scholarly journals Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan

2007 ◽  
Vol 56 (8) ◽  
pp. 1052-1057 ◽  
Author(s):  
Takayuki Wada ◽  
Shinji Maeda ◽  
Atsushi Hase ◽  
Kazuo Kobayashi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
Strain Typing ◽  
Beijing Family ◽  
Discrimination Power ◽  
Family Based ◽  
Vntr Analysis

Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter–Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.

scholarly journals Typing Method for the QUB11a Locus ofMycobacterium tuberculosis: IS6110Insertions and Tandem Repeat Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-6
Author(s):  
Eriko Maeda-Mitani ◽  
Koichi Murakami ◽  
Akira Oishi ◽  
Yoshiki Etoh ◽  
Nobuyuki Sera ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Variable Number ◽  
Typing Method ◽  
Repeat Analysis ◽  
Ofmycobacterium Tuberculosis ◽  
High Discrimination ◽  
Vntr Analysis

QUB11a is used as a locus for variable number of tandem repeats (VNTR) analysis ofMycobacterium tuberculosisBeijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp) that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110insertion may complicate VNTR analysis of large QUB11a fragments inM. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110insertion in the QUB11a locus ofM. tuberculosisusing capillary electrophoresis analysis andBsmBI digestion. All 29 large QUB11a fragments (>1,200 bp) investigated contained IS6110insertions and varied in the number of repeats (18 patterns) and location of IS6110insertions. This method allows VNTR analysis with high discrimination.

Genetic diversity of theMycobacterium tuberculosisBeijing family based on multiple genotyping profiles

2015 ◽  
Vol 144 (8) ◽  
pp. 1728-1735 ◽  
Author(s):  
Y. LIU ◽  
S. WANG ◽  
H. LU ◽  
W. CHEN ◽  
W. WANG
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeats ◽  
Cross Sectional Study ◽  
Variable Number ◽  
Beijing Genotype ◽  
Nucleotide Polymorphisms ◽  
Beijing Family ◽  
Cross Sectional ◽  
Discriminatory Ability ◽  
Family Based

SUMMARYAmong the most prevalentMycobacterium tuberculosis(Mtb) strains worldwide is the Beijing genotype, which has caused large outbreaks of tuberculosis (TB). Characteristics facilitating the dissemination of Beijing family strains remain unknown, but they are presumed to have been acquired through evolution of the lineage. To explore the genetic diversity of the Beijing family Mtb and explore the discriminatory ability of mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) loci in several regions of East Asia, a cross-sectional study was conducted with a total of 163 Beijing strains collected from registered TB patients between 1 June 2009 and 31 November 2010 in Funing County, China. The isolated strains were analysed by 15-MIRU-VNTR loci typing and compared with published MIRU-VNTR profiles of Beijing strains. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. The combination of SNP and MIRU-VNTR typing may be used to assess Mtb genotypes in areas dominated by Beijing strains. The modern subfamily in Shanghai overlapped with strains from other countries, whereas the ancient subfamily was genetically differentiated across several countries. Modern subfamilies, especially ST10, were prevalent. Qub11b and four other loci (MIRU 26, Mtub21, Qub26, Mtub04) could be used to discriminate Beijing strains.

scholarly journals Enhancing the differentiation of specific genotypes in Mycobacterium tuberculosis population

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shima Hadifar ◽  
Mansour Kargarpour Kamakoli ◽  
Abolfazl Fateh ◽  
Seyed Davar Siadat ◽  
Farzam Vaziri
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Allelic Diversity ◽  
Variable Number ◽  
Discriminatory Power ◽  
Discrimination Power ◽  
High Discrimination ◽  
High Discriminatory Power ◽  
Selection Of

AbstractToday, significant attention is directed towards the global lineages and sublineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains are recognized as growing and circulating Mtb genotypes, especially in Asian countries. It is crucial to develop or enhance Mtb genotyping methods for a more accurate and simple differentiation of these families. We used 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing for genotyping 217 Mtb isolates. To select the optimal MIRU-VNTR loci, we calculated the Hunter-Gaston discriminatory index (HGDI), allelic diversity, and accumulation of percentage differences (APDs) between the strains among different groups of genotypes (NEW-1 and non-NEW-1; CAS1-Delhi and non-CAS). Finally, the minimum spanning tree was constructed for clustering analysis. In the NEW-1 population, loci with APD > 60% were found to have a high discriminatory power. VNTR loci with APD > 50% showed high discrimination power for the CAS population. Our findings suggest that APDs, which are valuable for the selection of VNTR loci sets, may improve the discriminatory power of MIRU-VNTR typing for identification of Mtb genotypes in specific regions.

scholarly journals Distribution of Mycobacterium leprae genotypes from Surabaya and Bandung Clinical Isolates by Multiple Locus Variable Number of Tandem Repeat Analysis

2019 ◽  
Author(s):  
Cita Rosita Sigit Prakoeswa ◽  
Bayu Bijaksana Rumondor ◽  
Lina Damayanti ◽  
Muljaningsih Sasmojo ◽  
Dinar Adriaty ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Tandem Repeat ◽  
Copy Number ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Locus ◽  
Leprosy Patients ◽  
Transmission Studies ◽  
Multiple Locus Vntr Analysis ◽  
Vntr Analysis

Multiple Locus Variable Number of Tandem Repeat (VNTR) analysis has been proposed as a means of genotyping for tracking leprosy transmission due to tandem repeats’ potential as genetic markers to differentiate M. leprae strains. However, characteristics of polymorphism can vary depending on the population. This study aimed to compare the copy number of repeats in four genetic markers: TTC, AC8a, AC9 and 6-7 in leprosy patients from Surabaya and Bandung. Twenty three patients from Dr. Soetomo General Hospital and 21 from Hasan Sadikin Hospital were recruited. Multiple locus VNTR analysis was applied using total DNA extracts from Slit Skin Smear (SSS). From Surabaya, 7 samples showed the same copy number of four genetic markers (TTC=15; AC8a=10; AC9=10 and 6-7=6) and 2 showed another (TTC=16; AC8a=10; AC9=11 and 6-7=6); as for samples from Bandung, 2 showed the same copy number (TTC=15; AC8a=8; AC9=10 and 6-7=8) and 2 showed another (TTC=16; AC8a=10; AC9=11 and 6-7=6). The multiple locus VNTR analysis showed two identical M. leprae VNTR profiles from Bandung and Surabaya which supports the use of VNTR loci for transmission studies.

scholarly journals Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis

2008 ◽  
Vol 57 (7) ◽  
pp. 873-880 ◽  
Author(s):  
Yoshiro Murase ◽  
Satoshi Mitarai ◽  
Isamu Sugawara ◽  
Seiya Kato ◽  
Shinji Maeda
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Beijing Family

scholarly journals Insight into population structure of Mycobacterium tuberculosis isolates in the multiethnic province of Alborz, Iran

2021 ◽  
Author(s):  
Morassa Sadat Farnad ◽  
Hassan Momtaz ◽  
Nader Mosavari ◽  
Yahya Khosravi ◽  
Keyvan Tadayon
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Study Region ◽  
Tuberculosis Patients ◽  
Background Data ◽  
Study Panel ◽  
Insight Into ◽  
Vntr Analysis

Background and Objectives: Genetic diversity of Mycobacterium tuberculosis clinical isolates from tuberculosis patients in the multiethnic province of Alborz, Iran was assessed. Materials and Methods: A total of 17 isolates in the period of 2012-2013 were collected and subjected to a Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) consisted of 6 variable numbers of tandem repeats (VNTRs) including ETR-A, ETR-B, ETR-C, ElTR-D, ETR-E, ETR-F, 5 Mycobacterial Interspersed Repetitive Units including MIRU10, MIRU16, MIRU26, MIRU39, MIRU40, and 1 Queen University of Belfast locus, QUB11. Results: This classified all isolates into 17 distinct MIRU-VNTR types, a reflection of a highly heterogenic population. Within the 12 used VNTR loci, ten proved highly or moderately discriminant according to the calculated HGDI scores. No cluster of isolates was identified in the study panel, giving a clustering rate of 0%, several events of SVL (N=5) and DVL (N=4) and TVL (N=3) were detected. Conclusion: The greater heterogeneity observed here by MLVA-VNTR analysis is most likely due to limited background data in the study region rather than a genuine more heterogeneous population compared to other provinces of the country.

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