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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

Parsimony phylogenetic tree for cas genes.We constructed this parsimony tree with 100,000 iterations by TNT [38] based on concatenated sequences of the cas genes. This dendrogram indicated that cas genes of Lineages II and III were originated from distinct sources.
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pone-0055687-g003: Parsimony phylogenetic tree for cas genes.We constructed this parsimony tree with 100,000 iterations by TNT [38] based on concatenated sequences of the cas genes. This dendrogram indicated that cas genes of Lineages II and III were originated from distinct sources.

Mentions: We defined cas genes located at the 3′ end of mutS in Lineages II and III as cas Sequence 1 and 2, respectively. Multiple sequence alignments of concatenated nucleotide acids for cas Sequence 1 and 2 showed significant variations. Moreover, there are four collapsing groups in the parsimony tree because the sequence identities were almost 100% in each group, respectively. For example, there was only one substitution found at position 333 of strain from ground_turkey_MD_2003 in total 5,781 bp compared with other four sequences in the group (data not shown). A parsimony tree was generated based on cas alignments using TNT [38] with 100,000 bootstrap iterations (Figure 3), showing that cas proteins in Lineages II and III displayed divergent phylogenetic relatedness, and were separated by outgroup genomes. For example, cas genes of S. Paratyphi C and S. Choleraesuis displayed closer relatedness with cas Sequence 2 of Lineage III than Lineage II strains (Figure 3).


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)

Parsimony phylogenetic tree for cas genes.We constructed this parsimony tree with 100,000 iterations by TNT [38] based on concatenated sequences of the cas genes. This dendrogram indicated that cas genes of Lineages II and III were originated from distinct sources.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0055687-g003: Parsimony phylogenetic tree for cas genes.We constructed this parsimony tree with 100,000 iterations by TNT [38] based on concatenated sequences of the cas genes. This dendrogram indicated that cas genes of Lineages II and III were originated from distinct sources.
Mentions: We defined cas genes located at the 3′ end of mutS in Lineages II and III as cas Sequence 1 and 2, respectively. Multiple sequence alignments of concatenated nucleotide acids for cas Sequence 1 and 2 showed significant variations. Moreover, there are four collapsing groups in the parsimony tree because the sequence identities were almost 100% in each group, respectively. For example, there was only one substitution found at position 333 of strain from ground_turkey_MD_2003 in total 5,781 bp compared with other four sequences in the group (data not shown). A parsimony tree was generated based on cas alignments using TNT [38] with 100,000 bootstrap iterations (Figure 3), showing that cas proteins in Lineages II and III displayed divergent phylogenetic relatedness, and were separated by outgroup genomes. For example, cas genes of S. Paratyphi C and S. Choleraesuis displayed closer relatedness with cas Sequence 2 of Lineage III than Lineage II strains (Figure 3).

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