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PathoQuest Begins Cost-Benefit Study of Bloodstream Infection Test in Immunocompromised Patients

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NEW YORK (GenomeWeb) – French startup PathoQuest announced earlier this month that it has enrolled the first patient for a new cost-benefit study of its metagenomic next-generation sequencing test, iDtect, to identify pathogenic bacteria and viruses in the bloodstream of immunocompromised patients, beginning with febrile neutropenia cases.

As PathoQuest initiates the study, called IDENTIFY, in Paris, it is also eyeing the US market where it hopes to partner with laboratories to offer iDtect as a laboratory-developed test (LDT).

Founded as a spinout of The Pasteur Institute in Paris in 2010, PathoQuest's test integrates proprietary sample prep, untargeted next-generation sequencing, and a database of bacterial and viral genomic sequences to diagnose bloodstream infections (BSI). PathoQuest CEO and President Jean-François Brepson explained that the firm wants to minimize the time between sampling and laboratory processing.

Microbial diagnosis in the hospital setting can be challenging because immunocompromised patients are susceptible to numerous infectious and opportunistic pathogens, whose nature depends on the specific type of immunodeficiency, such as febrile neutropenia.

PathoQuest's iDetect assay, which is CE marked, is designed to identify more than 1,200 bacterial and viral pathogens in a single blood sample from a patient. Brepson said that PathoQuest decided to detect nucleic acids from whole infectious organisms, rather than cell-free pathogenic DNA in the bloodstream. In addition, he explained the assay's sample prep step allows the researcher to detect both DNA and RNA viruses.

Brepson noted that iDetect uses five milliliters of blood, which decreases the amount of human DNA in the sample before library preparation. The assay's database is regularly updated and curated by the firm's researchers, and the fully automated pathogen identification step produces a report in 15 minutes. According to Brepson, the overall process, from sample collection to the diagnostic report, requires around two days.

The ongoing IDENTIFY study will examine the performance of iDetect to find pathogens that cause BSIs in groups of immunocompromised patients. Centered at the microbiology department at the Saint Louis Hospital in Paris, the trial initially aims to enroll about 100 adult and pediatric patients by the end of 2018.

Brepson explained that the "medico-economic" study was prompted by the results of a proof-of-concept study published in Clinical Microbiology and Infection in January 2017. In the study, researchers compared iDetect with conventional microbiological methods for initial diagnosis of infection in 101 immunocompromised patients. The team found that iDtect was three times as likely to identify more clinically relevant viruses and bacterial infections than standard methods.

PathoQuest has therefore partnered with the Saint Louis Hospital and the French Society of Microbiology to validate the test's utility in the cost-evaluation study. The two-armed, randomized, comparative study will assess the test's impact on elements such as the duration of a patient's fever, length of hospital stay, level of antibiotic usage, and the need for additional infectious disease testing and biopsy collection. The researchers will then compare the test to standard blood culture results.

"We will [also] use the study to see what kind of ward is required for the patient, [whether] it is a regular room, a negative pressure room, or the intensive care unit," Brepson explained. "At the end, we will aim to generate convincing data to [demonstrate] the [test's] clinical and economic utility."

According to Brepson, PathoQuest's current business model involves charging for each test's diagnostic report, but he declined to disclose how much each test will cost the end user. In France, the firm offers a temporary reimbursed quote through an early access program. Brepson noted that the overall level of reimbursement for each test is currently set at €2,200 ($2,567).

In addition to France, PathoQuest aims to enter the US and a few, undisclosed European countries. While he believes the need for the iDtect is "everywhere," Brepson said that the firm is currently "focusing on France and the US while keeping in mind [specific] reimbursement approaches."

In the US, PathoQuest is separately collaborating with groups such as Memorial Sloan Kettering Cancer Center (MSK) and the Mayo Clinic in order to explore how to better diagnose of patients with febrile neutropenia using the firm's technology. In its partnership with MSK's microbiology lab, PathoQuest will compare iDtect with standard testing methods used to diagnose microbial infections. The Mayo Clinic will similarly use the test in a prospective US study to validate its utility. Brepson highlighted that in the future the firm may also collaborate with various National Comprehensive Cancer Network centers since it is initially focusing on hematology and oncology patients.

PathoQuest is also partnering with Charles River Laboratories to provide next-generation sequencing services in the biologics industry. Brepson noted that while the partnership will use the iDtect technology, the firm will develop a slightly different assay focusing on biological testing geared toward biotech and pharmaceutical companies.

Eventually PathoQuest aims to offer iDtect as a LDT in the US. PathoQuest will favor collaborations with existing US laboratories, including those with microbiology experts, rather than opening its own CLIA-CAP accredited lab. The firm is therefore identifying labs who are interested in adopting the iDtect assay in the future.

In addition, Brepson said the firm is currently developing a new version of iDtect which will include a new biomarker for an antibiotic resistant gene as well multiple fungal species.

Since 2010, PathoQuest has raised about €6.7 million in seed and series A funding from angel investors and European venture capital firms in healthcare. According to Brepson, the firm is finalizing a Series B round of funding, where it expects to raise about €10 million.

Brepson believes the iDtect's metagenomic approach could act as the new standard for BSI diagnosis, especially for pathogens that cause severe septic infections.

"We see a tremendous value for iDtect on other clinical populations where [it] may be more difficult to clearly identify organisms causing infections," Brepson noted. " [Our] research and development team is [currently] working on some of these options based on different types of biological samples."