title: [Identification of novel variable number tandem repeat (VNTR) loci in Mycobacterium avium and development of an effective means of VNTR typing].
abstract: BACKGROUND
  To make more effective use of variable number tandem repeat (VNTR) typing, we identified novel VNTR loci in Mycobacterium avium and used them for modified M. avium tandem repeat-VNTR (MATR-VNTR) typing.
  
  
  METHODS
  Analysis of a DNA sample extracted from a clinical isolate (strain HN135) with the FLX system genome sequencer (Roche Diagnostic System) led to discovery of several novel VNTR loci. The allelic diversity of the novel VNTR loci was evaluated for 71 clinical isolates and compared with the diversity of the MATR-VNTR loci. To improve efficacy of MATR-VNTR typing, we tested typing using 2 sets of loci selected from the newly identified loci and the MATR loci, i.e., one set containing 7 and another 16 loci. Hunter Gaston's discriminatory index (HGDI) was calculated for these sets.
  
  
  RESULTS
  Six VNTR loci were newly identified, of which 5 showed a high diversity. The HGDI was 0.980 for the improved new typing using a set of 7 loci, and 0.995 for another set of 16 loci, while it was 0.992 for the conventional MATR-VNTR typing.
  
  
  CONCLUSIONS
  VNTR typing with the set of the 7 loci enabled a rapid analysis, and another set of 16 loci enabled a precise analysis, as compared with conventional MATR-VNTR typing. A method that uses only VNTR loci with relatively high allelic diversity is considered to be a useful tool for VNTR typing of MAC isolates.
authors.affiliation: Department of Clinical Research, National Hospital Organization (NHO) Higashinagoya National Hospital, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Kurokawa
authors.forename: Kei-Ichi
authors.initials: K
authors.lastname: Uchiya
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yagi
authors.forename: Hiroyasu
authors.initials: H
authors.lastname: Takahashi
authors.forename: Masaki
authors.initials: M
authors.lastname: Niimi
authors.forename: Kazuya
authors.initials: K
authors.lastname: Ichikawa
authors.forename: Takayuki
authors.initials: T
authors.lastname: Inagaki
authors.forename: Makoto
authors.initials: M
authors.lastname: Moriyama
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Nikai
authors.forename: Yuta
authors.initials: Y
authors.lastname: Hayashi
authors.forename: Taku
authors.initials: T
authors.lastname: Nakagawa
authors.forename: Kenji
authors.initials: K
authors.lastname: Ogawa
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D018598:Minisatellite Repeats; D009162:Mycobacterium avium / Q000235:genetics* / Q000302:isolation & purification