Rapid Identification of Microbial Pathogens – Discovery and Innovation at University of Utah Health

Taxonomer is the engine behind IDbyDNA’s Explify platform. “A key barrier to adoption of next-generation sequencing for infectious disease testing has been the lack of simple, powerful bioinformatics software to turn the data generated by the sequencer into actionable insights. IDbyDNA’s Explify Platform combined with Illumina’s NGS systems and library preparation creates a powerful, comprehensive infectious disease workflow.” — Kathy Davy, Vice President of Clinical Marketing at Illumina.

The rapid identification of microbial pathogens is critical for timely and successful treatments. Improved capabilities in pathogen identification were the focus of a collaboration between physicians and scientists in the departments of Biomedical Informatics, Human Genetics, and Pathology. The product, a computational tool called Taxonomer, uses innovative algorithmic approaches to take next-generation sequencing reads and rapidly return a list of taxonomically classified organisms.

This tool was used to diagnose the cause of community-acquired pneumonia and has become the cornerstone of a University of Utah startup company IDbyDNA Inc. In March of 2020, Illumina announced a global strategic partnership with IDbyDNA Inc., to bring comprehensive next-generation sequencing-based workflows to the global microbiology market.

References:

Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R. J Clin Microbiol. 2016 Apr;54(4):1000.

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R. Genome Biol. 2016 May;17(1):111.

Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G; Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology; Microbiology Resource Committee of the College of American Pathologists. Arch Pathol Lab Med. 2017 Jun;141(6):776.