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PathoQuest to Launch Clinical Trials of NGS-Based Infectious Disease Diagnostic Assay


PathoQuest is preparing clinical trials of its next-generation sequencing-based infectious disease diagnostic assay, which it hopes to launch in Europe in early 2015 and later in the US, initially for use in immunocompromised patients.

The Paris-based company, a spinout of the Pasteur Institute and the Ecole Nationale Vétérinaire d'Alfort, ENVA, recently raised €3.8 million ($5 million) in a Series B private equity funding round that it will use to finance the trials as well as to develop its technology further.

While many firms are launching sequencing-based diagnostic assays for inherited diseases or to classify cancers, PathoQuest is among the few that applies the technology to diagnose infectious diseases, according to Luc Boblet, the company's CEO. "There is a lot of unmet need," he told Clinical Sequencing News.

Boblet and Marc Eloit, a professor of virology at ENVA and PathoQuest's president and CSO, founded the company in 2010. The following year, the firm raised €2 million from Kurma Life Science Partners, which was joined in the latest round by Idinvest and Aurinvest.

PathoQuest is housed in a new building within the Pasteur Institute campus in downtown Paris. The company has 12 employees, most of them biologists and bioinformaticians, and plans to increase its staff by at least a third next year.

The company's expertise lies in sample preparation for sequencing pathogens and in downstream data analysis to identify them. PathoQuest owns intellectual property around the selective extraction and amplification of pathogen DNA from host samples, and it has proprietary algorithms and databases for the taxonomic identification of pathogens from sequencing data.

Its workflow is compatible with any next-gen sequencing platform but the firm currently has an Ion Torrent Proton installed. In order to be able to increase its computing capabilities quickly if needed, the company uses cloud computing and follows a 'software as a service' business model.

Initially, PathoQuest focused on discovering new pathogenic viruses, mainly as part of research projects, but when the new benchtop sequencers from Illumina and Ion Torrent with their short run times appeared on the scene, "we switched from pathogen discovery to [infectious disease] diagnosis," Boblet said.

In its first clinical trial, to be launched in September, the company plans to validate its diagnostic assay, which is based on whole-genome sequencing, and to compare it against standard methods. "One of the key advantages of NGS is, you don't have to define the target a priori," Boblet said. "You can offer to the clinicians the full list of pathogens" present in a sample.

The main objective of the trial is "to demonstrate for the first time the clinical relevance of our technology" in order to "convince clinicians to prescribe our assay," he said.

For the trial, which PathoQuest is conducting in collaboration with the Hôpital Necker-Enfants Malades in Paris over 12 months, the company will analyze samples from about 300 immunocompromised patients with infections. It will compare the results with those of the hospital, which will use conventional approaches such as cell culture, PCR, and immunoassays.

Infections in immunocompromised patients can be caused by a wide range of pathogens, including viruses, bacteria, and fungi, including highly mutated drug resistant strains, and their detection may require a series of assays that can take 14 days to perform, Boblet said. Even after that, a diagnosis cannot be made in about 30 percent of cases. PathoQuest's assay, on the other hand, is comprehensive and only requires two days. Long term, the company plans to reduce the turnaround time to eight hours, which would allow it to offer the test to patients in critical care, which Boblet said would be the biggest market.

The identification of pathogens will help clinicians prescribe the best treatment for the infection. The potential for cost savings is great: "If you just save two to four days of hospitalization, that's going to generate massive savings for the entire [healthcare] system," he said.

Around mid next year, PathoQuest plans to launch a clinical trial in the US as well, where it is currently in discussions with potential partners. For that, it will transfer its sample prep technology to a US CLIA lab, which will also conduct the sequencing. PathoQuest will then analyze the data and send back a report containing the "entire flora of pathogens."

Following the trials, the company plans to launch a diagnostic infectious disease assay for immunocompromised patients in Europe in 2015, and in the US several months later. It is also considering assays for other indications, especially in the US, Boblet said, but he declined to provide further details for competitive reasons.

For the commercial assay, PathoQuest plans to offer a sample prep reagent kit in collaboration with an "established player" in the field, and is in early discussions with potential partners. In addition, it will offer distributed analysis services through its cloud computing model. "We clearly plan to work as a counterpart to the established diagnostic players by offering just the missing part, the upstream and the downstream," Boblet said.

The company will face some competition in the infectious disease arena from others betting on next-gen sequencing. For example, last year, Pathogenica launched a targeted sequencing-based kit on the Ion Torrent PGM that screens for 12 common pathogens in hospital-acquired infections (CSN 9/26/2012). Also, Qiagen recently said that it sees opportunities for next-gen sequencing in infectious disease diagnostics (CSN 7/17/2013).

Also, OpGen, which provides optical mapping technology, just opened a CLIA laboratory that will provide analysis services for monitoring and identifying healthcare-associated infections and human pathogens, combining next-gen sequencing, real-time PCR, and whole-genome mapping (GWDN 7/23/2013).