title: On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.
abstract: Facile laboratory tools are needed to augment identification in contamination events to trace the contamination back to the source (traceback) of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis). Understanding the evolution and diversity within and among outbreak strains is the first step towards this goal. To this end, we collected 106 new S. Enteriditis isolates within S. Enteriditis Pulsed-Field Gel Electrophoresis (PFGE) pattern JEGX01.0004 and close relatives, and determined their genome sequences. Sources for these isolates spanned food, clinical and environmental farm sources collected during the 2010 S. Enteritidis shell egg outbreak in the United States along with closely related serovars, S. Dublin, S. Gallinarum biovar Pullorum and S. Gallinarum. Despite the highly homogeneous structure of this population, S. Enteritidis isolates examined in this study revealed thousands of SNP differences and numerous variable genes (n = 366). Twenty-one of these genes from the lineages leading to outbreak-associated samples had nonsynonymous (causing amino acid changes) changes and five genes are putatively involved in known Salmonella virulence pathways. While chromosome synteny and genome organization appeared to be stable among these isolates, genome size differences were observed due to variation in the presence or absence of several phages and plasmids, including phage RE-2010, phage P125109, plasmid pSEEE3072_19 (similar to pSENV), plasmid pOU1114 and two newly observed mobile plasmid elements pSEEE1729_15 and pSEEE0956_35. These differences produced modifications to the assembled bases for these draft genomes in the size range of approximately 4.6 to 4.8 mbp, with S. Dublin being larger (∼4.9 mbp) and S. Gallinarum smaller (4.55 mbp) when compared to S. Enteritidis. Finally, we identified variable S. Enteritidis genes associated with virulence pathways that may be useful markers for the development of rapid surveillance and typing methods, potentially aiding in traceback efforts during future outbreaks involving S. Enteritidis PFGE pattern JEGX01.0004.
authors: Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America. marc.allard@fda.hhs.gov
authors: Marc W
authors: MW
authors: Allard
authors: Yan
authors: Y
authors: Luo
authors: Errol
authors: E
authors: Strain
authors: James
authors: J
authors: Pettengill
authors: Ruth
authors: R
authors: Timme
authors: Charles
authors: C
authors: Wang
authors: Cong
authors: C
authors: Li
authors: Christine E
authors: CE
authors: Keys
authors: Jie
authors: J
authors: Zheng
authors: Robert
authors: R
authors: Stones
authors: Mark R
authors: MR
authors: Wilson
authors: Steven M
authors: SM
authors: Musser
authors: Eric W
authors: EW
authors: Brown
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D016521:Electrophoresis, Gel, Pulsed-Field; D014644:Genetic Variation; D005828:Genetics, Population; D016680:Genome, Bacterial; D023281:Genomics; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012477:Salmonella enteritidis / Q000235:genetics* / Q000472:pathogenicity*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D026801:Synteny / Q000235:genetics; D014481:United States; D014774:Virulence
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