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DNAe Boasts Low Levels of Pathogen Detection for Forthcoming Sepsis, Antibiotic Resistance Test

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NEW YORK (GenomeWeb) – DNAe has moved closer to commercialization with its direct-from-blood semiconductor-based diagnostic platform by achieving a low limit of detection in identifying bloodstream pathogens that contribute to sepsis and markers that detect antimicrobial resistance.

Specifically, in a poster presentation last week at the Association of Molecular Pathology annual meeting in Salt Lake City, the firm presented the results of internal tests that reflected the end-to-end functionality of its testing platform, and showed that it could detect infection-causing pathogens in spiked samples at limits of detection as low as 1 CFU/ml.

DNAe also said that its sepsis panel can now detect 12 total pathogens, more than doubling the five pathogens it had reported detecting prior to the AMP meeting.

In previous poster presentations, including at the 2016 AMP annual meeting in Charlotte, North Carolina, the company had shared results from internal testing of subsystems of its semiconductor-based LiDia platform at an earlier stage of development, Nick McCooke, DNAe's chief business officer, said in an interview.

He noted that before the end of this year, the firm expects to test an integrated beta prototype that will resemble the eventual diagnostic test that that will go into clinical testing in hospitals. The firm expects to launch a CE marked commercial sepsis diagnostic in Europe in the latter half of 2018, McCooke said.

McCooke added that DNAe expects to present new data, which includes the results from testing its integrated beta prototype, at the European Congress of Clinical Microbiology and Infectious Diseases in Madrid, Spain, in April 2018.

"We expect that this test will be most suitable for use in hospital labs near patients, where a short turnaround time is required and where there's a need to quickly get results back to a relevant clinician," McCooke said.

The DNAe test would eliminate the need for a blood culture process that can take anywhere from two to six days, which could prove to be vital when it comes to detecting infections such as sepsis where the mortality rate increases quickly with time, McCooke noted. In addition, LiDia BSI could reduce unnecessary prescription of antibiotics by providing actionable results directing targeted treatment in just a few hours, the firm noted.

The LiDia platform leverages DNAe's Genalysis genomic technologies, which include sequencing and PCR-based methods that the company is developing for clinical use. The platform and a range of tests in development will enable DNA analysis directly on a microchip, he said.

The LiDia BSI test extracts pathogen DNA from intact bacteria and fungi, removes background matrix, performs nested PCR pre-amplification, and makes a final identification by real-time amplification on a pH-sensing complementary metal-oxide-semiconductor chip (CMOS). The CMOS technology is implemented in an integrated circuit that incorporates ion-sensitive field-effect transistors to detect the changes in pH associated with the release of hydrogen ions during PCR.

The firm said that it expects that LiDia BSI will be the first to launch in its pipeline. CE marking in the second half of 2018 would enable marketing of the test in Europe and other countries that accept the CE designation.

During 2018, the firm will also evaluate the test's sensitivity and specificity in patient samples within hospitals with a view to eventually obtaining US Food and Drug Administration clearance to market and sell the sepsis test in the US.

For now, however, DNAe is focused on obtaining the CE mark, and that is driving the timing of many of its activities, McCook said.

Nour Shublaq, DNAe's European product manager, said in an interview that the firm has shown that with one platform, it can detect and differentiate bacterial and fungal pathogens in blood, and at the same time identify markers that show when some pathogens are resistant to antibiotics that patients receive to help them ward off infections.

In internal tests using clinical samples contributed by the University of New Mexico, and samples that DNAe spiked with specific levels of pathogens, the LiDia BSI assay detected the most common pathogens linked to serious bloodstream infections and less frequent pathogens that are often mistreated empirically, the firm said.

The poster's authors, including Shublaq, confirmed not only the end-to-end functionality of the LiDia BSI workflow, but also that it correctly identified pathogens and resistance markers at 1 CFU/ml, a low level of detection that should translate into high levels of sensitivity, Shublaq said. At the same time, the test's sensitivity level is yet to be determined in clinical studies, she noted.

The test demonstrated a time to result of less than 5 hours, which was particularly noteworthy because this is a critical parameter for clinicians in treating some infections, she said. Turnaround time can probably be reduced to less than 3 hours, DNAe said.

In the poster presentation at AMP, the firm noted that its platform was able to correctly detect a number of pathogens — A. baumannii, K. oxytoca, K. pneumoniae, P. mirabilis, E. faecalis, E. faecium, S. aureus, C. albicans, and C. glabrata — in healthy blood samples spiked at 1 CFU/ml.

It also confirmed the absence of resistance markers in K. pneumoniae, E. faecalis, E. faecium, and S. aureus, and the presence of both pathogen and resistance markers in contrived whole blood specimens with vancomycin-resistant E. faecalis, vancomycin-resistant E. faecium, MRSA, and K. pneumoniae harboring blaKPC, a gram-negative resistance marker.

The system's ability to distinguish between specimens with either methicillin-resistant S. aureus or methicillin-sensitive S. aureus is of particular importance to healthcare systems, Shublaq noted.

The company expects that the assay will eventually be able to identify 20 pathogens, including bacterial and fungal, DNAe CEO Steve Allen recently told 360Dx. In doing so, the test will cover 95 percent of the pathogens in the bloodstream that could lead to sepsis and that are clinically actionable, he added.

Allen said in a statement that the data presented at AMP provides "evidence of the sensitivity, breadth of pathogen coverage, inclusion of resistance genes, and speed of the LiDia platform and test offering." He noted that the presentation is "an important stepping stone as we move swiftly towards commercialization of the LiDia BSI test."

The next stage in the development process, he said, is to fully integrate the workflow into the cartridge-based test "to allow the system to deliver clinically actionable results in less than three hours."

DNAe has granted limited, non-exclusive licenses to certain patents to a few life science companies, including Ion Torrent, which is now part of Thermo Fisher Scientific. DNAe noted that as a result, its technology is proven for next-generation sequencing in laboratories around the world.

In October 2016, the Biomedical Advanced Research and Development Authority (BARDA), a division of the Assistant Secretary for Preparedness and Response in the US Department of Health and Human Services, awarded DNAe a contract worth up to $51.9 million to develop Genalysis for rapid diagnosis in two applications — antimicrobial-resistant infections and pandemic influenza.

McCooke noted that although the LiDia platform uses multiplex PCR, the BARDA program uses NGS alone.

Several in vitro diagnostics companies including Roche, BioMérieux, and Thermo Fisher Scientific have launched tests for sepsis diagnosis and management. Some of them use procalcitonin as a biomarker that correlates with sepsis risk.

T2 Biosystems, a relatively new entrant in the marketplace, produces a panel that provides results directly from a blood draw in three to five hours, making it a direct competitor to DNAe if its test development is successful.

T2 may have an early-mover advantage over DNAe. Its instrument and the T2Candida Panel were both CE-marked and FDA-cleared in 2014. The firm received CE marking for its T2Bacteria Panel, which runs on the firm's proprietary T2Dx instrument and provides species-specific test results for targeted bacterial infections direct from whole blood in about 3.5 hours.

In September, T2 Biosystems said that it had filed a 510(k) premarket submission for its T2Bacteria Panel with the FDA. The firm also closed a public stock offering of about 4.4 million shares at $4 per share, raising $20.1 million in gross proceeds.

At AMP, T2 said that its research-use-only T2Bacteria Panel has shown clinical sensitivity in the range of 90 percent to 100 percent in more than 300 cases across several studies of known infected patients. The firm added that it has shown clinical specificity on average of about 98 percent across more than 3,000 patients tested at 15 institutions.