Identification and Characterization of Variable-Number Tandem Repeats in the
            <i>Yersinia pestis</i>
            Genome

Klevytska, Alexandra M.; Price, Lance B.; Schupp, James M.; Worsham, Patricia L.; Wong, Jane D.; Keim, Paul

doi:10.1128/jcm.39.9.3179-3185.2001

Cited by 192 publications

(150 citation statements)

References 25 publications

(17 reference statements)

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“…MNR are the most abundant SSR in V. cholerae genome, in agreement with previous reports for E. coli and for Yersinia pestis (30,43). The frequency of SSR (with repeats Ͼ3 and MNR of Ͼ5 bp) in the V. cholerae genome is similar to that found in the pathogenic E. coli O157:H7 EDL933 (one SSR every ϳ150 bp).…”

Section: Discussionsupporting

confidence: 80%

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing method that combines the variation in highly mutable SSR loci, with that of shorter, relatively more stable mononucleotide repeat (MNR) loci, for accurate and rapid typing of V. cholerae. Vibrio cholerae, a gram-negative bacterium, is the causal agent of the severe diarrheal disease cholera. Its natural reservoir is the aquatic environment (49, 84). Cholera pandemics are caused by specific serogroups of V. cholerae that are pathogenic only to humans (35,84). Since 1817, V. cholerae has caused a number of pandemics. The first seven were presumed to be caused by O1 serogroup of V. cholerae (68). In October 1992, a new serogroup, defined O139, caused a severe outbreak of cholera in southeast India. Within 10 months, the O139 serogroup was disseminated all over the Indian subcontinent and soon thereafter spread to 11 neighboring countries, temporarily displacing the O1 serogroups (64). Since then both serogroups coexist and are responsible for large outbreaks. Genomic studies indicated that O139 epidemic strain arose by horizontal acquisition of unique DNA (15, 47).Traditionally, V. cholerae classification is serological and requires about 200 antisera based on the somatic O antigen (72). Isolates of V. cholerae are divided into three major subgroups: O1, O139, and non-O1/non-O139, of which only the O1 and O139 serogroups are associated with cholera pandemics and epidemics. Non-O1, non-O139 serogroups are recognized as causative agents of sporadic and localized outbreaks (73). Pathogenic V. cholerae isolates carry virulence genes, such as the toxins genes ctxAB (25,65,68). The environmental V. cholerae strains from non-O1, non-O139 serogroups are a possible natural reservoir of potentially new emerging epidemic strains (67,73). This assumption is supported by the finding that some of these environmental strains harbor virulence genes (23) and thus are likely to evolve into novel pathogenic strains by horizontal gene transfer (24,25). The emergence of new pathogenic V. cholerae strains requires not only an efficient, rapid, and accurate identification tool but also a means for determining genetic relationships among environmental and clinical isolates.Genome-based bacterial identification and typing is essential for several disciplines, including taxonomy, epidemiology, determining phylogenetic relationships, and the study of evolutionary mechanisms. It allows distinguishing among strains within a species to monitor epidemics and routes of contamination. Recent advances in biotechnology have resulted in the development of numerous methods for microorganism typing that differ in their sensitivity, rapidity, complexity, discrimin...

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Section: Discussionsupporting

confidence: 80%

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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“…Such inaccurate branch orders are method-specific and can be recognized by comparing the results from independent methods with different clock rates. We therefore investigated the evolutionary history of Y. pestis by three independent high-resolution methods that have been applied to monomorphic species: synonymous SNPs (sSNPs) defined by genome scanning (22,23), MLVA (24,25), and screening for the presence of IS100 at defined locations (4).…”

Section: P Lague Decimated the Human Population Of Europe And Northmentioning

confidence: 99%

Microevolution and history of the plague bacillus, Yersinia pestis

Achtman

Morelli

Zhu

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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473

372

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The association of historical plague pandemics with Yersinia pestis remains controversial, partly because the evolutionary history of this largely monomorphic bacterium was unknown. The microevolution of Y. pestis was therefore investigated by three different multilocus molecular methods, targeting genomewide synonymous SNPs, variation in number of tandem repeats, and insertion of IS100 insertion elements. Eight populations were recognized by the three methods, and we propose an evolutionary tree for these populations, rooted on Yersinia pseudotuberculosis. The tree invokes microevolution over millennia, during which enzootic pestoides isolates evolved. This initial phase was followed by a binary split 6,500 years ago, which led to populations that are more frequently associated with human disease. These populations do not correspond directly to classical biovars that are based on phenotypic properties. Thus, we recommend that henceforth groupings should be based on molecular signatures. The age of Y. pestis inferred here is compatible with the dates of historical pandemic plague. However, it is premature to infer an association between any modern molecular grouping and a particular pandemic wave that occurred before the 20th century.insertion element ͉ SNP ͉ variable number tandem repeats ͉ pandemic ͉ molecular clock

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“…Primers designed to amplify the 12 chromosomal VNTRs published by Adair et al (2000), Le Flèche et al (2001) and Klevytska et al (2001) were used for PCR amplification in the Y. pestis cultures. It should be pointed out that some loci were given different names by different authors.…”

Section: Vntr Primersmentioning

confidence: 99%

“…However, analysis of multiple-locus variable number of tandem repeats (VNTR), also known as MLVA, has become a valuable tool to discriminate Y. pestis strains. Using MLVA, it is possible to trace the dispersion routes of bacterial populations at the local, regional and global levels (Adair et al, 2000;Klevytska et al, 2001;Achtman et al, 2004;Girard et al, 2004;Pourcel et al, 2004;Lowell et al, 2005;Vogler et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Yersinia pestis in Brazil

Oliveira¹,

Barros²,

Silveira-Filho³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Plague outbreaks are occasionally reported in Brazil. Unfortunately, due to great genetic similarity, molecular subtyping of Yersinia pestis strains is difficult. Analysis of multiple-locus variable number of tandem repeats (VNTR), also known as MLVA, has been found to be a valuable tool to discriminate among strains. To check for genetic differences, strains obtained from two different ecological complexes in Brazil collected during two different epidemiological events, an epizootic in Sítio Alagoinha in 1967 and an outbreak in Planalto da Borborema in 1986, were subtyped through MLVA using 12 VNTR loci. Three clusters (A, B and C) were observed. Of the 20 strains from the epizootic, 18 fit into cluster A. Cluster A was divided into two subgroups: A 1 (15 strains) and A 2 (3 strains). Of the 17 strains from the outbreak, 15 fit into cluster B. Cluster B was divided into three subgroups: B 1 (4 strains), B 2 (4 strains) and B 3 (7 strains). Cluster C is a singleton with one epizootic strain. The external standards, Y. pestis CO92 and Y. pseudotuberculosis IP32953, formed two clusters of singletons. The stability of 12 VNTR loci of three unrelated cultures ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 11 (3): 3414-3424 (2012) Brazilian Yersinia pestis diversity 3415 included in this study was assessed. The 12 VNTR loci were stable through multiple serial subcultures in the laboratory. MLVA revealed that Y. pestis populations in Brazil are not monomorphic, and that there is intraspecific genetic diversity among Brazilian plague strains. We conclude that there is some correlation among genetic groups of this species, related to the temporal and geographic origin of isolates.

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Identification and Characterization of Variable-Number Tandem Repeats in the Yersinia pestis Genome

Cited by 192 publications

References 25 publications

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Microevolution and history of the plague bacillus, Yersinia pestis

Genetic diversity of Yersinia pestis in Brazil

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