vaccination.