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Great Basin Preps Staph, Candida Dx Panels for Trials; Eyes European Sales in Q2


By Ben Butkus

A group led by researchers from early-stage molecular diagnostics firm Great Basin has published a study demonstrating 99 percent accuracy for the company's automated, DNA assay panel to identify major pathogenic strains of Staphylococcus and methicillin resistance in blood culture.

The company now plans to begin clinical trials for the assay, called Staph ID/R — as well as for another assay panel to detect Candida infections in blood — in the second quarter of this year, CEO Ryan Ashton told PCR Insider this week.

In addition, Great Basin expects to garner CE Marking for both assays — as well as for its first assay to detect Clostridium difficile — around the same time, leading the company to believe that it could see its first MDx test revenues by the end of the second quarter, Ashton said.

"We're working on the process now of our ISO certification and everything else, so we're feeling good about that," Ashton said. "We'll be launching products fairly soon — finally, after several years of hard work and development, we expect to see revenues in the second quarter if all goes well."

Meantime, the C. difficile test awaits 510(k) approval by the US Food and Drug Administration. The company submitted the assay for approval in November, and has received first response from the FDA, Ashton said, though he declined to speculate on the timing of the potential approval.

All of Great Basin's assays are cartridge-based and run on a yet-to-be-named benchtop instrument that features a chip-based detection component based on thin-film biosensor technology licensed from Yale University; as well as dedicated analysis software.

Both the C. difficile assay and Staph ID/R use an isothermal method called helicase-dependent amplification, licensed from New England Biolabs spinoff BioHelix, to amplify target nucleic acid sequences; while the Candida panel uses a proprietary signal amplification system as opposed to physically amplifying the target.

Great Basin has maintained that price would be a major differentiator for its products — last June the company said its platform could be manufactured for less than $5,000 — and Ashton this week reaffirmed that idea.

In addition, the platform can automatically provide a test result from a sample in less than 75 minutes, which compares favorably to both marketed platforms and those in development.

In terms of competition, Cepheid remains king of the hill for most HAI molecular testing, and in fact, Great Basin has said that it is modeling its platform on Cepheid's GeneXpert system.

However, the recently published study, which appears in the March issue of the Journal of Clinical Microbiology, demonstrates that Great Basin's assays, particularly those for Staphylococcus and Candida in blood culture, may also offer at least comparable sensitivity and specificity and "significantly more content than our competitors," Ashton said.

Although S. aureus — a "coagulase-negative" species — is the major culprit of most hospital-acquired infections, a number of other staphylococci referred to as "coagulase-negative" can be problematic.

"In the case of S. lugdunensis, which is not a terribly prevalent subspecies of Staph, it's just as virulent and every bit as dangerous as S. aureus; or, in the case of S. epidermidis, it can cause a positive blood culture result that is in fact more likely a contaminant … from the technician," Ashton said.

"Our assay will test for essentially all Staph, either by speciating the most prevalent of those species … or [providing] a universal positive so you know whether or not Staph is present in the sample," he added. "This allows hospitals to cease running backup culture, [because] once they know it's a gram-positive Staph … they don't have to run a backup test in the case that it's not S. aureus. So it adds some cost savings to the mix because they can eliminate some culture."

Furthermore, the ability of Staph ID/R to identify potential polymicrobial infections is important in pediatric and neonatal care, as well as in other immunocompromised patients, Ashton said.

In the JCM study, researchers from Great Basin, Denver Health Hospital, and Children's Memorial Hospital in Chicago tested blood cultures spiked with 25 unique Staphylococcus strains representing 19 different species.

They determined that Staph ID/R has an analytic sensitivity of one colony-forming unit per reaction for mecA, the gene that confers methicillin sensitivity in Staphylococcus species; and one to 250 CFUs per reaction for individual Staphylococcus species, depending on which was present in the culture. The group also found that Staph ID/R had excellent specificity with no observed cross-reactivity.

Next, the researchers validated the clinical performance of Staph ID/R by testing 104 frozen clinical positive blood cultures and comparing the results with rpoB gene or 16S rRNA gene sequencing for species identity determinations; and with mecA gene PCR to confirm mecA gene results.

The Staph ID/R test agreed with mecA gene PCR for all samples, and agreed with rpoB/16S rRNA gene sequencing in all cases except one that contained a mixture of two staphylococcal species, one of which Staph ID/R correctly identified.

Ashton said that the marketed version of Staph ID/R will ultimately test for seven different staphylococcal species, plus controls. Meantime, the Candida panel will also assay for several targets, although the exact number has not yet been determined. Great Basin's C. difficile assay only tests for one target, but a multiplex test for that organism is not as important as it is for Staphylococcus and Candida.

Besides its first three HAI tests, Great Basin has also begun exploring infectious disease testing – namely, for tuberculosis. Ashton said the company has set up a non-profit component to develop TB assays on the automated testing platform, and that an early-stage proof-of-principle study has been accepted by a peer-reviewed journal and is set to be published in the coming weeks.

"This is kind of a separate project inside Great Basin," Ashton said. "It's being funded a little differently, and we're looking at it largely as a low-resource environment project."

In the meantime, the company has begun ramping up its sales and marketing team in order to meet what it hopes is high demand for its products beginning in countries recognizing the CE Mark in the mid- to late second quarter. Great Basin has two distributors in place in Europe — Bühlmann Laboratories in Basel, Switzerland, and Pro-Lab in the UK.

The final piece of the puzzle is a name for Great Basin's testing platform.

"We're working on it now," Ashton said. "Our marketing department has to get that done quickly, because we're going to be shipping soon."

Have topics you'd like to see covered in PCR Insider? Contact the editor at bbutkus [at] genomeweb [.] com.