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Journal of Clinical Microbiology
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Mycobacteriology and Aerobic Actinomycetes

Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis

Philip Supply, Caroline Allix, Sarah Lesjean, Mara Cardoso-Oelemann, Sabine Rüsch-Gerdes, Eve Willery, Evgueni Savine, Petra de Haas, Henk van Deutekom, Solvig Roring, Pablo Bifani, Natalia Kurepina, Barry Kreiswirth, Christophe Sola, Nalin Rastogi, Vincent Vatin, Maria Cristina Gutierrez, Maryse Fauville, Stefan Niemann, Robin Skuce, Kristin Kremer, Camille Locht, Dick van Soolingen
Philip Supply
INSERM, U629Institut Pasteur de Lille, Lille, France
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  • For correspondence: Philip.Supply@pasteur-lille.fr
Caroline Allix
Institut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobactéries, Brussels, Belgium
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Sarah Lesjean
INSERM, U629Institut Pasteur de Lille, Lille, France
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Mara Cardoso-Oelemann
INSERM, U629Institut Pasteur de Lille, Lille, France
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Sabine Rüsch-Gerdes
Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
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Eve Willery
INSERM, U629Institut Pasteur de Lille, Lille, France
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Evgueni Savine
INSERM, U629Institut Pasteur de Lille, Lille, France
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Petra de Haas
Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute for Public Health and the Environment, 3720 Bilthoven
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Henk van Deutekom
Department of Tuberculosis Control, Municipal Health Service, Amsterdam, The Netherlands
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Solvig Roring
Veterinary Sciences Division, Department of Agriculture and Rural Development, Belfast, Northern Ireland
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Pablo Bifani
INSERM, U629Institut Pasteur de Lille, Lille, FranceInstitut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobactéries, Brussels, BelgiumTB Center, Public Health Research Institute, Newark, New Jersey
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Natalia Kurepina
TB Center, Public Health Research Institute, Newark, New Jersey
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Barry Kreiswirth
TB Center, Public Health Research Institute, Newark, New Jersey
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Christophe Sola
Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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Nalin Rastogi
Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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Vincent Vatin
Institut Pasteur de Lille, Lille, FranceCNRS, UMR 8090, Lille, France
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Maria Cristina Gutierrez
Laboratoire de Référence des Mycobactéries, Institut Pasteur, Paris, France
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Maryse Fauville
Institut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobactéries, Brussels, Belgium
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Stefan Niemann
Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
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Robin Skuce
Veterinary Sciences Division, Department of Agriculture and Rural Development, Belfast, Northern Ireland
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Kristin Kremer
Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
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Camille Locht
INSERM, U629Institut Pasteur de Lille, Lille, France
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Dick van Soolingen
Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
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DOI: 10.1128/JCM.01392-06
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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.

FOOTNOTES

    • Received 6 July 2006.
    • Returned for modification 18 August 2006.
    • Accepted 12 September 2006.
  • ↵▿ Published ahead of print on 27 September 2006.

  • ↵† Supplemental material for this article may be found at http://jcm.asm.org/.

  • American Society for Microbiology
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Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis
Philip Supply, Caroline Allix, Sarah Lesjean, Mara Cardoso-Oelemann, Sabine Rüsch-Gerdes, Eve Willery, Evgueni Savine, Petra de Haas, Henk van Deutekom, Solvig Roring, Pablo Bifani, Natalia Kurepina, Barry Kreiswirth, Christophe Sola, Nalin Rastogi, Vincent Vatin, Maria Cristina Gutierrez, Maryse Fauville, Stefan Niemann, Robin Skuce, Kristin Kremer, Camille Locht, Dick van Soolingen
Journal of Clinical Microbiology Dec 2006, 44 (12) 4498-4510; DOI: 10.1128/JCM.01392-06

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Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis
Philip Supply, Caroline Allix, Sarah Lesjean, Mara Cardoso-Oelemann, Sabine Rüsch-Gerdes, Eve Willery, Evgueni Savine, Petra de Haas, Henk van Deutekom, Solvig Roring, Pablo Bifani, Natalia Kurepina, Barry Kreiswirth, Christophe Sola, Nalin Rastogi, Vincent Vatin, Maria Cristina Gutierrez, Maryse Fauville, Stefan Niemann, Robin Skuce, Kristin Kremer, Camille Locht, Dick van Soolingen
Journal of Clinical Microbiology Dec 2006, 44 (12) 4498-4510; DOI: 10.1128/JCM.01392-06
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