Inflammatory bowel disease (IBD), defined as chronic inflammation of the gastrointestinal tract, is a condition that encompasses Crohn’s disease (CD) and ulcerative colitis.1 The diagnostic procedure for IBD always involves a challenging infection assessment.1 Identification of the microbes present and their pathogenic potential are essential for choosing a treatment plan. Gastrointestinal infections caused by nontuberculous mycobacteria (gNTM) are challenging to diagnose based on only disease symptoms. Diagnosis is especially difficult in the case of IBD patients suspected of having CD. Diagnostic studies that investigated symptom similarities have suggested the potential need for investigating mycobacteria-related infections in IBD cases.2, 3 Both CD and mycobacterial infections have been associated with the development of granuloma and branching fistula. However, conventional methods are likely insufficient for the identification of NTM associated with CD.4 Furthermore, the diagnosis and treatment of mycobacterial infection in an IBD patient could depend on the type of mycobacteria and the presence of certain chromosomally encoded virulence factors, such as the toxin-antitoxin (TA) elements parD, hipB, mazEF, and VapB.5 The TA loci have been implicated in mediating bacterial adaptive responses, resulting in the development of latent infections and virulence.5 Nontuberculous mycobacteria infections are exacerbated by their intrinsic drug resistance, their TA mechanisms, and the lack of adequate or timely identification.