Unite de Pathogenomique Mycobacterienne 1 article published in JoVE Immunology and Infection Identification of Virulence Markers of Mycobacterium abscessus for Intracellular Replication in Phagocytes Violaine Dubois*1, Laura Laencina*1, Anouchka Bories1, Vincent Le Moigne1, Alexandre Pawlik2, Jean-Louis Herrmann1, Fabienne Girard-Misguich1 12I, UVSQ, INSERM UMR1173, Université Paris-Saclay, 2Institut Pasteur, Unité de Pathogénomique Mycobactérienne Here, we present two protocols to study Phagocyte-Mycobacterium abscessus interactions: the screening of a transposon mutant library for bacterial intracellular deficiency and the determination of bacterial intracellular transcriptome from RNA sequencing. Both approaches provide insight into the genomic advantages and transcriptomic adaptations enhancing intracellular bacteria fitness.