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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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Pulsed Field Gel Electrophoresis (PFGE) profile digested with XbaI.We performed PFGE analysis of 24 S. Newport strains (without two environmental farm isolates) isolated from diverse sources and geographic locations. PFGE profiles divided these strains into two major clusters with different groupings compared with the phylogenetic tree based on whole genome wide SNPs.
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pone-0055687-g004: Pulsed Field Gel Electrophoresis (PFGE) profile digested with XbaI.We performed PFGE analysis of 24 S. Newport strains (without two environmental farm isolates) isolated from diverse sources and geographic locations. PFGE profiles divided these strains into two major clusters with different groupings compared with the phylogenetic tree based on whole genome wide SNPs.

Mentions: Conventional subtyping methods, such as MLST and Pulsed Field Gel Electrophoresis (PFGE), have been used to differentiate pathogenic strains during outbreaks and trace-back investigations and to study the phylogenetic organization of pathogens. MLST analyses (Figure 2) indicated that S. Newport was divided into two major clusters and was separated by outgroup genomes. Lineage II was grouped into three sublineages; however, sublineage IIA displayed closer relatedness with IIC than IIB, which was different with the genomic based parsimony tree (Figure 1). This was not unexpected as the genomic database was significantly larger than the MLST database. MLST indicated that these seven housekeeping genes were valuable to differentiate major and sublineages of S. Newport, though MLST may not accurately show the relationships among the sublineages. Therefore, whole genome sequencing data was able to provide more accurate phylogenetic relationship than small sets of genes. However, PFGE often may not be able to differentiate highly clonal strains [28], [32]. A combination of whole genome sequencing and phylogenetic analysis has been proven to provide enough accuracy and sensitivity for epidemiological investigations [28], [32]. In the current study, comparisons of PFGE (Figure 4) and the phylogenetic tree (Figure 1) illustrated that PFGE was not able to delineate the major lineages correctly, as expected. For example, according to the PFGE profile (Figure 4), three strains of sublineage IIB, namely, frog_Vietnam, fish_Hong_Kong and fish_Vietnam, were located with strains of Lineage III to form a lineage unsupported by sequence analysis. Bell et al. [9] demonstrated that whole genome sequencing and phylogenetic analysis were able to differentiate S. Newport strains with an identical PFGE pattern during an outbreak case study, providing detailed information about S. Newport’s complex ecology to the investigators.


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)

Pulsed Field Gel Electrophoresis (PFGE) profile digested with XbaI.We performed PFGE analysis of 24 S. Newport strains (without two environmental farm isolates) isolated from diverse sources and geographic locations. PFGE profiles divided these strains into two major clusters with different groupings compared with the phylogenetic tree based on whole genome wide SNPs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0055687-g004: Pulsed Field Gel Electrophoresis (PFGE) profile digested with XbaI.We performed PFGE analysis of 24 S. Newport strains (without two environmental farm isolates) isolated from diverse sources and geographic locations. PFGE profiles divided these strains into two major clusters with different groupings compared with the phylogenetic tree based on whole genome wide SNPs.
Mentions: Conventional subtyping methods, such as MLST and Pulsed Field Gel Electrophoresis (PFGE), have been used to differentiate pathogenic strains during outbreaks and trace-back investigations and to study the phylogenetic organization of pathogens. MLST analyses (Figure 2) indicated that S. Newport was divided into two major clusters and was separated by outgroup genomes. Lineage II was grouped into three sublineages; however, sublineage IIA displayed closer relatedness with IIC than IIB, which was different with the genomic based parsimony tree (Figure 1). This was not unexpected as the genomic database was significantly larger than the MLST database. MLST indicated that these seven housekeeping genes were valuable to differentiate major and sublineages of S. Newport, though MLST may not accurately show the relationships among the sublineages. Therefore, whole genome sequencing data was able to provide more accurate phylogenetic relationship than small sets of genes. However, PFGE often may not be able to differentiate highly clonal strains [28], [32]. A combination of whole genome sequencing and phylogenetic analysis has been proven to provide enough accuracy and sensitivity for epidemiological investigations [28], [32]. In the current study, comparisons of PFGE (Figure 4) and the phylogenetic tree (Figure 1) illustrated that PFGE was not able to delineate the major lineages correctly, as expected. For example, according to the PFGE profile (Figure 4), three strains of sublineage IIB, namely, frog_Vietnam, fish_Hong_Kong and fish_Vietnam, were located with strains of Lineage III to form a lineage unsupported by sequence analysis. Bell et al. [9] demonstrated that whole genome sequencing and phylogenetic analysis were able to differentiate S. Newport strains with an identical PFGE pattern during an outbreak case study, providing detailed information about S. Newport’s complex ecology to the investigators.

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