The rapidly growing mycobacterium M. abscessus sensu lato is the causative agent of emerging pulmonary and skin diseases and of infections following cosmetic surgery and postsurgical procedures. M. abscessus sensu lato can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Clinical isolates of rapidly growing mycobacteria were previously identified as M. abscessus by DNA-DNA hybridization. More than 30% of these 117 clinical isolates were differentiated as M. abscessus subsp. massiliense using combinations of multilocus genotyping analyses. A much more cost-effective technique to distinguish M. abscessus subsp. massiliense from M. abscessus subsp. abscessus, a multiplex PCR assay, was developed using the whole-genome sequence of M. abscessus subsp. massiliense JCM15300 as a reference. Several primer sets were designed for single PCR to discriminate between the strains based on amplicons of different sizes. Two of these single-PCR target sites were chosen for development of the multiplex PCR assay. Multiplex PCR was successful in distinguishing clinical isolates of M. abscessus subsp. massiliense from samples previously identified as M. abscessus. This approach, which spans whole-genome sequencing and clinical diagnosis, will facilitate the acquisition of more-precise information about bacterial genomes, aid in the choice of more relevant therapies, and promote the advancement of novel discrimination and differential diagnostic assays. bolletii, and that a new subspecies, M. abscessus subsp. abscessus, should be designated (9). However, a recent whole-genome study strongly supported the hypothesis that the species can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii (10). M. abscessus subsp. massiliense was initially isolated from the sputum of a patient with pneumonia in France in 2004 (5). In 2005, an outbreak of M. abscessus subsp. massiliense infection was linked to intramuscular injections of an antimicrobial agent in South Korea (11). This bacterium was also the source of a lethal case of sepsis in Italy (12) and has been found in cystic fibrosis patients in France (13). Several cases of bacteremia and cutaneous pulmonary infections have also been reported in Japan (14-17).A novel approach is required to differentiate M. abscessus subsp. massiliense from M. abscessus subsp. abscessus and M. abscessus subsp. bolletii because conventional methods such as biochemical assays and 16S rRNA genotyping cannot make the discrimination. Moreover, the clinical profile of M. abscessus subsp. massiliense is different from those of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii. In particular, antibiotic treatment with clarithromycin is more effective against M. abscessus subsp. massiliense lung infections, with resistance developing more readily in cases of M. abscessus subsp. abscessus lung disease. Therefore, differentiating ...