title: Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis.
abstract: Molecular typing based on 12 loci containing variable numbers of tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTRs) has been adopted in combination with spoligotyping as the basis for large-scale, high-throughput genotyping of Mycobacterium tuberculosis. However, even the combination of these two methods is still less discriminatory than IS6110 fingerprinting. Here, we define an optimized set of MIRU-VNTR loci with a significantly higher discriminatory power. The resolution and the stability/robustness of 29 loci were analyzed, using a total of 824 tubercle bacillus isolates, including representatives of the main lineages identified worldwide so far. Five loci were excluded for lack of robustness and/or stability in serial isolates or isolates from epidemiologically linked patients. The use of the 24 remaining loci increased the number of types by 40%--and by 23% in combination with spoligotyping--among isolates from cosmopolitan origins, compared to those obtained with the original set of 12 loci. Consequently, the clustering rate was decreased by fourfold--by threefold in combination with spoligotyping--under the same conditions. A discriminatory subset of 15 loci with the highest evolutionary rates was then defined that concentrated 96% of the total resolution obtained with the full 24-locus set. Its predictive value for evaluating M. tuberculosis transmission was found to be equal to that of IS6110 restriction fragment length polymorphism typing, as shown in a companion population-based study. This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies.
authors.affiliation: INSERM U629, Institut Pasteur de Lille, 1, rue du Prof. Calmette, F-59019 Lille Cedex, France. Philip.Supply@pasteur-lille.fr
authors.forename: Philip
authors.initials: P
authors.lastname: Supply
authors.forename: Caroline
authors.initials: C
authors.lastname: Allix
authors.forename: Sarah
authors.initials: S
authors.lastname: Lesjean
authors.forename: Mara
authors.initials: M
authors.lastname: Cardoso-Oelemann
authors.forename: Sabine
authors.initials: S
authors.lastname: Rüsch-Gerdes
authors.forename: Eve
authors.initials: E
authors.lastname: Willery
authors.forename: Evgueni
authors.initials: E
authors.lastname: Savine
authors.forename: Petra
authors.initials: P
authors.lastname: de Haas
authors.forename: Henk
authors.initials: H
authors.lastname: van Deutekom
authors.forename: Solvig
authors.initials: S
authors.lastname: Roring
authors.forename: Pablo
authors.initials: P
authors.lastname: Bifani
authors.forename: Natalia
authors.initials: N
authors.lastname: Kurepina
authors.forename: Barry
authors.initials: B
authors.lastname: Kreiswirth
authors.forename: Christophe
authors.initials: C
authors.lastname: Sola
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.forename: Vincent
authors.initials: V
authors.lastname: Vatin
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Gutierrez
authors.forename: Maryse
authors.initials: M
authors.lastname: Fauville
authors.forename: Stefan
authors.initials: S
authors.lastname: Niemann
authors.forename: Robin
authors.initials: R
authors.lastname: Skuce
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Camille
authors.initials: C
authors.lastname: Locht
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
mesh_terms: D015373:Bacterial Typing Techniques / Q000592:standards*; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics*; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D011237:Predictive Value of Tests; D015203:Reproducibility of Results; D014376:Tuberculosis / Q000382:microbiology
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial