Multilocus Variable-Number Tandem-Repeat Analysis for Molecular Typing of<i>Shigella sonnei</i>

Liang, Shiu-Yun; Watanabe, Haruo; Terajima, Jun; Li, Chun-Chin; Liao, Jui-Cheng; Tung, Shu-Chu; Chiou, Chien-Shun

doi:10.1128/jcm.00675-07

Cited by 54 publications

(57 citation statements)

References 23 publications

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“…Two strains of S. sonnei, two strains of S. boydii, three strains of E. coli, and two pairs of S. dysenteriae strains share the same genotype. Additional markers might allow further differentiation of Shigella strains, supposed to have been isolated in different places at different times (20). The HGDIs, however, are high and, by adding in the cluster analysis markers discarded previously, the strains remain un- distinguishable (data not shown), supporting the idea that they are in all likelihood epidemiologically related.…”

Section: Resultsmentioning

confidence: 76%

“…Loci with repeat units longer than 9 bp were favored in order to facilitate allele repeat number calling by a variety of DNA amplicon length estimation devices (24) and as a complement to a previous investigation (20). Selected primers pairs were validated in silico with available genome sequence data for Shigella and E. coli strains by using the multiple-PCR-primer BLAST Web service (http: //minisatellites.u-psud.fr/) which provides the expected size and sequence of the PCR products.…”

Section: Methodsmentioning

confidence: 99%

“…The present work aimed to set up MLVA for the Shigella genus to facilitate epidemiological follow-up, by providing easy-to-use typing tools, in countries suffering from a recrudescence of Shigella outbreaks. Recently, Liang et al (20) proposed an MLVA for molecular typing of S. sonnei and explored the capability of a 26-VNTR set for detecting clusters of infection. Because the proposed VNTRs have very short repeat units, this assay requires a high precision of DNA length measurement, as provided, for instance, by microcapillary electrophoresis and fluorescent markers.…”

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confidence: 99%

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Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing Shigella spp

et al. 2008

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The Shigella genus has historically been separated into four species, based on biochemical assays. The classification within each species relies on serotyping. Recently, genome sequencing and DNA assays, in particular the multilocus sequence typing (MLST) approach, greatly improved the current knowledge of the origin and phylogenetic evolution of Shigella spp. The Shigella and Escherichia genera are now considered to belong to a unique genomospecies. Multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses of highly homogeneous bacterial pathogens. Here, we assess the capability of MLVA for Shigella typing. Thirty-two potentially polymorphic VNTRs were selected by analyzing in silico five Shigella genomic sequences and subsequently evaluated. Eventually, a panel of 15 VNTRs was selected (i.e., MLVA15 analysis). MLVA15 analysis of 78 strains or genome sequences of Shigella spp. and 11 strains or genome sequences of Escherichia coli distinguished 83 genotypes. Shigella population cluster analysis gave consistent results compared to MLST. MLVA15 analysis showed capabilities for E. coli typing, providing classification among pathogenic and nonpathogenic E. coli strains included in the study. The resulting data can be queried on our genotyping webpage (http://mlva .u-psud.fr). The MLVA15 assay is rapid, highly discriminatory, and reproducible for Shigella and Escherichia strains, suggesting that it could significantly contribute to epidemiological trace-back analysis of Shigella infections and pathogenic Escherichia outbreaks. Typing was performed on strains obtained mostly from collections. Further studies should include strains of much more diverse origins, including all pathogenic E. coli types.

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Section: Resultsmentioning

confidence: 76%

Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing Shigella spp

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“…MLVA was performed as previously described (8). Twenty-six VNTR loci were characterized for every isolate studied.…”

Section: Methodsmentioning

confidence: 99%

“…In a previous study, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) method for fine typing of S. sonnei isolates. A total of 26 VNTR loci were identified, and MLVA typing based on the 8 most variable loci exhibited a higher discriminatory power than PFGE in distinguishing closely related isolates for outbreak investigation (8). Since the VNTR loci have a range of degrees of variability, they may also be applicable to establishing phylogenetic relationships among strains that have evolved over different timescales.…”

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confidence: 99%

Utility of Multilocus Variable-Number Tandem-Repeat Analysis as a Molecular Tool for Phylogenetic Analysis ofShigella sonnei

Chiou

Watanabe

Wang³

et al. 2009

J Clin Microbiol

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A panel of 916 isolates, including 703 closely related IST1 isolates, were characterized by inter-IS1 spacer typing (IST), pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to evaluate the utility of MLVA as a molecular tool for the phylogenetic analysis of Shigella sonnei. The global phylogenetic patterns determined by IST, PFGE, and MLVA were concordant. MLVA was carried out using 26 VNTR loci with a range of degrees of variability. MLVA data for the 703 IST1 isolates revealed that diversification among the closely related isolates was attributed mainly to four highly variable loci. The phylogenetic pattern for the closely related isolates determined using MLVA profiles of 8 highly variable loci was in agreement with that determined using the 26-locus profiles. A clustering analysis using the profiles of 18 loci with limited variability established clear phylogenetic relationships among IST clonal groups. Accordingly, MLVA is a useful tool for the phylogenetic analysis of S. sonnei. Combined VNTR loci with higher variability are useful markers for resolving closely related isolates, whereas combined loci with lower variability are suitable for establishing clear phylogenetic relationships between strains or clones that have evolved over a longer timescale.Shigella sonnei is one of the causative agents of shigellosis. Unlike the other three Shigella species, S. dysenteriae, S. flexneri, and S. boydii, which are prevalent in developing countries, S. sonnei is predominant in industrialized countries (6) and is one of the major causes of travel-associated diarrheal disease (3). Transmission of S. sonnei strains between countries occurs frequently via international travel (7,14).The analysis of bacterial isolates by various genotyping methods provides useful information for establishing the genetic relatedness among isolates for the purposes of epidemiological investigation and phylogenetic study. Among these genotyping methods, pulsed-field gel electrophoresis (PFGE) has been proven to be a powerful tool for discriminating Shigella strains and has become a standardized method for an international molecular-subtyping network for food-borne-disease surveillance (13). However, PFGE is, at times, too discriminatory for investigating clonal relationships among Shigella strains that have evolved over years or decades. In order to study an S. sonnei epidemic, we previously developed an inter-IS1 spacer typing (IST) method for subtyping of S. sonnei strains (1). IST is less discriminative than PFGE for S. sonnei, but it is more suitable than PFGE for investigating the clonal relationships among S. sonnei strains in circulation over a short timescale (15).Multilocus sequence typing (MLST) is a sequence-based typing method widely adopted for the phylogenetic study of a number of bacterial pathogens, as listed on the website http: //www.mlst.net/. The MLST method has been used for phylogenetic analysis of Shigella spp. with the protocol developed for Escherichia coli...

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Food Safety and Implications for Microbial Source Tracking

Graves

2011

Microbial Source Tracking: Methods, Applications, and Case Studies

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Multilocus Variable-Number Tandem-Repeat Analysis for Molecular Typing ofShigella sonnei

Cited by 54 publications

References 23 publications

Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing Shigella spp

Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing Shigella spp

Utility of Multilocus Variable-Number Tandem-Repeat Analysis as a Molecular Tool for Phylogenetic Analysis ofShigella sonnei

Food Safety and Implications for Microbial Source Tracking

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