The objective was to describe and validate a new and alternative software procedure for 24locus mycobacterial interspersed repetitive unitvariable numbertandem repeat miruvntr typing of mycobacterium tuberculosis mtb based on the multipurpose bionumerics software. How to use sitvit2 this is a user manual helping researchers how to navigate and analyze their data through the sitvit2 database. As outlined above, miru vntrplus allows for analysis of several types of mtbc genotyping data that correspond to the current, most frequently used standards for molecular epidemiological and phylogenetic analysis. In sum, this new automated method facilitates miruvntr genotyping and provides. The national mycobacterium reference servicesouth nmrs south is an accredited constituent. Mycobacteria interspersed repetitive unitsvariable number. Miru vntrplus provides also functions for the user to analyze own strains without interrogating the reference database. Evaluation and userstrategy of miruvntr plus, a multifunctional da tabase for online analysis of genotyping data and phylogenetic identi. 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. The conventional method for miruvntr genotyping requires. The bioinformatics tools developed for the miruvntrplus database will be detailed in a separate report. This confirms the relatedness to eai lineage of the sit459 isolates. Setup and validation of mycobacterial interspersed. Qiagen kit handbooks and user manuals are available at.
Pdf unusual miru alleles in locus 580 and 4348 among. Jun 11, 2008 on the basis of this evaluation, a user strategy was defined, which consisted of bestmatch analysis followed, if necessary, by treebased analysis. The miru vntr plus database is a powerful tool for highresolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far. Mycobacterium tuberculosis, database, spoligotyping, mycobacterial interspersed repetitive unitsvariable number of tandem repeats miru vntrs typing, evolution, phylogeny. The acronym miru is used to denote a mycobacterium tuberculosisspecific multiple locus vntr variable number of tandem repeats analysis mlva scheme. An overview of the information found in the manual is provided below. National mycobacterium reference servicesouth nmrssouth. A first assessment of the genetic diversity of mycobacterium. For the exchange of miruvntr data, the reporting of the full genotype with copy numbers of each locus in perfect order is mandatory.
Mycobacterial interspersed repetitive units variable number. Version 1 221120 introduction to strain typing module the strain typing module stm is an integrated part of the enhanced tuberculosis surveillance ets system. Pdf highthroughput miruvntr genotyping for mycobacterium. Data submitted by users of the miru vntrplus service is not stored permanently except for new miru vntr patterns expanding mlva mtbc159 nomenclature if explicitly agreed by the user privacy statement. Miruvntr clustered isolates is6110rflp 34 weeks additional 3 weeks genotyping. On the basis of this evaluation, a user strategy was defined, which consisted of bestmatch analysis followed, if necessary, by treebased analysis. The acronym miru is used to denote a mycobacterium tuberculosis specific multiple locus vntr variable number of tandem repeats analysis mlva scheme. The miruvntrplus web application allows for three main functionalities. In miruvntr plus database, a 4 loci strain variant 1277803 was found for this sit. Multi locus vntr analysis mlva is a molecular typing method to subtype microbial isolates based upon the variable copy numbers of tandem repeats vntr. Mycobacterial interspersed repetitive units variable number tandem repeats miruvntr, produces a pattern based on the number of repeat sequences at each locus. The miruvntrplus database is a powerful tool for highresolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.
The miruvntr plus database is a powerful tool for highresolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far. Evaluation and user strategy of miru vntrplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of mycobacterium tuberculosis complex isolates. Miruvntr manual in this manual you will learn how to install the miruvntr plugin in your bionumerics database, how to import curve files and peak tables, obtain copy numbers, and how to connect to the online miruvntrplus database to assign known types to your data and to submit new types. On the main page, a brief description of the techniques is provided and the user manual of the main functionalities can be downloaded. Miruvntr typing, has recently been adopted by the ecdc european centre for disease prevention and control and is now the international standardised molecular typing method for mycobacterium tuberculosis complex isolates. Bacterialstrainsforthevalidation four datasets were used to evaluate the accuracy of the miru profiler results with respect to experimental genotyping and a webbased tool for digital miru vntr typing of m.
National mycobacterium reference servicesouth user manual 4. The mlva mtbc159 type is a juxtaposition of two subtypes, i. In this manual you will learn how to install the miruvntr plugin in your bionumerics database, how to import curve files and peak tables, obtain copy numbers. Background for a long time differentiation of clinical mycobacterium tuberculosis mtb isolates was based on morphological and phenotypic characteristics such as growth morphology on loweinstein jensen medium eunogic or dysnogic or biochemical properties such as niacin test and nitrate reduction. Mycobacterium tuberculosis, database, spoligotyping, mycobacterial interspersed repetitive unitsvariable number of tandem repeats miruvntrs typing, evolution, phylogeny. Enhanced tb surveillance strain typing module user guide. Molecular epidemiology of mycobacterium bovis in cameroon. Dna from randomly selected isolates of mtb from two european laboratories, including external control samples for miru vntr. Loci analyzed in mycodb are vntr 2165, vntr 2461, vntr 0580, vntr 3192. Vm0808h user manual viii about this manual this user manual is provided to help you get the most from your vm0808h system. To facilitate scientific communication, miru vntrplus introduces an expanding nomenclature that assigns a numerical code to miru vntr patterns. In bionumerics, the miruvntr plugin is based on the successful mlva plugin.
Vntrmiru generate a 1524 digit strain designation number collated in uk national database geographical incidence of tb isolates with 15vntr profile 422225435173533, which corresponds to the leicester outbreak strain. Page 9 of 159 october 17, 2011 guide to the mvi69mnet user manual function section to read details introduction must do. Respirateur n95 contre les particules directives dutilisation important. Spoligotyping is widely used because of its low cost, high reproducibility, simplicity and ease of interpretation due to its binary results format, while the miruvntr assay is robust, reliable and easier to perform compared to is6110 rflp typing. Particulate respirator n95 8210 8210 mx8210 8210mx. This gives a measure of how much each locus contributes to the total discriminatory power of the miruvntr as a typing tool.
Extensive documentation manual and tutorials of the service is available to make best use of all features. Automated miruvntr genotyping of mycobacterium tuberculosis. Morphomanager user manual refer to end user license agreement for copyright notice page 3 screen 6 ma 100, ma j, ma 500 and ma vp settings52. Miruvntrplus provides also functions for the user to analyze own strains without interrogating the reference database. Miru vntrplus is a system with a focus on evaluation of a reference database. Miru vntr types cannot be obtained with the example data set provided, since it contains only information for three vntrs and miru vntr typing is based on 9 or 15 vntrs. The technical aspects and analysis methods of miru are the same as for other mlva schemes. Importing sequence assemblies from bam and sam files. This gives a measure of how much each locus contributes to the total discriminatory power of the miru vntr as a typing tool. Miru vntr alleles with incomplete tandem repeat units variant alleles and two alleles simultaneously detected for a given locus double alleles, cdc notation for miru vntr data by using a for 10 repeats, b for. The revolutionary qiaxcel advanced system replaces traditional, laborintensive gel analysis of dna and rna streamlining workflows and reducing time to result. Miru vntrplus allows users to upload data for up to 500 strains. The resulting trees may be exported in various data formats.
Mvi69mnet compactlogix and micrologix 1500 platform guide to the mvi69mnet user manual modbus tcpip communication module user manual prosoft technology, inc. Mycobacteria interspersed repetitive unitsvariable number of. Multilocus variable number tandem repeat genotyping of. National mycobacterium reference servicesouth nmrs. Genetic relatedness of mycobacterium tuberculosis strains.
Online tools for polyphasic analysis of mycobacterium. Mycobacterial interspersed repetitive units miru typing. For a selected set of tandem repeats, copy number analysis reveals insights about the relationships at a. Spoligotyping is widely used because of its low cost, high reproducibility, simplicity and ease of interpretation due to its binary results format, while the miru vntr assay is robust, reliable and easier to perform compared to is6110 rflp typing. Enhanced tuberculosis surveillance strain typing module user guide. Miruvntrtype search miruvntrtype earchs is a tool that allows miruvntr profile searches in.
Particulate respirator n95 user instructions 8210plus8210plusmx8210 8210mx070488110s 3 particulate respirator n95 user instructions important. This user handbook is intended for use by referral laboratories to the unit. The qiaxcel advanced system fully automates sensitive, highresolution capillary electrophoresis of up to 96 samples per run. Chapter 1, introduction, introduces you to the vm0808h system. Within the group of 52 isolates, 17 different miruvntr patterns were detected. 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. Evaluation and strategy for use of miruvntrplus, a. The miruvntr copy numbers stored in the miruvntr vals character experiment, the user infor mation and the strain ids of the selected entries are submitted to the miruvntrplus database. The miru vntrplus database is a powerful tool for highresolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.
The database has an additional viewer for visualization of the geographic distribution of mycobacterial isolations according to searching criteria introduced by the user such as year of. For all functions an extensive documentation is available online, including a user manual, multimedia. Qiaxcel advanced user manual en for use with qiaxcel advanced instruments and qiaxcel screengel software version 1. Miruvntr results are displayed as a 24 digit number that can be used to compare isolates for similarity or difference. Oct 02, 2019 mremoteng is the next generation of mremote, open source, tabbed, multiprotocol, remote connections manager. As it is based on amplification by pcr, miruvntr typing can be performed on heat. Tb control needs, such as identifying settings where transmission occurs note. In particular, for program mirpro, you need to add flag lpthread. Miru vntrtype search miru vntrtype earchs is a tool that allows miru vntr profile searches in order to view. For uptodate licensing information and productspecific disclaimers, see the respective qiagen kit handbook or user manual. You can access online user manuals for our bluetooth speakers and portable usb chargers. Vm0808h user manual about this manual this user manual is provided to help you get the most from your vm0808h system. One miruvntr pattern was found in 29 isolates, one pattern in four isolates, one pattern in three isolates, two times one miruvntr pattern was found occurring in two isolates, and 12 patterns were found only once.
Automated miruvntr genotyping of mycobacterium tuberculosis strains using the qiaxcel advanced systems 082016 3 results and discussion miruvntr loci the 15locus panel for epidemiological studies and the 24locus panel for phylogenetic resolution were used as the standard sets for identification of the main mycobacterial genotypes table 1. Find support for us digital media mobile accessories on this page. To locate your free radio shack manual, choose a product type below. Jul 01, 2010 for the exchange of miru vntr data, the reporting of the full genotype with copy numbers of each locus in perfect order is mandatory. To facilitate scientific communication, miruvntrplus introduces an expanding nomenclature that assigns a numerical code to miruvntr patterns. A vntr typically exhibits a large range of copy numbers, even among highly related bacterial strains. Nucleic acid or amino acid sequences, from import and assembly over multiple alignment to annotation, snp analysis, primer design and comparison of complete chromosomes. Deeplex myctb is an allinone test for specieslevel identification, genotyping and prediction of antibiotic resistance in mycobacterium tuberculosis complex strains. Miruvntrplus is a system with a focus on evaluation of a reference database.
The miruvntr typing method was widely described as an. In bionumerics, the miruvntr plugin is based on the successful mlva plugin miruspecific additions in the miru. Extensive documentation manual and tutorials of the service is. The plugin automatically interprets and analyzes miru vntr data and interacts with the miru vntrplus website for typing and global epidemiology of mycobacteria.
Miruvntr analysis of mycobacterium tuberculosis using. Highthroughput mycobacterial interspersed repetitiveunit. Displays all the data from each of the isolates sorted by region. Various formats for genotyping data are accepted, e. It covers all aspects of installation, configuration and operation. Page 9 of 159 october 17, 2011 guide to the mvi69mnet user manual function section to read details. The module is designed to identify strain typing clusters and assist with cluster investigation. A miru vntr based highspeed genotyping system has been developed, which combines the analysis of multiplex pcrs for the target loci on a fluorescencebased dna analyzer with computerized automation of the genotyping 16. As the first ever tool to exploit indepth dna sequencing technology and thus detect and analyze antibiotic resistance, deeplex myctb detects mutations responsible of antituberculosis drugs resistan. Dna from randomly selected isolates of mtb from two european laboratories, including external control. The numbers of manual corrections for allele assignments were 122 with. In addition, you can find source code, script, and user manual inside mirpro package. Visavet health surveillance centre is the institution responsible for the database where national data regarding animal mycobacteriosis are registered since 1996 to the present days. Allows a robustlineage identification based on the combination of different genotyping data.
298 855 1130 980 476 1197 648 516 933 363 671 225 1620 1374 513 554 1028 964 959 695 657 475 1569 118 1553 1521 498 429 228 1122 1561 1309 660 810 1586 438 877 1086 1322 932 158 835 992 638 553 1268 1128 289