Tag Archives: NGS

Stephanie Pollard, ClearLabs
In the Food Lab

The Power of Advanced NGS Technology in Routine Pathogen Testing

By Stephanie Pollard
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Stephanie Pollard, ClearLabs

The food industry is beginning to transition into an era of big data and analytics unlike anything the industry has ever experienced. However, while the evolution of big data brings excitement and the buzz of new possibilities, it also comes coupled with an element of confusion due to the lack of tools for interpretation and lack of practical applications of the newly available information.

As we step into this new era and begin to embrace these changes, we need to invest time to educate ourselves on the possibilities before us, then make informed and action-oriented decisions on how to best use big data to move food safety and quality into the next generation.

Stephanie Pollard will be presenting “The Power of Advanced NGS Technology in Routine Pathogen Testing” at the 2018 Food Safety Consortium | November 13–15One of the big questions for big data and analytics in the food safety industry is the exact origins of this new data. Next Generation Sequencing (NGS) is one new and disruptive technology that will contribute significantly to a data explosion in our industry.

NGS-based platforms offer the ability to see what was previously impossible with PCR and other technologies. These technologies generate millions of sequences simultaneously, enabling greater resolution into the microbial ecology of food and environmental surfaces.

This represents a seismic shift in the food safety world. It changes the age-old food microbiology question from: “Is this specific microbe in my sample?” to “what is the microbial makeup of my sample?”

Traditionally, microbiologists have relied on culture-based technologies to measure the microbial composition of foods and inform risk management decisions. While these techniques have been well studied and are standard practices in food safety and quality measures, they only address a small piece of a much bigger microbial puzzle. NGS-based systems allow more complete visibility into this puzzle, enabling more informed risk management decisions.

With these advances, one practical application of NGS in existing food safety management systems is in routine pathogen testing. Routine pathogen testing is a form of risk assessment that typically gives a binary presence/absence result for a target pathogen.

NGS-based platforms can enhance this output by generating more than the standard binary result through a tunable resolution approach. NGS-based platforms can be designed to be as broad, or as specific, as desired to best fit the needs of the end user.

Imagine using an NGS-based platform for your routine pathogen testing needs, but instead of limiting the information you gather to yes/no answers for a target pathogen, you also obtain additional pertinent information, including: Serotype and/or strain identification, resident/transient designation, predictive shelf-life analysis, microbiome analysis, or predictive risk assessment.

By integrating an NGS-based platform into routine pathogen testing, one can begin to build a microbial database of the production facility, which can be used to distinguish resident pathogens and/or spoilage microbes from transient ones. This information can be used to monitor and improve existing or new sanitation practices as well as provide valuable information on ingredient quality and safety.

This data can also feed directly into supplier quality assurance programs and enable more informed decisions regarding building partnerships with suppliers who offer superior products.

Similarly, by analyzing the microbiome of a food matrix, food producers can identify the presence of food spoilage microbes to inform more accurate shelf-life predictions as well as evaluate the efficacy of interventions designed to reduce those microbes from proliferating in your product (e.g. modified packaging strategies, storage conditions, or processing parameters).

Envision a technology that enables all of the aforementioned possibilities while requiring minimal disruption to integrate into existing food safety management systems. NGS-based platforms offer answers to traditional pathogen testing needs for presence/absence information, all the while providing a vast amount of additional information. Envision a future in which we step outside of our age-old approach of assessing the safety of the food that we eat via testing for the presence of a specific pathogen. Envision a future in which we raise our standards for safety and focus on finding whatever is there, without having to know in advance what to look for.

Every year we learn of new advancements that challenge the previously limited view on the different pathogens that survive and proliferate on certain food products and have been overlooked (e.g., Listeria in melons). Advanced NGS technologies allow us to break free of those associations and focus more on truly assessing the safety and quality of our products by providing a deeper understanding of the molecular makeup of our food.

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!

Mahni Ghorashi, Clear Labs
FST Soapbox

The Future of Food Safety: A Q&A with Mars, Inc.

By Mahni Ghorashi
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Mahni Ghorashi, Clear Labs

Food safety professionals often work behind-the-scenes, developing the systems and processes that keep our food supply free of harm. While a vital job, it’s often thankless work—recognition only comes when there’s a recall or an outbreak.

And yet, the food safety industry is evolving rapidly. New threats are emerging, new technologies are being deployed, and new regulations are causing changes in our fundamental infrastructure. “Good enough” pathogen detection is no longer good enough. As a result of new pressures, the food safety lab is emerging as one of the most promising centers of innovation in the entire supply chain. It’s time that the people who are driving this wave of innovation and change receive the positive recognition for their work that they deserve.

That’s why we’re starting this Q&A series—to hear the success stories, the best practices, the hurdles and the achievements from the best in the industry. We will dive deep with the experts into some of the biggest challenges and opportunities our industry faces, focused particularly on new technology that is advancing the industry by leaps and bounds—from blockchain to NGS to machine learning. As this series evolves, we hope that readers will be informed and inspired by what the future holds.

For our first interview, I had the pleasure of interviewing Bob Baker, corporate food safety science and capability director at Mars, Inc.. Bob leads the corporate food safety science strategy for Mars, Incorporated and provides leadership and consultation on food safety capability development and current and future challenges impacting global food security. Prior to his current role, Bob was responsible for the design, construction and leadership of the Mars Global Food Safety Center in Beijing, China.

Mahni Ghorashi: What are the biggest risks to our food safety infrastructure in 2018? What’s keeping you up at night?

Bob Baker: Food safety risks are increasing at an unprecedented rate, with new threats and hazards constantly emerging, changes in agricultural practices and food production, and the environment. The globalization of trade means that an issue in one part of the world often impacts the global supply chain.

To ensure safer food for all, the identification and isolation of potential and developing issues needs to happen at a much faster pace. At Mars, we believe industry has a crucial role to play in helping all stakeholders in the food supply chain identify risks and solutions, but no entity can do this alone. That’s why we have advocated for a new approach to food safety, one rooted in knowledge sharing and collaboration. That’s why we launched our Global Food Safety Center (GFSC) in 2015.

GFSC is conducting original research and collaborating in a number of areas that we see as critical—mycotoxin management, rapid detection and identification of pathogens, raw material and product authenticity, operational food safety optimization and transforming food safety through data integration.

Although we see improvements in some areas, some of them are becoming more complex. Mycotoxins are a prime example of that. Food fraud is another area of growing concern, and addressing that is going to take a focus on technology, regulation and enforcement and a number of other areas to deliver transparency, to verify sourcing, and ultimately ensure that customers and consumers are purchasing and consuming safe food.

Ghorashi: What are you most excited about? What’s changing in a good way in the food safety sector?

Baker: What’s encouraging is we’re seeing is a willingness to share information. At Mars we often bring together world experts from across the globe to focus on food safety challenges. We continue to see great levels of knowledge sharing and collaboration.

There are also new tools and new technologies being developed and applied. Something we’re excited about is a trial of portable ‘in-field’ DNA sequencing technology on one of our production lines in China. This is an approach that could, with automated sampling, reduce test times.

We’re also excited about the IBM-Mars Consortium for Sequencing the Food Supply Chain—early signs have been very encouraging. This is an approach that could change the nature of food safety management, taking us from testing for a specific pathogen, to a situation where we could map the entire makeup of an environment and predict food safety issues based on changes within that environment.

Ghorashi: If you take a look at the homepage of any of the food safety trade publications, all you see is recall after recall. Are transparency and technological advancement bringing more risks to light, and are things generally trending towards improvement?

Baker: At Mars, quality is our first principle and we take it seriously—if we believe that a recall needs to be made in order to ensure the safety of our consumers then we will do it. We also share lessons from recalls across our business to ensure that we learn from every experience.

Unfortunately, there does not seem to be a safe place for businesses to share such insights with each other. So although we are seeing more collaboration in the field of food safety generally, critical knowledge and experience from recalls is not being shared more broadly which may be having an impact.

Regarding the role of technological advancement, the hope is that as better tools and more advanced technology become available, it will be easier to pinpoint issues in the food supply chain much more effectively and much earlier than before which can only be a good thing.

Ghorashi: Do you see 2018 as the year when NGS technologies will find widespread adoption for food-safety testing applications? What can government and industry do to help accelerate adoption?

Baker: Next-generation sequencing has a lot of potential, but it may take time to be adopted fully.

We are very pleased to see the U.S. government continue to view food safety as a priority. The FDA and the CDC are already moving from single-cell cultures and single genes to mixed genomics and metagenomics. At Mars, we see metagenomics as the future of food safety because it may help identify sentinels of food safety and predict potential issues through microbiome shifts.

The key to the development and adoption of any successful technology is sharing knowledge so that all parties from the government, industry and NGOs can build on it. Early results from the IBM-Mars Consortium for Sequencing the Food Supply Chain have been encouraging and we are actively sharing these initial insights via publications and scientific forums.

Ghorashi: What are some new technology processes on the horizon for 2018, and where should industry and government be investing its time and resources?

Baker: Food safety challenges are increasing, and we need to collaborate and share insights if we are to ensure safe food.

One major area is informatics and how we can enable better application of data mining, more applied bioinformatics and statistics. How can key players –regulators, industry, NGOs—get together and share data? How do you better mine data to move to a predictive model? This is an area that could benefit from a more focused approach between government and industry.

Ghorashi: What is your #1 goal for the industry in 2018? Fewer recalls? New tech implementation? Better regulatory oversight?

Baker: We’d like to see progress in all of the above, and we will continue to work with a range of stakeholders to move the needle on food safety.

That said, the food safety challenges facing us all are complex and evolving. Water and environmental contaminants are areas that industry and regulators are also looking at, but all of these challenges will take time to address. It’s about capturing and ensuring visibility to the right insights and prioritizing key challenges that we can tackle together through collaboration and knowledge sharing.

Mahni Ghorashi, Clear Labs
In the Food Lab

The Food Safety Testing Lab as Profit Center

By Mahni Ghorashi
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Mahni Ghorashi, Clear Labs

It’s not that the industry has been more reluctant than others to embrace change; rather, the forces that will drive the food’s big data revolution have but recently come to bear.

Regulation is now playing a role. FSMA mandates that the industry embrace proactive food safety measures. That means higher testing volumes. Higher testing volumes means more data.

At the same time, new technologies like next-generation sequencing (NGS) are beginning to find wide-scale adoption in food-safety testing. And NGS technologies generate a lot of data—so much so that the food safety lab will soon emerge as the epicenter of the food industry’s big data revolution. As a result, the microbiology lab, a cost center, will soon emerge as one the industry’s most surprising profit centers.

A Familiar Trend

This shift may be unprecedented in food, but plenty of other industries touched by a technological transformation have undergone a similar change, flipping the switch from overhead to revenue generation.

Take the IT department, for instance. The debate about IT departments being a cost or profit center has been ongoing for many years. If data centers had simply kept doing what they have done in the past—data processing, enterprise resource planning, desktop applications, help desk—maintaining an IT department would have remained a cost center.

But things look quite different today. Companies in today’s fast-changing business environment depend on their IT departments to generate value. Now and for the foreseeable future, the IT department is on the hook to provide companies with a strategic advantage and to create new revenue opportunities.

Netflix, for example, recently estimated the value of their recommenders and personalization engines at $1 billion per year by quadrupling their effective catalog and dramatically increasing customer engagement and reducing churn.

Another great example are the call centers of customer support departments. For most of their history, call centers generated incredibly small margins or were outright cost centers.

Now, call centers armed with AI and chatbots are a source of valuable customer insights and are a treasure trove of many brands’ most valuable data. This data can be used to fuel upsells, inform future product development, enhance brand loyalty, and increase market share.

Take Amtrak as a prime example. When the commuter railway implemented natural language chatbots on their booking site, they generated 30% more revenue per booking, saved $1 million in customer service email costs, and experienced an 8X return on investment.

These types of returns are not out of reach for the food industry.

The Food Data Revolution Starts in the Lab

The microbiology lab will be the gravitational center of big data in the food industry. Millions of food samples flow in and out of these labs every hour and more and more samples are being tested each year. In 2016 the global food microbiology market totaled 1.14 billion tests—up 15% from 2013.1

I’d argue that the food-testing lab is the biggest data generator in the entire supply chain. These labs are not only collecting molecular data about raw and processed foods but also important inventory management information like lot numbers, brand names and supplier information, to name a few.

As technologies like NGS come online, the data these labs collect will increase exponentially.
NGS platforms have dramatically reduced turnaround times and achieve higher levels of accuracy and specificity than other sequencing platforms. Unlike most PCR and ELISA-based testing techniques, which can only generate binary answers, NGS platforms generate millions of data points with each run. Two hundred or more samples can be processed simultaneously at up to 25 million reads per sample.
With a single test, labs are able to gather information about a sample’s authenticity (is the food what the label says it is?); provenance (is the food from where it is supposed to be from?); adulterants (are there ingredients that aren’t supposed to be there?); and pathogen risk.

The food industry is well aware that food safety testing programs are already a worthwhile investment. Given the enormous human and financial costs of food recalls, a robust food-safety testing system is the best insurance policy any food brand can buy.

The brands that understand how to leverage the data that microbiology labs produce in ever larger quantities will be in a position to transform the cost of this insurance policy into new revenue streams.

Digitizing the Food Supply Chain

It’s clear that the food lab will generate massive amounts of data in the future, and it’s easy to see that this data will have value, but how, exactly, can food brands turn their data into revenue streams?

The real magic starts to happen when we can combine and correlate the trillions of data points we’re gathering from new forms of testing like NGS, with data already being collected, whether for inventory management, supply chain management, storage and environmental conditions, downstream sales data, or other forms of testing for additives and contaminant like pH, antibiotics, heavy metals and color additives.

When a food brand has all of this data at their fingertips, they can start to feed the data through an artificial intelligence platform that can find patterns and trends in the data. The possibilities are endless, but some insights you could imagine are:

  • When I procure raw ingredient A from supplier B and distributors X, Y, and Z, I consistently record higher-than-average rates of contamination.
  • Over the course of a fiscal year Supplier A’s product, while a higher cost per pound, actually increases my margin because, on average, it confers a greater nutritional value than the supplier B’s product.
  • A rare pathogen strain is emerging from suppliers who used the same manufacturing plant in Arizona.

Based on this information about suppliers, food brands can optimize their supplier relationships, decrease the risk associated with new suppliers, and prevent potential outbreaks from rare or emerging pathogen threats.

But clearly the real promise for revenue generation is in leveraging food data to inform R&D, and creating a tighter food safety testing and product development feedback loop.

The opportunity to develop new products based on insights generated in the microbiology lab are profound. This is where the upside lives.

For instance, brands could correlate shelf life with a particular ingredient or additive to find new ways of storing food longer. We can leverage data collected across a product line or multiple product lines to create new ingredient profiles that find substitutes for or eliminate unhealthy additives like corn syrup.

One of the areas I’m most excited about is personalized nutrition. With microbiome data collected during routine testing, we could develop probiotics and prebiotics that promote healthy gut flora, and eventually are even tailored to the unique genetic profile of individual shoppers. The holistic wellness crowd has always claimed that food is medicine; with predictive bioinformatic models and precise microbiome profiles, we can back up that claim scientifically for the first time.

Insights at Scale

Right now, much of the insight to be gained from unused food safety testing data requires the expertise of highly specialized bioinformaticians. We haven’t yet standardized bioinformatic algorithms and pipelines—that work is foundational to building the food genomics platforms of the future.

In the near future these food genomics platforms will leverage artificial intelligence and machine learning to automate bioinformatic workflows, dramatically increasing our ability to analyze enormous bodies of data and identify macro-level trends. Imagine the insights we could gain when we combine trillions of genomic data points from each phase in the food safety testing process—from routine pathogen testing to environmental monitoring to strain typing.

We’re not there yet, but the technology is not far off. And while the path to adoption will surely have its fair share of twists and turns, it’s clear that the business functions of food safety testing labs and R&D departments will grow to be more closely integrated than ever before.

In this respect the success of any food safety program will depend—as it always has—not just on the technology deployed in labs, but on how food brands operate. In the food industry, where low margins are the norm, brands have long depended on efficiently managed operations and superb leadership to remain competitive. I’m confident that given the quality and depth of its human resources, the food industry will be prove more successful than most in harnessing the power of big data in ways that truly benefit consumers.

The big data revolution in food will begin in the microbiology lab, but it will have its most profound impact at the kitchen table.

References

  1. Ferguson, B. (February/March 2017). “A Look at the Microbiology Testing Market.” Food Safety Magazine. Retrieved from https://www.foodsafetymagazine.com/magazine-archive1/februarymarch-2017/a-look-at-the-microbiology-testing-market/.
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.