ArticleBMC genomics2014
High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Outbreak investigations ofEpidemiology and infection · 2024Article
- Antimicrobial resistance genes, virulence markers and prophage sequences inCurrent research in microbial sciences · 2022Article
- Evaluation of the use of CRISPR loci for discrimination ofAIMS microbiology · 2022Article
- The Salmonella enterica Serovar TyphiJournal of bacteriology · 2020Article
- An UnusualFrontiers in microbiology · 2020Article
- Article
- Complete Genome Sequences of 12 Isolates ofGenome announcements · 2017Article
- Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity inFrontiers in microbiology · 2017Article
- Whole-genome sequencing targets drug-resistant bacterial infections.Human genomics · 2015Review
- Development of a new molecular subtyping tool for Salmonella enterica serovar Enteritidis based on single nucleotide polymorphism genotyping using PCR.Journal of clinical microbiology · 2014Article
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Authors and funding
7 authors.
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Abstract
backgroundThere is a need to characterize genomes of the foodborne pathogen, Salmonella enterica serovar Enteritidis (SE) and identify genetic information that could be ultimately deployed for differentiating strains of the organism, a need that is yet to be addressed mainly because of the high degree of clonality of the organism. In an effort to achieve the first characterization of the genomes of SE of Canadian origin, we carried out massively parallel sequencing of the nucleotide sequence of 11 SE isolates obtained from poultry production environments (n = 9), a clam and a chicken, assembled finished genomes and investigated diversity of the SE genome.
resultsThe median genome size was 4,678,683 bp. A total of 4,833 chromosomal genes defined the pan genome of our field SE isolates consisting of 4,600 genes present in all the genomes, i.e., core genome, and 233 genes absent in at least one genome (accessory genome). Genome diversity was demonstrable by the presence of 1,360 loci showing single nucleotide polymorphism (SNP) in the core genome which was used to portray the genetic distances by means of a phylogenetic tree for the SE isolates. The accessory genome consisted mostly of previously identified SE prophage sequences as well as two, apparently full-sized, novel prophages namely a 28 kb sequence provisionally designated as SE-OLF-10058 (3) prophage and a 43 kb sequence provisionally designated as SE-OLF-10012 prophage.
conclusionsThe number of SNPs identified in the relatively large core genome of SE is a reflection of substantial diversity that could be exploited for strain differentiation as shown by the development of an informative phylogenetic tree. Prophage sequences can also be exploited for SE strain differentiation and lineage tracking. This work has laid the ground work for further studies to develop a readily adoptable laboratory test for the subtyping of SE.
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