Tag Archives: WGS

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!

Stephen Ostroff, 2016 Food Safety Consortium

Blockchain Transformational, Says Ostroff. FDA Updates on Pathogens, FSMA, WGS and More

By Maria Fontanazza
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Stephen Ostroff, 2016 Food Safety Consortium

Stephen Ostroff, M.D. deputy commissioner for foods and veterinary medicine, sounds excited about the promise of blockchain. He also continues to enthusiastically wave the flag for whole genome sequencing (WGS) in solving foodborne illness cases. At the recent GMA Science Forum, Ostroff shared his usual update on incidents involving pathogens, agency progress in inspections and FSMA, and what the future holds.

The 2018 Food Safety Supply Chain conference features a Blockchain panel discussion | June 12–13 | Learn morePathogens

“There’s been essentially zero change in incidents of pathogens, and in some [cases there have been] increases—despite the fact that we’ve been doing quite a bit to improve the profile of food safety in the United States,” said Ostroff. This isn’t the first time that Ostroff pointed to the fact that foodborne illness is resistant to change, but he still emphasized the disappointment that industry is “way off” from the Healthy People 2020 target rate for pathogens established by the government. “None of these are close to where we thought we would be,” he said, referring to the government’s established target rates for Campylobacter, E.coli O157, Listeria, Salmonella, Vibrio and Yersinia.

Ostroff has previously pointed to improved diagnostics and surveillance systems as being partially responsible for a lack of improvement in the number of foodborne illness cases (due to higher detection rates), but during this particular presentation he brought attention to culture independent diagnostic tests (CIDTs)—which he said are having a “major impact on data collected in FoodNet.” CIDT is relatively new and is more rapid than the culture method, but it doesn’t allow for subtyping or antimicrobial resistance testing.

According to Ostroff, CIDTs have major implications for folks who work in food safety. The overall incidence of infection with foodborne pathogens is not decreasing, and the use of CIDTs makes assessment of trends difficult. CIDTs appear to be finding infections previously undiagnosed or unrecognized. In addition, they could affect the agency’s ability to monitor FSMA impact measures.

Inspections

The agency continues to look at inspection data from both the perspective of the number of inspections and their outcomes. During FY 2017, there were 1253 domestic and 146 foreign inspections. For FY 2018, there have already been 1610 domestic inspections to date.

Enforcement Discretion

In January, FDA issued new enforcement discretion for certain provisions in four FSMA rules. This included resolving issues related to the “farm” definition, requirements for food contact substances under FSVP, and certain written assurances in place for the Preventive Controls (human and animal) rule until FDA comes up with a practical solution to issues raised by stakeholders, Ostroff said.

Oversight of Food Imports

FDA continues to take a risk-based approach to FSVP and overseas inspections. Part of these efforts includes the agency’s systems recognition program where it looks at other mature food safety systems around the world to recognize countries that have programs similar to the United States. Thus far FDA has recognized Australia, Canada and New Zealand food safety systems; It is currently in the process of evaluating European Union members.

Intentional Adulteration Rule

The International Adulteration rule continues to be a hot topic of discussion, especially as it relates to associated costs. FDA is actively working on putting out a draft guidance that will discuss how to conduct vulnerability assessments, along with its interpretation of the rule, according to Ostroff. Part one of the draft should be out “in the very near future”, he said. He added that the agency is trying to be flexible with the rule and although food defense is an important component of food safety, companies should never do anything in the context of food defense that could pose a food safety risk.

Whole Genome Sequencing

WGS provides more precise identification at a genetic level and helps expedite recognition and response time for nearly all current foodborne illness and outbreak investigations. “It’s the new normal—it’s here and it’s here big time,” said Ostroff, adding that the GenomeTrakr network has more than 167,000 isolates sequences in the database and is becoming more and more powerful. “It’s amazing what this tool can do,” he said, citing two recent cases involving strains of Salmonella in papayas and kratom.

Blockchain

“I think blockchain can be really transformational in the world of food safety,” said Ostroff, calling it “traceability on steroids without question”. He thinks the technology could also be useful in addressing food fraud and economically motivated adulteration, and provide more consumer transparency. Right now the FDA is looking very closely at blockchain in context of traceability and FSMA.

Sasan Amini

NGS in Food Safety: Seeing What Was Never Before Possible

By Sasan Amini
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Sasan Amini

For the past year, Swedish food provider Dafgård has been using a single test to screen each batch of its food for allergens, missing ingredients, and even the unexpected – an unintended ingredient or pathogen. The company extracts DNA from food samples and sends it to a lab for end-to-end sequencing, processing, and analysis. Whether referring to a meatball at a European Ikea or a pre-made pizza at a local grocery store, Dafgård knows exactly what is in its food and can pinpoint potential trouble spots in its supply chains, immediately take steps to remedy issues, and predict future areas of concern.

The power behind the testing is next-generation sequencing (NGS). NGS platforms, like the one my company Clear Labs has developed, consist of the most modern parallel sequencers available in combination with advanced databases and technologies for rapid DNA analysis. These platforms have reduced the cost of DNA sequencing by orders of magnitude, putting the power to sequence genetic material in the hands of scientists and investigators across a range of research disciplines and industries. They have overtaken traditional, first-generation Sanger sequencing in clinical settings over the past several years and are now poised to supplement and likely replace PCR in food safety testing.

For Dafgård, one of the largest food providers in Europe, the switch to NGS has given it the ability to see what was previously impossible with PCR and other technologies. Although Dafgård still uses PCR in select cases, it has run thousands of NGS-based tests over the past year. One of the biggest improvements has been in understanding the supply chain for the spices in its prepared foods. Supply chains for spices can be long and can result in extra or missing ingredients, some of which can affect consumer health. With the NGS platform, Dafgård can pinpoint ingredients down to the original supplier, getting an unparalleled look into its raw ingredients.

Dafgård hopes to soon switch to an entirely NGS-based platform, which will put the company at the forefront of food safety. Embracing this new technology within the broader food industry has been a decade-long process, one that will accelerate in the coming years, with an increased emphasis on food transparency both among consumers and regulators globally.

Transitioning technology

A decade ago, very few people in food safety were talking about NGS technologies. A 2008 paper in Analytical and Bioanalytical Chemistry1 gave an outlook for food safety technology that included nanotechnology, while a 2009 story in Food Safety Magazine2 discussed spectrometric or laser-based diagnostic technologies. Around the same time, Nature magazine named NGS as its “method of the year” for 2007. A decade later, NGS is taking pathogen characterization and food authentication to the next level.

Over the last 30 years, multiple technology transitions have occurred to improve food safety. In the United States, for example, the Hazard Analysis and Critical Control Points (HACCP) came online in the mid-1990s to reduce illness-causing microbial pathogens on raw products. The move came just a few years after a massive outbreak of E. coli in the U.S. Pacific Northwest caused 400 illness and 4 deaths, and it was clear there was a need for change.

Before HACCP, food inspection was largely on the basis of sight, touch, and smell. It was time to take a more science-based approach to meat and poultry safety. This led to the use of PCR, among other technologies, to better measure and address pathogens in the food industry.

HACCP set the stage for modern-era food testing, and since then, efforts have only intensified to combat food-borne pathogens. In 2011, the Food Safety Modernization Act (FSMA) took effect, shifting the focus from responding to pathogens to preventing them. Data from 20153 showed a 30% drop in foodborne-related bacterial and parasitic infections from 2012 to 2014 compared to the same time period in 1996 to 1998.

But despite these vast improvements, work still remains: According to the CDC, foodborne pathogens in the Unites States alone cause 48 million illnesses and 3,000 fatalities every year. And every year, the food safety industry runs hundreds of millions of tests. These tests can mean the difference between potentially crippling business operations and a thriving business that customers trust. Food recalls cost an average of $10M per incident and jeopardize public health. The best way to stay ahead of the regulatory curve and to protect consumers is to take advantage of the new technological tools we now have at our disposal.

Reducing Errors

About 60% of food safety tests currently use rapid methods, while 40% use traditional culturing. Although highly accurate, culturing can take up to five days for results, while PCR and antigen-based tests can be quicker – -one to two days – but have much lower accuracy. So, what about NGS?

NGS platforms have a turnaround of only one day, and can get to a higher level of accuracy and specificity than other sequencing platforms. And unlike some PCR techniques that can only detect up to 5 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.

For PCR, very small segments of DNA are amplified to compare to potential pathogens. But with NGS tools, all the DNA is tested, cutting it into small fragments, with millions of sequences generated – giving many redundant data points for comparing the genome to potential pathogens. This allows for much deeper resolution to determine the exact strain of a pathogen.

Traditional techniques are also rife with false negatives and false positives. In 2015, a study from the American Proficiency Institute4 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. Research has shown that with robust data analytics and sample preparation, an NGS platform can bring false negative and positive rates down to close to zero for a pathogen test like Salmonella, Listeria, or E.coli.

Expecting the Unexpected

NGS platforms using targeted-amplicon sequencing, also called DNA “barcoding,” represent the next wave of genomic analysis techniques. These barcoding techniques enable companies to match samples against a particular pathogen, allergen, or ingredient. When deeper identification and characterization of a sample is needed, non-targeted whole genome sequencing (WGS) is the best option.

Using NGS for WGS is much more efficient than PCR, for example, at identifying new strains that enter a facility. Many food manufacturing plants have databases, created through WGS, of resident pathogens and standard decontamination steps to handle those resident pathogens. But what happens if something unknown enters the facility?

By looking at all the genomic information in a given sample and comparing it to the resident pathogen database, NGS can rapidly identify strains the facility might not have even known to look for. Indeed, the beauty of these technologies is that you come to expect to find the unexpected.

That may sound overwhelming – like opening Pandora’s box – but I see it as the opposite: NGS offers an unprecedented opportunity to protect against likely threats in food, create the highest quality private databases, and customize internal reporting based on top-of-the-line science and business practices. Knowledge is power, and NGS technologies puts that power directly in food companies’ hands. Brands that adopt NGS platforms can execute on decisions about what to test for more quickly and inexpensively – all the while providing their customers with the safest food possible.

Perhaps the best analogy for this advancement comes from Magnus Dafgård, owner and executive vice president at Gunnar Dafgård AB: “If you have poor eyesight and need glasses, you could be sitting at home surrounded by dirt and not even know it. Then when you get glasses, you will instantly see the dirt. So, do you throw away the glasses or get rid of the dirt?” NGS platforms provide the clarity to see and address problem directly, giving companies like Dafgård confidence that they are using the most modern, sophisticated food safety technologies available.

As NGS platforms continue to mature in the coming months and years, I look forward to participating in the next jump in food safety – ensuring a safe global food system.

Common Acronyms in Food Genomics and Safety

DNA Barcoding: These short, standardized DNA sequences can identify individual organisms, including those previously undescribed. Traditionally, these sequences can come from PCR or Sanger sequencing. With NGS, the barcoding can be developed in parallel and for all gene variants, producing a deeper level of specificity.

ELISA: Enzyme-linked immunosorbent assay. Developed in 1971, ELISA is a rapid substance detection method that can detect a specific protein, like an allergen, in a cell by binding antibody to a specific antigen and creating a color change. It is less effective in food testing for cooked products, in which the protein molecules may be broken down and the allergens thus no longer detectable.

FSMA: Food Safety Modernization Act. Passed in 2011 in the United States, FSMA requires comprehensive, science-based preventive controls across the food supply. Each section of the FSMA consists of specific procedures to prevent consumers from getting sick due to foodborne illness, such as a section to verify safety standards from foreign supply chains.

HACCP: Hazard analysis and critical control points. A food safety management system, HACCP is a preventative approach to quantifying and reducing risk in the food system. It was developed in the 1950s by the Pillsbury Company, the Natick Research Laboratories, and NASA, but did not become as widespread in its use until 1996, when the U.S. FDA passed a new pathogen reduction rule using HACCP across all meat and poultry raw products.

NGS: Next-generation sequencing. NGS is the most modern, parallel, high-throughput DNA sequencing available. It can sequence 200 to 300 samples at a time and generates up to 25 million reads per a single experiment. This level of information can identify pathogens at the strain level and can be used to perform WGS for samples with unknown pathogens or ingredients.

PCR: Polymerase chain reaction. First described in 1985, PCR is a technique to amplify a segment of DNA and generate copies of a DNA sequence. The DNA sequences generated from PCR must be compared to specific, known pathogens. While it can identify pathogens at the species level, PCR cannot provide the strain of a pathogen due to the limited amount of sequencing information generated.

WGS: Whole genome sequencing. WGS uses NGS platforms to look at the entire DNA of an organism. It is non-targeted, which means it is not necessary to know in advance what is being detected. In WGS, the entire genome is cut it into small regions, with adaptors attached to the fragments to sequence each piece in both directions. The generated sequences are then assembled into single long pieces of the whole genome. WGS produces sequences 30 times the size of the genome, providing redundancy that allows for a deeper analysis.

Citations

  1. Nugen, S. R., & Baeumner, A. J. (2008). Trends and opportunities in food pathogen detection. Analytical and Bioanalytical Chemistry, 391(2), 451-454. doi:10.1007/s00216-008-1886-2
  2. Philpott, C. (2009, April 01). A Summary Profile of Pathogen Detection Technologies. Retrieved September 08, 2017, from https://www.foodsafetymagazine.com/magazine-archive1/aprilmay-2009/a-summary-profile-of-pathogen-detection-technologies/?EMID
  3. Ray, L., Barrett, K., Spinelli, A., Huang, J., & Geissler, A. (2009). Foodborne Disease Active Surveillance Network, FoodNet 2015 Surveillance Report (pp. 1-26, Rep.). CDC. Retrieved September 8, 2017, from https://www.cdc.gov/foodnet/pdfs/FoodNet-Annual-Report-2015-508c.pdf.
  4.  Stombler, R. (2014). Salmonella Detection Rates Continue to Fail (Rep.). American Proficiency Institute.

New Whole Genome Sequencing Test Monitors Threat of Pathogens

By Maria Fontanazza
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Today food companies will have access to a new whole genome sequencing (WGS) test that could help them prevent dangerous pathogens from getting into their products. Released by Clear Labs, the test takes a detailed approach to identifying pathogen strains in samples, providing information about their geography and from which food groups they originate.

In an exclusive interview with Food Safety Tech, Mahni Ghorashi, co-founder of Clear Labs, explains how he expects the company’s new test, which has a five- to seven-day turnaround time, will offer companies with a more accurate yet less expensive alternative to protecting consumers by actively monitoring their supply chain for emerging pathogens.

Food Safety Tech: What differentiates this WGS test from current available solutions?

Mahni Ghorashi: No one has been able to provide the food industry with modern whole genome sequencing techniques for food safety. What we’re releasing is a quantum leap in terms of what’s been available on the market today. Whole genome sequencing has been largely siloed to regulatory bodies like FDA and CDC to trace outbreaks and inform investigations—the technologies and techniques that they’re using are actually fairly old; they’re some of the original WGS techniques that emerged on the next-gen sequencing platform. We’ve taken the most advanced techniques on the NGS platform for human disease exploration and personalized medicine and adapted them for food industry.

What gives our WGS test a competitive advantage over legacy-based methods is two fold:

1. Clear Labs has a 2-million+ entry-curated database of genomic information and sequences for the accurate ID of food ingredients (pathogenic organisms and microbiomes). Its accuracy and the confidence level that comes behind our matching is a huge step above anything that’s available in the public domain today.

2. Being able to place pathogenic strain information in the context of overall food ingredients and samples. The whole genome sequencing test we developed has been specifically catered for the food industry, and for food samples in particular, [versus] FDA’s GenomeTrakr, CDC’s PulseNet, or other food safety labs that are offering full genomic sequencing of pathogen strains—they’re using some of the earliest methods to do this. On the NGS platform, we’re able to put those strains in the context of food ingredients and suppliers: Specifically, [matching] bacterial strains with food ingredients [and] suppliers.

Clear Labs, whole genome sequencing

FST: Does this test target specific foods?

Ghorashi: Our platform particularly shines in complex foods. The value of next-gen sequencing and DNA barcoding over PCR-based technologies, which is the gold standard in food safety, is its stability to break down complex food ingredients into all of their known parts, and to look in a universal and unbiased way into food samples. It’s untargeted, so you don’t have know what it is that you’re looking for—and that’s the real power.

FST: What impact do you anticipate for this test, especially in the context of FSMA?

Ghorashi: Our customers are using [the test] for monitoring ingredient supplies and the effectiveness of preventive and sanitary controls [and] to match specific pathogen strains to specific food ingredients. They are using it for proactive testing for FSMA compliance—there’s a lot of movement in this direction and hefty budgets are being allocated to put new preventive controls in place in response to FSMA; whole-genome sequencing will play a big role, and we anticipate large-scale partnerships with agencies and private industry on that front. And the most obvious use case is that it’s being used for techniques to mitigate or reduce the risk of product recall and outbreak.

We’ve been able to significantly reduce the price point on whole-genome sequencing, and all of our tests across the board, because we’re intimately familiar with how the inner workings of these platforms and how to best optimize them for scale and cost efficiency. We think the test will be more accurate and leaps and bounds ahead of what’s available, as well as cost competitive. We’re excited about the work we’re doing and its impact on food safety. I don’t think the food industry—retailers and manufacturers—have ever had access to these kind of tools and they’re being made available just in time for FSMA, as the industry moves towards a more proactive approach to food safety and [takes] preventive measures in their supply chains.  Hopefully we’ll soon be living in a world where outbreaks, illness and the financial toll are a thing of a past.

Clear Labs also just released a microbiome test that helps companies associate microbiomes with specific food ingredients.

Mahni Ghorashi: The microbiome test we’ve developed is able to sequence samples from the human gut and from food, and look at how the microorganisms are interacting. Our customers for this test have been large brands that have advanced R&D departments and academic research centers that are looking for how diet research and the microbiome interact together and how new product development can help us move toward personalized diets when it comes to prebiotic and probiotic diets.”

The impact of the microbiome and the correlations between bacteria of the human gut and the bacteria in the food we eat. The prevailing thesis at the moment is that the microbiome has a significant impact on our health when it comes to disease risk and diet, inflammation and mood disorders. We’re seeing very forward thinking brands like Nestle, ConAgra and Mars putting a lot of attention on the impact of the microbiome when it comes the development of new products, [such as] prebiotics and probiotics, or even specific food products as it pertains to the microbiome. We believe that this intersection— nutrigenomics and the personalized diet—is going to be a massive market, and we’re at the early stages of that.