title: A new multilocus sequence analysis scheme for Mycobacterium tuberculosis.
abstract: OBJECTIVE
  Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis (M. tuberculosis) multilocus sequence analysis (MLSA) was established for the phylogenetic and epidemiology analysis.
  
  
  METHODS
  To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods.
  
  
  RESULTS
  After comparison of the genome, seven high discrimination gene loci (recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR) were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types (STs) were identified. Based on the Hunter-Gaston Index (HGI), MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types (ST) came into a main cluster, showing the major clonal complexes in those 44 strains.
  
  
  CONCLUSIONS
  MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.
authors.affiliation: State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, & National Tuberculosis Reference Laboratory Beijing 102206, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Lu
authors.forename: Hai Yan
authors.initials: HY
authors.lastname: Dong
authors.forename: Xiu Qin
authors.initials: XQ
authors.lastname: Zhao
authors.forename: Zhi Guang
authors.initials: ZG
authors.lastname: Liu
authors.forename: Hai Can
authors.initials: HC
authors.lastname: Liu
authors.forename: Yuan Yuan
authors.initials: YY
authors.lastname: Zhang
authors.forename: Yi
authors.initials: Y
authors.lastname: Jiang
authors.forename: Kang Lin
authors.initials: KL
authors.lastname: Wan
mesh_terms: D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D005838:Genotype; D058885:Multilocus Sequence Typing / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism*