The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level

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.

Figure 1. Genomic relatedness among the three representative strains based on genome sequences.

The percent values represent the average nucleotide identity (ANI) values by pairwise alignment of genome stretches based on BLAST. The numbers shown are the average of the ANI value calculated in both directions.

Figure 2. The genome tree based on ANI values showing the evolutionary relationships among 53 Mycobacterium abscessus genomes available in NCBI microbial genome resources (http://www.ncbi.nlm.nih.gov/genome).

To convert the ANI into a distance, its complement to 1 was taken. From this pairwise distance matrix, an ANI tree was constructed using the UPGMA clustering method.

Figure 3. The genome tree based on 262 highly conserved orthologous genes of 81 annotated genomes of Mycobacterium.

The evolutionary distance matrix was calculated using the Jukes & Cantor model, and the tree was constructed using the neighbor-joining method. Each node number represents the percentage of bootstrap support (>70%) from 1,000 resampled datasets. The bar represents 0.02 substitutions per site.

Figure 4. The phylogenetic tree based on 11 concatenated housekeeping genes conserved in the Mycobacterium abscessus group.

Each node number represents the percentage of bootstrap support (>70%) from 1,000 resampled datasets. The gene sequences of the argH, cya, gdhA, glpK, gnd, murC, pgm, pknA, pta, purH, and rpoB genes were obtained from 53 genome-sequenced Mycobacterium abscessus strains, and the sequences were aligned and concatenated (18,893 bp in length). The bar represents 0.002 substitutions per site.

Figure 5. The rpoB gene-based neighbor-joining tree showing the relationships among 53 genome-sequenced Mycobacterium abscessus strains.

Each node number represents the percentage of bootstrap support (>70%) from 1,000 resampled datasets. The bar represents 0.001 substitutions per site.