Open AccessHighly polymorphic variable‐number tandem repeats loci for differentiating Beijing genotype strains of Mycobacterium tuberculosis in Shanghai, China
Author(s) -
Zhang Lu,
Chen Jing,
Shen Xin,
Gui Xiaohong,
Mei Jian,
DeRiemer Kathryn,
Gao Qian
Publication year - 2008
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2008.01081.x
Subject(s) - variable number tandem repeat , tandem repeat , mycobacterium tuberculosis , genetics , genotype , restriction fragment length polymorphism , biology , tuberculosis , typing , population , molecular epidemiology , virology , gene , genome , demography , medicine , pathology , sociology
The PCR‐based variable‐number tandem repeats (VNTR) typing method is a very promising tool for the molecular epidemiological study of Mycobacterium tuberculosis . The discriminatory power of the VNTR loci that were optimized in many previous studies has not been evaluated in Shanghai, an area where Beijing genotype strains dominate. In the present study, we first performed a literature search to identify VNTR loci that were at least 45 bp in length. Second, we determined the Hunter–Gaston discriminatory index (HGI) values of each of the 45 VNTR loci that we identified, using Beijing genotype strains from a ‘test set’ of isolates from a population with low migration in Chongming Island, Shanghai, China. Third, we optimized two sets of VNTR loci, which we named VNTR‐7 and VNTR‐16. The HGI value of VNTR‐7 was slightly lower than that of IS 6110 restriction fragment length polymorphisms (RFLP), and the HGI values of VNTR‐16 and IS 6110 RFLP were comparable. Our results suggest that VNTR‐7, followed by VNTR‐16 and IS 6110 RFLP, can be used routinely as a tool to discriminate between M. tuberculosis isolates in population‐based epidemiologic studies of M. tuberculosis transmission in Shanghai, China.