Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method

@article{Groenen1993NatureOD,
  title={Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method},
  author={Peter M. A. Groenen and Annelies E. Bunschoten and Dick van Soolingen and Jan D. A. van Errtbden},
  journal={Molecular Microbiology},
  year={1993},
  volume={10}
}
Mycobacterium tuberculosis complex strains contain a unique chromosomal region, which consists of multiple 36bp direct repeats (DRs), which are interspersed by unique spacers 35 to 41 bp in length. In this study we investigated the nature of the DNA polymorphism of this DR cluster by sequencing part of this region in a large number of M. tuberculosis complex strains. Two types of genetic rearrangements were observed. One type consists of the variation in one or a few discrete, contiguous DRs… 
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Microevolution of the Direct Repeat Region of Mycobacterium tuberculosis: Implications for Interpretation of Spoligotyping Data
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The binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of Mycobacterium tuberculosis, having important implications for molecular epidemiologic strain tracking and for the application of spolgotype data to phylogenetic analysis of M. tuberculosis isolates.
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An evaluation of the utility of IS6110-based restriction fragment length polymorphism (RFLP) typing compared to a combination of variable number tandem repeat (VNTR) typing and mycobacterial interspersed repetitive unit (MIRU) typing found the speed of the combined VNTR and MIRU typing approach enabled results for some of the investigations to be supplied in “real time,” influencing choices in contact tracing.
IS6110 Transposition and Evolutionary Scenario of the Direct Repeat Locus in a Group of Closely Related Mycobacterium tuberculosis Strains
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DNA sequence analysis of the DR loci of these isolates revealed an evolutionary scenario, which allowed a reconstruction of the evolutionary steps and relationships among these closely related isolates, and suggested that IS6110 restriction fragment length polymorphism patterns are useful in grouping closely related isolate together.
Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG
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PCR-restriction enzyme analysis was applied to reference strains and clinical isolates with a worldwide distribution and provides rapid, sensitive, and specific identification of the important vaccine strain M. africanum.
University of Birmingham Mycobacterium tuberculosis complex genetic diversity
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The results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network.
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A novel method based on strain-dependent hybridization patterns of in vitro-amplified DNA with multiple spacer oligonucleotides was found to differentiate M. bovis from M. tuberculosis, a distinction which is often difficult to make by traditional methods.
Improvement of Differentiation and Interpretability of Spoligotyping for Mycobacterium tuberculosis Complex Isolates by Introduction of New Spacer Oligonucleotides
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The traditional commercialized first-generation membrane for spoligotyping is left unchanged for current applications and to introduce a second-generation spolgotyping membrane whenever extended discrimination is required, e.g., for low-copy-number IS6110 strains or for phylogenetic studies of Beijing genotype strains.
Use of Spoligotyping To Study the Evolution of the Direct Repeat Locus by IS6110 Transposition inMycobacterium tuberculosis
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The results show that the DR locus constitutes an idealIS6110 preferential locus (ipl), permitting the insertion of two or more copies of IS6110, and provide new clues for epidemiological and phylogenetic interpretation of changes in IS61 10-RFLP and spoligotyping profiles.
Insertion element IS6110-based restriction fragment length polymorphism genotyping of Mycobacterium tuberculosis.
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In this chapter, the method of IS6110 DNA fingerprinting is explained in such a way that it can be easily duplicated by molecular epidemiologists and will give reproducible results.
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