ArticleGenome biology and evolution2013
Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
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- Towards decentralization ofFrontiers in microbiology · 2025Article
- Comparative genomic analysis provides new insights into non-typhoidal Salmonella population structure in Peru.Scientific reports · 2024Article
- Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.International journal of molecular sciences · 2024Article
- Genetic Diversity inMicroorganisms · 2024Article
- Genomic and phenotypic characterization ofMicrobial genomics · 2023Article
- Genomic Surveillance ofAntibiotics (Basel, Switzerland) · 2023Article
- The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae.Current microbiology · 2023Article
- Large-scale comparative genomics to refine the organization of the globalMicrobial genomics · 2022Article
- EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.mSystems · 2022Article
- Genome analysis and virulence gene expression profile of a multi drug resistant Salmonella enterica serovar Typhimurium ms202.Gut pathogens · 2022Article
- Article
- Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria.Frontiers in microbiology · 2022Article
- Polyphyly in widespreadFrontiers in public health · 2022Article
- Salmonella Genomics in Public Health and Food Safety.EcoSal Plus · 2021Article
- Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium.G3 (Bethesda, Md.) · 2021Article
- Phylogeny ofMicrobial genomics · 2021Article
19 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles-some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.
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