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German Researchers Continue Commercializing Sequencing-Based Pathogen ID Test for Sepsis


NEW YORK – A team of German researchers from the Fraunhofer Institute for Interfacial Engineering and Biotechnology has commercialized their sequencing-based test that detects cell-free DNA to diagnose sepsis.

At the same time, they are also continuing to strengthen its use case in different settings.

The test, called Disqver, was developed to improve infectious disease diagnosis for severely ill patients and improve sensitivity for detecting bloodstream infections, said Kai Sohn, one of the test's developers and head of the IVD business unit at Fraunhofer. While blood culture is well established and inexpensive, it is not the most reliable or speedy form for diagnosing sepsis and ensuring the proper treatment, he noted.

Using evidence from other research groups that showed cell-free DNA from microbes could be used to detect infections earlier than the standard of care, Sohn and his colleagues tested whether they could translate that work to bloodstream infections.

To run the test, the cell-free DNA is isolated from a patient's plasma sample and the library is then prepared for sequencing, resulting in about 25 million to 30 million DNA fragments being sequenced overnight, Sohn said.

The "tiny fraction" of DNA in a sample that is of nonhuman origin is compared to a broader reference database containing the genomes of bacteria, viruses, parasites, and fungi to determine both qualitatively and quantitatively how many reads can be assigned to a specific pathogen, Sohn said. The researchers then use a bioinformatics algorithm to determine which of the identified pathogens are relevant to the infection and provide a final report to the clinician. It takes about 24 hours to receive a definitive result, not including the time it takes for a sample to be shipped to the laboratory for analysis.

The researchers' aim is to reduce the time to result for pathogen identification to the same hospital shift and it is still working to that end goal. The "time-limiting step" is the sequencing, which takes a little less than 12 hours, while the bioinformatics step only takes about an hour, Sohn noted. The team first published its work in 2016 using next-generation sequencing tools from Illumina, and in 2020 it published on the use of the test leveraging nanopore sequencing, which Sohn said is a much faster approach. According to the 2020 study, the researchers were able to reduce the turnaround time to about six hours after sample receipt for most samples. The nanopore sequencing works nicely "for really severely ill patients with high burdens of bacterial load," but isn't possible for all patients and thus "is not ready for prime time yet," Sohn said. The researchers are also working to shorten the sample and library preparation time.

In research published in 2019 in Critical Care Medicine, the team tested 256 plasma samples from 48 patients with sepsis at up to seven consecutive time points within a 28-day observation period and compared their results to blood culture. They found that blood culture had a positivity rate of 33 percent at sepsis onset, while the next-generation sequencing-based method had a positivity rate of 72 percent. Over the course of the entire study period, blood culture positivity was 11 percent and NGS positivity was 91 percent. In addition, 96 percent of positive NGS results for acute sepsis time points were plausible and would have led to a change to a more appropriate therapy in 53 percent of cases, according to an independent expert panel. 

Sohn noted that not every hospital has access to sequencing technology, which is "quite expensive," limiting the ability to integrate Disqver into hospital systems. However, the researchers are working on economic impact studies to show the benefits of introducing sequencing equipment into hospital laboratories for tests like Disqver, allowing patients to receive the adequate therapy sooner and thereby reducing intensive care unit stays and ventilator usage, as well as reducing use of the inappropriate therapy.

The researchers have spun out a startup firm called Noscendo to commercialize the test and offer it in clinical settings outside of clinical trials in 2017. It is currently available in Germany and a few other European countries. Disqver is CE-marked, and Noscendo is working on getting CE-IVDR marking to ensure it is compliant with Europe's In Vitro Diagnostic Regulation, said Silke Grumaz, the company's CSO.

Noscendo offers two ways to perform the test: Hospitals and laboratories without sequencing capabilities can send a sample to the firm's laboratory for sequencing and algorithmic analysis, or the company can do a technology transfer that allows hospitals and laboratory chains with access to sequencing to perform the test in-house and partner with Noscendo to use the algorithm.

Disqver costs a little less than €1,000 ($1,082) and is reimbursed by some payors in Germany in certain hospital settings, Sohn and Grumaz noted, and the firm is in ongoing discussions with other German insurers to cover the test. Noscendo also plans to expand the test outside of Europe to the US and other countries, although those plans are set for further into the future, Grumaz added.

Sohn added that he expects the cost of the test to decrease as it is performed more routinely in large central laboratories that are highly automated and can optimize the assay. Decreasing sequencing costs will also help lower the price of the test, he noted.

Noscendo is not the only company looking at cell-free DNA for sepsis diagnosis. For example, Stanford University spinout Karius detects pathogens by sequencing cell-free microbial DNA in a patient's blood using Illumina instruments, although Karius does take between 48 and 72 hours to return a result.

Currently, Noscendo's main customers are university hospitals that have deployed the test in emergency departments, hematology departments for fever of unknown origin, transplant medicine, and pediatrics, Grumaz said. However, use of Disqver by smaller hospitals is on the uptick as they can ship their samples to Noscendo for sequencing.

The next milestone for the company and the test is a plan to publish a multicenter trial, Next GeneSiS, with roughly 500 patients. The manuscript has been submitted to an unnamed journal for publication. The study protocol was published in 2018 in Medicine. The company is also currently recruiting patients for a two-arm interventional trial taking place in Germany, Sohn added.

Lastly, Noscendo is exploring the use of its technology for other infectious diseases and for antimicrobial resistance, Grumaz noted.