title: Heterogeneity of RNA polymerase gene (rpoB) sequences of Mycobacterium gordonae clinical isolates identified with a DNA probe kit and by conventional methods.
abstract: In a previous study, we have evaluated genetic identification by using the rpoB gene, which was recently introduced by Kim et al. (J. Clin. Microbiol. 39:2102-2109, 2001; J. Clin. Microbiol. 37:1714-1720, 1999). In this process, we examined the rpoB gene heterogeneity of clinical isolates identified as Mycobacterium gordonae with the conventional biological and biochemical tests and/or a commercially available DNA probe kit. Sequencing of the rpoB gene of 34 clinical isolates revealed that M. gordonae clinical isolates were classified into four major clusters (A, B, C, and D). Interestingly, organisms belonging to cluster D (15 isolates) did not hybridize with M. gordonae ATCC 14470 and specifically possessed urease activity. Therefore, it could be considered to be a novel mycobacterium. The identification of M. gordonae is known to have ambiguous results sometimes. On the other hand, identification of clinical isolates seems to be inconvenient and unsuitable because of a more than 99% 16S rRNA gene similarity value between clusters. These findings suggest that the existence of M. gordonae-like mycobacteria that share similar biochemical and biological characteristics with the 16S rRNA gene of an M. gordonae type strain but less similarity at the genomic DNA level may have complicated the identification of M. gordonae in many laboratories. Furthermore, compared with hsp65 PCR restriction analysis (PRA), rpoB PRA would have the advantage of producing no ambiguous results because of the intracluster homogeneity of the rpoB gene. In this case, rpoB would provide clearer results than hsp65, even if PRA analysis was used. We demonstrated that these M. gordonae-like mycobacteria were easily distinguished by PRA of the rpoB sequence. Additionally, the significance of this M. gordonae-like cluster may help to establish the comparison between the M. gordonae isolates from a clinical specimen and an infectious process in a given patient and to determine the true incidence of infection with this microorganism.
authors.affiliation: Bacteriology Division, The Research Institute of Tuberculosis, Japan Antituberculosis Association, Kiyose-shi, Tokyo 204-8533, Japan.
authors.forename: Saotomo
authors.initials: S
authors.lastname: Itoh
authors.forename: Yuko
authors.initials: Y
authors.lastname: Kazumi
authors.forename: Chiyoji
authors.initials: C
authors.lastname: Abe
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Takahashi
mesh_terms: D001426:Bacterial Proteins; D001483:Base Sequence; D018834:Chaperonin 60; D018833:Chaperonins; D004275:DNA, Ribosomal / Q000032:analysis; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D009165:Mycobacterium Infections, Nontuberculous / Q000382:microbiology*; D009170:Nontuberculous Mycobacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011933:Reagent Kits, Diagnostic; D015183:Restriction Mapping; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D018834:Chaperonin 60; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D011933:Reagent Kits, Diagnostic; C074119:heat-shock protein 65, Mycobacterium; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D018833:Chaperonins