NEW YORK – Clear Labs continues to drive into the microbiology testing market with its automated platform for sequencing-based infection prevention and control.
Last month, the San Carlos, California-based company said that following an evaluation of its technology, its Clear Dx platform can now be used by labs as part of the US Food and Drug Administration's GenomeTrakr program, a network of public health and academic laboratories that collects and shares whole-genome sequencing data from foodborne pathogens for real-time source tracking and outbreak detection.
According to Sasan Amini, Clear Labs' cofounder and CEO, to evaluate the suitability of Clear Dx for GenomeTrakr workflows, the FDA assessed performance across four GenomeTrakr labs.
"The outcome, as stated by the FDA, was, 'Clear Labs Clear Dx is an approved platform for performing WGS workflows on common foodborne pathogens, including Salmonella, Listeria, pathogenic E. coli, and Cronobacter species, within the GenomeTrakr network laboratories,'" Amini said.
In January, Clear Labs also raised $30 million in Series D funding to help accelerate the development and adoption of its automated microbial sequencing platform.
The round was led by an undisclosed strategic investor, along with contributions from the existing investors including Counterpoint Global, Felicis, GV, HBM Genomics, Khosla Ventures, Menlo Ventures, Nimble Ventures, Redmile Group, Wing Venture Capital, and funds and accounts advised by T. Rowe Price Associates.
Amini said the company plans to use the money to expand its assay menu for its automated NGS platform. Additionally, the firm, which currently has more than 50 employees, hopes to scale its operations in order to expand beyond the US market.
One new assay to be launched soon targets the 16S rRNA and ITS regions of bacteria and fungi to help identify infections in body fluids, according to Kyle Rhoden, the firm's director of product management.
Clear Dx, ClearLabs' flagship product, is an automated end-to-end platform for microbial WGS that the company started offering during the COVID pandemic. As that subsided, Clear Labs pivoted to microbial surveillance for infectious disease applications.
Clear Dx can carry out everything from DNA extraction all the way up to sequencing. According to Amini, the platform includes "a combination of in-house-developed components and commercially available hardware integrated through Original Equipment Manufacturer agreements."
Amini said Clear Labs has inked OEM partnerships with both Illumina and Oxford Nanopore Technologies, so the Clear Dx platform can come with either two Illumina iSeq sequencers or two Oxford Nanopore GridIon or MinIon devices. He declined to disclose other OEM partners for the platform.
Amini also noted that the company currently has "a relatively balanced" installed base of platforms using the Illumina and Oxford Nanopore sequencers, adding that many of the Clear Dx units in the field are equipped with both sequencers.
Besides the Clear Dx platform, Clear Labs supplies most of the sequencing reagents and consumables to its customers, including flow cells, nucleic acid extraction kits, and library prep kits. "The only consumable that we do not supply is 70 percent ethanol," Amini said. "Other than that, we are pretty much a one-stop shop."
Researchers can start with either purified nucleic acid or microbial isolates. Hands-on time for loading the instrument is about 30 minutes, Amini said, and the platform can typically accommodate two to 12 samples per batch, with tunable sequencing depth. Depending on the application, the turnaround time of Clear Dx can be between 10 and 24 hours, with FASTQ files being the output, he added. The platform is cloud connected, enabling users to integrate bioinformatics tools, and the company offers real-time technical support.
Amini declined to disclose the list price for Clear Dx, other than noting that it is "certainly in the six-figure range."
"The platform is very user-friendly; you don't need to have a lot of detailed microbiology experience in order to use this machine," said Amanda Bartling, a research technologist at Nebraska Public Health Lab and a Clear Labs customer.
Bartling's team used the Clear Dx platform for automated COVID sequencing since the pandemic. After Clear Labs released the microbial sequencing workflow, the lab has been using that for foodborne pathogen detection and surveillance, as well.
So far, Bartling's lab has sequenced over 1,000 bacterial isolates on the Clear Dx platform. The average hands-on time is roughly 30 to 40 minutes to set up the machine, followed by 27 hours of run time to get to FASTQ files, Bartling said, adding that the team typically batches 10 to 12 samples per run.
Cost is usually between $170 to $200 per sample for a full run on the Clear Dx platform, which she said is "right on board" with the cost of manual preparation followed by sequencing on the Illumina MiSeq.
The platform's automated reorder feature has also been beneficial for her lab. "The platform can track how many runs we have done, and once we hit a certain level, they just automatically resend us all the supplies we need, and we don't have to waste time putting in orders," Bartling explained.
Clear Labs is not the only company offering an automated, end-to-end NGS platform for the clinical microbial genomics market. Boston-based Next Gen Diagnostics, for instance, has also been commercializing an automated microbial WGS workflow, which includes a proprietary microfluidic instrument for library preparation as well as an automated bioinformatics pipeline for outbreak detection and antimicrobial analysis.
Despite the growing interest among microbiology labs to adopt automated NGS workflows, Bartling said bioinformatics can remain a bottleneck. "A big struggle with a lot of labs is being able to have those bioinformatics pipelines set," she said.
To help with that, Clear Labs integrates existing bioinformatics tools with its workflow. "One thing we usually try to do is that if there is a very good tool out there, we try not to reinvent the wheel, we lean more towards integrating with those types of best-in-class solutions versus developing them from scratch," Amini noted.
Meanwhile, if certain analysis tools do not exist, "those are opportunities for us to just build our own custom solutions and fill that gap for the customers," he said.