Phylogenetics and Differentiation of Salmonella Newport Lineages by Whole Genome Sequencing

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.

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

“…Among the latter four, we examined prophage panels from Typhimurium and Newport and found them to carry at least 10 and 5 different types of P22-like prophages, respectively (Figures S13 and S14). Newport, Agona and Bareilly are all polyphyletic serovars (Sangal et al , 2010; Achtman et al , 2012; Cao et al , 2013; Timme et al , 2013; Zhou et al , 2013) and Typhimurium is substantially more diverse than Typhi (Lan et al , 2009; Bell et al , 2011; Barco et al , 2015). Thus, there is a noticeable but imperfect correlation between uniformity of P22-like prophage contents and overall serovar genetic uniformity.…”

Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli

“…In contrast, group H8/H11was closer to O103:H25 strains than to O103:H2 strains based on subtype I-E cas sequences. Thus, concatenated subtype I-E cas genes could not be used to determine the same phylogenies as those found in genomic comparisons among serotypes (35).…”

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

“…The use of Salmonella CRISPR genotypes, either alone (39) or in combination with gene polymorphisms present in virulence-associated genes (35,40), has strongly improved the ability to separate Salmonella strain collections into individual outbreak isolates. Thus, elevated acquisition and turnover of CRISPR spacers of type I-F and I-E CRISPR-Cas systems in Y. pestis and Salmonella spp., respectively, do allow for high-resolution typing.…”