Tag Archives: Clear Labs

Sequencing pattern, pathogens

Pilot Program Aims to Advance NGS to a Routine Pathogen Testing Platform

By Maria Fontanazza
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Sequencing pattern, pathogens

NGS, or next generation sequencing, is described as the “most updated automated DNA sequencing technology available,” according to Eurofins’ Gregory Siragusa, Ph.D. and Douglas Marshall, Ph.D. Over the past few years, there’s been quite a bit of discussion around the technology and its role in transforming food safety testing.

Clear Labs has been especially vocal about the potential of NGS, as the company has built itself on an NGS platform with capabilities that include GMO testing, pathogen detection and ingredient authenticity. The company just announced a pilot program for its NGS platform that aims to bring the technology into the realm of routine food safety testing. Mahni Ghorashi, co-founder of Clear Labs, recently discussed the program with Food Safety Tech.

Food Safety Tech: Is the platform entering the pilot the same as the technology we talked about in the Q&A,“New Whole Genome Sequencing Test Monitors Threat of Pathogens” a couple of years back?. If so, have there been developments since? If this is a different platform, how long has it been in development and what is the novelty and advantages?

Mahni Ghorashi, Clear Labs
Mahni Ghorashi, co-founder of Clear Labs

Mahni Ghorashi: That’s a good question, and I understand why this could be a little confusing, especially for someone who has followed the development of Clear Labs over the years. (Thank you!).

The current platform being piloted is based on the same fundamental technology we’ve always had, but we have built it out considerably and adapted it for routine food safety testing.

At its core, our platform is based on industry-leading NGS technology paired with IP-protected bioinformatics. It’s always been backed by the world’s largest reference database for genomic food markers and food sample metadata.

Over the last year and a half, we’ve built capabilities into the core platform that allow our system to be deployed at high testing volumes for food safety testing, at scale.

We’ve built in robotics and automation to make this system truly “end-to-end” and to speed the process from start to finish.

We’ve reduced the cost by another order of magnitude, with faster turnaround time and greater accuracy than competing market products.

In short, the latest version of the platform is the first automated system that takes advantage of advanced DNA sequencing, bioinformatics, and robotics.

This pilot represents a new era for Clear Labs and the food safety industry at large. While our tests have always been higher-resolution and higher-accuracy than PCR, we now believe we can compete with the turnaround times and cost of PCR.

FST: What is the duration of the pilot study? What is the goal of the pilot?

Ghorashi: The goal of the pilot study is to demonstrate that NGS is ready to be adopted as the new standard for routine food safety testing. We believe that our pilot study will also help the industry to fully appreciate how NGS technologies will modernize food safety programs, without changing the way food safety is conducted today.

The pilots last for two weeks. Because our platform is for high-volume, routine safety testing, it doesn’t take long to have tested a statistically significant number of samples. We’re able to quickly provide our customers with a report comparing our results to that of their legacy, PCR-based tests.

FST: What feedback have you received about the platform thus far? What is its potential?

Ghorashi: The feedback we’ve gotten has been overwhelmingly positive. We can’t talk specifics until the pilot is complete, but I can tell you in broad terms that our early pilot customers have been overwhelmingly enthusiastic.

The potential is enormous. This NGS platform—the first of its kind—is going to usher in a new era of food safety testing.

Traditional techniques have high rates false negatives and false positives. In 2015, a study from the American Proficiency Institute on about 18,000 testing results from 1999 to 2013 for Salmonella found false negative rates between 2% and 10% and false positive rates between 2% and 6%. Several Food Service Labs claim false positive rates of 5% to 50%.

False positives can create a resource-intensive burden on food companies. Reducing false negatives is important for public health as well as isolating and decontaminating the species within a facility.

The costs savings, but even more important the peace of mind that comes from a near fail-proof system is invaluable to the leading food brand and service labs we’ve been working with.

FST: What are the clearest areas of impact for NGS in food safety?

Ghorashi: The impact of NGS is going to be felt broadly because it will replace existing PCR systems for high-throughput safety testing. Across the food industry, wherever there are PCR systems, we will soon see NGS-based system that will be more comprehensive, accurate, and cost-effective.

And unlike some PCR techniques that can only detect up to five targets on one sample at a time, the targets for NGS platforms are nearly unlimited, with up to 25 million reads per sample, with 200 or more samples processed at the same time. This results in a major difference in the amount of information yielded.

FST: Do you have any additional comments on the pilot program or NGS in general?

Ghorashi: While I can’t talk about specific customers, I should note that our pilot program is already deployed across half of the U.S.’s third-party service labs as well as major food production companies engaged in high-volume, routine safety testing.

The majority of the food safety industry is well aware of how transformative NGS systems can be for both their food safety programs and their bottom line. This pilot will go a long ways toward demonstrating that NGS technology has arrived for primetime in the food safety industry.

We’re still accepting applications for the pilot, and we’re excited to help brands recognize the value of and move forward with this vital progression in testing. After the pilot phase, we’ll be rolling out the full platform at IAFP in July of this year.

We’ll keep you updated!

North American Meat Institute Fires Back at Burger Report Findings

By Food Safety Tech Staff
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As Clear Labs’ latest report on burger products, The Hamburger Report, has gained widespread media attention, the North American Meat Institute is sounding an alarm about the findings. Clear Labs is a “fledging company” that is “up to its same old tricks”, using burgers as its target just in time for the grilling season, said Betsy Booren, Ph.D., vice president, scientific affairs at the North American Meat Institute, in a statement from the organization.

Read the article on Food Safety Tech: Next-Gen Sequencing Exposes Problems with Burgers

“A review of the company’s procedures suggest[s] collection methods prone to mistakes and a range of errors throughout the analysis process. A look at the company’s own promotional video featuring shots of overpacked freezers and technicians testing products using plastic forks and knives with paper towels would suggest cross contamination in the lab is a very good possibility,” said Booren. “When a single cell can generate a finding, precise methods are crucial. It’s entirely possible that the human DNA found could be linked back to the company’s own staff—we just don’t know.  Likewise, when the lab company suggests some products showed the presence of another species, like chicken in a beef product, this finding could also stem from a single cell and even result from the pulling samples from multiple packages in the same room, as the company appears to have done.”

Booren called Clear Labs’ report a marketing ploy and went on to assert that today’s ground beef is safer than ever, saying there have been significant reductions in pathogenic bacteria, which has been “further confirmed by this report [The Hamburger Report]”.

Clear Labs, The Hamburger Report

Next-Gen Genomic Sequencing Exposes Problems with Burgers

By Maria Fontanazza
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Clear Labs, The Hamburger Report

Burgers are the quintessential American food. But as prices continue to rise in the beef industry and U.S. consumers seek more health-conscious alternatives such as veggie and salmon burgers, some food companies may be cutting corners. Clear Labs used next-generation genomic sequencing (NGS) to conduct molecular analysis of 258 burger products (ground meat, frozen patties, fast food burgers and veggie burger products from 79 brands and 22 retailers) and found significant issues—instances of substitution, missing ingredients, pathogens or hygienic problems—in about 14% of samples. This is a red flag for industry, indicating a need to remain vigilant about vulnerabilities in the supply chain and the way in which products are tested.

Ironically, perhaps the biggest problems that The Hamburger Report revealed surrounded meat-alternative products. Out of 89 vegetarian samples, 23.6% were found to have issues, from ingredient substitutions to rat DNA to pathogens (see Figure 1). “We were surprised by the higher rate of problems in veggie burgers,” says Mahni Ghorashi, co-founder of Clear Labs. “There were nearly twice as many problems in those samples as their meat counterparts, which is surprising, because you normally think of a veggie product as perhaps a safer bet, but we actually found more cases of pathogen strains. And we found things like beef in veggie products, which isn’t acceptable. That was somewhat troubling.” Ghorashi suggests that manufacturers should be doing more to ensure consistency and adequate labeling of best-handling practices for consumers. “The message is that we need more awareness about the unknown risks and the potential need for more stringent safety measures,” he says. “We follow a great deal of these practices when it comes to meat-based products. Perhaps we’re not as sensitive toward veggie-based products.”

The Hamburger Report, Clear Labs
Figure 1. The Hamburger Report found a higher rate of issues with meat-alternative burger products. (Figure courtesy of Clear Labs)

The report also uncovered several high-risk pathogens in samples, but not the typical ones (i.e., Listeria, Salmonella, E. coli) that make news headlines. Out of the 258 samples, 4.3% contained pathogenic DNA, with vegetable products accounting for four of those instances. Pathogens found included Yersinia pseudotuberculosis, Yersinia enterocolitica, clostridium perfringens, and klebsiella pneumonia. Although these strains are often rare, they still have health implications and can cause tuberculosis-like symptoms, digestive issues and gastroenteritis. Typical methods such as polymerase chain reaction (PCR) are used to detect pathogenic strains such as Listeria, Salmonella and E. coli, but can potentially miss other strains. “The industry should take off their pathogen blinders and start to test for lesser known and potentially dangerous pathogens using these types of blind-testing techniques,” says Ghorashi. “It’s worth casting a wider net and filter in order to catch these [pathogens].”

Although the screening method that Clear Labs used is currently unable to determine whether a pathogen is dead or alive, nor the count, there are other benefits to using next-generation DNA sequencing, says Ghorashi, who thinks the method has the potential to become the technology of choice in the food industry. “The strength of this platform as it differentiates itself from existing solutions is its ability to look unbiasedly and universally into food samples and tell you everything that’s there,” he says. “It’s able to detect any type of DNA-based species within a sample as opposed to specific queries that you might be looking for. This technology can detect everything that’s there, so it often catches things that one might miss. Existing solutions look very focused on one particular item.”

What are the implications of The Hamburger Report in the context of FSMA?

Ghorashi: It’s very much in line with what FDA is rolling out with FSMA. This speaks back to where industry is headed in terms of rolling out more preventive measures versus responsive measures. It plays into economic adulteration and fraud. It also plays into the concept of proactive testing and measures, a better sense of the overall landscape of the supply chain and where the weaknesses are. These are all the areas that software-driven and data-driven platforms can help emphasize. We look at FDA as a forwarding-thinking organization and an ally in this initiative. Hopefully emerging companies, including ourselves, that have new disruptive technologies can help assist the food industry, whether producers, manufacturers, retailers or distributors, in building more air-tight safety programs and complying more closely with FSMA regulations.

Clear Labs is working towards building out its first product, Clear View. The software data analytics platform integrates NGS technology and is designed to aggregate test data in the cloud to provide food manufacturers, suppliers and retailers with insights about their supply chains. The company is also continually growing its internal database, which, according to Ghorashi, is currently the largest molecular food database in the world.