Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars

Brankatschk, K.; Blom, Jochen; Goesmann, Alexander; Smits, Theo H. M.; Duffy, Brion

doi:10.1016/j.ijfoodmicro.2012.01.024

Cited by 14 publications

(19 citation statements)

References 43 publications

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“…1) all showed previous phylogenetic support or had additional antigen characters that supported the relationship. “Section Typhi’s” antigen characters were variable, but these relationships were previously seen by eight studies (McClelland et al 2004; Vernikos et al 2007; den Bakker, Switt, Govoni, et al 2011; Fricke et al 2011; Jacobsen et al 2011; Brankatschk et al 2012; Yue et al 2012). “Section Typhimurium” serovars are characterized by an O:4 group, and most have H: 1,2 Phase 2 flagellar antigens as well as previous phylogenetic support (den Bakker, Switt, Govoni, et al 2011; Fey et al 2012; Leekitcharoenphon et al 2012).…”

Section: Discussionmentioning

confidence: 82%

“…“Section Typhimurium” serovars are characterized by an O:4 group, and most have H: 1,2 Phase 2 flagellar antigens as well as previous phylogenetic support (den Bakker, Switt, Govoni, et al 2011; Fey et al 2012; Leekitcharoenphon et al 2012). Along with previous molecular support (Vernikos et al 2007; Didelot et al 2011; Brankatschk et al 2012; Leekitcharoenphon et al 2012), “Section Enteritidis” serovars are characterized by having mostly O:9 groups and no Phase 2 flagellar antigens. Although no previous study uncovered the “Section Newport II” relationships (Newport + Muenchen + Litchfield), the lineage is very strongly supported in our ML tree and is also congruent with antigen characters: all have O:8 groups and 1,2 phase-2 flagellar antigens.…”

Section: Discussionmentioning

confidence: 86%

“…There has also been strong support coalescing around the sister relationship between S. Paratyphi C and S. Choleraesuis (Kingsley and Bäumler 2000; Liu et al 2009; Soyer et al 2009; Didelot et al 2011; Fricke et al 2011; Jacobsen et al 2011; Trujillo et al 2011; Achtman et al 2012; Brankatschk et al 2012). Because this is such a long, strongly supported branch (455 unique SNPs on our ML tree), it will be interesting to watch as our taxon sampling grows to include all ∼1,500 S. enterica subsp .…”

Section: Discussionmentioning

confidence: 99%

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Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

Timme

Pettengill

Allard

et al. 2013

Genome Biology and Evolution

126

117

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The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles—some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 99%

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Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

Timme

Pettengill

Allard

et al. 2013

Genome Biology and Evolution

126

117

View full text Add to dashboard Cite

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“…Several genes involved in carbohydrate metabolism were found to be more transcribed with only cspB and rfbK specific for mannose found on plants. We also found expression of three previously identified GIs specific for single Salmonella serovars encoding carbohydrate metabolism genes (Brankatschk et al ., ). Here, it was shown that GI_IV was not transcribed in presence of sprouts and in M9‐glucose medium whereas a low expression for GI_V was found and high expression for GI_VI (Brankatschk et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…In the genome of S . Weltevreden 2007‐60‐3289‐1, a strain isolated after an outbreak in Scandinavia in association with alfalfa sprouts, we found three serovar‐specific genomic islands (GIs), encoding carbohydrate metabolism genes (Brankatschk et al ., ). Analysis by reverse transcription‐polymerase chain reaction (RT‐PCR) showed that only genes of GI_VI encoding proteins putatively involved in mannitol degradation were transcribed with sprouts.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

Brankatschk

Kamber

Pothier

et al. 2013

Microbial Biotechnology

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Sprouted seeds represent a great risk for infection by human enteric pathogens because of favourable growth conditions for pathogens during their germination. The aim of this study was to identify mechanisms of interactions of Salmonella enterica subsp. enterica Weltevreden with alfalfa sprouts. RNA-seq analysis of S. Weltevreden grown with sprouts in comparison with M9-glucose medium showed that among a total of 4158 annotated coding sequences, 177 genes (4.3%) and 345 genes (8.3%) were transcribed at higher levels with sprouts and in minimal medium respectively. Genes that were higher transcribed with sprouts are coding for proteins involved in mechanisms known to be important for attachment, motility and biofilm formation. Besides gene expression required for phenotypic adaption, genes involved in sulphate acquisition were higher transcribed, suggesting that the surface on alfalfa sprouts may be poor in sulphate. Genes encoding structural and effector proteins of Salmonella pathogenicity island 2, involved in survival within macrophages during infection of animal tissue, were higher transcribed with sprouts possibly as a response to environmental conditions. This study provides insight on additional mechanisms that may be important for pathogen interactions with sprouts.

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Rapid and simultaneous analysis of five foodborne pathogenic bacteria using multiplex PCR

Guan

Jiang

Gao

et al. 2013

Eur Food Res Technol

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Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars

Cited by 14 publications

References 43 publications

Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

Rapid and simultaneous analysis of five foodborne pathogenic bacteria using multiplex PCR

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