Worldwide comparison of Salmonella Enteritidis genomes with and without the gyrA codon substitution D87Y

David J. Bradshaw II1,2*, Kaitlin A. Tagg3, Bradley L. Bearson4, Hattie E. Webb3, Shawn M.D. Bearson1*

1USDA-ARS, National Animal Disease Center, Ames, Iowa, 50010, U.S.A., Food Safety and Enteric Pathogens Research Unit

2Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, 37831, U.S.A. , Agricultural Research Service Participation Program

3Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Division of Foodborne, Waterborne, and Environmental Diseases

4USDA-ARS, National Laboratory for Agriculture and the Environment, Ames, Iowa, 50011, U.S.A., Agroecosystems Management Research Unit

*Corresponding authors: Shawn M.D. Bearson (shawn.bearson@usda.gov) & David J. Bradshaw II (david.bradshaw@usda.gov)

Salmonella enterica serovar Enteritidis (S. Enteritidis) with decreased susceptibility to ciprofloxacin (DSC) has emerged in the United States, driven by NCBI SNP Cluster PDS000065758 (denoted SE65758) strains with GyrA(D87Y). In the current study, metadata analysis of 79,476 S. Enteritidis genomes worldwide did not identify a similar increase of DSC Enteritidis in non-USA countries. Gene presence/absence differences from pangenomic analysis were not prominent between USA and non-USA SE65758 genomes with GyrA(D87Y), suggesting genetic content differences are not a major contributor to the USA-associated emergence of DSC Enteritidis. Variation between SE65758 genomes with and without GyrA(D87Y) was also not notable, but significant differences were identified between SE65758 and non-SE65758 genomes with GyrA(D87Y), including phage-like regions unique to each. In general, the data suggest the USA specific emergence of SE65758 genomes with GyrA(D87Y) was not solely driven by GyrA(D87Y) or a specific pangenomic element, warranting additional genomic and phenotypic analyses.