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Applied Biocode to Submit Gastrointestinal Pathogen Panel to FDA in Bid to Displace Luminex

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NEW YORK (GenomeWeb) – Applied Biocode intends to have a panel for identifying 18 different gastrointestinal pathogens on the clinical market by the end of the year.

CEO Winston Ho said that the Santa Fe Springs, California-based molecular diagnostics company will soon commence clinical trials for the assay, called the Gastrointestinal Pathogen Panel, which runs on its barcoded magnetic bead-based multiplex BioCode MDx 3000 system, at five sites in the US.

If all goes well, the company will submit the clinical trial data to the US Food and Drug Administration for 510(k) clearance by the end of June. Should the agency clear the test and system, it will become Applied Biocode's first in vitro diagnostic product on the clinical market. It will also allow the firm to directly challenge Luminex, which offers its own FDA-cleared xTAG Gastrointestinal Pathogen Panel for 14 microorganisms on several instruments.

Luminex has been offering xTAG GPP to high-volume laboratories for clinical use since 2013 and the firm has considered the assay to be a growth driver. However, according to Ho, as well as to Bob Wessel, a marketing and strategic planning consultant who works for Applied Biocode, the availability of their GPP and BioCode MDx 3000 system could temper Luminex's dominant market position.

"This is a very rapidly growing market and customers with whom we have talked about the system really want it badly," Wessel said of Applied Biocode's offering. "We are planning to displace Luminex," he noted. "Luminex is a non-automated system, some of their customers have not been happy with that, and they are looking for another solution."

Representatives for Luminex declined to comment on Applied Biocode's statements.

Ho, who is also Applied Biocode's CTO, founded the firm in 2008 to commercialize its barcoded magnetic bead technology, where DNA targets are coupled to barcoded beads, providing a high-contrast transmitted signal, no fluorescence background, and nearly 100 percent decoding accuracy, according to the company. Applied Biocode's BMB technology provides up to 4,096 unique digital barcodes for multiplex analysis, he noted, and the technology is protected by several US patents.

The new BioCode MDx 3000 system is based on a 96-well microplate format, which should spur its adoption in clinical labs, Ho said. The system automates the PCR amplification, hybridization, and detection steps of the assay, and it can process up to 94 patient samples in less than five hours.

"It's a high-throughput, automated multiplex system, and we are targeting the high-volume labs with it," said Ho of the company's offering.

Applied Biocode has long eyed the infectious disease testing market as a primary opportunity for the technology, and its GPP has been in development for years. The assay simultaneously detects and differentiates between 18 diarrhea-causing pathogens, including bacteria like Campylobacter and E. coli O157, viruses such as Rotavirus A, and parasites like Giardia lamblia.

Ho said that the company also has a respiratory virus panel in its pipeline, and would seek FDA clearance for that test, too, once it sees its BioCode MDx 3000 system cleared for clinical use. Wessel commented that Applied Biocode also offers a version of the system that will enable users to run their own custom assays, therefore easing its path to adoption for laboratory-developed tests. For this, the company will also have Luminex as a main competitor, which already offers an FDA-cleared xTAG Respiratory Virus Panel and enables customers to develop their own tests.

Applied Biocode recently concluded beta site trials for its GPP assay at the University of California, Los Angeles, and at Poplar Healthcare, a Memphis, Tennessee-based laboratory services company. Ho said that one of the beta users will take part in the clinical trial as well, although he declined to say which one or name any of the other sites.

Anami Patel, vice president of genomics operations and development at Poplar Healthcare, oversaw the beta trial at that site and said that it is possible that Applied Biocode could win over customers who are looking for greater automation for gastrointestinal pathogen testing.

"When Luminex introduced multiplex testing for that indication, it brought a very good molecular tool into the market as a first mover," Patel said. "Our physicians were very excited about ordering that test when it became available and I had never seen such excitement for such a test."

Though the xTAG GPP takes about six or seven hours to complete, he said, it was "still better than culture," the conventional method that many labs still employ, and "brought a lot of efficiency" to his laboratory.

While he noted that Applied Biocode's GPP has a few more targets than Luminex's offering, he said that its greater degree of automation is also a positive for Applied Biocode's offering as there is "less room for error." To date, Poplar has run about 400 specimens on the system, and Patel said that Applied Biocode's automation, as well as its software, which he described as easy to use, are both important for lab efficiency.

Pricing for the system remains unknown, although Ho said it will be competitive. Patel said that he is "very curious" about how much Applied Biocode's offering might cost, adding that an automated system like the BioCode MDx 3000 would certainly fit into Poplar's workflow, where about 90 specimens are analyzed every day. Because of that volume load, other, less automated offerings, such as BioMérieux's BioFire Diagnostics FilmArray Gastrointestinal Panel, which gained FDA clearance in 2016 and allows users to test for the presence of 22 different pathogens in one sample at a time, are not directly competitive for Poplar's lab. "BioFire won't fit into our workflow," he said.

It is unclear if Luminex is planning to update the GPP to counter any challenge from Applied Biocode. In recent months, the company has progressed with bringing in vitro diagnostics to market, albeit on its newer, real-time PCR-based ARIES system. In January, for instance, it gained FDA clearance for its Aries Group B Streptococcus (GBS) assay for antepartum detection of GBS colonization in pregnant women. Last year, the company also acquired Nanosphere for $58 million, and integrating the molecular diagnostics company has also been a focus for Luminex.

Like Patel, Sanjib Bhattacharyya, laboratory director of the City of Milwaukee Health Department, who has used Luminex's xTAG GPP, described the assay as "the first of its kind" on the market but acknowledged that there would be many more and that molecular testing had become "very popular" in labs that conduct infectious disease testing versus conventional culture.

However, he said that some public health reference labs are concerned that these new platforms miss the opportunity for culture-based antimicrobial susceptibility testing, which he described as "critical" for assessing microbial drug resistance as well as for future drug development. He also said that the availability of such high-throughput multiplex systems, like the ones offered by Applied Biocode, would only increase the need for skilled clinical interpretation.

"Since these panels will bring in lots of information, understanding the cause of diseases and symptoms, [and] infection versus colonization for some of those pathogens will be important for optimal therapy and antibiotic use, for those [in] need," said Bhattacharyya.

He added that while resistance detection is currently limited on such panels, it may become available as the field moves from phenotypic to genotypic susceptibility testing. He suggested that test developers increase their cooperation with clinical and public health reference laboratories, to spur such advances.

"Infection control practitioners will be valuable for defining algorithms and judicious use of these enteric panels," Bhattacharyya said.

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