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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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Parsimony phylogenetic tree of S. Newport and outgroup genomes.This phylogenetic tree was reconstructed by TNT [38] with 100,000 iterations based on 147,780 genome wide SNPs. All S. Newport strains were grouped into two major clusters, S. Newport Lineages II and III. Lineage II was further grouped into three sublineages, IIA, IIB and IIC. S. Newport displayed clear geographic structure. Asian strains were grouped together and divergent from ones from Americas. At the locus between invH and mutS genes, Lineage II and all outgroup genomes shared Gene Cluster 1; however, Lineage III strains shared Gene Cluster 2. Gene Cluster 3 was only found in strain from fish_Hong_Kong at the 3′ end of Gene Cluster 1. GC1 = Gene Cluster 1; GC2 = Gene Cluster 2; GC3 = Gene Cluster 3. Additionally, Node M includes most MDR strains in the current study.
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pone-0055687-g001: Parsimony phylogenetic tree of S. Newport and outgroup genomes.This phylogenetic tree was reconstructed by TNT [38] with 100,000 iterations based on 147,780 genome wide SNPs. All S. Newport strains were grouped into two major clusters, S. Newport Lineages II and III. Lineage II was further grouped into three sublineages, IIA, IIB and IIC. S. Newport displayed clear geographic structure. Asian strains were grouped together and divergent from ones from Americas. At the locus between invH and mutS genes, Lineage II and all outgroup genomes shared Gene Cluster 1; however, Lineage III strains shared Gene Cluster 2. Gene Cluster 3 was only found in strain from fish_Hong_Kong at the 3′ end of Gene Cluster 1. GC1 = Gene Cluster 1; GC2 = Gene Cluster 2; GC3 = Gene Cluster 3. Additionally, Node M includes most MDR strains in the current study.

Mentions: A total of 147,780 informative SNPs were obtained from multiple genome alignment and were used to construct a parsimony phylogenetic tree (Figure 1) with 100,000 iterations by TNT [38]. All 28 S. Newport genomes (including S. Newport SL254 and SL317) were grouped into two major lineages (Figure 1), S. Newport Lineages II and III [14]. S. Newport Lineage II was further divided into sublineages IIA, IIB and IIC. Our data demonstrated that S. Newport displayed a clear geographic structure. For example, isolates from frog_Vietnam, fish_Hong_Kong, fish_Vietnam, shrimp_India, squid_Vietnam and pepper_Vietnam were placed in two sublineages (IIA and IIB) within Lineage II, and divergent from those from the Americas (IIC). The two Vietnamese strains in IIA grouped together to the exclusion of the other Asian strain and the same grouping of Vietnamese strains was also seen in IIB. Furthermore, IIC including one Mexican strain (cheese_Mexico) and many North American strains defined an Americas clade and were separated from the Asian clades within Lineage II. However, this structure was imperfect with pig_ear_CA located in IIA, an otherwise Asian clade. The U.S. strains from various sources were diverse and grouped into both major lineages. All strains in Lineage III were isolated from the United States. S. Newport Lineages II and III were polyphyletic, namely, Lineage III displayed closer evolutionary relationship with S. Hadar and S. Typhimurium outgroups than Lineage II (Figure 1).


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 of S. Newport and outgroup genomes.This phylogenetic tree was reconstructed by TNT [38] with 100,000 iterations based on 147,780 genome wide SNPs. All S. Newport strains were grouped into two major clusters, S. Newport Lineages II and III. Lineage II was further grouped into three sublineages, IIA, IIB and IIC. S. Newport displayed clear geographic structure. Asian strains were grouped together and divergent from ones from Americas. At the locus between invH and mutS genes, Lineage II and all outgroup genomes shared Gene Cluster 1; however, Lineage III strains shared Gene Cluster 2. Gene Cluster 3 was only found in strain from fish_Hong_Kong at the 3′ end of Gene Cluster 1. GC1 = Gene Cluster 1; GC2 = Gene Cluster 2; GC3 = Gene Cluster 3. Additionally, Node M includes most MDR strains in the current study.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0055687-g001: Parsimony phylogenetic tree of S. Newport and outgroup genomes.This phylogenetic tree was reconstructed by TNT [38] with 100,000 iterations based on 147,780 genome wide SNPs. All S. Newport strains were grouped into two major clusters, S. Newport Lineages II and III. Lineage II was further grouped into three sublineages, IIA, IIB and IIC. S. Newport displayed clear geographic structure. Asian strains were grouped together and divergent from ones from Americas. At the locus between invH and mutS genes, Lineage II and all outgroup genomes shared Gene Cluster 1; however, Lineage III strains shared Gene Cluster 2. Gene Cluster 3 was only found in strain from fish_Hong_Kong at the 3′ end of Gene Cluster 1. GC1 = Gene Cluster 1; GC2 = Gene Cluster 2; GC3 = Gene Cluster 3. Additionally, Node M includes most MDR strains in the current study.
Mentions: A total of 147,780 informative SNPs were obtained from multiple genome alignment and were used to construct a parsimony phylogenetic tree (Figure 1) with 100,000 iterations by TNT [38]. All 28 S. Newport genomes (including S. Newport SL254 and SL317) were grouped into two major lineages (Figure 1), S. Newport Lineages II and III [14]. S. Newport Lineage II was further divided into sublineages IIA, IIB and IIC. Our data demonstrated that S. Newport displayed a clear geographic structure. For example, isolates from frog_Vietnam, fish_Hong_Kong, fish_Vietnam, shrimp_India, squid_Vietnam and pepper_Vietnam were placed in two sublineages (IIA and IIB) within Lineage II, and divergent from those from the Americas (IIC). The two Vietnamese strains in IIA grouped together to the exclusion of the other Asian strain and the same grouping of Vietnamese strains was also seen in IIB. Furthermore, IIC including one Mexican strain (cheese_Mexico) and many North American strains defined an Americas clade and were separated from the Asian clades within Lineage II. However, this structure was imperfect with pig_ear_CA located in IIA, an otherwise Asian clade. The U.S. strains from various sources were diverse and grouped into both major lineages. All strains in Lineage III were isolated from the United States. S. Newport Lineages II and III were polyphyletic, namely, Lineage III displayed closer evolutionary relationship with S. Hadar and S. Typhimurium outgroups than Lineage II (Figure 1).

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