Methods and Challenges in Detecting Subspecies of Mycobacterium abscessus Based on a Case of Otitis Media

Abstract

In recent years, the number of cases of non-tuberculosis mycobacterial infection has increased in Japan; Mycobacterium abscessus is the third most common after M. avium and M. intracellulare. There are three subspecies of M. abscessus; their identification is important because the presence or absence of inducible macrolide resistance differs between these subspecies. Diagnostic advancements, such as mass spectrometry and genetic methods, have facilitated identification. However, subspecies identification remains challenging. We report a method for M. abscessus subspecies identification based on an isolate identified in a patient with otitis media and mastoiditis. Multiplex polymerase chain reaction (PCR) was initially used to identify the subspecies. However, the band pattern of the PCR products differed from that of any known M. abscessus subspecies. Whole-genome sequencing was performed, using 16S rRNA, hsp65, and rpoB as sequence references. Although these sequences were compared with those of the reference strain, no matches were found. The isolate was finally identified as M. abscessus subsp. massiliense by phylogenetic analysis of the core genome. M. abscessus subspecies identification remains difficult despite the availability of various testing methods. The development of new techniques and the accumulation of results from newly developed kits are needed.