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Mycobacteriology and Aerobic Actinomycetes

Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification of Mycobacterium tuberculosis Complex Isolates

Caroline Allix-Béguec, Dag Harmsen, Thomas Weniger, Philip Supply, Stefan Niemann
Caroline Allix-Béguec
1Genoscreen, 1, rue du Professeur Calmette, Lille 59019 Cedex, France
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Dag Harmsen
2Department of Periodontology, University Hospital Münster, Waldeyerstrasse 30, Münster D-48149, Germany
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Thomas Weniger
2Department of Periodontology, University Hospital Münster, Waldeyerstrasse 30, Münster D-48149, Germany
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Philip Supply
4INSERM U629
5Institut Pasteur de Lille, 1, rue du Professeur Calmette, Lille 59019 Cedex, France
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  • For correspondence: philip.supply@pasteur-lille.fr
Stefan Niemann
3Forschungszentrum Borstel, National Reference Center for Mycobacteria, Parkallee 1-40, Borstel 23845, Germany
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DOI: 10.1128/JCM.00540-08
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  • FIG. 1.
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    FIG. 1.

    Typical output of a best-match analysis. Visualization of the MIRU-VNTR copy numbers and spoligotype patterns of a test isolate and its best matches among the reference strain collection is presented along with information on the best-match reference strains, including the strain lineage, country of isolation, MIRU-VNTR type, SNP and RD types, and SpolDB4 shared type and lineage classification. Differences in genotype profiles between the test strain and strains in the reference database are highlighted in red for better recognition.

  • FIG. 2.
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    FIG. 2.

    Phylogenetic distribution of isolates with unassigned or T spoligotypes. A radial tree was constructed by using the 24-locus MIRU-VNTR typing data for the reference strains in the MIRU-VNTRplus database and 187 genotypes with unassigned or T spoligotypes from the Brussels population-based collection by using the neighbor-joining algorithm and categorical distance coefficient. The positions of Brussels genotypes with unassigned or T spoligotypes are indicated by yellow circles. Lineages containing exclusively T-spoligotype strains or lineages corresponding to well-characterized, classical clades of the Euro-American superlineage (such as the Haarlem lineage) comprising T-spoligotype strains are denoted T-specific and T-aspecific, respectively. EAI, East African-Indian; West Afri 2, West African 2 (M. africanum 2); West Afri 1, West African 1 (M. africanum 1); Tur, Turkish; BJ, Beijing; CAS, Central Asian; LAM, Latin American-Mediterranean.

  • FIG. 3.
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    FIG. 3.

    Strategy for use of phylogenetic identification. If no match is detected after an initial best-match analysis with a stringent distance cutoff of 0.17, tree-based analysis is preferred upon best-match analysis with a relaxed distance cutoff of 0.3 as a second step, because the former method minimizes the fine-tuned mismatching that can occur as an exception among strains belonging to the Euro-American superlineage (see text). NJ, neighbor-joining.

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  • TABLE 1.

    Internal database evaluationa

    ResultNo. (%) of isolates with the indicated result by the following method(s) with the indicated cutoff
    24-locus MIRU-VNTR typing24-locus MIRU-VNTR typing + spoligotypingSpoligotyping
    0.170.30.170.30.170.3
    Lineage confirmationb147 (79.0)177 (95.1)170 (91.4)183 (98.4)175 (94.1)178 (95.7)
    No match39 (21.0)7 (3.8)16 (8.6)1 (0.5)4 (2.2)0 (0.0)
    Conflictc0 (0.0)2 (1.1)0 (0.0)2 (1.1)7 (3.8)8 (4.3)
    • ↵ a The self-consistency of the strain lineage identification was evaluated by testing the best matches of the genotyping data for the 186 isolates of the reference collection against the collection itself.

    • ↵ b For lineage confirmation data, percentages correspond to sensitivity of lineage identification, defined here as the proportion of correct best matches identified among the test samples.

    • ↵ c The specificity for lineage identification equals 100 − conflict (in percent). Specificity is defined here as the portion of correct best matches found among the total best matches identified.

  • TABLE 2.

    External evaluation with isolates whose lineages were preidentifieda

    Cutoff and resultNo. (%) of isolates with the indicated result by:
    24-locus MIRU-VNTR typing + spoligotyping15-locus MIRU-VNTR typing + spoligotyping24-locus MIRU-VNTR typing15-locus MIRU-VNTR typing
    Cutoff of 0.17
        Lineage confirmationb319 (72.2)278 (62.9)240 (54.3)160 (36.2)
        No match123 (27.8)163 (36.9)199 (45.0)282 (63.8)
        Conflictc0 (0.0)1 (0.2)3 (0.7)0 (0.0)
    Cutoff of 0.3
        Lineage confirmationb419 (94.8)403 (91.2)392 (88.7)327 (74.0)
        No match8 (1.8)32 (7.2)36 (8.1)106 (24.0)
        Conflictc15 (3.4)7 (1.6)14 (3.2)9 (2.0)
    • ↵ a Best-match-based analyses were performed with the 442 isolates with a preidentified lineage from the Brussels-Capital Region collection.

    • ↵ b For lineage confirmation data, percentages correspond to sensitivity of lineage identification, defined here as the proportion of correct best matches identified among the test samples.

    • ↵ c The specificity for lineage identification equals 100 − conflict (in percent). Specificity is defined here as the portion of correct best matches found among the total best matches identified.

  • TABLE 3.

    External evaluation with unknown or T-spoligotype isolatesa

    Cutoff and resultNo. (%) of isolates with the indicated result by:
    24-locus MIRU-VNTR typing + spoligotyping15-locus MIRU-VNTR typing + spoligotyping24-locus MIRU-VNTR typing15-locus MIRU-VNTR typing
    Cutoff of 0.17
        Best match62 (33.2)21 (11.2)16 (8.6)8 (4.3)
        No match125 (66.8)166 (88.8)171 (91.4)179 (95.7)
    Cutoff of 0.17
        Best match179 (95.7)172 (92.0)164 (87.7)57 (30.5)
        No match8 (4.3)15 (8.0)23 (12.3)130 (69.5)
    • ↵ a Best-match-based analyses were performed with the 187 unknown or T-spoligotype isolates from the Brussels-Capital Region collection.

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Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification of Mycobacterium tuberculosis Complex Isolates
Caroline Allix-Béguec, Dag Harmsen, Thomas Weniger, Philip Supply, Stefan Niemann
Journal of Clinical Microbiology Aug 2008, 46 (8) 2692-2699; DOI: 10.1128/JCM.00540-08

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Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification of Mycobacterium tuberculosis Complex Isolates
Caroline Allix-Béguec, Dag Harmsen, Thomas Weniger, Philip Supply, Stefan Niemann
Journal of Clinical Microbiology Aug 2008, 46 (8) 2692-2699; DOI: 10.1128/JCM.00540-08
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KEYWORDS

Bacterial Typing Techniques
DNA, Bacterial
Databases, Genetic
Interspersed Repetitive Sequences
molecular epidemiology
Mycobacterium tuberculosis
tuberculosis

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