Optimization of variable number tandem repeat typing set for differentiating Mycobacterium tuberculosis strains in the Beijing family

• Published in: FEMS microbiology letters Vol. 256; no. 2; pp. 258 - 265
• Main Authors: Kam, Kai Man, Yip, Chi Wai, Tse, Lai Wa, Leung, Ka Ling, Wong, Kin Lai, Ko, Wai Mei, Wong, Wai Sum
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.03.2006; Blackwell Science Ltd; Blackwell; Oxford University Press
• Subjects: Bacterial Typing Techniques - methods; Bacteriological methods and techniques used in bacteriology; Bacteriology; Beijing family; Biological and medical sciences; DNA Fingerprinting; DNA Transposable Elements - genetics; DNA, Bacterial - genetics; Fundamental and applied biological sciences. Psychology; Gene polymorphism; Genetics; Hong Kong; Humans; Interspersed Repetitive Sequences - genetics; IS6110; Loci; Microbiology; Minisatellite Repeats - genetics; multidrug resistance; Mycobacterium tuberculosis; Mycobacterium tuberculosis - classification; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Optimization; Polymorphism; Polymorphism, Restriction Fragment Length; Restriction fragment length polymorphism; RFLP; Strains (organisms); Tandem Repeat Sequences - genetics; Tuberculosis; Tuberculosis - microbiology; VNTR; Hong Kong; Beijing China; China; Beijing family; multidrug resistance; IS; VNTR; RFLP; tuberculosis; Typing; Mycobacterial infection; Tandemly repeated sequence; Statistics; Optimization; Strain; Infection; Restriction fragment length polymorphism; Tuberculosis; Mycobacterium tuberculosis; Mycobacteriales; Minisatellite DNA; Multiple resistance; Bacteriosis; Mycobacteriaceae; Bacteria; Actinomycetes; tuberculosis; Beijing family; multidrug resistance; VNTR; IS6110
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2006.00126.x

Abstract Variable number tandem repeat (VNTR) typing of Mycobacterium tuberculosis, as presently used, has often failed to differentiate clonal strains especially in areas where the Beijing family genotype is predominant. We have evaluated mycobacterial interspersed repetitive units (MIRUs), Queen's University of Belfast (QUB) loci and exact tandem repeat (ETR) loci individually for their abilities to differentiate the Beijing and non-Beijing genotype families of M. tuberculosis. The best locus was QUB 3232 followed by QUB 11b. Available MIRU, QUB and ETR loci were then consecutively arranged in declining order of discriminatory power, and combined to form an optimal set of 12-loci VNTR typing (MIRU 10, 26, 39, 40; QUB 11a, 11b, 15, 18, 26, 3232, 3336; ETR A) that possessed comparable discriminatory ability to IS6110 restriction fragment length polymorphism. This optimized 12-loci VNTR typing set can become an important tool for tracking M. tuberculosis of the Beijing family.