title: Optimization of variable number tandem repeat typing set for differentiating Mycobacterium tuberculosis strains in the Beijing family.
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.
authors.affiliation: Tuberculosis Reference Laboratory, Public Health Laboratory Centre, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Kowloon, Hong Kong. kmkam@dh.gov.hk
authors.forename: Kai Man
authors.initials: KM
authors.lastname: Kam
authors.forename: Chi Wai
authors.initials: CW
authors.lastname: Yip
authors.forename: Lai Wa
authors.initials: LW
authors.lastname: Tse
authors.forename: Ka Ling
authors.initials: KL
authors.lastname: Leung
authors.forename: Kin Lai
authors.initials: KL
authors.lastname: Wong
authors.forename: Wai Mei
authors.initials: WM
authors.lastname: Ko
authors.forename: Wai Sum
authors.initials: WS
authors.lastname: Wong
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D016172:DNA Fingerprinting; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D006723:Hong Kong; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D018598:Minisatellite Repeats / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012150:Polymorphism, Restriction Fragment Length; D020080:Tandem Repeat Sequences / Q000235:genetics*; D014376:Tuberculosis / Q000382:microbiology
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial