ArticlePloS one2013
On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed.
- Molecular epidemiology ofAntimicrobial agents and chemotherapy · 2025Article
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- vSNP: a SNP pipeline for the generation of transparent SNP matrices and phylogenetic trees from whole genome sequencing data sets.BMC genomics · 2024Article
- Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade ofMicrobial genomics · 2023Article
- Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization inFrontiers in public health · 2023Article
- Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014.Transactions of the Royal Society of Tropical Medicine and Hygiene · 2022Article
- Multi-Omics Approach in Amelioration of Food Products.Frontiers in microbiology · 2022Review
- Salmonella Genomics in Public Health and Food Safety.EcoSal Plus · 2021Article
- Whole-Genome Analysis of Multidrug-ResistantPathogens (Basel, Switzerland) · 2021Article
- The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety.Pathogens (Basel, Switzerland) · 2021Review
- Whole genome sequencing and protein structure analyses of target genes for the detection of Salmonella.Scientific reports · 2021Article
- AT Homopolymer Strings inMicroorganisms · 2021Article
- Phylogenetic structure of Salmonella Enteritidis provides context for a foodborne outbreak in Peru.Scientific reports · 2020Article
- Review
- ClosingFrontiers in microbiology · 2020Article
- Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.EFSA journal. European Food Safety Authority · 2019Article
- Multistate outbreak ofEpidemiology and infection · 2019Article
- Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis.Poultry science · 2019Article
- The use of next generation sequencing for improving food safety: Translation into practice.Food microbiology · 2019Review
- Complete Assembly of the Genome of anFrontiers in microbiology · 2019Article
12 more citing papers are in PubMed but not listed here.
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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.
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