Genome maps of eleven Canadian isolates of Salmonella Enteritidis. Genome maps of contiguous DNA fragments of Salmonella Enteritidis isolates (n = 11) obtained following digestion with Nco I restriction enzyme (OpGen Inc., Gaithersburg, MD) were compared to an in silico map of the reference P125109 strain obtained from the GenBank (Accession Number AM933172.1) and all showed high similarity. The two main types of genetic variations observed were single nucleotide polymorphism within the component of the genome shared by all isolates (core genome; also see Table 1) and presence of prophage sequences (accessory genome). Six prophage sequences consisting of 4.0, 8.0, 8.2, 11.5, 14.8 and 42.0 kb depicted on the maps as “Green Square Symbol” were present in the reference genome and all field isolates with the exception of SE 11 which was missing the 8.2 kb prophage. Previously described prophages φSE 10, φSE 12&12A, and φSE 14 (reference ) match the 8.2, 42.0, and 14.8 kb prophage sequences, respectively, both in location and gene content. The unique prophage sequence in the reference genome “Blue Square Symbol” is the P125109 phage and matches previously described φSE20 (reference ). A 28 kb prophage designated as OLF-10058 (3) is depicted as “Red Square Symbol” and was observed in three isolates, namely: SE 7, 10 and 11. The recently described 36 kb ELPHis prophage (reference ) depicted in the maps as “Pink Square Symbol”, was found in all Canadian field isolates except one, SE 9, which was obtained from a clam (Table 3). SE 9 had a unique prophage, termed OLF-10012 “Yellow Square Symbol”, which has not been previously reported as a full 43 kb prophage in Salmonella Enteritidis.