Human tuberculosis (TB) remains a global public health problem and the main cause of human death due to an infectious disease. TB is caused by a group of closely related bacteria known as the Mycobacterium tuberculosis Complex (MTBC). The outcome of TB infection and disease is highly variable, ranging from rapid bacterial clearance by innate immunity and life-long asymptomatic latent infection to active pulmonary- and extra-pulmonary disease. This variation has traditionally been attributed to host and environmental factors. Indeed, early twin studies have demonstrated a high degree of heritability in TB susceptibility. However, more recent human genetic studies have largely failed to identify TB susceptibility loci reproducibly. The limited success of these studies partially stems from the fact that the role of human variation has rarely been studied together with pathogen variation. The human-adapted MTBC is an obligate human pathogen with no animal or environmental reservoir that has affected humankind for thousands of years. Hence, co-evolution between humans and the human-adapted MTBC is likely to have contributed to some of the characteristics of the host-pathogen interactions in human TB. This notion is supported by evidence for local adaptation of different MTBC genotypes to particular human populations that are perturbed by HIV co-infection. However, formal demonstration of host-pathogen co-evolution in human TB is lacking. Moreover, no study to date has explored the combined effects of human- and MTBC genomic variation on clinically relevant phenotypes. The goal of this project is to test for genetic and functional evidence of host-pathogen co-evolution in human TB, and explore the joint effects of human and pathogen variation on ex vivo and in clinico phenotypes, including those associated with virulence and disease severity, immunogenicity, patient outcome, and bacterial transmission. We hypothesize that i) paired human- and MTBC genome data from TB patients exhibit signals of host-pathogen co-evolution that are perturbed by HIV co-infection, ii) MTBC genomic variation is driven by specific human genomic variation in TB patients (and/or vice versa), iii) MTBC virulence and transmission phenotypes measured ex vivo and in clinico vary as a function of the particular combination of human- and bacterial genotypes, and iv) specific interacting host- and bacterial genomic loci are associated with these phenotypic differences. We will test these hypotheses by addressing the following three Specific Objectives:1)Detect and characterize signals of host-pathogen co-evolution in the paired genome-wide diversity data from HIV-negative and HIV-coinfected TB patients and their cognate MTBC strains from Tanzania;2)Identify and validate interacting genomic loci in the paired genomes of TB patients and their MTBC isolates associated with ex vivo, in clinico and epidemiological phenotypes;3)Measure the virulence, immunogenicity and transmission of TB in Tanzanian patients as a function of human- and MTBC genomic diversity.This projects benefits from the multidisciplinary and complementary expertise of the study team, and from access to an ongoing cohort of TB patients in Dar es Salaam, Tanzania that is separately funded. Through this cohort, we have access to 1,200 TB patients who have already been recruited and consented, as well as to the relevant patient information, blood samples for human genomic studies, their MTBC isolates and genome sequences. In addition to analyzing these retrospective data, we will get access to samples from 650 prospectively recruited TB patients during the first two years of the project, and perform additional assays to validate and complement the findings from the retrospective analyses. These assays include measuring the Molecular Bacterial Load in sputum at the time of diagnosis, a TAM-TB assay to measure the level of immune activation, and a set of ex vivo macrophage infection experiments. The quantitative read-outs of these assays will be combined with the corresponding human- and MTBC genomic information to identify host-pathogen interacting loci that together influence these phenotypes. Our study will provide new genomic and functional insights into the role of host-pathogen co-evolution, and the relevance of both human- and bacterial variation in the biology and epidemiology of one of humankind’s most devastating diseases.