The Mycobacterium avium complex (MAC) is a group of nontuberculous mycobacteria (NTM) responsible of infections in humans and animals. Diagnostic and treatments of pulmonary MAC infections are challenging. These bacteria are commonly resistant to first line antituberculosis drugs and current treatments consist of a lengthy multi-drug therapy which represents a burden for the patients who often experience adverse effects and treatment failure. Therefore, new candidates for the design of alternative diagnostic methods and therapies are needed, which requires a better understanding of MAC virulence and pathogenesis. Several NTM, including M. avium can reversibly switch between smooth transparent (SmT) and smooth opaque (SmO) colony morphologies, discernible on agar plates. Interestingly, these two forms differ in virulence and antibiotic resistance. The virulent SmT, commonly isolated from patients, is more resistant to antibiotics and if grown repeatedly under laboratory conditions, gives rise to isogenic derived avirulent SmO colonies. Although they could be targeted for therapy, the underlying regulatory processes of the SmO/SmT reversible switch in NTM are still unknown. The aim of this project is to perform genomic analysis of SmO and SmT morphotypes to identify DNA modification patterns potentially related to virulence and/or involved in the process of phenotypic switching. For this project, two strains of MAC will be analysed, using the Oxford Nanopore sequencing technology.