First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains
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TLDR
This first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future.Abstract:
Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future.read more
Citations
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Journal ArticleDOI
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.
Josephine M. Bryant,Anita C. Schürch,Anita C. Schürch,Henk van Deutekom,Simon R. Harris,Jessica L. de Beer,Victor de Jager,Victor de Jager,Kristin Kremer,Sacha A. F. T. van Hijum,Sacha A. F. T. van Hijum,Roland J. Siezen,Roland J. Siezen,Martien W. Borgdorff,Stephen D. Bentley,Julian Parkhill,Dick van Soolingen +16 more
TL;DR: This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies, but the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
Journal ArticleDOI
Current Methods in the Molecular Typing of Mycobacterium tuberculosis and Other Mycobacteria.
Tomasz Jagielski,Jakko van Ingen,Nalin Rastogi,Jarosław Dziadek,Pawel K. Mazur,Jacek Bielecki +5 more
TL;DR: This review summarizes currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease.
Journal ArticleDOI
Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey
Jessica L. de Beer,Jakko van Ingen,Gerard de Vries,Connie Erkens,M. M. G. G. Sebek,Arnout Mulder,Rosa Sloot,Anne-Marie van den Brandt,Mimount Enaimi,Kristin Kremer,Philip Supply,Dick van Soolingen +11 more
TL;DR: VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an R FLP-clustering-based cluster investigation, which makes VNTR typed a suitable method for tuberculosis surveillance systems.
Journal ArticleDOI
A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study.
David H. Wyllie,David H. Wyllie,Jennifer Davidson,Grace Smith,Priti Rathod,Derrick W. Crook,Derrick W. Crook,Tim E. A. Peto,Tim E. A. Peto,Esther Robinson,Timothy M Walker,Colin Campbell +11 more
TL;DR: This molecular epidemiological study shows MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness, assessed by SNV.
Book ChapterDOI
The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex.
TL;DR: This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods, and provides suggestions on what method to use depending on the specific research question.
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TL;DR: In this article, the authors proposed a standardized technique which exploits variability in both the number and genomic position of IS6110 to generate strain-specific patterns for DNA fingerprinting of Mycobacterium tuberculosis.
Journal ArticleDOI
Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis
Philip Supply,Philip Supply,Caroline Allix,Sarah Lesjean,Sarah Lesjean,Mara Cardoso-Oelemann,Mara Cardoso-Oelemann,Sabine Rüsch-Gerdes,Eve Willery,Eve Willery,Evgueni Savine,Evgueni Savine,Petra E. W. de Haas,Henk van Deutekom,Solvig Roring,Pablo Bifani,Natalia Kurepina,Barry N. Kreiswirth,Christophe Sola,Nalin Rastogi,Vincent Vatin,Vincent Vatin,Maria Cristina Gutierrez,Maryse Fauville,Stefan Niemann,Robin A. Skuce,Kristin Kremer,Camille Locht,Camille Locht,Dick van Soolingen +29 more
TL;DR: A discriminatory subset of 15 loci with the highest evolutionary rates was defined that concentrated 96% of the total resolution obtained with the full 24-locus set, and its predictive value for evaluating M. tuberculosis transmission was found to be equal to that of IS6110 restriction fragment length polymorphism typing.
Journal ArticleDOI
Automated High-Throughput Genotyping for Study of Global Epidemiology of Mycobacterium tuberculosis Based on Mycobacterial Interspersed Repetitive Units
TL;DR: Kremer et al. as mentioned in this paper used variable-number tandem repeat (VNTR) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 mammalian minisatellite-like loci of M. tuberculosis.
Journal ArticleDOI
Comparison of Methods Based on Different Molecular Epidemiological Markers for Typing of Mycobacterium tuberculosis Complex Strains: Interlaboratory Study of Discriminatory Power and Reproducibility
Kristin Kremer,D. van Soolingen,Richard Frothingham,Walter H. Haas,Peter W. M. Hermans,Carlos Martin,Prasit Palittapongarnpim,Bonnie B. Plikaytis,Lee W. Riley,Mitchell A. Yakrus,James M. Musser,J. D. A. Van Embden +11 more
TL;DR: Strain differentiation by IS6110 RFLP or mixed-linker PCR are the methods of choice for epidemiological investigations, indicating a clonal population structure of M. tuberculosis strains.
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