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 Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands

2017 ◽  
Vol 56 (2) ◽  
Author(s):  
Rana Jajou ◽  
Miranda Kamst ◽  
Rianne van Hunen ◽  
Carolina Catherina de Zwaan ◽  
Arnout Mulder ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
The Netherlands ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Structural Basis ◽  
Nucleotide Polymorphisms ◽  
Bacterial Populations ◽  
Content Type ◽  
Source Case

ABSTRACTSince 2004, variable-number tandem-repeat (VNTR) typing ofMycobacterium tuberculosiscomplex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084;P= 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386;P= 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants.

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 A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing

2017 ◽  
Vol 56 (2) ◽  
Author(s):  
Rana Jajou ◽  
Albert de Neeling ◽  
Erik Michael Rasmussen ◽  
Anders Norman ◽  
Arnout Mulder ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
The Netherlands ◽  
Genetic Distance ◽  
Genome Sequencing ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Whole Genome ◽  
Average Genetic Distance ◽  
Content Type

ABSTRACT In many countries, Mycobacterium tuberculosis isolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigate M. tuberculosis transmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in those countries was unlikely. Whole-genome sequencing (WGS) was applied to analyze transmission in depth and to assess the precision of VNTR typing. WGS was applied to 40 M. tuberculosis isolates from refugees in the Netherlands and Denmark (most of whom were from the Horn of Africa) that shared the exact same VNTR profile. Cluster investigations were undertaken to identify in-country epidemiological links. Combining WGS results for the isolates (all members of the central Asian strain [CAS]/Delhi genotype), from both European countries, an average genetic distance of 80 single-nucleotide polymorphisms (SNPs) (maximum, 153 SNPs) was observed. The few pairs of isolates with confirmed epidemiological links, except for one pair, had a maximum distance of 12 SNPs. WGS divided this refugee cluster into several subclusters of patients from the same country of origin. Although the M. tuberculosis cases, mainly originating from African countries, shared the exact same VNTR profile, most were clearly distinguished by WGS. The average genetic distance in this specific VNTR cluster was 2 times greater than that in other VNTR clusters. Thus, identical VNTR profiles did not represent recent direct M. tuberculosis transmission for this group of patients. It appears that either these strains from Africa are extremely conserved genetically or there is ongoing transmission of this genotype among refugees on their long migration routes from Africa to Europe.

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.

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 Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System

2015 ◽  
Vol 81 (16) ◽  
pp. 5395-5410 ◽  
Author(s):  
Salwa Essakhi ◽  
Sophie Cesbron ◽  
Marion Fischer-Le Saux ◽  
Sophie Bonneau ◽  
Marie-Agnès Jacques ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Type Iii Secretion ◽  
Variable Number Tandem Repeat ◽  
Type Iii Secretion System ◽  
Variable Number ◽  
Secretion System ◽  
Content Type ◽  
Type Iii ◽  
Xanthomonas Arboricola ◽  
Canonical Type

ABSTRACTXanthomonas arboricolais conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed thatX. arboricolaalso encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess theX. arboricolapopulation structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100X. arboricolastrains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection ofX. arboricolastrains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containingXanthomonas arboricolapv. juglandis strains. Some nonpathogenic strains ofX. arboricoladid not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity inX. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity inX. arboricola.

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 Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak

2012 ◽  
Vol 78 (20) ◽  
pp. 7290-7298 ◽  
Author(s):  
Sonia M. Hernandez ◽  
Kevin Keel ◽  
Susan Sanchez ◽  
Eija Trees ◽  
Peter Gerner-Smidt ◽  
...  
Keyword(s):  
United States ◽  
Salmonella Enterica ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Pfge Type ◽  
Eastern United States ◽  
Typing Method ◽  
Content Type ◽  
Typhimurium Strain ◽  
Serovar Typhimurium

ABSTRACTSalmonella entericasubsp.entericaserovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. ThisSalmonellaserovar is also responsible for die-offs in songbird populations. In 2009, there was anS. Typhimurium epizootic reported in pine siskins in the eastern United States. At the time, there was also a human outbreak with this serovar that was associated with contaminated peanuts. As peanuts are also used in wild-bird food, it was hypothesized that the pine siskin epizootic was related to this human outbreak. A comparison of songbird and humanS. Typhimurium pulsed-field gel electrophoresis (PFGE) patterns revealed that the epizootic was attributed not to the peanut-associated strain but, rather, to a songbird strain first characterized from an American goldfinch in 1998. This sameS. Typhimurium strain (PFGE type A3) was also identified in the PulseNet USA database, accounting for 137 of 77,941 totalS. Typhimurium PFGE entries. A second molecular typing method, multiple-locus variable-number tandem-repeat analysis (MLVA), confirmed that the same strain was responsible for the pine siskin epizootic in the eastern United States but was distinct from a genetically related strain isolated from pine siskins in Minnesota. The pine siskin A3 strain was first encountered in May 2008 in an American goldfinch and later in a northern cardinal at the start of the pine siskin epizootic. MLVA also confirmed the clonal nature ofS. Typhimurium in songbirds and established that the pine siskin epizootic strain was unique to the finch family. For 2009, the distribution of PFGE type A3 in passerines and humans mirrored the highest population density of pine siskins for the East Coast.

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