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.

scholarly journals Can 15-Locus Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis Provide Insight into the Evolution of Mycobacterium tuberculosis?

2005 ◽  
Vol 71 (12) ◽  
pp. 8207-8213 ◽  
Author(s):  
Andrea Gibson ◽  
Timothy Brown ◽  
Lucy Baker ◽  
Francis Drobniewski
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Molecular Techniques ◽  
Nucleotide Polymorphisms ◽  
East African ◽  
Phylogeny And Evolution ◽  
Phylogenetic Lineages

ABSTRACT The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

scholarly journals Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 75 ◽  
Author(s):  
Olha Konstantynovska ◽  
Mariia Rekrotchuk ◽  
Ivan Hrek ◽  
Anton Rohozhyn ◽  
Nataliia Rudova ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Outcomes ◽  
Tandem Repeats ◽  
Genotypic Variation ◽  
Variable Number Tandem Repeat ◽  
Severe Infection ◽  
Variable Number ◽  
Beijing Genotype ◽  
Multiple Drug ◽  
Public Health Response

Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.

Mycobacterium tuberculosis Diversity by Exact Tandem Repeats-Variable Number Tandem Repeat Method in Azerbaijan, Iran

2018 ◽  
Vol 26 (2) ◽  
pp. 80-83
Author(s):  
Mostafa Danandeh ◽  
Seyed Reza Moadab ◽  
Mohammad Asgharzadeh ◽  
Naser Alizadeh ◽  
Reza Ghotaslou
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Variable Number

scholarly journals Mycobacterium tuberculosis Lineage 7 Strains Are Associated with Prolonged Patient Delay in Seeking Treatment for Pulmonary Tuberculosis in Amhara Region, Ethiopia

2015 ◽  
Vol 53 (4) ◽  
pp. 1301-1309 ◽  
Author(s):  
Solomon A. Yimer ◽  
Gunnstein Norheim ◽  
Amine Namouchi ◽  
Ephrem D. Zegeye ◽  
Wibeke Kinander ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Variable Number Tandem Repeat ◽  
Bioinformatic Analysis ◽  
Variable Number ◽  
Patient Delay ◽  
Contact Tracing ◽  
Amhara Region ◽  
Study Region ◽  
Content Type ◽  
Delay In Seeking Treatment

Recent genotyping studies ofMycobacterium tuberculosisin Ethiopia have reported the identification of a new phylogenetically distinctM. tuberculosislineage, lineage 7. We therefore investigated the genetic diversity and association of specificM. tuberculosislineages with sociodemographic and clinical parameters among pulmonary TB patients in the Amhara Region, Ethiopia. DNA was isolated fromM. tuberculosis-positive sputum specimens (n= 240) and analyzed by PCR and 24-locus mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR) analysis and spoligotyping. Bioinformatic analysis assigned theM. tuberculosisgenotypes to global lineages, and associations between patient characteristics and genotype were evaluated using logistic regression analysis. The study revealed a high diversity of modern and premodernM. tuberculosislineages, among which approximately 25% were not previously reported. Among theM. tuberculosisstrains (n= 138) assigned to seven subgroups, the largest cluster belonged to the lineage Central Asian (CAS) (n= 60; 26.0%), the second largest to lineage 7 (n= 36; 15.6%), and the third largest to the lineage Haarlem (n= 35; 15.2%). Four sublineages were new in the MIRU-VNTRplus database, designated NW-ETH3, NW-ETH1, NW-ETH2, and NW-ETH4, which included 24 (10.4%), 18 (7.8%), 8 (3.5%), and 5 (2.2%) isolates, respectively. Notably, patient delay in seeking treatment was significantly longer among patients infected with lineage 7 strains (Mann-Whitney test,P< 0.008) than in patients infected with CAS strains (adjusted odds ratio [AOR], 4.7; 95% confidence interval [CI], 1.6 to 13.5). Lineage 7 strains also grew more slowly than otherM. tuberculosisstrains. Cases of Haarlem (OR, 2.8; 95% CI, 1.2 to 6.6) and NW-ETH3 (OR, 2.8; 95% CI, 1.0 to 7.3) infection appeared in defined clusters. Intensified active case finding and contact tracing activities in the study region are needed to expedite diagnosis and treatment of TB.

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 Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tsung-Yu Lu ◽  
Katherine M. Munson ◽  
Alexandra P. Lewis ◽  
Qihui Zhu ◽  
Luke J. Tallon ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Traditional Approach ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Population Diversity ◽  
Protein Coding ◽  
Short Reads ◽  
Repeat Structure ◽  
Continental Population ◽  
Develop Software

AbstractVariable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

Convenient PCR method for variable-number tandem-repeat typing of Mycobacterium tuberculosis clinical isolates

2017 ◽  
Vol 139 ◽  
pp. 12-14 ◽  
Author(s):  
Junji Seto ◽  
Takayuki Wada ◽  
Yu Suzuki ◽  
Tatsuya Ikeda ◽  
Katsumi Mizuta ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Clinical Isolates ◽  
Pcr Method

scholarly journals Comparison of Multilocus Variable-Number Tandem-Repeat Analysis with Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis for Enterococcus faecalis

2011 ◽  
Vol 60 (4) ◽  
pp. 335-339 ◽  
Author(s):  
EWA SADOWY ◽  
ALEKSANDRA SIEŃKO ◽  
WALERIA HRYNIEWICZ
Keyword(s):  
Enterococcus Faecalis ◽  
Gel Electrophoresis ◽  
Tandem Repeats ◽  
Diversity Index ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Pulsed Field Gel Electrophoresis ◽  
Discriminatory Power ◽  
Pulsed Field ◽  
High Discriminatory Power

Enterococcus faecalis represents recently an important etiological agent of health care-associated infections (HAIs) and there is a need for evaluation and comparison of typing methods available for this microorganism. We tested multilocus VNTR (variable-number tandem repeats) analysis (MLVA) on a well-characterized collection of 153 clinical isolates of E. faecalis, corresponding to 52 multilocus sequence types and 67 pulsed-field gel electrophoresis (PFGE) profiles. MLVA showed high discriminatory power, discerning 111 different types (diversity index equal 98.9%). The concordance MLVA/MLST and MLVA/PFGE was 0.95 and 0.74, respectively. High discriminatory power of MLVA indicates its utility for local epidemiology such as outbreak investigation, and for differentiation of clones defined by other methods.

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