Genomic Epidemiology of<i>Salmonella enterica</i>Serotype Enteritidis based on Population Structure of Prevalent Lineages

Deng, Xiangyu; Desai, Prerak; Bakker, Henk C. den; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, René S.; Frye, Jonathan G.; Porwollik, Steffen; Weimer, Bart C.; Wiedmann, Martin; Weinstock, George M.; Fields, Patricia I.; McClelland, Michael

doi:10.3201/eid2009.131095

Cited by 82 publications

(115 citation statements)

References 40 publications

Supporting

Mentioning

101

Contrasting

Unclassified

Order By: Relevance

“…Average coverage of sequencing is summarized in Table S3 in the supplemental material. SNP detection was performed similarly to what was described in our previous study (15). Briefly, trimmed and filtered sequencing reads were mapped to a reference genome (P125109; GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

“…Powered by whole-genome-sequencing (WGS) technologies, recent implementations of whole-genome single-nucleotidepolymorphism (SNP) typing (WGST) have led to substantial improvements of both molecular subtyping and phylogenetic analyses, particularly for genetically homogenous bacterial pathogens such as S. enterica serotype Enteritidis (14,15). A recent WGSbased survey of S. enterica serotype Enteritidis isolates resolved the commonly circulating S. enterica serotype Enteritidis populations in the United States into five major genetic lineages, revealing potential patterns in their geographical and epidemiological distribution (15).…”

mentioning

confidence: 99%

“…A recent WGSbased survey of S. enterica serotype Enteritidis isolates resolved the commonly circulating S. enterica serotype Enteritidis populations in the United States into five major genetic lineages, revealing potential patterns in their geographical and epidemiological distribution (15).…”

mentioning

confidence: 99%

“…In this study, we assembled a cohort of 52 S. enterica serotype Enteritidis isolates from 15 major foodborne disease outbreaks and three sporadic cases in the United States and 1 outbreak in Mauritius between 2001 and 2012. A retrospective investigation of these isolates was performed with a combination of WGST, MLVA, CRISPR-MVLST, and PFGE analyses to compare their respective performances in delineating each individual outbreak under the guidance of the recently proposed phylogenetic framework and population structure of S. enterica serotype Enteritidis (15).…”

mentioning

confidence: 99%

See 3 more Smart Citations

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

et al. 2015

Self Cite

View full text Add to dashboard Cite

A retrospective investigation was performed to evaluate whole-genome sequencing as a benchmark for comparing molecular subtyping methods for Salmonella enterica serotype Enteritidis and survey the population structure of commonly encountered S. enterica serotype Enteritidis outbreak isolates in the United States. A total of 52 S. enterica serotype Enteritidis isolates representing 16 major outbreaks and three sporadic cases collected between 2001 and 2012 were sequenced and subjected to subtyping by four different methods: (i) whole-genome single-nucleotide-polymorphism typing (WGST), (ii) multiple-locus variablenumber tandem-repeat (VNTR) analysis (MLVA), (iii) clustered regularly interspaced short palindromic repeats combined with multi-virulence-locus sequence typing (CRISPR-MVLST), and (iv) pulsed-field gel electrophoresis (PFGE). WGST resolved all outbreak clusters and provided useful robust phylogenetic inference results with high epidemiological correlation. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed the other methods in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of S. enterica serotype Enteritidis. Our results suggested that whole-genome sequencing makes a viable platform for the evaluation and benchmarking of molecular subtyping methods. Salmonella enterica is currently the most common bacterial foodborne pathogen in the United States, causing over 1 million cases of illnesses annually, including approximately 20,000 hospitalizations and 400 deaths (1). Serotyping is commonly used to subtype strains below the species level for epidemiologic purposes. Salmonella enterica serotype Enteritidis was the serotype most commonly linked to foodborne outbreaks between 1998 and 2008 in the United States, with shell eggs being the major vehicle for foodborne transmission (2). In recent years, S. enterica serotype Enteritidis was also found to cause multistate outbreaks associated with other foods such as ground beef (2012), Turkish pine nuts (2011), and alfalfa and spicy sprouts (2011), in addition to shelled eggs (2010) (3).During outbreak investigations, it is critical to employ subtyping methods capable of distinguishing outbreak isolates from epidemiologically distinct but genetically related bacterial strains. Most S. enterica serotype Enteritidis isolates have been shown to be genetically homogeneous, making it difficult for conventional subtyping methods such as pulsed-field gel electrophoresis (PFGE), the current gold standard for strain-level Salmonella subtyping, to discriminate between strains (4, 5). Among the S. enterica serotype Enteritidis isolates reported to PulseNet (6), approximately 45% display a single PFGE pattern using XbaI (JEGX01.0004), rendering PFGE ineffective in some foodborne outbreak investigations. One strategy to improve subtype resolution is to target hypervariable regions (i.e., regions of the bacterial chromosome with less genetic stability) in the ba...

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…En varios estudios e investigaciones epidemiológicas ha quedado de manifiesto la limitación del PFGE, sobre todo en casos donde las cepas involucradas son de tipo monomórficas o clonales. Por ejemplo, para algunos serotipos de Salmonella la sub-tipificación con PFGE no es útil, ya que no discrimina entre cepas muy clonales 12 ; es el caso de Salmonella Enteritidis, el serotipo más común de este patógeno. Cuando las cepas de S. Enteritidis se discriminan con PFGE, entre 40 y 50 % de las cepas presentan el mismo patrón 13,14 ; por lo tanto, realizar la investigación epidemiológica, rastrear la fuente e identificar la ruta de transmisión se convierte en un proceso altamente complejo y la utilidad de PFGE, es más bien dudosa.…”

unclassified

Infectología en la era de la genómica

Switt

Toledo

2015

Rev. chil. infectol.

View full text Add to dashboard Cite

Genomic Diversity in Salmonella enterica

Wain

O’Grady

2017

Applied Genomics of Foodborne Pathogens

View full text Add to dashboard Cite

Salmonella enterica is a bacterial species which contains diversity within the limits of a single species ancestry. Selection by different habitats, represented by the extraordinary number of host species colonised by S. enterica, and the need to successfully transmit through water, soil, or fomites (from host to host) has driven this diversity. An understanding of the impact of this diversity needs to drive the naming of isolates which should be clinically and biologically relevant in terms of niche occupation as well as in terms of ancestry; all we need is an accurate sequence of the entire genome and a comprehensive understanding of the biology of the variation seen. Currently serotype is the working unit of classification but the variation seen within each serotype is itself very variable and so not all serotypes are equal. Here we describe the current genomic data from several common serotypes and discuss the biology behind the different levels of variation

show abstract

Genomic Epidemiology ofSalmonella entericaSerotype Enteritidis based on Population Structure of Prevalent Lineages

Abstract: Major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s.

Cited by 82 publications

References 40 publications

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

Infectología en la era de la genómica

Genomic Diversity in Salmonella enterica

Contact Info

Product

Resources

About