Molecular Epidemiology of Xanthomonas euvesicatoria Strains from the Balkan Peninsula Revealed by a New Multiple-Locus Variable-Number Tandem-Repeat Analysis Scheme

Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.

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Genotyping North American Animal Mycobacterium Bovis Isolates Using Multilocus Variable Number Tandem Repeat Analysis

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870802000601 ◽

2008 ◽

Vol 20 (6) ◽

pp. 707-715 ◽

Cited By ~ 13

Author(s):

Lorene R. Martinez ◽

Beth Harris ◽

William C. Black ◽

Robert M. Meyer ◽

Patrick J. Brennan ◽

...

Keyword(s):

North America ◽

Mycobacterium Bovis ◽

Tandem Repeat ◽

North American ◽

Variable Number Tandem Repeat ◽

Epidemiological Data ◽

Variable Number ◽

Repeat Analysis ◽

Trace Back ◽

Animal Isolates

Multilocus variable number tandem repeat analysis (MLVA) has recently emerged as a genotyping method that is both robust and highly discriminatory for the differentiation of Mycobacterium tuberculosis complex (MTBC) strains, including Mycobacterium bovis. However, MLVA assessment of M. bovis isolates recovered from animals in North America has been limited. Using an epidemiologically diverse set of 41 North American M. bovis animal isolates, MLVA, based on 27 published variable number tandem repeat (VNTR) loci, was evaluated. Nineteen loci displayed polymorphism, which resulted in differentiation of 21 unique MLVA genotypes. A subset of 6 loci differentiated the isolates into 14 genetically related groups that displayed remarkable concordance with the epidemiological data gathered via traditional trace-back methods. In most cases, MLVA exhibited greater resolution than spoligotyping, which differentiated the isolates into 11 groups. MLVA genotyping of M. bovis shows great potential as a molecular typing tool for characterizing the epidemiology of M. bovis animal infections in North America. However, the greatest resolution was achieved by using a combination of both MLVA and spoligotyping.

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Multiple-Locus Variable-Number Tandem Repeat Analysis Scheme for Non-O157 Shiga Toxin-Producing Escherichia coli: Focus on Serogroups O103, O121, O145, O165, and O91

Japanese Journal of Infectious Diseases ◽

10.7883/yoken.jjid.2020.095 ◽

2020 ◽

Vol 73 (6) ◽

pp. 481-490 ◽

Cited By ~ 1

Author(s):

Hidemasa Izumiya ◽

Kenichi Lee ◽

Nozomi Ishijima ◽

Sunao Iyoda ◽

Makoto Ohnishi

Keyword(s):

Escherichia Coli ◽

Tandem Repeat ◽

Shiga Toxin ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Multiple Locus ◽

Repeat Analysis ◽

Analysis Scheme

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Application of Variable-Number Tandem-Repeat Typing To Discriminate Ralstonia solanacearum Strains Associated with English Watercourses and Disease Outbreaks

Applied and Environmental Microbiology ◽

10.1128/aem.01219-13 ◽

2013 ◽

Vol 79 (19) ◽

pp. 6016-6022 ◽

Cited By ~ 20

Author(s):

Neil Parkinson ◽

Ruth Bryant ◽

Janice Bew ◽

Christine Conyers ◽

Robert Stones ◽

...

Keyword(s):

River Water ◽

Tandem Repeat ◽

Ralstonia Solanacearum ◽

Tandem Repeats ◽

Variable Number Tandem Repeat ◽

Disease Outbreaks ◽

Variable Number ◽

Content Type ◽

Clonal Type ◽

The United Kingdom

ABSTRACTVariable-number tandem-repeat (VNTR) analysis was used for high-resolution discrimination amongRalstonia solanacearumphylotype IIB sequevar 1 (PIIB-1) isolates and further evaluated for use in source tracing. Five tandem-repeat-containing loci (comprising six tandem repeats) discriminated 17 different VNTR profiles among 75 isolates from potato, geranium, bittersweet (Solanum dulcamara), tomato, and the environment.R. solanacearumisolates from crops at three unrelated outbreak sites where river water had been used for irrigation had distinct VNTR profiles that were shared with PIIB-1 isolates from infected bittersweet growing upriver of each site. The VNTR profiling results supported the implication that the source ofR. solanacearumat each outbreak was contaminated river water. Analysis of 51 isolates from bittersweet growing in river water at different locations provided a means to evaluate the technique for studying the epidemiology of the pathogen in the environment. Ten different VNTR profiles were identified among bittersweet PIIB-1 isolates from the River Thames. Repeated findings of contiguous river stretches that produced isolates that shared single VNTR profiles supported the hypothesis that the pathogen had disseminated from infected bittersweet plants located upriver. VNTR profiles shared between bittersweet isolates from two widely separated Thames tributaries (River Ray and River Colne) suggested they were independently contaminated with the same clonal type. Some bittersweet isolates had VNTR profiles that were shared with potato isolates collected outside the United Kingdom. It was concluded that VNTR profiling could contribute to further understanding ofR. solanacearumepidemiology and assist in control of future disease outbreaks.

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

Infectious Diseases in Clinical Practice ◽

10.1097/ipc.0000000000000561 ◽

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

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Genotyping of pathogenic leptospira by Multiple Locus Variable-number Tandem Repeat Analysis (MLVA)

Online Journal of Public Health Informatics ◽

10.5210/ojphi.v10i1.8902 ◽

2018 ◽

Vol 10 (1) ◽

Author(s):

Vitalii Ukovskyi ◽

Taras Tsarenko ◽

Nataliia Vydayko ◽

Leonid Korniienko ◽

Igor Nebogatkin

Keyword(s):

Tandem Repeat ◽

Tandem Repeats ◽

Reference Strain ◽

Field Isolate ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Pathogenic Leptospira ◽

Molecular Genotyping ◽

Repeat Analysis ◽

Multispacer Sequence Typing

ObjectiveTo introduce the method of molecular genotyping (MLVA) to determine the genotype of field isolates of leptospira.IntroductionLeptospirosis (ictherohemoglobinuria, Leptospirosis biliousness) is a natural focal and zoonotic infectious disease dangerous for humans and farm animals. It is important to identify specific leptospira strains isolated from rodents or sick and suspicious animals by the serotype or genotype. In comparison with serotyping using micro agglutination test (MAT), molecular genotyping makes it possible to accurately identify a specific pathogen strain. The genetic classification now becomes more significant than the phenotypic classification.MethodsSpecific oligonucleotide primers, which flank fragments of the genome locus of pathogenic leptospira varies in terms of the number of tandem repeats VNTR-4, -7, -10 specific for L.interrogans, L.kirschneri, and L.borgpetersenii were used. The amplification products were detected using agar gel electrophoresis with the following identification of the fragment length with a molecular weight marker and comparison with the collection of VNTR profiles of the strains described in the literature.ResultsIt was established that the method of leptospira molecular genotyping by determining the number of variable tandem repeats of a locus (VNTR-variable number tandem repeats analysis) is suitable for molecular epizootology studies in Ukraine. The advantages of the method are the simplicity of performance and availability for diagnostic and research laboratories in Ukraine compared to other pathogen genome sequencing based genotyping methods, in particular Multilocus sequence typing (MLST) or Multispacer Sequence Typing (MST), which require complex equipment and operating conditions. The reference strain of Leptospira M20 serotype Copengageni serogroup Icterohaemorrhagiae from the NAAS IVM collection of was studied and its VNTR profile was identified with the genotype of the strain Fiocruz L1-130 that is described in the literature as a serotype of Copengageni serogroup Icterohaemorrhagiae. The genotype of the leptospira field isolate obtained from a rat in Lviv Oblast of Ukraine was specified and its identity was established in the aforementioned genotype. The obtained data support the prospects of using MLVA genotyping method to study the distribution of different genotypes of leptospira. The research will continue to study the specificities of molecular epizootology of leptospirosis in Ukraine.ConclusionsThe method of leptospira molecular genotyping by multilocus analysis of the number of variable tandem repeats has been tested in the Leptospirosis Research Laboratory in collaboration with the Museum of Microorganisms at the National Academy of Sciences, the Ukraine Institute of Veterinary Medicine, the ELISA and PCR Research Laboratory, and the Bila Tserkva National Agrarian University. The genotype of the reference strain has been correlated with its serological profile; identification of the genotype of the field isolate pathogenic leptospira has been completed. The tested method is planned to be implemented in surveillance and control over leptospirosis spreading in Ukraine, and aimed to help in development and improvement of leptospirosis vaccine formulations. Additionally, method of Multiple-Locus Variable number tandem repeat Analysis will be used for molecular epidemiology research in Ukraine.ReferencesSalaün L, Mérien F, Gurianova S, Baranton G, Picardeau M. Application of multilocus variable-number tandem-repeat analysis for molecular typing of the agent of leptospirosis. J Clin Microbiol. 2006;44(11):3954-3962. doi:10.1128/JCM.00336-06.Caimi K, Repetto SA, Varni V, Ruybal P. Infection , Genetics and Evolution Leptospira species molecular epidemiology in the genomic era. Infect Genet Evol. 2017;54(July):478-485. doi:10.1016/j.meegid.2017.08.013.Ayral F, Zilber AL, Bicout DJ, Kodjo A, Artois M, Djelouadji Z. Distribution of leptospira interrogans by multispacer sequence typing in urban Norway rats (Rattus norvegicus): A survey in France in 2011-2013. PLoS One. 2015;10(10):1-14. doi:10.1371/journal.pone.0139604.

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Multilocus Variable Number of Tandem Repeat Analysis for molecular typing of uropathogenic Escherichia coli

10.21203/rs.3.rs-84882/v1 ◽

2020 ◽

Author(s):

Reza Ranjbar ◽

Farhad Safarpoor Dehkordi ◽

Morteza Mashhouri ◽

Omid Farahani

Keyword(s):

Escherichia Coli ◽

Tandem Repeat ◽

Tandem Repeats ◽

Genetic Relationships ◽

Variable Number Tandem Repeat ◽

Pcr Amplification ◽

Variable Number ◽

E Coli ◽

Repeat Analysis

Abstract Background: The aim of this study was genotyping of Uropathogenic Escherichia coli (UPEC) based on Variable Number of Tandem Repeats (VNTRs) sequences. Methods: E. coli strains isolated from urine samples were included in this study. Seven VNTR loci were subjected to Multilocus variable-number tandem repeat analysis (MLVA) based on PCR amplification. Then data was analyzed via online mlvaplus software and the information was displayed in the form of MST analysis. Results: A total of 100 E. coli strains were isolated and subjected to the study. MLVA was able to differentiate 56 different genotypes. Also, the technique could classify E. coli isolates in 5 clonal complexes. Based on UPGMA dendrograms, E. coli isolates were classified into 4 clusters (clusters A to D). The strains associated with Complex No. 1 appeared to be dominant pathogens of UPEC in Tehran's patients. The present study provides valuable insights into the genetic relationships of E. coli isolates recovered from clinical cases in a major hospital in Iran. Conclusions: The analysis of MLVA profiles using the MST algorithm showed the usefulness of the MLVA method in the classification of uropathogenic E. coli collected in different periods. We evaluated MLVA in a laboratory equipped with simple molecular equipment. Based on these results, it has been assumed that the E. coli strains were derived from a limited number of clones that have undergo a small genetic change during this period.

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Relatedness of Vibrio cholerae O1/O139 Isolates from Patients and Their Household Contacts, Determined by Multilocus Variable-Number Tandem-Repeat Analysis

Journal of Bacteriology ◽

10.1128/jb.00698-10 ◽

2010 ◽

Vol 192 (17) ◽

pp. 4367-4376 ◽

Cited By ~ 46

Author(s):

Emily A. Kendall ◽

Fahima Chowdhury ◽

Yasmin Begum ◽

Ashraful I. Khan ◽

Shan Li ◽

...

Keyword(s):

Vibrio Cholerae ◽

Tandem Repeat ◽

Tandem Repeats ◽

Genetic Relatedness ◽

Variable Number Tandem Repeat ◽

Index Patient ◽

Variable Number ◽

Repeat Analysis ◽

Household Contacts ◽

Vibrio Cholerae O1

ABSTRACT The genetic relatedness of Vibrio cholerae O1/O139 isolates obtained from 100 patients and 146 of their household contacts in Dhaka, Bangladesh, between 2002 and 2005 was assessed by multilocus variable-number tandem-repeat analysis. Isolate genotypes were analyzed at five loci containing tandem repeats. Across the population, as well as within households, isolates with identical genotypes were clustered in time. Isolates from individuals within the same household were more likely to have similar or identical genotypes than were isolates from different households, but even within a household, isolates from different individuals often had different genotypes. When household contacts were sampled regularly for 3 weeks after the illness of the household index patient, isolates with genotypes related to the index patient appeared in contacts, on average, ∼3 days after the index patient, while isolates with unrelated genotypes appeared in contacts ∼6 days after. Limited data revealed that multiple isolates from the same individual collected within days of each other or even from a single stool sample may have identical, similar, or unrelated genotypes as well. Our results demonstrate that genetically related V. cholerae strains cluster in local outbreaks but also suggest that multiple distinct strains of V. cholerae O1 may circulate simultaneously within a household.

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