title: Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains.
abstract: In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
authors.affiliation: Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands. kristin.kremer@rivm.nl
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Catherine
authors.initials: C
authors.lastname: Arnold
authors.forename: Angel
authors.initials: A
authors.lastname: Cataldi
authors.forename: M Cristina
authors.initials: MC
authors.lastname: Gutiérrez
authors.forename: Walter H
authors.initials: WH
authors.lastname: Haas
authors.forename: Stefan
authors.initials: S
authors.lastname: Panaiotov
authors.forename: Robin A
authors.initials: RA
authors.lastname: Skuce
authors.forename: Philip
authors.initials: P
authors.lastname: Supply
authors.forename: Adri G M
authors.initials: AG
authors.lastname: van der Zanden
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics; D009841:Oligonucleotides / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D009841:Oligonucleotides