Mycobacterium tuberculosis (Mtb) has been a serious threat to human health globally. However, the diagnosis, therapy, prevention and increasing drug resistance remain to be major problems for tuberculosis control in China. Our group focused on the genome microevolution and pathogenesis of Mtb and the development of novel rapid diagnosis for tuberculosis and Mtb drug susceptibility test. So far, we have made some significant progress in the Mtb virulence evolution and tuberculosis clinical applications.