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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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Neighbor-joining phylogenetic tree based on the rpoB or 35 concatenated genes from 6 Mycobacterium intracellulare strains.(A) A tree based on the whole rpoB gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. (B) A tree based on the 35 concatenated gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. The bootstrap values were calculated from 1,000 replications and values <50% were not shown. The bar indicates the number of substitutions per nucleotide position. M. tuberculosis H37Rv and M. avium 104 were used as outgroups in the rpoB gene- or concatenated genes-based phylogenetic trees, respectively.
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pone.0152703.g003: Neighbor-joining phylogenetic tree based on the rpoB or 35 concatenated genes from 6 Mycobacterium intracellulare strains.(A) A tree based on the whole rpoB gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. (B) A tree based on the 35 concatenated gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. The bootstrap values were calculated from 1,000 replications and values <50% were not shown. The bar indicates the number of substitutions per nucleotide position. M. tuberculosis H37Rv and M. avium 104 were used as outgroups in the rpoB gene- or concatenated genes-based phylogenetic trees, respectively.

Mentions: The entire sequences of rpoB and the 35 selected genes were retrieved from the genome sequences of 6 mycobacterial strains [3 M. intracellulare strains (M. intracellulare ATCC 13950T, MOTT-02, and MOTT-64), 2 INT-5 strains (MOTT-36Y and MOTT-H4Y) and M. yongonense DSM 45126T] (Table 1) and subjected to phylogenetic analysis. In the rpoB gene (3,375 to 3,462 bp)-based phylogenetic analysis, the two INT-5 strains MOTT-H4Y and MOTT-36Y were clustered into the group including the M. intracellulare strains (M. intracellulare ATCC 13950T, MOTT-02, and MOTT-64) and were separated from M. yongonense DSM 45126Tand M. parascrofulaceum ATCC BAA-614 (Fig 3A). However, in the phylogenetic analyses based on the sequences of the 35 selected genes, the two INT-5 strains MOTT-H4Y and MOTT-36Y were clustered into M. yongonense DSM 45126T and separated from the other 3 M. intracellulare strains with a high bootstrap value (> 99%), as shown in the genome sequence-based phylogenetic analysis (Figs 1 and 3B). These results suggest that there may be a distinct M. yongonense genotype having an rpoB gene sequence that is almost identical to M. intracellulare.


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)

Neighbor-joining phylogenetic tree based on the rpoB or 35 concatenated genes from 6 Mycobacterium intracellulare strains.(A) A tree based on the whole rpoB gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. (B) A tree based on the 35 concatenated gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. The bootstrap values were calculated from 1,000 replications and values <50% were not shown. The bar indicates the number of substitutions per nucleotide position. M. tuberculosis H37Rv and M. avium 104 were used as outgroups in the rpoB gene- or concatenated genes-based phylogenetic trees, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0152703.g003: Neighbor-joining phylogenetic tree based on the rpoB or 35 concatenated genes from 6 Mycobacterium intracellulare strains.(A) A tree based on the whole rpoB gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. (B) A tree based on the 35 concatenated gene sequences from 3 M. intracellulare, 2 INT-5 strains, M. yongonense, and M. parascrofulaceum. The bootstrap values were calculated from 1,000 replications and values <50% were not shown. The bar indicates the number of substitutions per nucleotide position. M. tuberculosis H37Rv and M. avium 104 were used as outgroups in the rpoB gene- or concatenated genes-based phylogenetic trees, respectively.
Mentions: The entire sequences of rpoB and the 35 selected genes were retrieved from the genome sequences of 6 mycobacterial strains [3 M. intracellulare strains (M. intracellulare ATCC 13950T, MOTT-02, and MOTT-64), 2 INT-5 strains (MOTT-36Y and MOTT-H4Y) and M. yongonense DSM 45126T] (Table 1) and subjected to phylogenetic analysis. In the rpoB gene (3,375 to 3,462 bp)-based phylogenetic analysis, the two INT-5 strains MOTT-H4Y and MOTT-36Y were clustered into the group including the M. intracellulare strains (M. intracellulare ATCC 13950T, MOTT-02, and MOTT-64) and were separated from M. yongonense DSM 45126Tand M. parascrofulaceum ATCC BAA-614 (Fig 3A). However, in the phylogenetic analyses based on the sequences of the 35 selected genes, the two INT-5 strains MOTT-H4Y and MOTT-36Y were clustered into M. yongonense DSM 45126T and separated from the other 3 M. intracellulare strains with a high bootstrap value (> 99%), as shown in the genome sequence-based phylogenetic analysis (Figs 1 and 3B). These results suggest that there may be a distinct M. yongonense genotype having an rpoB gene sequence that is almost identical to M. intracellulare.

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