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Clear Labs Expands Pilot Ahead of Food Testing Platform Launch


This article has been updated to correct the previously reported number of people infected with food-borne diseases annually.

NEW YORK (GenomeWeb) – Clear Labs is seeking additional participants for an ongoing pilot program it launched about a month ago that aims to put the company's next-generation sequencing-based platform for high-volume food safety testing through its paces ahead of a full launch in July.

As part of the pilot, participants will have access to a version of Clear Labs' sequencing and analysis platform, which is designed for high-volume food safety and quality testing. Reports generated at the end compare the accuracy of Clear Labs' platform to PCR-based testing methods currently used by the food safety market.

The Menlo Park, California-based company sees its platform as a replacement for PCR-based testing, which has hitherto been the gold standard for the food safety industry, and is confident that its results will be superior to existing systems on the market, according to CEO Sasan Amini.

"PCR tests are targeted and therefore limited in their data reporting capabilities," Amini said in a statement. "They also have a history of high false positive and false negative rates that costs the industry millions." In comparison, "NGS technologies provide a far more accurate, granular, and comprehensive view of the risks in any supply chain and can compete head-to-head with PCR."

In 2015, Clear Labs raised $6.5 million in a Series A private financing round and unveiled its flagship product, called Clear View, which the company claims is used by 40 customers globally. Clear Labs offers testing as a service using Clear View, which can be run either in its own laboratory or a traditional food-testing laboratory.

When the company releases the newest iteration of its platform this year, which will be called Clear Safety, it will target leading food brands and food safety testing laboratories as potential customers. Specifically, it will pursue companies with in-house laboratories that are looking to upgrade from their legacy PCR systems, as well as contract research labs that offer food safety testing as a service. "We have a direct sales and marketing team here at Clear Labs with deep roots and ties to the food industry," Mahni Ghorashi, Clear Labs' chief commercial officer, said in an interview. Initial sales efforts will focus on the North American market and then broaden out to include Europe and Asia.

Customers who license Clear Safety will have access to sequencing capabilities, a proprietary bioinformatics pipeline, and cloud-based infrastructure. "We are following exact models currently used in the food-testing industry, including a reagent rental model that incorporates any cap-ex costs," Ghorashi said. "The final reaction and media cost is equal with PCR through Clear Labs’ innovation and IP. It’s a 1:1 swap out for PCR platforms."

For food manufacturing companies, recalls can be crippling, costing as much as $10 million a year or more, according to Ghorashi. In 2017, for example, there were nearly 500 food recall cases. There is also a public health cost, with some 50 million people in the United States suffering from diseases caused by food-borne pathogens annually, he said.

For the last decade or so, PCR-based testing methods have largely dominated the food safety testing market. However, it is limited in the sense that food companies need to know what they are looking for up front, and there are multiple possible sources of contamination. Testing can "take up to three to five days. So the food company is now holding inventory and incurring incredible costs as a result," Ghorashi said.

In contrast, next-generation sequencing-based testing offers a more detailed picture about the state of food samples, including any potential pathogens and which specific serotypes are present, which makes it appealing to food companies. "It's a big era shift," not unlike the transformation that occurred when the industry moved from antibody-based methods to PCR, Ghorashi noted.

When it launches the platform in July, Clear Labs will charge an undisclosed price per test performed using Clear Safety. However, the company claims that its prices are on par with PCR-based testing, and exactly how it got those costs down is the core of its business. "There's a lot of variables involved and a lot of those are trade secrets," Ghorashi explained. "Every lever you can imagine is being pulled to get that turnaround time down [to] 24 hours because that’s what the food industry needs, and roughly $10 a sample on average, which is what PCR testing kind of averages out in the food industry today."

The company's process includes proprietary protocols for prepping samples for sequencing as well as for analyzing the data. "We have kitting with all of our consumables to prepare samples for sequencing. We have the sequencing process for pathogen testing [and] there is an enrichment step before that to grow the bacteria signal easily," Ghorashi said.

Data from the sequencing step is uploaded to the cloud, where it is analyzed by the company's proprietary bioinformatics pipeline. "Our informatics have been tailor-made for looking at the precise markers and regions of the genome that give us the information on the pathogen species and subtype information," he said.

Completing the analysis in 24 hours or less is non-trivial, requiring an "immense amount of development and IP to target those regions and customize the information in a way that gives you the right answer." Furthermore, there is little room for error in the food industry. "If a run fails, that’s not acceptable because product is waiting to ship and … [the company] can't risk a recall," he said. As part of the analysis, Clear Safety utilizes Clear Labs' database of genomic markers relevant to food safety testing.

So far, the company has deployed its platform in several third-party service labs as well as major food production companies that are performing high-volume testing. Specifically, about 10 companies with in-house labs are participating in the Clear Safety pilot, as well as over half of the third-party labs in the US. However, the company has spots open for more partners. Pilots typically run for about two weeks. "It doesn't take long to come back with a statistically significant number, so we are able to quickly provide customers with a report comparing our results against the legacy PCR platforms," Ghorashi said.

Moving forward, Clear Labs anticipates more NGS-based companies will begin to target the food safety market in the near future. It will have to compete with companies like SGS, Eurofins, and Covance, for example, but these firms offer mostly microbiology-based testing solutions or whole-genome sequencing for one-off testing rather than high-throughput testing, he said. A second category of competitors are the NGS platform providers themselves, such as Illumina and Oxford Nanopore Technologies. However, these companies are not currently focused on the food safety space and do not have a presence in the industry at this point in time, he said.

PCR platform providers such as Bio-Rad, Dupont, and 3M are more direct competitors for Clear Labs' market share. Also, other startups are developing PCR-based food testing systems, for example LexaGene, which is working on a microfluidics-based platform to perform qPCR tests for identifying pathogens in food samples.

However, when Clear Safety goes on sale, Ghorashi believes it will draw customers away from these providers. "That's really who we are going head to head with, and we believe with a far superior solution," he said. In fact, Ghorashi believes that his company is at least two years ahead of any potential competitors. "The food industry is a $4 trillion global market, and food safety testing alone is a $10 billion market" with about 400 million food safety tests run globally per annum. "It's not only the diagnostic testing revenue that is exciting for Clear Labs but it's also the data that we are gathering, which is so rich and can be leveraged for … predictive risk assessment."

Jack Regan, CEO of LexaGene, disagreed. He noted that while there are benefits to NGS-based testing, there are significant time and cost constraints, among other factors, that limit its use for food safety. "The NGS platform has a benefit of trying to determine whether or not foodborne illnesses that have been detected across the country are all from the same strain or subtype of bacteria that originated from a single farm," he said. "The disadvantage is that generally, NGS is more expensive to run, [takes] more time, and [the sequencing] is not done onsite." 

Furthermore, NGS offers far more information than is needed for risk assessment in the food safety industry, he said. In cases of widespread food contamination, access to such data is useful for tracing the initial sources of the contamination but the greater demand in the food industry is for very fast risk assessment of items being packaged and sent for consumer use. According to Regan, that is the sweet spot for PCR-based methods, making it unlikely that companies in the space will switch to NGS-based testing anytime soon. Furthermore, there are standard markers that denote the presence of particular pathogens that are well characterized and easily detectable by PCR. "A food packing plant wants to know if there is Salmonella [in their sample] … they don't care if there is a mutation in the non-coding region of an unimportant segment of the genome," he said. "You don't need all of that information."

Regan pointed to the results of an internal market survey that LexaGene conducted to find out how many markers food companies want tests to be able to detect. The results showed that most companies only want to detect three or four markers at most. NGS offers far more data than necessary, and more is not always better, he said. "Once you have too much information, you have to figure out what you are going to do with that information," Regan said. With the LexaGene platform, "we can look for up to 22 different targets at once, which is more than enough coverage."

Clear Labs claims that it can return results in about 24 hours. But PCR-based methods still offer a much shorter time to results, since they deal with smaller quantities of data. "We return your results in about an hour [and] we are very low cost, which is extremely important to the food industry, where for the most part, it’s a very high-volume, low-cost per sample market," Regan said. "NGS will help you identify the causative farm or packing plant which is causing the contamination but it does not prevent you from having the contamination … and we hope to prevent these things happening in the first place."

Like Clear Labs, LexaGene is not disclosing specific details about pricing. However, Regan did say that the cost will range from $25 to $35 per sample.