Multiple-locus variable-number tandem repeat analysis for subtyping of Salmonella enterica subsp. enterica serovar Enteritidis

Beranek, Andreas; Mikula, Claudia; Rabold, Peter; Arnhold, Daniela; Berghold, C; Lederer, I.; Allerberger, Franz; Kornschober, Christian

doi:10.1016/j.ijmm.2008.06.002

Cited by 51 publications

(40 citation statements)

References 28 publications

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“…Several nucleic acid-based molecular subtyping methods have been used to subtype Salmonella, including amplified fragment length polymorphism (AFLP) (18,32,36,42,46), multiple-locus variable-number tandem-repeat analysis (MLVA) (2,30,31,37), and pulsed-field gel electrophoresis (PFGE) (35). PFGE is currently considered the "gold standard" method for subtyping food-borne pathogens and is the subtyping method used by PulseNet, the molecular surveillance network in the United States and throughout the world to investigate food-borne illnesses and outbreaks (17).…”

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confidence: 99%

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica

Liu

Barrangou

Gerner‐Smidt

et al. 2011

Appl Environ Microbiol

129

119

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Salmonella enterica subsp. enterica is the leading cause of bacterial food-borne disease in the United States. Molecular subtyping methods are powerful tools for tracking the farm-to-fork spread of food-borne pathogens during outbreaks. In order to develop a novel multilocus sequence typing (MLST) scheme for subtyping the major serovars of S. enterica subsp. enterica, the virulence genes sseL and fimH and clustered regularly interspaced short palindromic repeat (CRISPR) loci were sequenced from 171 clinical isolates from nine Salmonella serovars, Salmonella serovars Typhimurium, Enteritidis, Newport, Heidelberg, Javiana, I 4,[5],12:i:؊, Montevideo, Muenchen, and Saintpaul. The MLST scheme using only virulence genes was congruent with serotyping and identified epidemic clones but could not differentiate outbreaks. The addition of CRISPR sequences dramatically improved discriminatory power by differentiating individual outbreak strains/clones. Of particular note, the present MLST scheme provided better discrimination of Salmonella serovar Enteritidis strains than pulsed-field gel electrophoresis (PFGE). This method showed high epidemiologic concordance for all serovars screened except for Salmonella serovar Muenchen. In conclusion, the novel MLST scheme described in the present study accurately differentiated outbreak strains/clones of the major serovars of Salmonella, and therefore, it shows promise for subtyping this important food-borne pathogen during investigations of outbreaks.

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confidence: 99%

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica

Liu

Barrangou

Gerner‐Smidt

et al. 2011

Appl Environ Microbiol

129

119

View full text Add to dashboard Cite

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“…Several molecular subtyping methods have been developed for studying the epidemiology of S. Enteritidis, including amplified fragment length polymorphism (AFLP) (15,19,27,28,39), multiple-locus variable-number tandem-repeat analysis (MLVA) (3,5,12,37), and pulsed-field gel electrophoresis (PFGE) (18). PFGE is currently the "gold standard" method used by public health surveillance laboratories for tracking food-borne pathogens, including Salmonella (18).…”

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confidence: 99%

Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

Liu

Kariyawasam

Jayarao

et al. 2011

Appl Environ Microbiol

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Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

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“…MLVA has been particularly effective in typing homogenous clones including Yersinia pestis (1,14,21,25), Bacillus anthracis (8,11,12,34), and Mycobacterium tuberculosis (7,16,32,35,36). In S. enterica, a few serovars, including serovars Enteritidis, Typhimurium, and Typhi have been studied by MLVA (3,4,(18)(19)(20)27). Two MLVA studies of serovar Typhi showed different levels of variation of VNTR loci analyzed (20,27).…”

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confidence: 99%

Multiple-Locus Variable-Number Tandem-Repeat Analysis of Salmonella enterica Serovar Typhi

Octavia

Lan

2009

J Clin Microbiol

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Multilocus variable-number tandem repeats (VNTRs) are widely used as molecular markers to differentiate isolates of homogenous pathogenic clones. We explored the genomes of Salmonella enterica serovar Typhi strains CT18 and Ty2 for potential VNTRs. Among the 43 potential VNTRs screened, 2 were found to be polymorphic. Together with seven polymorphic VNTRs from previous studies, they were used to type 73 global serovar Typhi isolates. A total of 70 multilocus VNTR analysis (MLVA) profiles were found, distinguishing all except three pairs of isolates into individual profiles. The discriminatory power was 0.999. Phylogenetic analysis showed that the MLVA profiles can be divided into seven clusters. However, except for the closely related isolates, the relationships derived were in conflict with those inferred from single nucleotide polymorphism (SNP) typing using 38 SNPs done previously. We concluded that MLVA can resolve the relationships only among closely related isolates. A combination of SNP typing and MLVA typing offers the best approach for local and global epidemiology and the evolutionary analysis of serovar Typhi. We suggest that seven of the nine most polymorphic VNTRs be used as a standardized typing scheme for epidemiological typing.

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Multiple-locus variable-number tandem repeat analysis for subtyping of Salmonella enterica subsp. enterica serovar Enteritidis

Cited by 51 publications

References 28 publications

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica

Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

Multiple-Locus Variable-Number Tandem-Repeat Analysis of Salmonella enterica Serovar Typhi

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