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High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis

Dele Ogunremi1*, John Devenish1, Kingsley Amoako2, Hilary Kelly1, Andrée Ann Dupras1, Sebastien Belanger1 and Lin Ru Wang3

Author Affiliations

1 Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario K2H 8P9, Canada

2 Lethbridge Laboratory, Canadian Food Inspection Agency, Township Road 9-1, P. O. Box 640, Lethbridge, Alberta T1J 3Z4, Canada

3 Greater Toronto Area Laboratory, Canadian Food Inspection Agency, 2301 Midland Avenue, Scarborough, Ontario M1P 4R7, Canada

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BMC Genomics 2014, 15:713  doi:10.1186/1471-2164-15-713

Published: 25 August 2014



There 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.


The 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.


The 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.

Salmonella Enteritidis; Genomes; Core; Accessory; Single nucleotide polymorphism; Subtyping; Tracking