Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis.
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.
Supply
Philip
P
INSERM U629, Institut Pasteur de Lille, 1, rue du Prof. Calmette, F-59019 Lille Cedex, France. Philip.Supply@pasteur-lille.fr
Allix
Caroline
C
Lesjean
Sarah
S
Cardoso-Oelemann
Mara
M
Rüsch-Gerdes
Sabine
S
Willery
Eve
E
Savine
Evgueni
E
de Haas
Petra
P
van Deutekom
Henk
H
Roring
Solvig
S
Bifani
Pablo
P
Kurepina
Natalia
N
Kreiswirth
Barry
B
Sola
Christophe
C
Rastogi
Nalin
N
Vatin
Vincent
V
Gutierrez
Maria Cristina
MC
Fauville
Maryse
M
Niemann
Stefan
S
Skuce
Robin
R
Kremer
Kristin
K
Locht
Camille
C
van Soolingen
Dick
D
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
D004251:DNA Transposable Elements; D004269:DNA, Bacterial