Improved subspecies identification in clinicalMycobacterium abscessuscomplex isolates using whole genome sequence

Mycobacterium abscessus complex, which is frequently reported causing a variety of skin and soft tissues diseases in humans, is composed of three subspecies, namely M. abscessus subsp. abscessus, M. abscessus subsp. massiliense and M. abscessus subsp. bolletii . Currently, the differentiation of these three subspecies in clinical isolates still largely depend on single gene identification methods like the genes namely hsp65, 16s with a limited accuracy. This study confirmed the limitations of the single gene based method in the subspecies identification. We performed a comprehensive analysis of MABC genomes in the NCBI database and tried to build an accurate and user-friendly identify method. Here, we describe an improved assay for Mycobacterium abscessus complex fast identification using WGS data, based on the identities of rpoB, erm (41) and rpls . Comprehensive analysis has been performed to compare our software results with the traditional method. The result showed that the method built-in this study could 100% identification the subspecies for the Mycobacterium abscessus complex in the public genome database (893 genomes from NCBI database and 6 clinical isolates from this study). Because this software can be easily integrated into a routine workflow to quickly and precisely provide subspecies-level identification and discrimination MABC different subspecies in clinical isolates by WGS. This assay will facilitate accurate molecular identification of species from the MABC complex in a variety of clinical specimens and diagnostic contexts.