A new Multilocus Sequence Analysis Scheme for Mycobacterium tuberculosis

作     者：LU Bing DONG Hai Yan ZHAO Xiu Qin LIU Zhi Guang LIU Hai Can ZHANG Yuan Yuan JIANG Yi WAN Kang Lin 

作者机构：State Key Laboratory for Infectious Diseases Prevention and Control National Institute for Communicable DiseaseControl and Prevention Chinese Center for Disease Control and Prevention & National Tuberculosis ReferenceLaboratory Beijing 102206 China 

出 版 物：《Biomedical and Environmental Sciences》 (生物医学与环境科学（英文版）)

年 卷 期：2012年第25卷第6期

页      面：620-629页

核心收录：

学科分类：090603[农学-临床兽医学] 0711[理学-系统科学] 07[理学] 081104[工学-模式识别与智能系统] 08[工学] 09[农学] 0906[农学-兽医学] 0811[工学-控制科学与工程] 071102[理学-系统分析与集成] 081103[工学-系统工程] 

基　　金：supported by the fund of State Key Laboratory for Infectious Diseases Prevention and Control (2011SKLID208) the project "Transmission Mode of Tuberculosis"of National Key Program of Mega Infectious Diseases (2008ZX100/03-010) 

主　　题：M. tuberculosis Multilocus sequence analysis Genotyping 

摘      要：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. Conclusion MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.