Allelic diversity of variable number of tandem repeats provides phylogenetic clues regarding the Mycobacterium tuberculosis Beijing family

2009 ◽  
Vol 9 (5) ◽  
pp. 921-926 ◽  
Author(s):  
Takayuki Wada ◽  
Tomotada Iwamoto
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Allelic Diversity ◽  
Variable Number ◽  
Beijing Family

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 Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Anna Engström ◽  
Uladzimir Antonenka ◽  
Abdylat Kadyrov ◽  
Gulmira Kalmambetova ◽  
Katharina Kranzer ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Population Structure ◽  
Central Asia ◽  
Tandem Repeats ◽  
Relative Size ◽  
Multidrug Resistant ◽  
Variable Number ◽  
Health Concern ◽  
Drug Resistant ◽  
Recent Emergence

Abstract Background Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. Methods The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. Results The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. Conclusions Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.

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.

Molecular epidemiology of Mycobacterium tuberculosis in adult Filipino TB-HIV co-infected patients

2021 ◽  
Vol 25 (4) ◽  
pp. 285-291
Author(s):  
J. C. M. Malabad ◽  
C. F. Ang ◽  
F. A. R. Palabrica ◽  
M. A. M. Cajucom ◽  
N. G. Gloriani ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Molecular Epidemiology ◽  
Disease Transmission ◽  
Tandem Repeats ◽  
The Philippines ◽  
Variable Number ◽  
People Living With Hiv ◽  
East African ◽  
Living With Hiv

BACKGROUND: TB is the leading cause of death from a single infectious disease, particularly among people living with HIV (PLHIV). Molecular epidemiology provides information on prevalent genotypes of Mycobacterium tuberculosis and disease transmission dynamics, which aid in TB control. Identification of mutations that confer drug resistance is essential for the rapid diagnosis of drug-resistant TB, especially in high TB burden settings, like the Philippines.METHODS: This study aimed to determine mutations in M. tuberculosis drug resistance-conferring genes and circulating genotypes in PLHIV. MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem repeats) typing using a set of 24-loci and sequencing of drug resistance-conferring genes were performed in 22 M. tuberculosis isolates from TB-HIV co-infected patients.RESULTS: The prevalence of resistance to any drug was 31.8%, 18.2% for isoniazid monoresistance, 4.5% for streptomycin monoresistance and 9.1% for multidrug resistance. The identified mutations in the katG, rpoB, pncA, rpsL and gyrA genes have been reported in the literature; none was found in the inhA and embB genes. All isolates belonged to the EAI2-Manila family and were grouped into four clusters based on their phenotypic drug resistance and mutation profiles.CONCLUSION: The use of 24-loci set may be used as a more discriminatory MIRU-VNTR typing in settings where the East African-Indian lineage is predominant, like the Philippines.

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.

Variable-number tandem repeats typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 in Thailand

Tuberculosis ◽  
2010 ◽  
Vol 90 (1) ◽  
pp. 9-15 ◽  
Author(s):  
Arunee Thong-On ◽  
Nat Smittipat ◽  
Tada Juthayothin ◽  
Hideki Yanai ◽  
Norio Yamada ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Copy Numbers ◽  
Variable Number Tandem Repeats

scholarly journals Polymorphism of Variable-Number Tandem Repeats at Multiple Loci in Mycobacterium tuberculosis

2005 ◽  
Vol 43 (10) ◽  
pp. 5034-5043 ◽  
Author(s):  
N. Smittipat ◽  
P. Billamas ◽  
M. Palittapongarnpim ◽  
A. Thong-On ◽  
M. M. Temu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Loci ◽  
Variable Number Tandem Repeats

scholarly journals Pulmonary Tuberculosis Outbreak in a High School, China

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
◽  
Yang Zhou ◽  
Bing Zhao ◽  
Tao Li ◽  
Qian Cheng ◽  
...  
Keyword(s):  
High School ◽  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Skin Testing ◽  
Drug Susceptibility ◽  
Variable Number ◽  
Hunan Province ◽  
Tuberculin Skin Testing ◽  
Nucleotide Polymorphisms ◽  
Symptom Screening

This study reports an outbreak of Tuberculosis (TB) in a high school in Hunan province, China during January 2017-April 2018. Contact investigation and TB screening were conducted through symptom screening, tuberculin skin testing, chest radiography and smear examination. Identification of positive isolates and drug susceptibility phenotype were assessed by standard method. Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) and Whole Genome Sequencing (WGS) were performed to investigate the relationships among the positive isolates. A total of 90 students and one teacher were diagnosed active pulmonary TB among 2908 students and 188 staff, with an attack rate of 2.94%. Thirteen positive isolates were identified as drug susceptible Beijing family of Mycobacterium tuberculosis. Results of MIRU-VNTR typing and WGS revealed two clones of Mycobacterium tuberculosis circulating during outbreak. One hundred and twenty-nine Single Nucleotide Polymorphisms (SNPs) discriminated the isolates in two clusters; the maximum number of SNPs between any pair of isolates in each cluster was five or fewer. Our findings highlight the importance of early identification and isolation of the TB cases to prevent spread of TB. WGS provides better resolution than MIRU-VNTR to identify recent transmission in TB outbreak.

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