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Title: Single nucleotide polymorphisms that differentiate two subpopulations of Salmonella Enteritidis within phage type.

Author
item Guard, Jean
item Morales, Cesar
item Cray, Paula
item Gast, Richard

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/23/2011
Publication Date: 9/26/2011
Citation: Guard, J.Y., Morales, C., Cray, P.J., Gast, R. K. 2011. Single nucleotide polymorphisms that differentiate two subpopulations of salmonella enteritidis within phage type. BMC Research Notes. 4:369

Interpretive Summary: Salmonella Enteritidis is the world’s leading cause of human salmonellosis. It has only recently become feasible to do whole genome analysis of multiple bacterial genomes for the purpose of locating all differences between isolates implicated in outbreaks. It is also difficult to look at collections of genetic differences to know which ones alter the behavior of bacteria in a way that impacts their ability to cause disease in people. By using stringent phenotypic assays to evaluate the ability of the pathogen to contaminate eggs and to form biofilm, strains of Salmonella Enteritidis were selected for the purpose of comparing their whole genomes. Results indicate that very little genetic change is needed to define genetic lineages of Salmonella Enteritidis that vary in their ability to contaminate eggs, colonize the poultry environment and to otherwise be pathogenic. These results support that it may be possible to identify certain genes that are of more value than others for assaying the outbreak potential of Salmonella Enteritidis

Technical Abstract: Salmonella enterica serovar Enteritidis is currently the world’s leading cause of salmonellosis, in part because of its ability to contaminate the internal contents of eggs. Comparative whole genome mutational mapping of two PT13a strains that historically varied in the ability to contaminate eggs and to form biofilm was achieved using high density tiling of fluorescently labeled DNA samples with overlapping primers designed from a PT4 reference genome. A total of 250 sequence-confirmed single nucleotide polymorphisms were detected. Polymorphisms differentiating the PT13a subpopulations ranged in size from single base pair substitutions to a deletion of 215bp. A total of 15 polymorphisms (3 in egg-contaminating PT13a 21046 and 12 in biofilm forming PT13a 21027) altered coding sequences of 16 genes, because one deletion created a fusion of two open reading frames. Less than 0.01% of the genome was different between the two PT13a subpopulations, which varied in virulence potential. However, 1.3 and 1.6% of genes, respectively, diverged in sequence for PT13a 21046 and PT13a 21027 from the reference genome (excluding synonymous and intergenic polymorphisms). Codon analysis suggested that nucleotide substitutions involving the acidic amino acids aspartate and glutamate occur frequently. None of the polymorphisms occurring in intergenic regions had obvious associations with known regulatory elements. An interval map constructed by cross-referencing annotation of S. Enteritidis polymorphisms to the S. Typhimurium LT2 genome located 2 genomic differences between S. Enteritidis and S. Typhimurium that have not yet been reported, suggesting SNP interval mapping between Salmonella serotypes might be useful for plotting larger genome rearrangements. Overall, mutation was skewed towards non-synonymous rather than synonymous mutation, suggesting that adaptive radiation rather than randomly occurring genetic drift is driving evolution of S. Enteritidis.