Polymorphic locus sequence typing of foodborne pathogens

Strain typing plays a central role in detection and investigation of foodborne outbreaks, particularly those mediated by Salmonella, Listeria, and Shiga toxigenic E. coli (STEC). To a much lesser extent, strain typing is used by food processors to monitor pathogens within their facilities (e.g., introduction of new strains or persistence of established strains), although increasing this practice would undoubtedly reduce outbreaks. The gold standard for strain typing has been pulsed-field gel electrophoresis (PFGE), but its multiple disadvantages have encouraged development of alternative methods, in particular whole genome sequence-based single nucleotide polymorphism analysis (WGS-SNP). Although providing high resolution, WGS-SNP requires major investments in equipment, reagents, and personnel, largely limiting its use to government-supported labs. Neither PFGE nor WGS-SNP are practical alternatives for food processors, and government labs would also benefit from a complementary sequence-based typing approach that is more rapid, less costly, and user-friendly. MicrobiType was founded in 2014 to address this need. Its technology platform ? polymorphic locus sequence typing (PLST) ? is based on standard PCR and dideoxy sequencing, and is hence simple, affordable, and robust. Its novelty is in its targeting of specific genomic loci (patent pending) that have been bioinformatically determined to be the most phylogenetically informative, as a consequence of highly polymorphic tandem repeats. This Phase I proposal will build upon recently published and commercially implemented PLST services for Salmonella and Listeria by developing and evaluating similar services for STEC, along with the relatively neglected but increasingly important foodborne pathogens Campylobacter and Vibrio parahaemolyticus.