Open AccessMolecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis
Author(s) -
Byoung Jun Kim,
Bo Ram Kim,
So Young Lee,
Ga Na Kim,
Yoon Hoh Kook,
Bum Joon Kim
Publication year - 2016
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0152703
Subject(s) - biology , rpob , phylogenetic tree , genotype , genetics , genome , phylogenetics , single nucleotide polymorphism , gene , typing , 16s ribosomal rna
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 .