Multiplex real-time PCR for detection and quantification of mycotoxigenic Aspergillus, Penicillium and Fusarium

The most agriculturally and economically important classes of mycotoxins are produced by species of Aspergillus, Penicillium, and Fusarium. Rapid methods to detect mycotoxigenic fungi could help prevent mycotoxins from entering the food chain. The purpose of this research was to develop a multiplex real-time PCR assay to detect and quantify multiple species of mycotoxigenic fungi. A pair of broad-spectrum PCR primers was designed for amplification of the internal transcribed spacer (ITS) regions of rDNA from the mycotoxigenic species. An in silico analysis of the primers revealed the presence of amplification in more than 40 Aspergillus species, 23 Fusarium species, and 32 Penicillium species as well as 64 other fungal genera. Genus-specific Taqman probes were designed from the ITS sequences of the most important mycotoxigenic species of Fusarium, Penicillium, and Aspergillus. The specificity of the probes was established against a wide range of fungal species. As a multiplex assay, the linear range of detection was 1 pg to 10 ng of DNA. The assay was validated by analyzing fungal growth in distiller's grain (DG), an animal feedstock that is a by-product when ethanol is produced from corn. This assay could be used as an initial step to evaluate the mycotoxigenic potential of DG and various other agricultural commodities.