Purpose: A comparative whole genome single nucleotide polymorphism (SNP) analysis of Salmonella Enteritidis strains isolated in Brazil over a period of 48 years was performed to check the diversity of the strains in the pre- and postpandemic period.
Methods: DNA from 267 Salmonella Enteritidis strains isolated from food (85), humans (113), chickens (52) and the farm environment (17) in Brazil between 1968 and 2016 were sequenced using the Illumina Nextseq platform. The sequencing reads were mapped to the reference strain Salmonella Enteritidis P125109 to build a SNP
matrix and construct the phylogenetic tree. We also included 30 Salmonella Enteritidis strains isolated in the United States in the analysis for comparison purposes.
Results: Based on the SNP analysis, 18 of the 26 strains isolated until 1993 clustered together and in a different cluster from the strains isolated between 1994 and 2016. The United States strains clustered together in a separated cluster. We analyzed the genomic diversities of Salmonella pathogenicity islands, Salmonella genomic islands and other virulence factors.
Significance: The study demonstrates that use of next-generation sequencing identifies stable SNP targets that can be used for differentiating closely related Salmonella Enteritidis isolates, providing a better understanding of virulence and evolutionary history. The results suggest a genomic difference among strains isolated before and after the pandemic in Brazil, which helps to explain the emergence and the outbreak transmission dynamics of Salmonella Enteritis in Brazil after the mid-90s.