scholarly journals Ruminant Rhombencephalitis-Associated Listeria monocytogenes Alleles Linked to a Multilocus Variable-Number Tandem-Repeat Analysis Complex

2011 ◽  
Vol 77 (23) ◽  
pp. 8325-8335 ◽  
Author(s):  
Lina Balandyté ◽  
Isabelle Brodard ◽  
Joachim Frey ◽  
Anna Oevermann ◽  
Carlos Abril
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Genetic Relatedness ◽  
Clonal Complex ◽  
Variable Number Tandem Repeat ◽  
Virulence Gene ◽  
Variable Number ◽  
Content Type ◽  
Repeat Analysis ◽  
Cns Infections

ABSTRACTListeria monocytogenesis among the most important food-borne pathogens and is well adapted to persist in the environment. To gain insight into the genetic relatedness and potential virulence ofL. monocytogenesstrains causing central nervous system (CNS) infections, we used multilocus variable-number tandem-repeat analysis (MLVA) to subtype 183L. monocytogenesisolates, most from ruminant rhombencephalitis and some from human patients, food, and the environment. Allelic-profile-based comparisons groupedL. monocytogenesstrains mainly into three clonal complexes and linked single-locus variants (SLVs). Clonal complex A essentially consisted of isolates from human and ruminant brain samples. All but one rhombencephalitis isolate from cattle were located in clonal complex A. In contrast, food and environmental isolates mainly clustered into clonal complex C, and none was classified as clonal complex A. Isolates of the two main clonal complexes (A and C) obtained by MLVA were analyzed by PCR for the presence of 11 virulence-associated genes (prfA,actA,inlA,inlB,inlC,inlD,inlE,inlF,inlG,inlJ, andinlC2H). Virulence gene analysis revealed significant differences in theactA,inlF,inlG, andinlJallelic profiles between clinical isolates (complex A) and nonclinical isolates (complex C). The association of particular alleles ofactA,inlF, and newly described alleles ofinlJwith isolates from CNS infections (particularly rhombencephalitis) suggests that these virulence genes participate in neurovirulence ofL. monocytogenes. The overall absence ofinlGin clinical complex A and its presence in complex C isolates suggests that the InlG protein is more relevant for the survival ofL. monocytogenesin the environment.

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 Multilocus Variable-Number Tandem-Repeat Analysis ofYersinia ruckeriConfirms the Existence of Host Specificity, Geographic Endemism, and Anthropogenic Dissemination of Virulent Clones

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Snorre Gulla ◽  
Andrew C. Barnes ◽  
Timothy J. Welch ◽  
Jesús L. Romalde ◽  
David Ryder ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Tandem Repeat ◽  
Minimum Spanning Tree ◽  
Clonal Complex ◽  
Variable Number Tandem Repeat ◽  
Geographic Origin ◽  
Variable Number ◽  
Yersinia Ruckeri ◽  
Content Type ◽  
Repeat Analysis

ABSTRACTA multilocus variable-number tandem-repeat analysis (MLVA) assay was developed for epizootiological study of the internationally significant fish pathogenYersinia ruckeri, which causes yersiniosis in salmonids. The assay involves amplification of 10 variable-number tandem-repeat (VNTR) loci in two five-plex PCRs, followed by capillary electrophoresis. A collection of 484Y. ruckeriisolates, originating from various biological sources and collected from four continents over 7 decades, was analyzed. Minimum-spanning-tree cluster analysis of MLVA profiles separated the studied population into nine major clonal complexes and a number of minor clusters and singletons. The major clonal complexes could be associated with host species, geographic origin, and serotype. A single large clonal complex of serotype O1 isolates dominating the yersiniosis situation in international rainbow trout farming suggests anthropogenic spread of this clone, possibly related to transport of fish. Moreover, subclustering within this clonal complex indicates putative transmission routes and multiple biotype shift events. In contrast to the situation in rainbow trout,Y. ruckeristrains associated with disease in Atlantic salmon appear as more or less geographically isolated clonal complexes. A single complex of serotype O1 exclusive to Norway was found to be responsible for almost all major yersiniosis outbreaks in modern Norwegian salmon farming, and site-specific subclustering further indicates persistent colonization of freshwater farms in Norway. Identification of genetically diverseY. ruckeriisolates from clinically healthy fish and environmental sources also suggests the widespread existence of less-virulent or avirulent strains.IMPORTANCEThis comprehensive population study substantially improves our understanding of the epizootiological history and nature of an internationally important fish-pathogenic bacterium. The MLVA assay developed and presented represents a high-resolution typing tool particularly well suited forYersinia ruckeriinfection tracing, selection of strains for vaccine inclusion, and risk assessment. The ability of the assay to separate isolates into geographically linked and/or possibly host-specific clusters reflects its potential utility for maintenance of national biosecurity. The MLVA is internationally applicable and robust, and it provides clear, unambiguous, and easily interpreted results. Typing is reasonably inexpensive, with a moderate technological requirement, and may be completed from a harvested colony within a single working day. As the resulting MLVA profiles are readily portable, anyY. ruckeristrain may rapidly be placed in a global epizootiological context.

An Optimized Multilocus Variable-Number Tandem Repeat Analysis Typing Scheme for Listeria monocytogenes from Three Western Provinces in China

2018 ◽  
Vol 81 (12) ◽  
pp. 1956-1962
Author(s):  
RENDONG FANG ◽  
BING JIANG ◽  
JIANHUA XIE ◽  
ZICHUN WANG ◽  
WANGWANG LIANG ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Multilocus Sequence Typing ◽  
Variable Number Tandem Repeat ◽  
Foodborne Pathogen ◽  
Variable Number ◽  
Western China ◽  
Typing Scheme ◽  
Repeat Analysis ◽  
Outbreak Investigations

ABSTRACT Listeria monocytogenes is a foodborne pathogen worldwide. Multilocus variable-number tandem repeat analysis (MLVA) has been used for listeriosis surveillance and outbreak investigations. MLVA typing schemes have been proposed, but their usefulness for typing isolates from the People's Republic of China has not been assessed. To this aim, all L. monocytogenes strains (79) isolated from 1,445 raw meat and abattoir environmental samples of three western provinces in China were characterized with PCR serogrouping, multilocus sequence typing, and MLVA. The isolates were typed into the four PCR serogroups IIb (38.0%), IIc (26.6%), IIa (24.0%), and IVb (11.4%), with a Simpson's index (SI) of 0.7235. With multilocus sequence typing, they were typed into 18 sequence types (STs), including two new STs, ST1029 and ST1011, with an SI of 0.8880. With the 14 MLVA loci from the previous five schemes, the isolates were typed into 39 MLVA genotypes, with an SI of 0.9656. The typing data indicated that MLVA had the highest typing capability among the three methods. A subsequent optimization analysis identified an optimal combination of eight loci (LMV2, LMV9, LMV1, Lm10, Lm11, Lm15, Lm23, and LMTR6) producing the same SI as that of the 14 loci. The present optimized combination shared only six loci with the optimal nine-loci combination proposed in Australia, verifying for the first time that the optimal combinations varied with the isolates' sets. The current optimal typing scheme was ideal for L. monocytogenes isolates from western China.

scholarly journals Development of a Multiple-Locus Variable-Number Tandem-Repeat Typing Scheme for Genetic Fingerprinting of Burkholderia cenocepacia and Application to Nationwide Epidemiological Analysis

2014 ◽  
Vol 53 (2) ◽  
pp. 398-409 ◽  
Author(s):  
Christine Segonds ◽  
Michelle Thouverez ◽  
Antoine Barthe ◽  
Nadège Bossuet-Greif ◽  
Lenka Tisseyre ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Burkholderia Cepacia ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Cost Effective ◽  
Variable Number ◽  
Discriminatory Power ◽  
Burkholderia Cenocepacia ◽  
Content Type ◽  
Burkholderia Multivorans

Organisms of theBurkholderia cepaciacomplex are especially important pathogens in cystic fibrosis (CF), with a propensity for patient-to-patient spread and long-term respiratory colonization.B. cenocepaciaandBurkholderia multivoransaccount for the majority of infections in CF, and major epidemic clones have been recognized throughout the world. The aim of the present study was to develop and evaluate a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme forB. cenocepacia. Potential VNTR loci were identified upon analysis of the annotated genome sequences ofB. cenocepaciastrains AU1054, J2315, and MCO-3, and 10 of them were selected on the basis of polymorphisms and size. A collection of 100B. cenocepaciastrains, including epidemiologically related and unrelated strains, as well as representatives of the major epidemic lineages, was used to evaluate typeability, epidemiological concordance, and the discriminatory power of MLVA-10 compared with those of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Longitudinal stability was assessed by testing 39 successive isolates from 14 patients. Typeability ranged from 0.91 to 1, except for that of one marker, which was not amplified in 53% of theB. cenocepaciaIIIA strains. The MLVA types were shown to be stable in chronically colonized patients and within outbreak-related strains, with excellent epidemiological concordance. Epidemic and/or globally distributed lineages (epidemic Edinburgh-Toronto electrophoretic type 12 [ET-12], sequence type 32 [ST-32], ST-122, ST-234, and ST-241) were successfully identified. Conversely, the discriminatory power of MLVA was lower than that of PFGE or MLST, although PFGE variations within the epidemic lineages sometimes masked their genetic relatedness. In conclusion, MLVA represents a promising cost-effective first-line tool inB. cenocepaciasurveillance.

A multiple-locus variable-number tandem repeat analysis (MLVA) ofListeria monocytogenesisolated from Norwegian salmon-processing factories and from listeriosis patients

2012 ◽  
Vol 141 (10) ◽  
pp. 2101-2110 ◽  
Author(s):  
B. T. LUNESTAD ◽  
T. T. T. TRUONG ◽  
B.-A. LINDSTEDT
Keyword(s):  
Listeria Monocytogenes ◽  
Salmo Salar ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis ◽  
Great Heterogeneity ◽  
Sporadic Cases ◽  
Farmed Atlantic Salmon

SUMMARYThe objective of this study was to characterizeListeria monocytogenesisolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65L. monocytogenesisolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients.L. monocytogeneswith this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

scholarly journals New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

2014 ◽  
Vol 81 (2) ◽  
pp. 688-698 ◽  
Author(s):  
L. Poulin ◽  
P. Grygiel ◽  
M. Magne ◽  
L. Gagnevin ◽  
L. M. Rodriguez-R ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Leaf Blight ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Blight ◽  
Bacterial Leaf Streak ◽  
Content Type ◽  
Genetic Lineages ◽  
Repeat Analysis

ABSTRACTMultilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars ofXanthomonas oryzaecan cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused byX. oryzaepv. oryzicola, and bacterial leaf blight is caused byX. oryzaepv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the threeX. oryzaegenetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the threeX. oryzaelineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains ofX. oryzaerepresenting different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56X. oryzaestrains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.

scholarly journals Multilocus Variable-Number Tandem-Repeat Analysis of Clostridioides difficile Clusters in Ribotype 027 Isolates and Lack of Association with Clinical Outcomes

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Julian R. Garneau ◽  
Claire Nour Abou Chakra ◽  
Louis-Charles Fortier ◽  
Annie-Claude Labbé ◽  
Andrew E. Simor ◽  
...  
Keyword(s):  
Clinical Outcomes ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Content Type ◽  
Repeat Analysis ◽  
Ribotype 027 ◽  
Clostridioides Difficile ◽  
Significant Difference ◽  
Pcr Ribotyping

ABSTRACT The epidemiology of Clostridioides difficile infection (CDI) has drastically changed since the emergence of the epidemic strain BI/NAP1/027, also known as ribotype 027 (R027). However, the relationship between the infecting C. difficile strain and clinical outcomes is still debated. We hypothesized that certain subpopulations of R027 isolates could be associated with unfavorable outcomes. We applied high-resolution multilocus variable-number tandem-repeat analysis (MLVA) to characterize C. difficile R027 isolates collected from confirmed CDI patients recruited across 10 Canadian hospitals from 2005 to 2008. PCR ribotyping was performed first to select R027 isolates that were then analyzed by MLVA (n = 450). Complicated CDI (cCDI) was defined by the occurrence of any of admission to an intensive care unit, colonic perforation, toxic megacolon, colectomy, and if CDI was the cause or contributed to death within 30 days after enrollment. Three major MLVA clusters were identified, MC-1, MC-3, and MC-10. MC-1 and MC-3 were exclusive to Quebec centers, while MC-10 was found only in Ontario. Fewer cases infected with MC-1 developed cCDI (4%) than those infected with MC-3 and MC-10 (15% and 16%, respectively), but a statistically significant difference was not reached. Our data did not identify a clear association between subpopulations of R027 and different clinical outcomes; however, the data confirmed the utility of MLVA’s higher discrimination potential to better characterize CDI populations in an epidemiological analysis. For a patient with CDI, the progression toward an unfavorable outcome is a complex process that probably includes several interrelated strain and host characteristics.

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