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

Cho YJ, Yi H, Chun J, Cho SN, Daley CL, Koh WJ, Shin SJ - PLoS ONE (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Chunlab, Inc., Seoul National University, Seoul, Korea.

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.

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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.
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pone-0081560-g005: 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.

Mentions: A comparative analysis at genus level from 81 annotated Mycobacterium genomes available in NCBI microbial genome resources (http://www.ncbi.nlm.nih.gov/genome) was performed. All ORFs from one genome was compared to those from other genome, and bidirectional best hits (BBHs) were made for each pair of 81 strains using BLASTP to find orthologs [41,42]. A set of highly conserved orthologous ORFs (262 genes in total, 237,940 bp) showing greater than 50% amino acid sequence similarity to Mycobacterium abscessus subsp. abscessus ATCC 19977T (PRJNA61613) was selected to represent highly conserved proteins of the genus Mycobacterium [43]. An orthologous gene tree was built using aligned amino acid sequences, demonstrating that the three representative strains clustered among the other Mycobacterium strains (Figure 3). In addition, 11 housekeeping genes (argH, cya, gdhA, glpK, gnd, murC, pgm, pknA, pta, purH, and rpoB, 18,893 bp) were selected for the species-level comparison from a previous study [44] of 53 Mycobacterium abscessus genomes (Figure 4). Their nucleotide sequences were aligned using CLUSTALW and the phylogenetic tree was drawn. Finally, phylogenetic tree was built using the rpoB single-gene nucleotide sequence (Figure 5) because the rpoB sequence has been widely used as a taxonomic-classification marker [45,46]. The overall tree structure was similar, with the representative strains forming their own clusters (Figures 4 and 5). In addition, a comparative BLASTP analysis based on the three representative strains revealed group-specific genes among the representative strains (see Information S1).


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

Cho YJ, Yi H, Chun J, Cho SN, Daley CL, Koh WJ, Shin SJ - PLoS ONE (2013)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3842311&req=5

pone-0081560-g005: 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.
Mentions: A comparative analysis at genus level from 81 annotated Mycobacterium genomes available in NCBI microbial genome resources (http://www.ncbi.nlm.nih.gov/genome) was performed. All ORFs from one genome was compared to those from other genome, and bidirectional best hits (BBHs) were made for each pair of 81 strains using BLASTP to find orthologs [41,42]. A set of highly conserved orthologous ORFs (262 genes in total, 237,940 bp) showing greater than 50% amino acid sequence similarity to Mycobacterium abscessus subsp. abscessus ATCC 19977T (PRJNA61613) was selected to represent highly conserved proteins of the genus Mycobacterium [43]. An orthologous gene tree was built using aligned amino acid sequences, demonstrating that the three representative strains clustered among the other Mycobacterium strains (Figure 3). In addition, 11 housekeeping genes (argH, cya, gdhA, glpK, gnd, murC, pgm, pknA, pta, purH, and rpoB, 18,893 bp) were selected for the species-level comparison from a previous study [44] of 53 Mycobacterium abscessus genomes (Figure 4). Their nucleotide sequences were aligned using CLUSTALW and the phylogenetic tree was drawn. Finally, phylogenetic tree was built using the rpoB single-gene nucleotide sequence (Figure 5) because the rpoB sequence has been widely used as a taxonomic-classification marker [45,46]. The overall tree structure was similar, with the representative strains forming their own clusters (Figures 4 and 5). In addition, a comparative BLASTP analysis based on the three representative strains revealed group-specific genes among the representative strains (see Information S1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Chunlab, Inc., Seoul National University, Seoul, Korea.

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.

Show MeSH
Related in: MedlinePlus