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CogenDx Uses Molecular Methods to ID 'Unusual Suspect' Pathogens in Wound Care

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This article has been amended to clarify the relationship between CogenDx and Millenium Health.

NEW YORK (GenomeWeb) – CogenDx recently launched a molecular testing product that it hopes can help expedite treatment of patients with infected wounds by providing a clearer picture of the infecting organisms and their resistance to antibiotics.

According to a 2009 study in Wound Repair and Regeneration, the total costs per year to treat the 6.5 million patients with wound related complications is around $25 billion. CogenDx wants to reduce the costs by offering its rapid tests clinically, providing doctors with information that will help guide antibiotic treatment.

The genetics brand of Millennium Health, CogenDx was established earlier this year to focus on developing genetic technologies of use to clinicians. CogenDx runs a CLIA-certified, full-service clinical lab with a national commercial footprint. Its new product, DxWound, examines the DNA of microorganisms in a patient's wound that will potentially lead to life-threatening skin and soft tissue infections (SSTIs).

Officially launched and featured by the company at the IDWeek meeting earlier this month in San Diego, DxWound provides clinicians with a swab collection device containing preservation buffer to collect a specimen from a patient's wound site via the recommended Levine technique, expressing the liquid from the tissue and placing it in a preservation buffer. The solution preserves the wound microbiome, where "it essentially inactivates the microorganism and preserves the DNA," and therefore prevents "any overgrowth and any types of competitive interactions that" might cause" what you see when you [collect] the specimen in the lab" to have "a different microbial population [from] what you collected from the wound itself," CogenDx VP of Genetics Naissan Hussainzada said during an interview. Clinicians then ship the tube in a transport bag and send it to CogenDx's laboratory.

When the sample arrives at the lab, CogenDx's staff performs the downstream work, including DNA isolation and extraction, followed byPCR tests for specific organisms, antibiotic resistance genes, and a virulence gene. They then generate a consolidated report including all detected microbes found in the sample and return it to doctors typically within a business day from sample receipt, said Hussainzada. The sample report allows a clinician to quickly identify potential pathogens causing the infection and ultimately guide antibiotic selection and therapy.

At IDWeek, CogenDx highlighted DxWound's ability to detect a wide spectrum of microbes that can lead to debilitating bacterial and fungal diseases. As of now, DxWound can test for 13 antibiotic resistance genes, 1 virulence gene, and 27 different microorganisms in infected soft tissues. These include drug-resistant threats such as carbapenem-resistant Enterobacteriaceae, extended-spectrum beta-lactamase, methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, in addition to species of Candida and Clostridium.

In addition to a wide array of antibiotic resistant pathogens listed as public health threats by the US Centers for Disease Control and Prevention and the World Health Organization, CogenDx's DxWound also detects anaerobic bacteria and fungi that are normally much more challenging to diagnose in standard biopsies.

"Generally, they are those organisms that are a bit more challenging to grow and cultivate in traditional culture methods," Hussainzada said. "However, we know, based on many published studies, that anaerobic bacteria and fungi can be detected [and are] potentially pathogenic within wounds and the causative organisms underlying infections." Hussainzada referred to separate studies that identify the two types of microorganisms in up to 25 percent of wound infections.

In the first study, published in 2011 in the Journal of Wound Care, researchers from the Research and Testing Laboratory of the South Plains (RTL) assessed the incidence, abundance, and diversity of fungi in chronic wounds of 915 patients, as well as describing the associations of major fungi populations. They found that 208 (23 percent) patients were positive for fungal species, subclassified among the four major chronic wound types. Results demonstrated that fungi are more important wound pathogens and opportunistic pathogens than reported previously. 

In the second study, published in 2015 in Wound Repair and Regeneration, scientists from RTL and the Southwest Regional Wound Care Center performed 16S rDNA pyrosequencing to analyze the composition of bacterial communities present in samples obtained from patients with chronic ulcers and nonhealing wounds. Wolcott saw that up to 25 percent of SSTIs included anaerobic pathogens. Their results indicated that anaerobes comprise a significant proportion of the chronic wound microbiome.

DxWound is CogenDx's third product offering in its genetics brand. Hussainzada explained that the company started its testing within pharmacogenetics four years ago, when the technology and applications were relatively new in the clinical setting.

She emphasized that the company was one of the first to commercialize and grow a pharmacogenetic testing service, and that it has since used that experience to develop subsequent products.

While the test does not currently offer tissue as a specimen type, initial testing is underway for validating tissue biopsies. CogenDx plans to release tissue as a specimen option in 2018.  

Hussainzada explained that CogenDx's technology is not trying to replace current techniques, but instead act as a complement. Because molecular tests are based on identifying genes with well-characterized sequences and confirmed associations with observed drug resistance patterns, they may not be able to detect newly emerging or previously uncharacterized resistance mechanisms and genes.

Additionally, the presence of a resistance gene does not guarantee expression of the gene, nor does the absence of a resistance gene exclude the possibility of other resistance mechanisms. Hussainzada believes that clinicians may find the most benefit for now  when molecular methods and susceptibility testing are used in tandem to understand antimicrobial resistance.

Hussainzada declined to comment about early adopters, as clinical use of the test only began earlier this month. She did say that CogenDx has received samples at its laboratories, and that it already has clinicians who have signed up with its services and see the value in the test.

In terms of future plans, Hussainzada said that the CogenDx will focus on leveraging its  pharmacogenetic capabilities to get more out of medication, as well as growing within the infectious disease market. The company views infectious disease detection as a high-growth market with a lot of unmet need, particularly in the area of antimicrobial resistance.

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