Discovery of Salmonella signature SNPs by microarrays.

DESCRIPTION (provided by applicant): To meet the challenge of bio-terrorism, pathogen genome sequencing with a view to the development of new reagents and applications is a high priority of NIAID. Salmonella is a NIAID Category B pathogen. Worldwide, Salmonella typhi is responsible for 16 million cases of typhoid fever and 600,000 deaths annually. Previous Samonella outbreaks in the United States have resulted from the deliberate anthropogenic introduction of Salmonella typhi to cause typhoid fever and Salmonella typhimurium to cause gastroenteritis. The goal of this research is to identify polymorphic loci in Salmonella to enable rapid and accurate identification of Salmonella subspecies and strains. To this end, we will use high-density oligonucleotide microarray (HDOMA) technology to re-sequence the genomes (and associated plasmids) of 44 representative strains of Salmonella, including 15 strains of S. typhi, 15 strains of S. typhimurium, two strains each of S. enterica subspecies II, IlIa, IIIb, IV, VI, and VII, and two strains of S. bongori. We will then develop and employ a Salmonella genotyping HDOMA to characterize 8000 polymorphic loci we discover in the resequencing phase in a total of 130 strains of Salmonella, including the strains discussed above plus 30 additional strains of S. enterica subspecies I; 8 additional strains each of S. enterica sub-species II, IlIa, IIIb, IV, VI, and VII; and 8 additional strains of S. bongori. These data will be used to establish a Salmonella comparative genome sequence resource containing the strain resequencing data and a Salmonella genotype database containing the strain genotype data. These resources should prove useful in characterizing the epidemiology of Salmonella outbreaks. Successful application of HDOMA-based polymorphism discovery in this study could be extended to characterizing variation in other sequenced microbial pathogens.