Data analysis
Antibiotic resistance genes were identified using the Resfinder . SNPs between the whole genomes of the sequenced Salmonella Enteritidis strains in this study and those of the Korean SalmonellaEnteritidis strains deposited in the public database were identified and aligned with the PhaME using default parameter. The genomic sequence ofSalmonella Enteritidis P125109 strain (GenBank no. NC011294) was used as reference genome for SNP calling. A whole genome SNP tree was constructed based on 819 SNPs generated by the PhaME using the RAxML, with the General Time Reversible gamma substitution model and 100 bootstrap replicates. Plasmids were compared using the BLAST Ring Image Generator (BRIG) and the MAUVE .