Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans, is estimated to infect one third of the human population leading to circa two million deaths a year. While many work has been done onto the socio-economic and host factors affecting the different outcomes of the disease, little is still known about the possible influence of Mycobacterium tuberculosis strain variation. Compare to other bacteria, Mtb has very low polymorphism which have prevented until now a detailed study of the evolutionary forces behind this pathogen. With the advent of next-generation sequencing this gap in our knowledge on the population genetics of Mtb with respect other bacteria is starting to close. This project will be aimed to analyze 100 Mtb strains currently being sequenced by the Sanger institute using Illumina technology which added to our previous panel of 30 strains already generated will allow detail population genetics and evolutionary studies with an special focus on the evolution of known Mtb antigens. Collaborations with laboratories with expertise in immunology, transcriptomics and molecular epidemiology will allow us to put in context the consequences of the Mtb genomic variation found in this study.