Abstract
Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, ‘M. massiliense’, and ‘M. bolletii’. In 2011, ‘M. massiliense’ and ‘M. bolletii’ were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of ‘M. massiliense’ within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of ‘Mycobacterium massiliense’ (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of ‘M. bolletii’ and ‘M. massiliense’ at the subspecies level. The genome tree also clearly illustrated that ‘M. bolletii’ and ‘M. massiliense’ form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known ‘M. massiliense’ and ‘M. bolletii’ strains.
Highlights
Growing mycobacteria (RGM) are nontuberculous mycobacteria that cause a wide spectrum of human infections; the Mycobacterium abscessus complex is the most frequent group associated with pulmonary, skin, soft tissue, and bone diseases [1,2]
(39) This study the genomes of the M. abscessus complex (Figure 1 and Table 1)
We evaluated the current taxonomic status of M. abscessus and its subspecies using a similarity analysis based on the single gene, multilocus gene, several hundreds of orthologous gene, and whole-genome levels
Summary
Growing mycobacteria (RGM) are nontuberculous mycobacteria that cause a wide spectrum of human infections; the Mycobacterium abscessus complex is the most frequent group associated with pulmonary, skin, soft tissue, and bone diseases [1,2]. Because of the heterogeneity within the group, the M. abscessus complex (M. abscessus sensu lato) was divided into three species in 2006, namely M. abscessus sensu stricto, ‘M. massiliense’ [12], and ‘M. bolletii’ [13]. The three independent species were proposed primarily based on differences in the rpoB sequences and phenotypic patterns of the type strains [12,14]. The differentiation of these three species has relied upon the sequencing of one or more housekeeping genes, such as rpoB, hsp, and secA, the emergence of isolates with interspecific composite patterns has led to conflicting identification results [16]. Isolates from recent Brazilian outbreaks display genetic characteristics consistent with either ‘M. massiliense’ or ‘M. bolletii’, depending on the housekeeping genes selected for the identification [15]
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