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.

A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes

2015 ◽  
Vol 33 ◽  
pp. 233-241 ◽  
Author(s):  
Yolande Hauck ◽  
Charles Soler ◽  
Patrick Gérôme ◽  
Rithy Vong ◽  
Christine Macnab ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Propionibacterium Acnes ◽  
Variable Number ◽  
Multiple Locus ◽  
Vntr Analysis

scholarly journals Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for the Molecular Subtyping of Enterobacter sakazakii

2007 ◽  
Vol 74 (4) ◽  
pp. 1223-1231 ◽  
Author(s):  
N. R. Mullane ◽  
M. Ryan ◽  
C. Iversen ◽  
M. Murphy ◽  
P. O'Gaora ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Fluorescent Dyes ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Enterobacter Sakazakii ◽  
Multiple Locus ◽  
Epidemiological Tool ◽  
Genescan Analysis ◽  
Variable Number Tandem Repeats ◽  
Multiple Locus Vntr Analysis

ABSTRACT The genomic content of Enterobacter sakazakii strain ATCC BAA-894 was analyzed for variable-number tandem repeats (VNTRs). In this study we report the development of a multiple-locus VNTR analysis (MLVA) strategy for the subtyping of E. sakazakii. The method is based on a GeneScan analysis of four VNTR loci labeled with multiple fluorescent dyes. This approach was applied to a collection of 112 isolates representing all 16 of the currently defined E. sakazakii biogroups. MLVA successfully discriminated among these isolates and compared favorably with pulsed-field gel electrophoresis. The method was relatively fast and easy to perform. The potential value of MLVA as an epidemiological tool is discussed.

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.

scholarly journals Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

2004 ◽  
Vol 186 (16) ◽  
pp. 5496-5505 ◽  
Author(s):  
Leo M. Schouls ◽  
Han G. J. van der Heide ◽  
Luc Vauterin ◽  
Paul Vauterin ◽  
Frits R. Mooi
Keyword(s):  
The Netherlands ◽  
Tandem Repeat ◽  
Bordetella Pertussis ◽  
Minimum Spanning Tree ◽  
Whooping Cough ◽  
Variable Number Tandem Repeat ◽  
Clonal Expansion ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis

ABSTRACT Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected.

scholarly journals Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

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