Publication:
Prospective universal application of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping to characterize Mycobacterium tuberculosis isolates for fast identification of clustered and orphan cases.

Loading...
Thumbnail Image

Date

2009-05-20

Authors

Alonso-Rodríguez, Noelia
Martínez-Lirola, Miguel
Sánchez, M Luisa
Herranz, Marta
Peñafiel, Teresa
Bonillo, Magdalena del Carmen
Gonzalez-Rivera, Milagros
Martínez, Juan
Cabezas, Teresa
Diez-García, Luis Felipe

Advisors

Journal Title

Journal ISSN

Volume Title

Publisher

American Society for Microbiology
Metrics
Google Scholar
Export

Research Projects

Organizational Units

Journal Issue

Abstract

The use of molecular tools for genotyping Mycobacterium tuberculosis isolates in epidemiological surveys in order to identify clustered and orphan strains requires faster response times than those offered by the reference method, IS6110 restriction fragment length polymorphism (RFLP) genotyping. A method based on PCR, the mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping technique, is an option for fast fingerprinting of M. tuberculosis, although precise evaluations of correlation between MIRU-VNTR and RFLP findings in population-based studies in different contexts are required before the methods are switched. In this study, we evaluated MIRU-VNTR genotyping (with a set of 15 loci [MIRU-15]) in parallel to RFLP genotyping in a 39-month universal population-based study in a challenging setting with a high proportion of immigrants. For 81.9% (281/343) of the M. tuberculosis isolates, both RFLP and MIRU-VNTR types were obtained. The percentages of clustered cases were 39.9% (112/281) and 43.1% (121/281) for RFLP and MIRU-15 analyses, and the numbers of clusters identified were 42 and 45, respectively. For 85.4% of the cases, the RFLP and MIRU-15 results were concordant, identifying the same cases as clustered and orphan (kappa, 0.7). However, for the remaining 14.6% of the cases, discrepancies were observed: 16 of the cases clustered by RFLP analysis were identified as orphan by MIRU-15 analysis, and 25 cases identified as orphan by RFLP analysis were clustered by MIRU-15 analysis. When discrepant cases showing subtle genotypic differences were tolerated, the discrepancies fell from 14.6% to 8.6%. Epidemiological links were found for 83.8% of the cases clustered by both RFLP and MIRU-15 analyses, whereas for the cases clustered by RFLP or MIRU-VNTR analysis alone, links were identified for only 30.8% or 38.9% of the cases, respectively. The latter group of cases mainly comprised isolates that could also have been clustered, if subtle genotypic differences had been tolerated. MIRU-15 genotyping seems to be a good alternative to RFLP genotyping for real-time interventional schemes. The correlation between MIRU-15 and IS6110 RFLP findings was reasonable, although some uncertainties as to the assignation of clusters by MIRU-15 analysis were identified.

Description

MeSH Terms

Medical Subject Headings::Health Care::Environment and Public Health::Public Health::Epidemiologic Methods::Statistics as Topic::Cluster Analysis
Medical Subject Headings::Disciplines and Occupations::Social Sciences::Criminology::Forensic Sciences::Forensic Medicine::DNA Fingerprinting
Medical Subject Headings::Chemicals and Drugs::Nucleic Acids, Nucleotides, and Nucleosides::Nucleic Acids::DNA::DNA, Bacterial
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genotype
Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Genome Components::Interspersed Repetitive Sequences
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Genome Components::Tandem Repeat Sequences::Minisatellite Repeats
Medical Subject Headings::Health Care::Environment and Public Health::Public Health::Epidemiologic Methods::Molecular Epidemiology
Medical Subject Headings::Organisms::Bacteria::Gram-Positive Bacteria::Gram-Positive Rods::Gram-Positive Asporogenous Rods::Gram-Positive Asporogenous Rods, Regular::Mycobacteriaceae::Mycobacterium::Mycobacterium tuberculosis
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Nucleic Acid Amplification Techniques::Polymerase Chain Reaction
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::Polymorphism, Genetic::Polymorphism, Restriction Fragment Length
Medical Subject Headings::Health Care::Environment and Public Health::Public Health::Epidemiologic Methods::Statistics as Topic::Sensitivity and Specificity
Medical Subject Headings::Diseases::Bacterial Infections and Mycoses::Bacterial Infections::Gram-Positive Bacterial Infections::Actinomycetales Infections::Mycobacterium Infections::Tuberculosis
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Clinical Laboratory Techniques::Microbiological Techniques::Bacteriological Techniques::Bacterial Typing Techniques

DeCS Terms

CIE Terms

Keywords

Técnicas de Tipificación Bacteriana, Análisis por Conglomerados, Dermatoglifos de ADN, ADN bacteriano, Genotipo, Secuencias Repetitivas Esparcidas, Repeticiones de Minisatélite, epidemiología molecular, Mycobacterium tuberculosis, Reacción en Cadena de la Polimerasa, Polimorfismo de Longitud del Fragmento de Restricción, Tuberculosis

Citation

Alonso-Rodriguez N, Martínez-Lirola M, Sánchez ML, Herranz M, Peñafiel T, Bonillo M del C, et al. Prospective universal application of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping to characterize Mycobacterium tuberculosis isolates for fast identification of clustered and orphan cases. J. Clin. Microbiol. 2009 Jul; 47(7):2026-32