<OL> <LI>To assemble a diverse panel of 10 to 20 STEC O157 isolates from beef and beef cattle environments. <LI>To utilize Comparative Genome Sequencing (CGS) to survey the entire microbial genome of each of 10 STEC beef diversity panel strains and then identify DNA polymorphisms in each strain. <LI>To combine and integrate the new DNA polymorphism data generated from the bovine diversity panel with the existing corresponding data from human STEC O157 isolates to develop a first generation human-animal DNA polymorphism-based STEC O157 typing system.
Approach: We will (a) define optimal selection criteria for and then (b) assemble a panel of at least 10 diverse STEC O157 animal and environmental origin isolates. Purified DNA from these judicially selected isolates will then be provided to NimbleGen to identify and characterize SNPs and indels in the beef isolate panel. Following NimbleGen sequencing, the SNP data will be subjected to bioinformatics data reduction and analysis to identify informative DNA polymorphisms.