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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Analysis of Poultry-Associated Salmonella enterica to Identify and Characterize Properties and Markers Associated with Egg-Borne Transmission of Illness

Location: Egg Safety and Quality

Title: Evolutionary relationships between known serotypes and unique variants of Salmonella enterica as determined by ISR secondary structure

Authors
item Guard, Jean
item Desai, Prerak -
item Mcclelland, Michael -

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: November 13, 2013
Publication Date: January 27, 2014
Citation: Guard, J.Y., Desai, P., Mcclelland, M. 2014. Evolutionary relationships between known serotypes and unique variants of Salmonella enterica as determined by ISR secondary structure. International Poultry Scientific Forum. p. 5.

Technical Abstract: Intergenic Sequence Ribotyping (ISR) near the dkgB gene of Salmonella enterica subspecies I genome is now used to assign serotype in a manner that is largely concordant with the historical Kauffman-White-LeMinor (KWL) antibody-based scheme. ISR has a number of advantages over the KWL scheme, and it can be used to i) assign serotype to strains lacking O- and/or H-antigens, ii) detect mixtures of serotypes, and to iii) find strain variation within a single serotype as designated by the KWL scheme. Other DNA-based methods detect genomic variation within a single serotype, but ISR is more suitable for use in larger scale projects that continuously monitor environments due to its simplicity of application. A limitation of ISR is that sequence cannot be evaluated by phylogenetic analysis for evolutionary relatedness, because there is a disproportionate impact of size of sequence on clade formation and no parameters have been found to circumvent inappropriate clustering. We wanted to know if comparing secondary structures generated from ISR sequences was a better approach for understanding the evolutionary relationship within Salmonella enterica serotypes. To explore this issue, secondary structures were generated from a database of ISR sequences and then compared for similarity. Results were that strains with ISRs of different sizes but with common KWL serotype shared considerable structure. Size differences within a KWL serotype were observed as hairpins projecting from a similar backbone. Serotypes Newport and the Group D poultry-associated serotypes Gallinarum, Pullorum and Enteritidis were revealed to have new variants that maintained structural similarities regardless of ISR size. We suggest that the roadblock preventing assignment of unique ISR variants within an evolutionary framework of existing serotypes can thus be overcome by recognizing that blocks of sequences rather than individual bases are better for assessing evolutionary relatedness. ISR secondary structure to assign serotype relatedness within Salmonella enterica subspecies I may be adequate to recognize new variants within serotypes, but other approaches for studying blocks of nucleotides as individual elements should also be assessed.

Last Modified: 12/22/2014
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