Cannabis has a complex microbiome that can, in rare circumstances, contain four Aspergillus species of clinical and regulatory concern. Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus are regulated pathogens in many legal cannabis jurisdictions in the U.S. (21 states) and Canada. Molecular methods that interrogate the DNA of these pathogenic species have been adopted due to the challenges in resolving these species from other benign and ubiquitous Aspergillus species with culture or plating methods. Despite the rapid and competitive adoption of qPCR in this field, discordances still arise and require resolution. We describe the use of two different next generation sequencing methods to better characterize the targets of Aspergillus qPCR assays used in the cannabis field.

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