Rapid pan-fungal detection and quantification


Researchers at TGen and Northern Arizona University have developed technology to rapidly detect and quantify the total fungal load from human, animal, and environmental samples without requiring priori knowledge of the fungi present in a sample.  This technology enables quicker and more accurate diagnosis of fungal infections in clinical medicine and public health arenas, measurement of fungal abundance changes over time in response to treatment or among multiple study groups, and assessment of fungal diversity in environmental studies.  Additionally, the technology can be used to create a fungal clone library used for identification and quantification of individual fungal species, and in conjunction with quality monitoring technology in industries such as pharmaceutics and food production.


Fungal infections are underdiagnosed in a clinical setting due to the low sensitivity of fungal cultures and are an important cause of disease, especially with respect to immunocompromised patients.  Traditional methods of detecting fungi, such as culturing, serological detection of antigens, molecular test panels, and next generation sequencing, do not provide broad coverage or quantitative results, and may be prohibitively expensive due to the required complex analysis.  Customary methods of measuring fungal abundance, such as biochemical methods targeting ergosterol, chitin, or fatty acid profiles, further require performing an extraction.  Other alternatives to measuring fungal abundance, such as microscopy or quantitative culturing, are time consuming, subject to operator error, and lack broad coverage.


Researchers at TGen and Northern Arizona University developed pan-fungal TaqMan® quantitative polymerase chain reaction (qPCR) assays (FungiQuant) targeting conserved regions of the fungal 18S rRNA gene.  These assays allow the fungal diversity to be rapidly detected in a real-time PCR format, followed by highly sensitive sequencing based on characterization to detect, quantify, and characterize the fungal population in a single test. In validation, the assay successfully matched 90.0% of the thousands of fungal species analyzed and 91.4% of the over one thousand fungal genera analyzed, confirming the ability to provide comprehensive coverage against fungal diversity and a marked improvement over previously published broad coverage qPCR assays.  Further, the assay delineates between fungal genes and other non-target human or contaminating DNA, increasing the accuracy of the detection and quantification results. 


Link to Issued US Patent 8,722,335


Link to Issued US Patent 9,434,986


Link to Issued AU Patent 2011209624 A1


Link to Issued CA Patent 2803401 A1


Link to Granted EP Patent 2529034 A2 [Validation in CH, GB, DE, FR, IE]

Patent Information:
For Information, Contact:
Katie Bray
Intellectual Property Counsel
The Translational Genomics Research Institute
Cindy Liu
Sergey Kachur
Lance Price
Paul Keim