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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg Safety & Quality Research » Research » Publications at this Location » Publication #352565

Research Project: Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments

Location: Egg Safety & Quality Research

Title: Whole genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

Author
item Guard, Jean
item Cao, Guojie - Food And Drug Administration(FDA)
item Luo, Yan - Food And Drug Administration(FDA)
item Baugher, Joseph - Food And Drug Administration(FDA)
item Davison, Sherrill - University Of Pennsylvania
item Yao, Kuan - Food And Drug Administration(FDA)
item Hoffman, Maria - Food And Drug Administration(FDA)
item Zhang, Guodong - Food And Drug Administration(FDA)
item Likens, Nathan
item Bell, Rebecca - Food And Drug Administration(FDA)
item Zheng, Jie - Food And Drug Administration(FDA)
item Brown, Eric - Food And Drug Administration(FDA)
item Allard, Marc - Food And Drug Administration(FDA)

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2019
Publication Date: 4/9/2019
Citation: Guard, J.Y., Cao, G., Luo, Y., Baugher, J.D., Davison, S., Yao, K., Hoffman, M., Zhang, G., Likens, N., Bell, R., Zheng, J., Brown, E., Allard, M. 2019. Whole genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s. Genomics. GENO_2018_447_R1.
DOI: https://doi.org/10.1016/j.ygeno.2019.04.005

Interpretive Summary: Salmonella Enteritidis is a foodborne pathogen of global concern because of the high frequency isolated from foods and patients. Genomes of 91 S. Enteritidis strains from intestines and spleens of mice were reported. One genome was closed and completed as a reference genome. The availability of these genomes provides useful information on genomic diversity and invasion capability of S. Enteritidis in Northeastern United States during a time when foodborne outbreaks traced to internal contamination of eggs was prevalent. This work was conducted via a Material Transfer Agreement between USDA and FDA (06-2016).

Technical Abstract: Salmonella enterica serovar Enteritidis (SE), the most commonly reported serovar of human salmonellosis, has been frequently associated with poultry farms, eggs and egg products. Mice are known vectors of SE contamination in these facilities. The objective of this study was to use whole-genome sequencing (WGS) to analyze SE from mice obtained at poultry farms in Pennsylvania. Documenting pathogen diversity can identify reliable biomarkers for rapid detection and speed up outbreak investigations. We sequenced 91 SE isolates from 83 mice (62 spleen isolates, 29 intestinal isolates) caught at 15 poultry farms between 1995-1998 using an Illumina NextSeq 500. We identified 742 single nucleotide polymorphisms (SNPs) capable of distinguishing each isolate from one another. Isolates were divided into two major clades: there were more SNPs differences within Clade B than counterparts in Clade A. All isolates containing antimicrobial resistance genes belong to Subgroup B2. Clade-defining SNPs provided biomarkers distinguishing isolates from 12 individual subgroups, which were separated by farm location or year of collection. Nonsynonymous changes from the clade-defining SNPs proffered a better understanding of possible genetic variations among these isolates. For a broader view of SE diversity, we included data from NCBI Pathogen Detection Isolates Browser, in which subgroups in Clade B formed new SNP Clusters.