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Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis.

Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJ - PLoS ONE (2016)

Bottom Line: These results suggest their taxonomic transfer from M. intracellulare into M. yongonense.The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs.In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea.

ABSTRACT
Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950(T) and Mycobacterium yongonense DSM 45126(T). Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126(T) than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.

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Venn diagrams based on genome information of INT-5 strains.Venn diagrams showing orthologous ORFs among four mycobacterial species as determined by BLASTCLUST analysis. Numbers in parenthesis include paralogous ORFs.
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pone.0152703.g002: Venn diagrams based on genome information of INT-5 strains.Venn diagrams showing orthologous ORFs among four mycobacterial species as determined by BLASTCLUST analysis. Numbers in parenthesis include paralogous ORFs.

Mentions: To assess the number of genes shared between each genome, we performed a BLASTCLUST analysis on the four genomes (M. intracellulare ATCC 13950T, MOTT-H4Y, and M. yongonense DSM 45126T or M. intracellulare ATCC 13950T, MOTT-36Y, and M. yongonense DSM 45126T). At the level of 95% identity, M. intracellulare MOTT-36Y or MOTT-H4Y shared more orthologous coding sequences (CDSs) with M. yongonense DSM 45126T (4,271/5,128 CDSs, 83.3% or 4,287/5,020 CDSs, 85.4%, respectively) than M. intracellulare ATCC 13950T (4,101/5,128 CDSs, 80.0% or 4,052/5,020 CDSs, 80.7%, respectively) (Fig 2). This finding supported the results of our phylogenetic study that the two INT-5 strains might belong to M. yongonense rather than to M. intracellulare (Fig 1).


Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis.

Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJ - PLoS ONE (2016)

Venn diagrams based on genome information of INT-5 strains.Venn diagrams showing orthologous ORFs among four mycobacterial species as determined by BLASTCLUST analysis. Numbers in parenthesis include paralogous ORFs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816341&req=5

pone.0152703.g002: Venn diagrams based on genome information of INT-5 strains.Venn diagrams showing orthologous ORFs among four mycobacterial species as determined by BLASTCLUST analysis. Numbers in parenthesis include paralogous ORFs.
Mentions: To assess the number of genes shared between each genome, we performed a BLASTCLUST analysis on the four genomes (M. intracellulare ATCC 13950T, MOTT-H4Y, and M. yongonense DSM 45126T or M. intracellulare ATCC 13950T, MOTT-36Y, and M. yongonense DSM 45126T). At the level of 95% identity, M. intracellulare MOTT-36Y or MOTT-H4Y shared more orthologous coding sequences (CDSs) with M. yongonense DSM 45126T (4,271/5,128 CDSs, 83.3% or 4,287/5,020 CDSs, 85.4%, respectively) than M. intracellulare ATCC 13950T (4,101/5,128 CDSs, 80.0% or 4,052/5,020 CDSs, 80.7%, respectively) (Fig 2). This finding supported the results of our phylogenetic study that the two INT-5 strains might belong to M. yongonense rather than to M. intracellulare (Fig 1).

Bottom Line: These results suggest their taxonomic transfer from M. intracellulare into M. yongonense.The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs.In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea.

ABSTRACT
Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950(T) and Mycobacterium yongonense DSM 45126(T). Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126(T) than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.

Show MeSH
Related in: MedlinePlus