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Clear Labs Pushing Automated Whole-Genome Sequencing Into Clinical Market for Infection Control


NEW YORK – During the pandemic, Clear Labs expanded the market for its automated sequencing system from environmental pathogen detection in the food industry to SARS-CoV-2 surveillance and wastewater monitoring. Now, the San Carlos, California-based company is hoping to find new customers among hospital labs, particularly for whole-genome sequencing-based infection prevention and control.

In-house sequencing technologies have long been considered unfeasible in most clinical labs because of the cost and expertise they require. But automation may change these dynamics, Clear Labs CSO Ramin Khaksar said in a recent interview.

Khaksar, who is also chief operating officer and a cofounder of Clear Labs, said the firm's Clear Dx system pairs robotics with nanopore sequencing in a "sample-in, result-out" platform that eliminates some of the expert labor typically needed for sequencing interpretation.

For example, Clear Labs can perform troubleshooting on the system via its cloud connectivity, Khaksar said. Approximately 90 percent of issues can be solved within one hour via the cloud, he said, with less than five minutes of response time and no need to wait days for a field service technician to physically visit the system.

Clear Labs sponsored a presentation at IDWeek last month highlighting the benefits of in-house hospital lab WGS for infection control. Jen Bruursema, VP of marketing at Clear Labs, said that the intent was to bring awareness of WGS and begin a dialogue with clinicians.

According to Charles Vaske, Clear Lab's head of bioinformatics, the focus on democratizing sequencing, "to the extent that anybody can do it in any location," differentiates the firm from other genomics companies.

After its founding in 2014, Clear Labs gained traction in food safety — specifically detection and serotyping of Salmonella and Listeria — to help reduce contamination in processing facilities.

The main competing technology in this space is reliably fast and cheap PCR, but Vaske said that some food processors found that the improved accuracy of sequencing actually leads to faster remediation. 

In one exemplary case, the sequencing technology was used to determine that an ongoing outbreak in a factory was caused by many separate strains, leading to an improved investigation that sought more than one source of contamination. 

"When the pandemic came, we had an instrument that was fully automated for doing sequencing, and it turned out public health labs were having a lot of difficulty with staffing and with getting sequencing done quickly for COVID surveillance," Vaske said.

Now, Clear Labs has a presence in about 60 percent of US public health labs, he said, which have all adopted the Clear Dx system for SARS-CoV-2 surveillance.

Vaske said the system's ease of use is particularly attractive to public health labs. "It is down to just one touch point for the operator," he said.

Furthermore, the system performs sample preparation, PCR, and sequencing automatically, and runs the analytics in the cloud. "You don't need to have specialized bioinformaticians to run pipelines, and your wet lab techs can get back to more interesting things," Vaske said. Automation can also reduce human error and improve the reproducibility of results.

The turnkey nature of the system can also overcome the hurdle of logistics, since reagents and supplies are provided by Clear Labs, as well, Vaske said.

"We are in the golden age of sequencers right now — but the challenges to using them in practice stop everyone except the most well-resourced facilities," he said. Clear Labs enables sequencing in labs "that would not be able to do sequencing otherwise," he added, and also can save money and time even for customers with fully staffed expert labs.

In 2018, University of Washington clinical virologist Alex Greninger presented at the American Association for Clinical Chemistry meeting on the question of whether clinical sequencing was "ready for prime time." He concluded that, although it has amazing applications in diagnosing unusual infections and tracking outbreaks in hospitals, clinical sequencing remained too slow and expensive.

Four years and one pandemic later, and despite the uptake in public health labs, Greninger still sees cost-related challenges in hospital lab adoption of in-house sequencing systems. In an email, he noted that public health labs got funding from Congress for capital equipment to use in genomic surveillance, enabling them to more easily bring on systems like Clear Labs' system. Unfortunately, the main things Congress has offered to clinical microbiology labs is the Protecting Access to Medicare Act and inflation, Greninger said.

Kyle Rodino, assistant director of clinical microbiology at the Hospital of the University of Pennsylvania and an assistant professor of pathology and lab medicine, also highlighted some of the challenges for in-house WGS in a Clear Labs-sponsored event at IDWeek last month.

WGS has demonstrated strengths in supporting infection prevention and control efforts. For example, it can provide more accuracy and resolution than other assays in evaluating transmission chains of hospital-acquired pathogens, and it can also detect horizontal gene transfer of plasmids between bacteria. This enables better tracking of infections, which can save lives.

But, in his IDWeek presentation, Rodino said there is currently limited capacity for in-house WGS-based epidemiological investigations in clinical microbiology labs. Approximately 80 percent of labs currently have staff vacancies, he said, with 33 percent experiencing a shortage of as many as five staff members.

Standard sequencing also requires that these scarce technicians be in the lab at many different points in the workflow, which also increases cost.

The American Society of Microbiology is expected to launch a 50-hour NGS training program in 2023, Rodino said, but in the meantime the level of sequencing expertise among many laboratorians necessitates having dedicated salaried staff to operate sequencing platforms. In addition, the workflow is time-intensive, with sample prep and sequencing taking up to four days of technician efforts, and bioinformatics steps taking another day.

In his presentation, Rodino also noted that although WGS-based infection prevention can save hospitals money through averting outbreaks, it is essentially a non-billable test.

Documenting the cost of outbreaks and send-out investigations, and establishing collaborations with public health labs — for example through the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) program — can potentially help labs in justifying the capital expense, he said.

Overall, Rodino concluded that successful WGS requires teamwork between infection prevention and clinical microbiology labs.

The capital cost may still be a hurdle for some — the publicly disclosed cost of the Clear Dx system is around $200,000 — but Clear Labs now hopes to reach clinical microbiology lab customers by expanding its marketing, in part through generating awareness at conferences, Bruursema said.

The firm also seeks to understand the day-to-day needs of clinicians, infection prevention specialists, and epidemiologists, so it can potentially build flexibility into the solution to help address the clinical market. 

Vaske noted that the team hopes to collaborate with leaders in clinical microbiology and infection prevention in order to add to the literature on WGS-based cost savings as well as show the efficacy of the Clear Dx system.

And so, while WGS-based infection prevention is showing increasing benefits, Khaksar said he now hopes that by lowering the barriers of staffing, turnaround time, computing infrastructure, and bioinformatics, the firm's solution can allow further uptake.

Khaksar said it may also now be "prime time" for sequencing regulation, and he anticipates sequencing assays and products to be granted regulatory clearance by the US Food and Drug Administration within the next few years, further stimulating adoption.