title: Evaluation of four candidate VNTR Loci for genotyping 225 Chinese clinical Mycobacterium tuberculosis complex strains.
abstract: OBJECTIVE
  To evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.
  
  
  METHODS
  Genomic sequences for two M. tuberculosis strains (CCDC5079 and CCDC5180) were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software.
  
  
  RESULTS
  The Hunter-Gaston Index (HGI) for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. bovis and M. africanum strains from the four loci.
  
  
  CONCLUSIONS
  We have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Jiang
authors.forename: Hai Can
authors.initials: HC
authors.lastname: Liu
authors.forename: Hua Jun
authors.initials: HJ
authors.lastname: Zheng
authors.forename: Biao
authors.initials: B
authors.lastname: Tang
authors.forename: Xiang Feng
authors.initials: XF
authors.lastname: Dou
authors.forename: Xiu Qin
authors.initials: XQ
authors.lastname: Zhao
authors.forename: Yong Qiang
authors.initials: YQ
authors.lastname: Zhu
authors.forename: Bing
authors.initials: B
authors.lastname: Lu
authors.forename: Sheng Yue
authors.initials: SY
authors.lastname: Wang
authors.forename: Hai Yan
authors.initials: HY
authors.lastname: Dong
authors.forename: Guo Ping
authors.initials: GP
authors.lastname: Zhao
authors.forename: Yuan Yuan
authors.initials: YY
authors.lastname: Zhang
authors.forename: Biao
authors.initials: B
authors.lastname: Kan
authors.forename: Kang Lin
authors.initials: KL
authors.lastname: Wan
mesh_terms: D016000:Cluster Analysis; D060005:Genotyping Techniques; D006801:Humans; D018598:Minisatellite Repeats; D009163:Mycobacterium bovis / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics*