title: Progression toward an improved DNA amplification-based typing technique in the study of Mycobacterium tuberculosis epidemiology.
abstract: While high-copy-number IS6110-based restriction fragment length polymorphism (HCN-RFLP) is the gold standard for typing most Mycobacterium tuberculosis strains, the time taken for culturing and low throughput make it impractical for large-scale prospective typing of large numbers of isolates. The development of a new method, mycobacterial interspersed repetitive units (MIRU), a variation of the original variable-number tandem repeat (VNTR) technique, may provide a viable alternative. Panels based on the original 12-loci MIRU (12MIRU), a combination of 12MIRU and remaining ETR loci (15MIRU-VNTR), and an extended panel with an additional 10 novel regions (25VNTR) were used to study three populations with varying degrees of epidemiological data. MIRU discrimination increased with panel size and the addition of spoligotyping. Combining these two techniques enabled a reduction in the panel size from 25 to 14 loci without a significant loss in discrimination. However, 25VNTR alone or in combination with spoligotyping still possessed weaker discrimination than RFLP for high-copy-number isolates.
authors.affiliation: Health Protection Agency Mycobacterium Reference Unit, Clinical Research Centre, Barts and the London Medical School, Queen Mary College, University of London, 2 Newark St., London E1 2AT, United Kingdom.
authors.forename: Krishna K
authors.initials: KK
authors.lastname: Gopaul
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Brown
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Gibson
authors.forename: Malcolm D
authors.initials: MD
authors.lastname: Yates
authors.forename: Francis A
authors.initials: FA
authors.lastname: Drobniewski
mesh_terms: D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D017720:Molecular Epidemiology / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial