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. In this project, we are interested in the characterization of these two morphotypes by using genomics, transcriptomics, and methylation analysis to get insights into the potential mechanism behind morphology and thus virulence variation in M. avium. Genomic and transcriptomic analyses were completed and we would like now to investigate DNA methylation in these morphologies. This will be performed using the DNA sequencing data with Nanopore which also offers the possibility to detect DNA modifications, such as methylation. This work will be done for the two strains of M. avium that we use as model systems. The objectives of this project are: - Map the methylation data for each morphotypes to their corresponding reference genome; - Define methylation characteristics for the two strains (methylation types, motifs, location) - Determine if there are differential methylation regions (DMRs) between the morphotypes; - If there are differences, correlate with changes in gene expression we already observed.