Single Nucleotide Polymorphism (SNP) Genotyping of E. Coli 0157:H7
Introduction E. coli O157:H7 is a major health problem causing infection in more than 70,000 patients a year in the United States. These infections may be both in large outbreaks as well as isolated sporadic infections in small numbers of individuals. The Center for Disease Control (CDC) typically uses Pulse Field Gel Electrophoresis (PFGE) for identifying an E. coli outbreak, but it is neither a rapid nor inexpensive method. Enzyme immunoassay (EIA) is used in clinics, but the test is too expensive and does not provide rapid results. A need exists for a quick real-time assay that will detect single nucleotides. Description of Technology Michigan State University’s technology utilizes SNP (single nucleotide polymorphism) to classify the O157 strains into clade groupings. The classification into clades is based upon the presence (or absence) of 96 SNPs that vary among the O157 subtypes. Some of these clades were found to be more epidemiologically relevant because they cause more disease than others. In particular, the frequency and distribution of the Shiga toxin genes were found to be important in the progression of the disease and in the types of disease reported. The SNP method is more useful in circumstances of outbreak investigations over current methods because it can directly translate into populating genetics and phylogenetic analysis, thus pinpointing genotypes that can cause disease. As such, it could be useful in determining the precise nature of a patient’s infection, allowing for effective and timely treatment. Key BenefitsRapid, precise, and inexpensive diagnosis of E. coli infection: The SNP genotyping approach is able to provide for a quick real-time assay capable of detecting single nucleotides. Directly pinpoints genotype that causes disease: The SNP method is useful in outbreak investigations because it can directly translate into populating genetics and phylogenetic analysis, thus pinpointing genotypes that can cause disease and allowing for effective and timely treatment.Pathogen tracking: Allows pathogen strain tracking across time and geography Compatible: Works with rapid SNP Stream analysis, so it could be expanded to other strains. ApplicationsClinical testing kits for pathogen infection CDC or state lab outbreak tracking Food supply monitoring Patent Status Patent pending Inventors Thomas Whittam, Shannon Manning, David Alland, Alifiya Motiwala Tech ID TEC2009-0010 Alternative contact due to temporary leave: Nina (Isi) Davis, Technology Marketing Manager, email: davisnin@msu.edu, phone (direct): (517)884-1829.
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