Whole Genome SNP Analysis of <i>Salmonella</i> Enteritidis Strains Isolated between 1968 and 2016 in Brazil

Campioni, Fabio; Campioni, Fabio

Tuesday, July 11, 2017

Exhibit Hall (Tampa Convention Center)

Fabio Campioni , University of São Paulo, School of Pharmaceutical Sciences of Ribeirao Preto , Ribeirao Preto , Brazil

George Kastanis , U.S. Food and Drug Administration, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition , College Park , MD

Guojie Cao , U.S. Food and Drug Administration, Center for Food Safety & Applied Nutrition , College Park , MD

Maria Hoffmann , U.S. Food and Drug Administration , College Park , MD

Yan Luo , U.S. Food and Drug Administration , College Park , MD

Alzira Maria Morato Bergamini , Adolfo Lutz Institute , Ribeirao Preto , Brazil

Dalia dos Prazeres Rodrigues , Oswaldo Cruz Foundation , Rio de Janeiro , Brazil

Marc Allard , U.S. Food and Drug Administration , College Park , MD

Juliana Pfrimer Falcao , University of São Paulo, School of Pharmaceutical Sciences of Ribeirao Preto , Ribeirao Preto , Brazil

Introduction: Salmonella Enteritidis emerged after the 1980s as the most common foodborne isolated serovar in several countries. In Brazil the emergence was observed after the 1990s and it is believed that an epidemic and more virulent clone was introduced in the country. This serovar remains as one of the most isolated one from clinical and food sources in Brazil.

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.

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P2-68 Whole Genome SNP Analysis of Salmonella Enteritidis Strains Isolated between 1968 and 2016 in Brazil