scholarly journals Hypervariable loci that enhance the discriminatory ability of newly proposed 15-loci and 24-loci variable-number tandem repeat typing method onMycobacterium tuberculosisstrains predominated by the Beijing family

2007 ◽  
Vol 270 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Tomotada Iwamoto ◽  
Shiomi Yoshida ◽  
Katsuhiro Suzuki ◽  
Motohisa Tomita ◽  
Riyo Fujiyama ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Beijing Family ◽  
Typing Method ◽  
Discriminatory Ability ◽  
Hypervariable Loci

scholarly journals Prediction of Local Transmission of Mycobacterium tuberculosis Isolates of a Predominantly Beijing Lineage by Use of a Variable-Number Tandem-Repeat Typing Method Incorporating a Consensus Set of Hypervariable Loci

2017 ◽  
Vol 56 (1) ◽  
Author(s):  
Yoshiro Murase ◽  
Kiyohiko Izumi ◽  
Akihiro Ohkado ◽  
Akio Aono ◽  
Kinuyo Chikamatsu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Trend Test ◽  
Typing Method ◽  
Content Type ◽  
Tuberculosis Transmission ◽  
High Prevalence ◽  
Hypervariable Loci

ABSTRACT Strain genotyping based on the variable-number tandem repeat (VNTR) is widely applied for identifying the transmission of Mycobacterium tuberculosis. A consensus set of four hypervariable loci (1982, 3232, 3820, and 4120) has been proposed to improve the discrimination of Beijing lineage strains. Herein, we evaluated the utility of these four hypervariable loci for tracing local tuberculosis transmission in 981 cases over a 14-month period in Japan (2010 to 2011). We used six different VNTR systems, with or without the four hypervariable loci. Patient ages and weighted standard distances (a measure of the dispersion of genotype-clustered cases) were used as proxies for estimating local tuberculosis transmission. The highest levels of isolate discrimination were achieved with VNTR systems that incorporated the four hypervariable loci (i.e., the Japan Anti-Tuberculosis Association [JATA]18-VNTR, mycobacterial interspersed repetitive unit [MIRU]28-VNTR, and 24Beijing-VNTR). The clustering rates by JATA12-VNTR, MIRU15-VNTR, JATA15-VNTR, JATA18-VNTR, MIRU28-VNTR, and 24Beijing-VNTR systems were 52.2%, 51.0%, 39.0%, 24.1%, 23.1%, and 22.0%, respectively. As the discriminative power increased, the median weighted standard distances of the clusters tended to decrease (from 311 to 80 km, P < 0.001, Jonckheere-Terpstra trend test). Concurrently, the median ages of patients in the clusters tended to decrease (from 68 to 60 years, P < 0.001, Jonckheere-Terpstra trend test). These findings suggest that strain typing using the four hypervariable loci improves the prediction of active local tuberculosis transmission. The four-locus set can therefore contribute to the targeted control of tuberculosis in settings with high prevalence of Beijing lineage strains.

scholarly journals Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015

2017 ◽  
Vol 22 (9) ◽  
Author(s):  
Tansy Peters ◽  
Sophie Bertrand ◽  
Jonas T Björkman ◽  
Lin T Brandal ◽  
Derek J Brown ◽  
...  
Keyword(s):  
North America ◽  
Tandem Repeat ◽  
Validation Study ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
European Economic Area ◽  
The European Union ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Typing Method ◽  
Repeat Analysis

Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S. Enteritidis targeting five loci. Following normalisation of fragment sizes using a set of reference strains, a blinded set of 24 strains with known allele sizes was analysed by each participant. The S. Enteritidis 5-loci MLVA protocol was shown to produce internationally comparable results as more than 90% of the participants reported less than 5% discrepant MLVA profiles. All 14 participating laboratories performed well, even those where experience with this typing method was limited. The raw fragment length data were consistent throughout, and the inter-laboratory validation helped to standardise the conversion of raw data to repeat numbers with at least two countries updating their internal procedures. However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data.

scholarly journals Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable ResistantMycobacterium tuberculosisComplex Isolates in the Netherlands from 2004 to 2016

2018 ◽  
Vol 56 (11) ◽  
Author(s):  
Inge Roof ◽  
Rana Jajou ◽  
Miranda Kamst ◽  
Arnout Mulder ◽  
Albert de Neeling ◽  
...  
Keyword(s):  
The Netherlands ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Multivariate Logistic Regression Analysis ◽  
Variable Number ◽  
Linkage Data ◽  
Nucleotide Polymorphisms ◽  
Typing Method ◽  
Content Type ◽  
Heterogeneous Clustering

ABSTRACTThe variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering ofMycobacterium tuberculosisisolates with identical VNTR patterns is assumed to reflect recent transmission. Hence, clusters are thought to be homogeneous regarding antibiotic resistance. In practice, however, heterogeneous clusters are also identified. This study investigates the prevalence and characteristics of heterogeneous VNTR clusters and assesses whether isolates in these clusters remain clustered when subjected to whole-genome sequencing (WGS). In the period from 2004 to 2016, 9,072 isolates were included. Demographic and epidemiological linkage data were obtained from the Netherlands Tuberculosis Register. VNTR clusters were defined as homogeneous when isolates shared identical resistance profiles or as heterogeneous if both susceptible and (variable) resistant isolates were found. Multivariate logistic regression analysis was performed to identify factors associated with heterogeneous clustering. Isolates from 2016 were subjected to WGS, and a genetic distance of 12 single nucleotide polymorphisms (SNPs) was used as the cutoff for WGS clustering. In total, 4,661/9,072 (51%) isolates were clustered into 985 different VNTR clusters, of which 217 (22%) were heterogeneous. Patient characteristics associated with heterogeneous clustering were non-Dutch ethnicity (odds ratio [OR], 1.46 [95% confidence interval {CI}, 1.22 to 1.75]), asylum seeker (OR, 1.51 [95% CI, 1.24 to 1.85]), extrapulmonary TB (OR, 1.26 [95% CI, 1.09 to 1.46]), previous TB diagnosis (OR, 1.38 [95% CI, 1.04 to 1.82]), and not being a contact of a TB patient (OR, 1.35 [95% CI, 1.08 to 1.69]). With WGS, 34% of heterogeneous and 78% of homogeneous isolates from 2016 remained clustered. Heterogeneous VNTR clusters are common but seem to be explained by a substantial degree of false clustering by VNTR typing compared to WGS.

scholarly journals Subtyping of a Large Collection of Historical Listeria monocytogenes Strains from Ontario, Canada, by an Improved Multilocus Variable-Number Tandem-Repeat Analysis (MLVA)

2013 ◽  
Vol 79 (20) ◽  
pp. 6472-6480 ◽  
Author(s):  
S. Saleh-Lakha ◽  
V. G. Allen ◽  
J. Li ◽  
F. Pagotto ◽  
J. Odumeru ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Food Chain ◽  
Diversity Index ◽  
Variable Number Tandem Repeat ◽  
Diversity Indices ◽  
Variable Number ◽  
Typing Method ◽  
Content Type ◽  
Repeat Analysis

ABSTRACTListeria monocytogenesis responsible for severe and often fatal food-borne infections in humans. A collection of 2,421L. monocytogenesisolates originating from Ontario's food chain between 1993 and 2010, along with Ontario clinical isolates collected from 2004 to 2010, was characterized using an improved multilocus variable-number tandem-repeat analysis (MLVA). The MLVA method was established based on eight primer pairs targeting seven variable-number tandem-repeat (VNTR) loci in two 4-plex fluorescent PCRs. Diversity indices and amplification rates of the individual VNTR loci ranged from 0.38 to 0.92 and from 0.64 to 0.99, respectively. MLVA types and pulsed-field gel electrophoresis (PFGE) patterns were compared using Comparative Partitions analysis involving 336 clinical and 99 food and environmental isolates. The analysis yielded Simpson's diversity index values of 0.998 and 0.992 for MLVA and PFGE, respectively, and adjusted Wallace coefficients of 0.318 when MLVA was used as a primary subtyping method and 0.088 when PFGE was a primary typing method. Statistical data analysis using BioNumerics allowed for identification of at least 8 predominant and persistentL. monocytogenesMLVA types in Ontario's food chain. The MLVA method correctly clustered epidemiologically related outbreak strains and separated unrelated strains in a subset analysis. An MLVA database was established for the 2,421L. monocytogenesisolates, which allows for comparison of data among historical and new isolates of different sources. The subtyping method coupled with the MLVA database will help in effective monitoring/prevention approaches to identify environmental contamination by pathogenic strains ofL. monocytogenesand investigation of outbreaks.

scholarly journals Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

2015 ◽  
Vol 81 (16) ◽  
pp. 5318-5325 ◽  
Author(s):  
Punnida Techaruvichit ◽  
Hajime Takahashi ◽  
Mongkol Vesaratchavest ◽  
Suwimon Keeratipibul ◽  
Takashi Kuda ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Campylobacter Jejuni ◽  
Tandem Repeat ◽  
Diversity Index ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Chicken Meat ◽  
Typing Method ◽  
Content Type ◽  
Multiple Locus

ABSTRACTCampylobacter jejuniis a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation ofC. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring ofC. jejuniand investigation of epidemics caused byC. jejuni.

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