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HelixBind Developing Culture-Free Molecular Testing System for Bloodstream Infections


NEW YORK (GenomeWeb) - HelixBind, a Marlborough, Massachusetts-based startup, recently became the first entity to receive funding for a molecular diagnostic testing system through CARB-X, an international group intent on combating antibiotic-resistant superbugs.

The HelixBind test system, called RaPID, uses a number of novel approaches, including peptide nucleic acid-, or PNA-based amplification to detect bloodstream infections, said David Steinmiller, the firm's chief business officer.

Bloodstream infections — which can lead to sepsis — present challenges both in diagnosis and in treatment. Symptoms can be similar to other conditions, Steinmiller said, making it a diagnostic challenge, and sepsis treatment is costly, often requiring long hospital stays.

"The only way to diagnose a bloodstream infection now is to do blood culture," Steinmiller said. But culture can be slow, depending on the bacteria in question. There are also bacteria that refuse to grow in culture, and growth can be inhibited if a patient is already on an antibiotic.

The primary hurdle to direct-from-blood testing, however, is the fact that a milliliter of blood from a patient with sepsis may contain only a few bacteria, but also millions of white blood cells.

"Trying to find that bacteria is truly trying to find a needle in a haystack," Steinmiller said, particularly because molecular tests are looking for bacterial genomic DNA in a background of millions of human DNA copies.

HelixBind was started in 2013 by Alon Singer, a biomedical engineer, with the intention of bringing together or developing a suite of technologies specifically to address bloodstream infections, Steinmiller said. The goal was to find the best way to pull out the small amounts of bacteria from whole blood and perform sensitive and specific detection and identification as well as determine any antibiotic resistance.

"To make an effective diagnostic test you need to take a systems-level approach and incorporate a wide range of technologies," Steinmiller said. "Our solution isn't just a detection technique or a clever way of doing lysis, it is a collection of many different technologies that work together," he added.

The entire suite, which encompasses both licensed and in-house-developed methods, works in concert to yield a rapid, direct-from-blood BSI test.

Although he declined to provide granular detail at this time, the HelixBind method for concentrating bacteria from blood samples involves eliminating all of the white blood cells and cell-free DNA in a way that does not require centrifugation.

Because the system requires larger volumes of blood to find a few bacterial cells, however, rather than being a microfluidic it is more like a macrofluidic device. It comprises a disposable element in which users would snap in an EDTA blood collection tube with milliliter volumes of patient sample. That device then goes into an analyzer instrument, and the user can "press 'Go' and walk away," Steinmiller said.

After PCR for 16s genomic DNA, as well as 18s, a non-bacterial sequence present in fungi, the system uses artificial nucleic acid probes rather than DNA hybridization.

"The problem with DNA hybridization is it doesn't have perfect specificity … so when you are trying to differentiate very closely related species with DNA hybridization you can't be 100 percent sure you are detecting what you think you are," Steinmiller said.

Instead, the HelixBind system uses an artificial nucleic acid called a peptide nucleic acid, or PNA.

The technique of PNA-PCR has been used by other groups, for example in liquid biopsy applications, or as a combined clamp and sensor probe.

The HelixBind PNA technology binds within the helical structure of double-stranded DNA, hence the name of the company. It is sensitive enough to differentiate species that differ by only a few bases, Steinmiller said.

The system can also perform genotypic resistance testing, but HelixBind is mindful of phenotypic testing systems in development or currently available and sees itself as potentially complementary or as an upstream system for those assays. The firm is also looking into combining phenotypic testing with a future product, Steinmiller said.

Some aspects of the HelixBind technology were described in a 2016 mBio article, which presented a PNA-mediated method that could identify species from a 21-pathogen panel in under two and a half hours, with a sensitivity of single colony-forming units per milliliter. That study also showed 95 percent sensitivity and greater than 90 percent overall correlation to blood culture in a cohort of 61 clinical specimens.

Although the sepsis diagnostic market is becoming highly competitive, Steinmiller noted that there are no commercially available devices quite like the one HelixBind plans to launch, particularly none that do not require any bacterial culture step.

A test in development at Johns Hopkins aims to do direct-from-blood testing and melt curve analysis, while a direct test from DNAe is semiconductor-based using pH-sensing CMOS chips. Qvella is developing multiplexed PCR-based assays to detect infectious disease agents directly from patient samples using its proprietary electrical sample prep technique called Field Activated Sample Treatment, or FAST.

Now, the CARB-X funding will provide HelixBind up to $2 million to further develop RaPID.

Short for Combating Antibiotic Resistant Bacteria Accelerator, CARB-X comprises a portfolio of about 20 antibacterial products in clinical development. The organization, a nonprofit partnership headquartered at Boston University's School of Law, plans to invest $455 million over five years toward the fight against antibiotic resistance using funding provided by the Biomedical Advanced Research and Development Authority (BARDA), the Wellcome Trust, and the National Institute of Health's National Institute of Allergy and Infectious Diseases. CARB-X partners also include RTI International, the Broad Institute, MassBio, and the California Life Sciences Institute.

According to the CARB-X 2016-2017 annual report, the group chose 18 projects in its first year from 368 applications. These were primarily projects developing new antibiotics, with the one funded diagnostics project encompassing an endoscopy-based fluorescent imaging test for lung infections.

"We crafted our [CARB-X] application to emphasize how absolutely critical it is to have diagnostic solutions in parallel to therapeutic solutions," Steinmiller said.

He noted that many of the novel antibiotics being developed today are narrow-spectrum, and identifying the type of bacteria causing infection should be particularly important to correctly applying these therapies. Diagnostics might also be important in the development and clinical trials for these new compounds, Steinmiller suggested.

HelixBind has also been awarded around $3 million in funding from NIAID and the National Institute of Child Health and Human Development for the overall platform and device as well as projects specific for endocarditis and neonatal bloodstream infections. The company also has several patents and patent applications on the technology, Steinmiller said, such as one on its PNA probe method.

HelixBind is not currently disclosing a timeline for launching a product, nor pricing information, though Steinmiller said the company expects it to be competitively priced.

When the firm has a product, it plans to pursue regulatory clearance with the US Food and Drug Administration, most likely a de novo submission, Steinmiller said, and will also pursue CE marking in parallel.

The company also plans to launch a research instrument with additional features such as measuring pathogen load.