Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-specific Detection

Single-nucleotide polymorphisms (SNPs) are one of the most common forms of genetic variation and as such are powerful tools for the identification of bacterial strains, their genetic diversity, phylogenetic analysis, and outbreak surveillance. In this study, we used 15 sets of SNP-containing primers to amplify and sequence the target . Based on the combination of the 15-sequence primer sets, each SNP site encompassing forward and reverse primer sequences (620-919 bp) were aligned and an SNP-based marker was designed. Each SNP marker exists in at least two SNP sites at the 3' end of each primer; one natural and the other artificially created by transition or transversion mutation. Thus, 12 sets of SNP primers (225-488 bp) were developed for validation by amplifying the target . Finally, a temperature gradient triplex PCR kit was designed to detect target strains. The selected primers were amplified in three genes (, and ), with fragment sizes of 401, 337, and 232 bp for O157:H7, , and O145:H28, respectively. This allele-specific SNP-based triplex primer assay provides serotype-specific detection of strains in one reaction tube. The developed marker would be used to diagnose, investigate, and control food-borne outbreaks.