Development of a Real-time PCR to Detect Genotypes A and B in Flavobacterium psychrophilum

Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is classified into two genotypes (A and B) based on peptidyl-prolyl cis-trans isomerase C (PPIC) gene polymorphism. These are routinely detected using restriction fragment length polymorphism of the PCR amplicon (PCR-RFLP). Since this method is difficult and time-consuming, a simple method is required. Here we developed a new method using real-time PCR assay (TaqMan probe assay) to detect single nucleotide polymorphism (SNP) in PPIC region. We designed the probes on a SNP site and performed TaqMan probe genotyping. The results obtained using this method was in line with those of RFLP. This new method could easily and rapidly determine F. psychrophilum genotypes.