Nucleotide Sequence Comparison of the Mycobacterial dnaJ Gene and PCR-Restriction Fragment Length Polymorphism Analysis for Identification of Mycobacterial Species

Takewaki, Shun-ichi; Okuzumi, Katsuko; Manabe, Ichiro; Tanimura, Masako; Miyamura, Kikuko; Nakahara, Ken-ichi; Yazaki, Yoshio; Ohkubo, Akihiro; Nagai, Ryozo

doi:10.1099/00207713-44-1-159

Cited by 77 publications

(55 citation statements)

References 34 publications

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“…M15467) (Takewaki et al, 1994) and the resulting phylogenetic tree (available as Supplementary Fig. S1 in IJSEM Online) confirmed the very close phylogenetic relationship between the test strains and M. doricum.…”

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confidence: 52%

Mycobacterium monacense sp. nov.

Reischl

Melzl

Kroppenstedt

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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Four bacterial strains were isolated from independent clinical specimens in different countries and their genotypic and phenotypic characters support their classification in a novel species within the genus Mycobacterium. One strain was clearly responsible for a severe, post-traumatic wound infection in a healthy boy. The novel species, for which the name Mycobacterium monacense sp. nov. is proposed, is yellow-pigmented, non-photochromogenic and grows in less than a week on solid medium. Based on phenotypic investigations alone, distinction of these four strains from known scotochromogenic rapidly growing strains is problematic. However, the novel strains differ from any other mycobacterium in each of the molecular species markers investigated: the 16S rRNA gene, the 16S-23S rRNA gene internal transcribed spacer and the hsp65 gene. Of the strains investigated, two different sequevars were detected for the hsp65 region. Phylogenetic analysis revealed that these four strains were most closely related to Mycobacterium doricum. The type strain of Mycobacterium monacense sp. nov. is B9-21-178 T (=DSM 44395 T =CIP 109237 T ).

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mentioning

confidence: 52%

Mycobacterium monacense sp. nov.

Reischl

Melzl

Kroppenstedt

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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“…The use of molecular genetic techniques to identify infectious mycobacteria has been widely adopted. In particular, 16S rRNA gene sequences have been used to describe phylogenetic relationships between mycobacterial species (7,16,22,24,26). Similar tests that use sequences of the Mycobacterium-specific dnaJ gene, the 32-kDa protein gene, hsp 65, superoxide dismutase, and the recA, rpoV, and gyrB genes have been reported (2,5,15,20,21,24,25).…”

mentioning

confidence: 99%

“…In particular, 16S rRNA gene sequences have been used to describe phylogenetic relationships between mycobacterial species (7,16,22,24,26). Similar tests that use sequences of the Mycobacterium-specific dnaJ gene, the 32-kDa protein gene, hsp 65, superoxide dismutase, and the recA, rpoV, and gyrB genes have been reported (2,5,15,20,21,24,25). The molecular genetic approach offers a fast and accurate means to identify Mycobacterium spp., from which information can be gained even if the isolate represents a new taxon or is nonculturable, nonviable, or archived only in formalin-fixed, paraffinembedded tissue.…”

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confidence: 99%

Histologic and Genotypic Characterization of a Novel Mycobacterium Species Found in Three Cats

Appleyard

Clark

2002

J Clin Microbiol

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Three cases of feline atypical mycobacteriosis from different geographical regions in North America were characterized by large clusters of filamentous bacteria visible on hematoxylin-and-eosin-stained tissue sections. PCR amplification demonstrated the presence of Mycobacterium-specific nucleic acid in samples of skin lesions from these cases. PCR-assisted cloning and DNA sequence analysis of a 541-bp length of the Mycobacterium 16S rRNA gene generated DNA sequences which were >95% identical, suggesting that the three isolates were closely related. Two of the sequences were 99% identical and may represent the same species. Alignment with comparable 16S rRNA gene sequences from 66 Mycobacterium species and partially characterized isolates highlighted similarities (>94%) with Mycobacterium bohemicum, Mycobacterium haemophilum, Mycobacterium ulcerans, Mycobacterium avium subsp. avium, and isolate IWGMT 90242. Parsimony analysis of sequence data suggested relatedness to M. leprae. Significant molecular genetic and pathobiological differences between these three similar isolates and other known species of mycobacteria suggested that the organisms may not have been described previously and that these cases may represent a new form of mycobacterial disease in cats. We suggest the term "Mycobacterium visibilis" to describe the organism from which the two nearly identical sequences were obtained.

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“…Genotypic taxonomy is typically based on the detection of highly conserved regions within the genome that harbor hypervariable sequences in which species-specific deletions, insertions, or replacements of single nucleotides are present in 16S rRNA, hsp65 gene and more recently on a fragment of the gene coding for the beta sub-unit of RNA polymerase (rpoB) are also contributing to this field, mostly for RGM (da Costa et al, 2009;da Costa et al, 2010). Several amplification molecular methods, have been proposed to correct NTM identification, including specific DNA probes (AccuProbe: GenProbe, Inc., San Diego, CA, U.S.A) and PRA method based on 16S rRNA (Domenech et al, 1994), 16S-23S rRNA internal transcribed spacer (ITS) (Roth et al, 1998), hsp65 (Telenti et al, 1993), rpoB (Lee et al, 2000), cold-shock protein gene (dnaJ) (Takewaki et al, 1994), DNA repair protein gene (recA) (Blackwood et al, 2000) and elongation factor Tu gene (tuf) (Shin et al, 2009), but all have limitations as the variety of mycobacteria to be identified (da Costa et al, 2010a, b).…”

Section: Discussionmentioning

confidence: 99%