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Background   Mycobacterium yongonense,  as a novel member of the  M. avium  complex (MAC), was recently reported to be isolated from human specimens in South Korea and Italy. Due to its close relatedness to other MAC members, particularly  M. intracellulare  in taxonomic aspects, the development of a novel diagnostic method for its specific detection is necessary for clinical or epidemiologic purposes.    Methods  Using the  Mycobacterium yongonense  genome information, we have identified a novel IS-element, IS Myo2 . Targeting the IS Myo2  sequence, we developed a real-time PCR method and applied the technique to Mycobacterial genomic DNA.    Results  To identify proper nucleic acid targets for the diagnosis, comparisons of all insertion sequence (IS) elements of 3  M. intracellulare  and 3  M. yongonense  strains, whose complete genome sequences we reported recently, led to the selection of a novel target gene, the  M. yongonense -specific IS element, IS Myo2  (2,387 bp), belonging to the IS 21  family. Next, we developed a real-time PCR method using SYBR green I for  M. yongonense -specific detection targeting IS Myo2 , producing a 338-bp amplicon. When this assay was applied to 28  Mycobacterium  reference strains and 63 MAC clinical isolates, it produced amplicons in only the 6  M. yongonense  strains, showing a sensitivity of 100 fg of genomic DNA, suggesting its feasibility as a diagnostic method for  M. yongonense  strains .Conclusions  We identified a novel IS Myo2  IS element belonging to the IS 21  family specific to  M. yongonense  strains via genome analysis, and a real-time PCR method based on its sequences was developed.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1978-2) contains supplementary material, which is available to authorized users.

Identification of ISMyo2, a novel insertion sequence element of IS21 family and its diagnostic potential for detection of Mycobacterium yongonense