HybProbes-based real-time PCR assay for specific identification of Streptomyces scabies and Streptomyces europaescabiei, the potato common scab pathogen.

Xu, R., Falardeau, J., Tyler, J.A., and Tambong, J.T. (2015). "HybProbes-based real-time PCR assay for specific identification of Streptomyces scabies and Streptomyces europaescabiei, the potato common scab pathogen.", Letters in Applied Microbiology. doi : 10.1111/lam.12522  Access to full text

Abstract

The aim of this study was to develop and validate a HybProbes-based real-time PCR assay targeting the trpB gene for specific identification of S. scabies and S. europaeiscabiei. Four primer pairs and a fluorescent probe were designed and evaluated for specificity in identifying S. scabies and S. europaescabiei, the potato common scab pathogens. The specificity of the HybProbes-based real-time PCR assay was evaluated using 46 bacterial strains, 23 Streptomyces strains and 23 non-Streptomyces bacterial species. Specific and strong fluorescence signals were detected from all 9 strains of S. scabies and S. europeascabies. No fluorescence signal was detected from 14 strains of other Streptomyces species and all non-Streptomyces strains. The identification was corroborated by the melting curve analysis that was performed immediately after the amplification step. Eight of the 9 S. scabies and S. europeascabies strains exhibited a unique melting peak, at Tm of 69.1 °C while one strain, Warba-6, had a melt peak at Tm of 65.4 °C. This difference in Tm peaks could be attributed to a guanine to cytosine mutation in strain Warba-6 at the region spanning the donor HybProbe. The reported HybProbes assay provides a more specific tool for accurate identification of S. scabies and S. europaeiscabiei strains.

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