Project Number: 6612-32000-007-02
Project Type: Nonfunded Cooperative Agreement

Start Date: Jun 15, 2009
End Date: Jun 14, 2012

Objective:
1) Develop new knowledge about evolution occurring in Salmonella enterica and 2) develop molecular typing tools that will help identify, detect, impede and control food- and water-borne disease.

Approach:
In order to deal with the combinatorial complexity presented by the Salmonella bacterium, there is a need for receiving and processing thousands of strains, performing massive amounts of sequencing, conducting downstream analysis and then organizing a database that will produce a fine map of critical changes occurring in the genome (fine genome map). The Environment Research Institute (ERI) in Ireland has received funds to establish a high-throughput molecular evolution group with a strong focus on Salmonella enterica. The ERI group is being fed strains from the international community (Institut Pasteur in Paris, Health Protection Agency in London, Sanger Institute in Cambridge, Food and Drug Administration in Washington, Sidney Kimmel Cancer Center in San Diego, plus other laboratories in Bonn, Africa, Philadelphia and elsewhere around the world). The ERI will perform Multilocus Seqence Typing (MLST), other types of fingerprinting and high resolution sequence-based typing that will locate single nucleotide polymorphisms (SNPs) and other small-scale evolutionary events that tend to escape detection by current typing methodologies. Using a set of proprietary strains, USDA has independently identified a set of small-scale polymorphisms, which differentiate strains that vary in virulence behavior within one serotype, namely Salmonella enterica serovar Enteritidis. More specifically, the set of polymorphisms distinguish between subpopulations occurring within a single phage type lineage, namely PT13a. The USDA strains vary in their ability to contaminate eggs, to grow to high cell density, to form biofilm and to produce a type of capsule called HMM LPS. Most of the characterized polymorphisms are SNPs, but there are a few deletions not exceeding 500 contiguous base pairs that have been located. The USDA Salmonella Enteritidis SNP Set (USDA-SE-SNP SET) has been published initially as putative polymorphisms and then as confirmed polymorphisms after sequencing. The database is available at the National Center for Biotechnology Information (currently at http://www.ncbi.nlm.nih.gov/genomes/static/Salmonella_SNPS.html). USDA would like to contribute its foundation strains and other strains in its collection that have been used to develop the USDA-SE-SNP SET to the ERI for high-throughput analyses in order to aid development of the fine genome map of Salmonella enterica. USDA would like the SET assessed for its usefulness as a separate typing strategy when compared to other SNPs that are independently identified by the ERI as suitable for analysis of Salmonella enterica in general. Each polymorphism in the USDA-SE-SNP SET will be assigned a unique identifier to aid collaboration and discussion of results. For example, polymorphisms will be accessioned as USDA-SEnt1 and thereon consecutively.