This form can be accessed on all pages that use calculated distances. The tool can accurately infer repeat numbers at the standard 24 or 2124 miru vntr loci from the complete or howtocitethisarticlerajwani et al. Methods we studied isolates from the english midlands. Its discriminatory power is high, and it can be used for samples that are not typable by rflp because of. Molecular typing of mycobacterium kansasii using pulsed. The module is designed to identify strain typing clusters and assist with cluster investigation. Mycobacterial interspersed repetitive units miru typing. Screening can be done for all entries present in the database, or for any selection of entries in database. Miru vntr is more predictive of close relatedness in lineage 4. The results of 24 loci miru vntr typing are unlikely to directly influence the treatment and management of patients. Miru vntr, a global reference the miru vntr typing. Highresolution minisatellitebased typing as a portable.
Mycobacterial interspersed repetitive units variable number tandem repeat miru vntr typing by the 24loci is a minisatellite typing system that was first proposed by supply et al. Miru vntr typing of drugresistant tuberculosis isolates in greece nikoletta rovina, simona karabela, pantelis constantoulakis, vassiliki michou, konstantinos konstantinou, vassileios sgountzos, charis roussos and nikolaos poulakis abstract. The miru vntr mycobacterial identification repetitiv unit vntr analysis is an mlva multiple loci vntr analysis analysis scheme specific to mycobacterium tuberculosis. Background mycobacterial interspersed repetitive unitvariable number tandem repeat miru vntr typing is widely used in highincome countries for mycobacterium tuberculosis typing. Variable number of tandem repeat vntr typing is based on analysis of dna segments containing tandem repeated sequences in which the number of copies of the repeated sequence varies among strains. Having combined miruvntr and etr vntr data, we increased the discriminatory power of typing method, thus 25 clusters were identified.
Dna from randomly selected isolates of mtb from two european laboratories, including external control samples for miru vntr. The qiaxcel advanced system might offer a costeffective medium. Mtbc isolates with identical miru vntr profiles can be clustered to identify epidemiologically linked cases supply et al. Miru vntrplus supports polyphasic typing by calculating a combined distance for different types of genotyping data. A variable number tandem repeat or vntr is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. This is used in the genotyping of strains by numbering copies of vntr present in 24 identified loci. Mycobacterial interspersed repetitive unitvariable number.
Once the most polymorphic miru vntr loci were identified, additional analysis was performed to identify combinations for improved differentiation of mycobacteria included in the present study in the first approach, five miru vntr typing loci excluding qub 3232 showed a very high discriminatory index for our set of isolates and were particularly useful to differentiate almost all the. Only 8% of miru vntr linked pairs in lineage 1 were within 5 snv, compared to 31% in lineage 4. Proposal for standardization of optimized mycobacterial. Primer sequences for target loci were selected from previous reports 4, 5, 6. In addition, phenotypic drug suceptibility was performed. A quantitative evaluation of miruvntr typing against. The objective was to describe and validate a new and alternative software procedure for 24locus mycobacterial interspersed repetitive unitvariable numbertandem repeat miru vntr typing of mycobacterium tuberculosis mtb based on the multipurpose bionumerics software. The aim of the national strain typing service is to enable the rapid detection of potential clusters or outbreaks and identify associated transmission settings to inform targeted screening for active and latent tb. Miru vntr loci most appropriate to use for typing mtbc organisms isolated from sika deer in china. Current methods in the molecular typing of mycobacterium. Inthesetting studied, thismolecular epidemiologicalstudy shows miru vntr typing andepidemiological risk factors are poorly predictive of close genomic relatedness, assessed by snv.
The miru profiler is a rapid tool for inference of digital miru vntr profile from the assembled genome sequences. Miru is a mtbc specific name of a multiple locus vntr variable number of tandem repeats analysis mlva bacterial typing scheme. Miru vntr typing generally proved efficacy and high discriminatory power, with a collective alleles diversification of 0. This has rendered 24locus miru vntr typing the new gold standard in molecular typing of m. The combination of the two typing methods confirms the relatedness of the strains. Synchronization with the miru vntrplus server is possible with a single click, while new types are assigned automatically. In a combined spoligotyping and miru vntr typing protocol, the number of vntr loci could be reduced to four qub 11a, qub 11b, etr a, and 4052 while maintaining a high level of strain. Our data supports a different relationship between miru vntr and snv in the most common sublineages present. Insilico miru vntr typing using long reads 42 commits 2 branches 0 packages 0 releases fetching contributors mit python. For a selected set of tandem repeats, copy number analysis reveals insights about the relationships at a.
In our setting rflp typing and miru vntr typing provided a high level of both reproducibility and genetic diversity. The classtr approach for classification based on miru vntr typing indicated that 5. Setup and validation of mycobacterial interspersed. Population structure of drugresistant mycobacterium. Because of its portable data format, miru typing has the potential to be a versatile tool for individual strain identification based on large reference databases. This typing method opens the way to the construction of digital global databases for molecular. We report a molecular epidemiology study that used spoligotyping, mycobacterial interspersed repetitive unitsvariablenumber tandem repeat miru vntr typing, and region of. Only 8% of miru vntr linked pairs in lineage 1 were 39 within 5 snv, compared to 31% in lineage 4. Like spoligotyping and miru vntr typing, reppcr is a fast time and laboursaving method that can generate realtime strain typing results. In addition to the automated import and analysis tools for vntr s, the miru vntr plugin provides specific functionality for mycobacterium interspersed repetitive units typing. Moreover, concomitant use of the matr vntr method and is 1245 rflp typing increased the hgdi to 0.
Comparison of variablenumber tandemrepeat markers typing. Miruvntr genotyping of mycobacterium tuberculosis strains. Enhanced tuberculosis surveillance strain typing module user guide. Evaluation of miruvntr for typing of mycobacterium bovis. Background molecular genotyping of rculosis is an important laboratory tool in the context of emerging drug resistant tb. The plugin automatically interprets and analyzes miru vntr data and interacts with the miru vntrplus website for typing and global epidemiology of mycobacteria. Each variant acts as an inherited allele, allowing them to be used for personal or parental identification.
Multilocus variable number tandem repeat genotyping of. The method relies on pcr amplification and calculation of the number of repeats on the basis of the size of the amplified product. Molecular genotyping of mycobacterium tuberculosis in xian, china, using miru vntr typing. Molecular strain typing of mycobacterium tuberculosis. Miru vntr typing names manually, please note that information. The diversity analysis showed that the discriminatory power of individual loci differed greatly, with h ranging from 0. Multi locus vntr analysis mlva is a molecular typing method to subtype microbial isolates based upon the variable copy numbers of tandem repeats vntr. Accuracy of the qiaxcel automated system for miruvntr. Miru vntr typing of dna samples was performed using the primers shown in table 1. Although the panel of miru vntr loci has been modified over the years, the standardized 24locus miru vntr typing is currently recognized as the reference typing. Citeseerx document details isaac councill, lee giles, pradeep teregowda.
The increasing immigration rate in greece from countries with a high prevalence of. Qiaxcel system is proposed as an affordable tool that could replace conventional gel electrophoresis and provide high concordance with. Miru typing in bionumerics the miru vntr application creates a database environment for the import and analysis of miru vntr data, making it an easy to use typing application. Miruvntr typing of drugresistant tuberculosis isolates. Among a large cohort of pulmonary tb patients in lima, peru, we found evidence of withinhost m. International journal of tuberculosis and lung disease. Version 1 221120 introduction to strain typing module the strain typing module stm is an integrated part of the enhanced tuberculosis surveillance ets system. Among different sets of miru vntr loci described for typing m. Next to the proposed standardized miru vntr 15 or 24loci sets, the use of another three loci, the socalled hypervariable loci i. The national strain typing service involves prospectively typing tb isolates using 24 loci mycobacterial interspersed repeat units variable number tandem repeats miru vntr. The copy numbers and allelic diversity h in miru vntr loci were recorded table 1. Mycobacterial interspersed repetitive units miru vntr ios ebptm 004 rev.
The study set consisted of 607 isolates with 235 from uzbekistan, 206 from tajikistan, and 166 from kyrgyzstan. So far, this optimized system has been assessed in a single, 1year populationbased study performed in germany. These can be found on many chromosomes, and often show variations in length number of repeats among individuals. Mycobacterial interspersed repetitive units variable number tandem repeat miru vntr typing of mycobacterium tuberculosis complex mtbc isolates, based on 24 loci, is still widely used as the standard for routine molecular surveillance of tuberculosis tb. Molecular typing systems for pathogenic mycobacteria are important for epidemiologic control because they enable caselinking and outbreak tracing 6. Loci 10, 26, 40 in miru and etra were highly discriminatory.
The standard 24loci miru vntr typing includes pcr amplification followed by the detection and sizing of pcr fragments using capillary electrophoresis on automated sequencers or using agarose gels. Polyclonal pulmonary tuberculosis infections and risk for. Screening can be done for all entries present in the database, or. Genotyping guide description of genotyping methods.
Standardized mycobacterial interspersed repetitiveunitvariablenumber tandem repeat miru vntr typing based on 15 and 24 loci recently has been proposed for mycobacterium tuberculosis genotyping. However, is 1245 rflp and miru vntr typing yielded hgdis of 0. Miru vntr typing has the considerable advantages of being fast, appropriateforall rculosis isolates,includingstrainsthathave a few is6110 copies, and permitting easy and rapid comparison of results from independent laboratories. Enhanced tb surveillance strain typing module user guide. Molecular genotyping of mycobacterium tuberculosis in xi. Scope this protocol describes all the steps and information needed to perform 24locus vntr typing of m. Wholegenome sequencing wgs is known to deliver greater specificity, but no quantitative prospective comparison has yet been undertaken. When 24locus miru vntr typing and 43spacer spoligotyping methods are combined with equal weights, the respective tolerances are i loci and j spacers, with i equal to 0 to 8, j equal to 0 to 14, and 0. Results analysis of individual miru vntr locus miru vntr typing results of m.
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