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MicroGen Dx Focusing on Urological, Prosthetic Joint Infection Diagnostics


SAN FRANCISCO (GenomeWeb) – MicroGen Dx is developing PCR and next-generation sequencing tests to diagnose microbial infections, with its initial focus on urological and prosthetic joint infections.

The company, which is headquartered in Orlando, Florida and has a CLIA-certified, CAP-accredited laboratory in Lubbock, Texas, changed its name from Pathogenius after current CEO Rick Martin purchased it last year.

The firm sees the potential for molecular tools to replace culture-based diagnostics. Martin predicted that would result in a "massive paradigm shift," enabling the detection of "complex organisms that can cause infection and inflammation."

Currently, the company offers a PCR-based panel and an NGS assay based on targeted 16S sequencing. The two assays are run concurrently for $250, with the PCR results delivered within 24 hours and the NGS results within three to five days, Martin said.

Recently, the firm demonstrated with collaborators from Thomas Jefferson University that its technology could diagnose prosthetic joint infections better than culture-based techniques in a study published in the Journal of Bone and Joint Surgery.

In the prospective study, researchers collected samples from 82 patients, including 65 patients who were undergoing revision surgery due to a failed knee or hip replacement joint and 17 patients who were undergoing primary joint replacement.

The samples from the revision surgeries were cultured and also assessed by PCR and NGS.  The primary surgery samples were analyzed only by molecular techniques, since they had no symptoms of being infected

Of the 65 samples from patients whose joint replacements failed, 28 were thought to be infected based on criteria set by the Musculoskeletal Infection Society. However, culture-based techniques were only positive for 17 of those samples, while the NGS assay identified pathogens in 25 samples. The NGS assay also identified infection in 10 patients who did not meet the MSIS criteria for infection but whose joint replacement had failed. The culture-based technique confirmed one of those cases.

Joint infection is rare, occurring in about 2 percent of cases, but with around 1.2 million joint replacements performed annually in the US, there are a large number of cases, according to Javad Parvizi, senior author of the study and an orthopedic surgeon at the Rothman Institute at Thomas Jefferson University. "It's an incredibly complex issue when it occurs," he adds and "is very difficult to diagnose." Culture fails to identify the causative organism nearly 50 percent of the time. Not identifying the responsible microorganism makes treatment difficult, Parvizi said. Rather than using a targeted antibiotic, broad-spectrum antibiotics must be used, which can cause liver and kidney issues, he said.

Parvizi said that he's been interested in molecular techniques to help improve the diagnosis of prosthetic joint infections, which eventually led to his lab partnering with MicroGen Dx. Parvizi added that he also has a financial stake in the company, although is not an employee.

He said that this initial study demonstrated that NGS techniques can diagnose the infected organism in nearly 90 percent of cases, and in addition, because of its unbiased nature it has shown that in many cases there is more than one microbe responsible for the infection.

"What we've done historically is concentrate on the most dominant organism and ignore the others," he said. "When patients' [revision] surgery fails because of reinfection, that may be because of persistence of the organisms that were there in the first place but that we ignored."

The other important aspect of molecular techniques is that resistance genes can be identified, Parvizi said.

Parvizi added that he has now enrolled over 400 patients in the study, and following that he said his lab would look to make this standard of care for any patient that must undergo revision surgery for a joint implant. "I'm very encouraged by the results," he said.

In addition, Parvizi said that the lab is conducting a separate study using MicroGen Dx's assays to identify infections in patients with broken bones.

Other groups have also turned toward NGS to diagnose prosthetic joint infections, including a research team at the Mayo Clinic that has been developing a metagenomic sequencing protocol for prosthetic joint infections. Because that technique involves metagenomic sequencing, it is more expensive and time consuming than the targeted approach used by MicroGenDx, but is also more comprehensive.

German molecular diagnostics firm Curetis also markets a PCR panel for joint and tissue infection in Europe and is conducting trials in the US.

Martin said that MicroGenDx chose targeted approaches in order to reduce turnaround time and costs as much as possible, while still having a higher sensitivity than culture-based techniques.

The company's quantitative PCR panel can identify 17 common microbes as well as resistance factors that can determine resistance to eight classes of antibiotics, Martin said. That panel enables the firm to "within 24 hours say if we've detected the most common species and what they're resistant to."

The firm then runs an NGS panel to more comprehensively analyze the microbes that are present. Currently, the company runs the NGS panel on Thermo Fisher Scientific's Ion Torrent PGM, Martin said, but added that it is also in the process of validating Illumina's MiSeq.

The turnaround time for the NGS assay is currently three to five days, but Martin said that the company aims to reduce that to two to four days.

The firm's main customers are urologists looking for better ways to diagnose urinary tract and prostate infections. "Chronic UTIs are a huge problem," Martin said, "and has a big impact on antibiotic stewardship, resulting in an overuse of antibiotics and development of resistance."

He said that the firm recently completed a single-site study testing its assays for UTI diagnosis that will be published soon in a peer-reviewed journal. Patients with UTIs were enrolled and half of each patient's sample went to a culture lab and half were sent to MicroGenDx's lab. Then patients were randomized to be treated either on the basis of the culture results or the molecular results. There was a "massive difference" in patients' outcomes, Martin said. Patients treated based on the molecular results saw their symptoms decrease quicker and were more likely to have their infections cleared compared to patients who were treated based on the culture results, he said.

The company is also involved in a multi-center trial for orthopedic infections, Martin said, which he expected would bolster the results found with the Thomas Jefferson University collaborators.

Martin added that the firm is seeking to distinguish itself from potential competitors by its assay cost and turnaround times. In addition, while most companies either offer PCR-based panels or NGS testing, he said that doing both is beneficial, so that critical information can be returned immediately with a more comprehensive analysis a few days later.