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Phylogenetics and differentiation of Salmonella Newport lineages by whole genome sequencing.

Cao G, Meng J, Strain E, Stones R, Pettengill J, Zhao S, McDermott P, Brown E, Allard M - PLoS ONE (2013)

Bottom Line: A resulting phylogenetic tree consisted of four sublineages and indicated that S.Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes.Newport and also provided additional markers for epidemiological response.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA.

ABSTRACT
Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks from 1995 to 2011 in the United States. In the current study, we selected 26 S. Newport strains isolated from diverse sources and geographic locations and then conducted 454 shotgun pyrosequencing procedures to obtain 16-24 × coverage of high quality draft genomes for each strain. Comparative genomic analysis of 28 S. Newport strains (including 2 reference genomes) and 15 outgroup genomes identified more than 140,000 informative SNPs. A resulting phylogenetic tree consisted of four sublineages and indicated that S. Newport had a clear geographic structure. Strains from Asia were divergent from those from the Americas. Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes. We selected loci around the mutS gene of S. Newport to differentiate distinct lineages, including those between invH and mutS genes at the 3' end of Salmonella Pathogenicity Island 1 (SPI-1), ste fimbrial operon, and Clustered, Regularly Interspaced, Short Palindromic Repeats (CRISPR) associated-proteins (cas). These genes in the outgroup genomes held high similarity with either S. Newport Lineage II or III at the same loci. S. Newport Lineages II and III have different evolutionary histories in this region and our data demonstrated genetic flow and homologous recombination events around mutS. The findings suggested that S. Newport Lineages II and III diverged early in the serotype evolution and have evolved largely independently. Moreover, we identified genes that could delineate sublineages within the phylogenetic tree and that could be used as potential biomarkers for trace-back investigations during outbreaks. Thus, whole genome sequencing data enabled us to better understand the genetic background of pathogenicity and evolutionary history of S. Newport and also provided additional markers for epidemiological response.

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Related in: MedlinePlus

MLST analysis of S. Newport and outgroup genomes.Seven housekeeping genes were selected and MLST dendrogram was performed by TNT [38] with 100,000 iterations. S. Newport was divided into two major clusters, which were separated by outgroup genomes. Lineage II was divided into three sublineages, which display minor differences compared with the parsimony tree. Sublineage IIA showed closer relatedness with IIC than IIB.
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pone-0055687-g002: MLST analysis of S. Newport and outgroup genomes.Seven housekeeping genes were selected and MLST dendrogram was performed by TNT [38] with 100,000 iterations. S. Newport was divided into two major clusters, which were separated by outgroup genomes. Lineage II was divided into three sublineages, which display minor differences compared with the parsimony tree. Sublineage IIA showed closer relatedness with IIC than IIB.

Mentions: Since multilocus sequence typing (MLST) has been used as a common analysis tool to study the phylogenetic relatedness and epidemiology of Salmonella, we extracted seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) of genomes in the current study (except strain from canine_AZ_2003 because of sequence quality) and performed MLST analyses (Figure 2). MLST indicated that S. Newport Lineage II was grouped into three sublineages with minor differences. For example, sublineage IIA showed closer relatedness with IIB than IIC. Additionally, Lineages II and III were separated by outgroup genomes, although outgroups displayed different relatedness compared with the parsimony phylogenetic tree (Figure 1). For example, S. Virchow, S. Paratyphi C and S. Choleraesuis showed closer relationship with Lineage II.


Phylogenetics and differentiation of Salmonella Newport lineages by whole genome sequencing.

Cao G, Meng J, Strain E, Stones R, Pettengill J, Zhao S, McDermott P, Brown E, Allard M - PLoS ONE (2013)

MLST analysis of S. Newport and outgroup genomes.Seven housekeeping genes were selected and MLST dendrogram was performed by TNT [38] with 100,000 iterations. S. Newport was divided into two major clusters, which were separated by outgroup genomes. Lineage II was divided into three sublineages, which display minor differences compared with the parsimony tree. Sublineage IIA showed closer relatedness with IIC than IIB.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569456&req=5

pone-0055687-g002: MLST analysis of S. Newport and outgroup genomes.Seven housekeeping genes were selected and MLST dendrogram was performed by TNT [38] with 100,000 iterations. S. Newport was divided into two major clusters, which were separated by outgroup genomes. Lineage II was divided into three sublineages, which display minor differences compared with the parsimony tree. Sublineage IIA showed closer relatedness with IIC than IIB.
Mentions: Since multilocus sequence typing (MLST) has been used as a common analysis tool to study the phylogenetic relatedness and epidemiology of Salmonella, we extracted seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) of genomes in the current study (except strain from canine_AZ_2003 because of sequence quality) and performed MLST analyses (Figure 2). MLST indicated that S. Newport Lineage II was grouped into three sublineages with minor differences. For example, sublineage IIA showed closer relatedness with IIB than IIC. Additionally, Lineages II and III were separated by outgroup genomes, although outgroups displayed different relatedness compared with the parsimony phylogenetic tree (Figure 1). For example, S. Virchow, S. Paratyphi C and S. Choleraesuis showed closer relationship with Lineage II.

Bottom Line: A resulting phylogenetic tree consisted of four sublineages and indicated that S.Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes.Newport and also provided additional markers for epidemiological response.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA.

ABSTRACT
Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks from 1995 to 2011 in the United States. In the current study, we selected 26 S. Newport strains isolated from diverse sources and geographic locations and then conducted 454 shotgun pyrosequencing procedures to obtain 16-24 × coverage of high quality draft genomes for each strain. Comparative genomic analysis of 28 S. Newport strains (including 2 reference genomes) and 15 outgroup genomes identified more than 140,000 informative SNPs. A resulting phylogenetic tree consisted of four sublineages and indicated that S. Newport had a clear geographic structure. Strains from Asia were divergent from those from the Americas. Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes. We selected loci around the mutS gene of S. Newport to differentiate distinct lineages, including those between invH and mutS genes at the 3' end of Salmonella Pathogenicity Island 1 (SPI-1), ste fimbrial operon, and Clustered, Regularly Interspaced, Short Palindromic Repeats (CRISPR) associated-proteins (cas). These genes in the outgroup genomes held high similarity with either S. Newport Lineage II or III at the same loci. S. Newport Lineages II and III have different evolutionary histories in this region and our data demonstrated genetic flow and homologous recombination events around mutS. The findings suggested that S. Newport Lineages II and III diverged early in the serotype evolution and have evolved largely independently. Moreover, we identified genes that could delineate sublineages within the phylogenetic tree and that could be used as potential biomarkers for trace-back investigations during outbreaks. Thus, whole genome sequencing data enabled us to better understand the genetic background of pathogenicity and evolutionary history of S. Newport and also provided additional markers for epidemiological response.

Show MeSH
Related in: MedlinePlus