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PathoGene Reels in $750K in Seed Funds to Develop PCR-Based Infectious Disease Dxs

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By Ben Butkus

Upstart molecular diagnostics firm PathoGene said yesterday that it has raised $750,000 in seed money, exceeding its original goal of $500,000, to fund clinical evaluation of its PCR-based molecular assays for difficult-to-treat and drug-resistant infectious diseases.

In addition, the company hopes to use the funding and potential grant money to outlicense its assays to existing in vitro diagnostic providers, who would then take the tests to market, Todd Snowden, PathoGene's president, said this week.

PathoGene, based in Flagstaff, Ariz., was founded in 2008 based on intellectual property licensed from the Translational Genomics Research Institute and Northern Arizona University. The IP is based on technology developed in the laboratory of Paul Keim, director of TGen's Pathogen Genomics division and professor of microbiology at NAU.

The company is developing and validating infectious disease assays for clinical use based primarily on disease targets, genetic biomarkers, and PCR primers developed in Keim's laboratory.

According to its website, PathoGene's assays could also be re-developed for other molecular technologies using the same targets; however, Snowden told PCR Insider that the assays would likely remain PCR-based for the foreseeable future.

"At this point I think they're all going to be PCR based because that's really what's being implemented in the clinical environment right now," Snowden said. "As next-generation sequencing and other technologies come to fruition and are used in the clinical environment, then we would pursue those, as well.

"Certainly the targets that have been defined for the diseases and resistance could be used with other technologies," Snowden added. "But if you built them for some other technology now, no one is going to be able to use them clinically, and we're all about getting this into the clinical environment to impact patient care."

PathoGene will initially focus on assays to diagnose methicillin-resistant Staphylococcus aureus infections and to determine the antibiotic resistance profile of the infection; followed by assays to diagnose Valley fever, a fungal disease that is caused by one of two strains of Coccidioides and is isolated to the Phoenix-Tucson corridor, the California San Joaquin valley, and a few other pockets in the Southwest US.

"Valley fever is an orphan disease that affects a very small geographical area, but basically there is no good diagnostic for it," Snowden told PCR Insider. "Right now, the average time to diagnosis from when a patient first seeks medical care is about five months. It doesn't affect huge numbers of people … but it's very debilitating, and there is really no good way to diagnose it today."

PathoGene will create diagnostic assays for Valley fever in both humans and animals, and currently has studies ongoing in both clinical and veterinary environments, Snowden said. PathoGene is also developing diagnostic assays for influenza, including H1N1 strains.

PathoGene's assays are currently being developed around TaqMan real-time PCR technology, but with "a variety of different probe technologies depending on what is required to produce the most specific and sensitive assay for a particular disease," Snowden said.

"For example, the probe technology we're using in our Valley fever assay is different from the technology we're using in the MRSA assays," he added. "It just depends on what is required to produce the best result, and also the lowest cost, because that’s important once you get into the clinical environment."

The company will also continue to work closely with Keim's laboratory to evaluate potential discoveries for conversion into diagnostic assays. Keim is known for his work in DNA-based pathogen identification, particularly for anthrax.

A search of the US Patent and Trademark Office patent database revealed that he is named as an inventor on patents and patent applications surrounding PCR-based detection and diagnosis of infectious agents such as Bacillus anthracis; Burkholderia pseudomallei, the causative agent of melioidosis; pathogenic E. coli; and Mycobacterium tuberculosum. It is unclear whether PathoGene plans to pursue diagnostic development in any of these disease areas.

"Currently all of our technology is out of Dr. Keim's lab, and the company was really started because he has been doing work for 25 plus years, and has made a lot of very interesting discoveries and developed some very interesting assays, and none of it has ever been commercialized," Snowden said.

PathoGene's overarching business model is to "in-license, develop, and outlicense" technology; and the company will also pursue IP developed at research institutes besides TGen and NAU, Snowden said. PathoGene is particularly interested in licensing IP that is "consistent with its focus on infectious diseases where strain identification and/or antimicrobial resistance is important to clinical decision making and or disease surveillance," the company said.

Meantime, the company's end goal is to develop assays based on these molecular targets and license them to larger in vitro diagnostic companies. PathoGene will make licenses available for research use, clinical diagnostics, and veterinary markets; and its current licensing opportunities include MRSA identification and resistance profiling, influenza A and H1N1 identification, and Tamiflu resistance identification, according to its website.

Snowden said that PathoGene will attempt to strike deals with companies that offer both "large-volume-type platforms" designed for more centralized diagnostic testing and newer platforms directed at "smaller community hospital-based labs, the moderate complexity and random access-type analyzers." The latter types of platforms are "really being driven into the community hospital setting because of the movement of PCR-type techniques into infectious disease."

PathoGene's offices are currently located in the Northern Arizona Center for Emerging Technologies, a technology accelerator partially funded by the city of Flagstaff.

The $750,000 in seed money is the first outside investment received by PathoGene, which has thus far subsisted on contributions from its founders. "We've also submitted grant applications, and hope to fund some future development using grant money — like everybody else," Snowden said.

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