Tag Archives: whole genome sequencing

Sandra Eskin, OSU

Highlights from Food Safety Tech’s Hazards Conference

By Food Safety Tech Staff
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Sandra Eskin, OSU

The Food Safety Tech’s Hazards Conference + CFI Think Tank “Industry & Academia Advancing Food Safety Practices, Technology and Research” took place April 3-5 in Columbus, Ohio. The event offered two days of practical education on the detection, mitigation, control and regulation of key food hazards, followed by discussion geared toward identifying gaps for research and innovation.

Sandra Eskin, OSU

Sandra Eskin, Deputy Under Secretary for Food Safety, USDA FSIS, opened the program to discuss the agency’s proposed Salmonella in poultry framework. She highlighted the need for a more comprehensive approach that includes incentives to bring down the Salmonella load in birds entering the slaughterhouse, enhanced monitoring of safety measures within the facility, and enforceable product standards for raw poultry products.

Day one continued with a focus on Salmonella and Listeria. Barb Masters, VP of Regulatory Policy at Tyson Foods presented “Salmonella: What We’ve Learned and Remaining Gaps in Detection and Mitigation.” Masters highlighted key gaps in Salmonella detection, mitigation and research including:

  • Correlating what comes from the farm to what is entering a plant
  • Potential benefits of quantification testing
  • A better understanding of products that have the highest levels of Salmonella
  • Identification of virulence factors of different serotypes
  • The need for rapid testing methods that can be used at the plant level

Sanja Ilic, Ph.D., presented findings on the risks and most effective mitigation methods for listeria in hydroponic systems, followed by a session from Stacy Vernon, Ph.D., on recent listeria outbreaks in RTE meats and ice cream.

Shawn Stevens and Bill Marler

Attorneys Bill Marler, founder of Marler Clark, and Shawn Stevens of the Food Industry Counsel opened day two with an overview of the legal and financial risks of food safety hazards. The program continued with a focus on detection and mitigation of pathogens and biofilms.

 

Session Highlights

Application of Ozone for Decontamination of Fresh Produce with Al Baroudi, Ph.D., VP of Quality Assurance and Food Safety, The Cheesecake Factory, and Ahmed Yousef, Ph.D., Professor and Researcher with the Department of Food Science & Technology, OSU

Estimating Mycotoxin Exposure in Guatemala and Nigeria with Ariel Garsow, Ph.D., Food Safety Technical Specialist at the Global Alliance for Improved Nutrition (GAIN)

Mitigating the Risks of Salmonella and Listeria in Your Facility & Products with Sanjay Gummalla of the American Frozen Food Institute, and Rashmi Rani, Senior Manager of Food Safety and Quality Assurance, Schwan’s Foods

How to Use Whole Genome Sequencing in Operations To Improve Food Safety and Root Cause Analysis with Fabien Robert, Head of Zone AMS, Nestlé

Biofilm Prevention and Control Practices with Charles Giambrone, Food Safety Manager, Rochester Midland

On April 5, attendees joined the Ohio State University Center for Foodborne Illness Research and Prevention (CFI), founded and directed by Barbara Kowalcyk, for its annual “Think Tank.” The program featured student research presentations and an “Einstein Lunch” that brought members of industry together with graduate students and OSU researchers to identify gaps in research in the areas of pathogen detection and mitigation, handwashing and mycotoxins.

“We’re hoping this is the first of future collaborations with CFI and Food Safety Tech, where we have industry and academia presenting together,” said Rick Biros, founder of Food Safety Tech, the Food Safety Consortium and the Food Safety Tech Hazards Conference series. “This is something I feel both academia and industry benefit from, and I look forward to working with Barbara and CFI in the future.”

“I learned a lot myself, and it was great to see this program come together,” said Kowalcyk. “I want to thank the presenters, attendees and all the people who worked behind the scenes to make this event happen.”

Scenes from Food Safety Hazards Conference + CFI Thinktank

OSU 2023   OSU reception 2023  Sanja Ilic

Al Baroudi and Ahmed Yousef  CFI Think tank 2023  Saldesia OSU

Rick and Barbara Kowalcyk  OSu Reception - Steve Mandernach  Fabien Robert

 

 

OSU_CFI Logo
Food Safety Think Tank

It is Time for Industry to Embrace Whole Genome Sequencing

By Food Safety Tech Staff
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OSU_CFI Logo

Whole genome sequencing (WGS) has become a powerful tool to track the origins of foodborne illness, but if industry views WGS simply as a tool for regulators, it is missing out on a valuable instrument to improve food safety within its facilities. Join Fabien Robert, head of zone AMS for Nestlé Quality Assurance centres, and Food Safety Tech on April 3-5 at Ohio State University, as we take a closer look at:

Fabien Robert
Fabien Robert
  • How WGS can help industry mitigate food safety risks and enhance root cause analysis
  • How to use WGS in your operations to improve food safety

The Food Safety Tech’s Hazards Conference + CFI Think Tank brings together leading minds in industry and academia for two days of practical education on the detection, mitigation, control and regulation of key food hazards, followed by discussion geared toward identifying gaps for research and innovation.

In person and virtual registration options available

Additional speakers include:

Biofilm Prevention and Control Practices

Charles Giambrone, Food Safety Manager, Rochester Midland

Giambrone received his M.S. degree in Microbiology from Rutgers University in 1978, where his research focus was applied and environmental microbiology. In his current and previous roles as VP & Sr. Technical Support Manager for Rochester Midland Corp, he provides applied research and technical support in the whole area of food safety and sanitation including processing and preparation, membrane cleaning, and water treatment systems plus supervision of R & D projects. Giambrone has a broad and in-depth expertise in the areas of hygiene, disinfection, and biocides. This includes working with systems to remove or prevent biofilm formation in food processing and water system lines as well as other applications.

The USDA’s Proposed Approach to Salmonella Control in Poultry Products

Sandra Eskin, Deputy Under Secretary for Food Safety, Food Safety and Inspection Service, USDA

Sandra Eskin leads the Office of Food Safety at the USDA, overseeing the Food Safety and Inspection Service (FSIS), which has regulatory oversight for ensuring that meat, poultry and egg products are safe, wholesome and accurately labeled. Prior to joining USDA, Eskin was the Project Director for Food Safety at The Pew Charitable Trusts in Washington, D.C. She also served as the Deputy Director of the Produce Safety Project (PSP), a Pew-funded initiative at Georgetown University from 2008-2009.

RTE Meats and Ice Cream – Mitigating Listeria Risks & Responding to Contamination

Stacy Vernon, Food Safety Specialist & Project Manager, CIFT

Stacy Vernon is the Food Safety and Operations Program Manager at CIFT, where she works alongside food manufactures of all sizes to help them achieve their food safety goals and objectives. She delivers business solutions and technical expertise to her clients as they work towards achieving, maintaining and improving their regulatory and third party food safety certification compliance. Stacy has over 15 years of experience in the food and beverages industry as prior to joining CIFT in 2016, she worked in food safety and quality assurance management roles for Smithfield Foods, Inc. and Rudolph Foods Company.

View the full agenda

Listeria in the Retail Food Environment

Janet Buffer, Center for Foodborne Illness & Prevention, OSU

Janet Buffer’s expertise spans across multidisciplinary medical and clinical research centers, higher education institutions, extension agencies, and regulatory departments. Throughout her 28-year professional career, Janet has served in various capacities; relentlessly utilizing her unique skill sets and ability to connect with students and consumers, to thoroughly educate and actively train those around her. She has spearheaded food safety information accuracy efforts and prioritized food production and food safety regulatory compliance in the healthcare and business spheres above all else. All the while, advising and aiding in corporate administration and the improvement of food technologies.

Application of Ozone for Decontamination of Fresh Produce

Al Baroudi, Ph.D., Vice President of Quality Assurance & Food Safety, The Cheesecake Factory

In addition to his current role, Dr. Baroudi has conducted workshops, published White Papers and introduced the HACCP program to developing countries on behalf of the U.S. government. He is the recipient of Borden’s “President Award”, the Sani “Food Safety Champion Award”, and the “Outstanding Food Safety Program Innovation Award,” and the Southern California IFT “Distinguished Achievement Award.” In 2022, NR News named, Dr. Baroudi as one of the top 50 most influential restaurant executives in the country, and The NRA presented him their inaugural Lifetime Achievement Award for “Outstanding Leader in Food Safety.” He was instrumental in passing the Food Facilities Sanitization Bill “AB 1427” in the California State Assembly that cleared the way for the ozone to be approved in California Cal Code (2012).

Ahmed Yousef, Ph.D., Department of Food Science & Technology, Ohio State University

Dr. Yousef earned his Ph.D. in Food Science from University of Wisconsin-Madison. He worked as a postdoctoral researcher at the University of Wisconsin-Madison before joining Ohio State as an Assistant Professor in 1991. Since the late 1990s, Dr. Yousef and his research team have worked to develop methods to pasteurize shell eggs and to decontaminate fresh produce while maintaining products’ fresh qualities. His ozone research led to developing methods to decontaminate spinach, apples, and other fresh produce. As a result of this research, Dr. Yousef established the largest ozone research laboratory in the U.S. at Ohio State.

View the full agenda and register here.

 

CDC, FDA, USDA logos

IFSAC to Continue Focus on Finding Sources of Foodborne Illnesses

By Food Safety Tech Staff
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CDC, FDA, USDA logos

The Interagency Food Safety Analytics Collaboration (IFSAC) has published its 2022–2023 Interim Strategic Plan, placing continued emphasis on foodborne illness source attribution for Salmonella, E. coli O157:H7, Listeria monocytogenes and Campylobacter. Over the next year, IFSAC will address several short-term goals surrounding improvement of methods to evaluate and identify foodborne illness source attribution through the use of outbreak and non-outbreak-associated disease data, and continued collaboration with external partners in an effort to boost data access and capabilities. The group will be targeting several efforts in the coming year, including:

  • Analysis of trends related to foodborne disease outbreak-associated illnesses over the past two decades, with a subsequent peer-reviewed journal article that reveals results.
  • Development and improvement of machine-learning methods used to predict food sources of illnesses that have an unknown source. WGS will be used to compare Salmonella isolates of known and unknown sources.
  • Collaboration with FoodNet when assessing key food sources for sporadic Salmonella Enteritidis and Campylobacter illnesses. The group will develop case-control studies using specific FoodNet data.

Formed in 2011, IFSAC is a partnership between FDA, FSIS and the CDC that seeks to strengthen federal interagency efforts and maximize use of food safety data collection, analysis and use. During 2022–2023, IFSAC will publish its yearly reports on foodborne illness source attribution for the previously mentioned priority pathogens.

El Abuelito Cheese

Recall Alert: Listeria Outbreak Linked to Hispanic-Style Fresh and Soft Cheeses

By Food Safety Tech Staff
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El Abuelito Cheese

–UPDATE March 9, 2021 — Today the FDA confirmed that the recalled cheeses were also distributed to Rhode Island. “States with confirmed distribution now include: AL, CT, FL, GA, IA, IL, IN, KS, KY, MA, MD, MI, MN, MO, MS, NC, NJ, NY, NE, OH, PA, RI, SC, TN, VA, and WI.”

–UPDATE February 24, 2021 — FDA has expanded its warning related to El Abuelito Cheese to include all cheese branded by the company “until more information is known”.

—END UPDATE—

A multistate outbreak of Listeria monocytogenes has been linked to Hispanic-style fresh and soft cheeses produced by El Abuelito Cheese, Inc. As a result, the company has recalled all Questo Fresco products with sell by dates through March 28 (032821).

Join Food Safety Tech on April 15 for the complimentary Food Safety Hazards Series: Listeria Detection, Mitigation, Control & Regulation“As the FDA stated, about this outbreak investigation, the Connecticut Department of Public Health collected product samples of El Abuelito-brand Hispanic-style fresh and soft cheeses from a store where a sick person bought cheeses. Sample analysis showed the presence of Listeria monocytogenes in samples of El Abuelito Queso Fresco sold in 10 oz packages, marked as Lot A027 with an expiration date of 02/26/2021,” the company stated in an announcement posted on FDA’s website. “Samples are currently undergoing Whole Genome Sequencing (WGS) analysis to determine if the Listeria monocytogenes found in these samples is a match to the outbreak strain. At this time, there is not enough evidence to determine if this outbreak is linked to El Abuelito Queso Fresco.”.

The recalled products were distributed to Connecticut, Maryland, New Jersey, North Carolina, New York, Pennsylvania and Virginia. Thus far seven people, all of whom have been hospitalized, have fallen ill.

FDA recommends that consumers, restaurants and retailers do not consume, sell or serve any of the recalled cheeses. The agency also states that anyone who purchased of received the recalled products use “extra vigilance in cleaning and sanitizing any surfaces and containers that may have come in contact with these products to reduce the risk of cross-contamination.”

Cantaloupe

Nearly 100 People Sick from Salmonella ‘Potentially Linked’ to Tailor Cut Produce Fruit Mix

By Food Safety Tech Staff
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Cantaloupe

Using whole genome sequencing (WGS), FDA has confirmed 96 illnesses in 11 states that were caused by Salmonella Javiana. Thus far, traceback evidence indicates that a fruit mix from New Jersey-based Tailor Cut Produce is the possible source of the outbreak.

FDA provided its latest update about the ongoing investigation today: Of the 96 illnesses, 27 have been hospitalized, and no deaths have been reported. The highest number of illnesses have been reported in Delaware (39), Pennsylvania (34) and New Jersey (12). The agency stated its inspection at Tailor Cut Produce continues and it is collecting records to support a traceback investigation.

Tailor Cut Produce recalled the Fruit Luau fruit mix earlier in December, along with its cut honeydew, cantaloupe and pineapple products.

Recall

Almark Foods Expands Hard Boiled Egg Recall As Listeria Outbreak Continues

By Food Safety Tech Staff
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Recall

Today FDA provided an update about its outbreak investigation of Listeria monocytogenes linked to hard-boiled eggs manufactured by Almark Foods’ facility in Gainesville, Georgia. On December 23, Almark expanded its recall to include all eggs manufactured at the Gainesville plant. In addition, the company is not producing products at this facility.

Thus far, four companies have recalled products containing the eggs from Almark Foods, as they have the potential to be contaminated with Listeria monocytogenes:

As of December 17, seven infections were reported, with four hospitalizations and one death across five states. The hard-boiled eggs were sold both in bulk pails to food processors, restaurants and retailers, as well as directly to consumers at the retail level, and have “Best If Used By Dates” through March 2, 2020.

FDA used whole genome sequencing to find a genetic match in the outbreak strain from samples collected at Almark’s facility during agency inspections in February and December of this year.

The agency investigation is ongoing.

John Besser, CDC, 2018 Food Safety Consortium

CDC: Quite a Year for Outbreaks, Exciting Time in Food Safety

By Maria Fontanazza
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John Besser, CDC, 2018 Food Safety Consortium

This year Salmonella outbreaks hit chicken, shell eggs, ground beef, pre-cut melon, dried and frozen coconut, pasta salad, chicken salad, turkey, ground beef, raw sprouts and breakfast cereal. There were also significant Cyclospora infections linked to salads sold at McDonalds as well as vegetable trays. For the first time in 10 years, a Listeria outbreak was linked to an FSIS regulated product (deli ham); ground beef was affected by E. coli O26. And perhaps the most notable outbreak of the year was the E.coli O157:H7 outbreak linked to romaine lettuce from the Yuma growing region.

“It’s been quite a year for outbreaks,” said John Besser, Ph.D., deputy chief, enteric diseases laboratory branch, at CDC, referring to the pathogens that have plagued a variety of consumer products in 2018. “Out of this group, there are a lot of the things you’d expect, but also some brand new unexpected [products affected] like shredded coconut and Honey Smacks cereal.”

Despite the number of outbreaks that have hit the food industry in 2018, “this is a really exciting time to be in public health and food safety, because there are a lot of tools we can use to help make food safer,” said Besser. Most of the diseases that impact the food industry are preventable if their source can be identified, and using big data can have a tremendous impact on improving food safety.

Yesterday John Besser informed attendees at the 2018 Food Safety Consortium about CDC’s latest efforts in foodborne disease surveillance, which he defines as the
systematic collection, analysis and interpretation of health data. The agency is actively working to identify unrecognized gaps in the food supply chain and provide the industry with information it can use to make products safer. “The most important reason for detecting outbreaks is so we can identify the problem and fix it,” said Besser.

There are two ways that CDC detects outbreaks. The first is via the “citizen reporters” who are observant and alert the agency. (This is actually how E.coli O157 was discovered). The second is through pathogen-specific surveillance where CDC takes lab information and links cases that are geographically diverse. These cases are often widely dispersed and are the most effective way to find food production and distribution problems, and are often easier to address than local issues, according to Besser.

He went on to review the successes of PulseNet and the promise of whole genome sequencing (WGS) and metagenomics. The CDC’s PulseNet nationwide WGS implementation project is underway and will result in a “tsunami of data”, with the timeline as follows:

  • January 15, 2018: Listeria monocytogenes
  • October 15, 2018: Campylobacter jejuni/coli
  • January 15, 2019: Diarrheagenic E.coli (including STEC)
  • March 15, 2019: Salmonella enterica

Metagenomics will continue to play a large role in enabling unbiased sequencing of all nucleic acids in an environment. It will help to directly characterize sequences from samples, food and people (i.e., the gut), and could aid in pathogen discovery.

“I think within just a few years, it’s going to be the standard for tests,” said Besser. “My prediction is that you’ll be able to do this test in the production environment.”

Deadly Outbreaks and the Role of Metagenomics

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, Clear Labs

NGS in Food Safety: Seeing What Was Never Before Possible

By Sasan Amini
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Sasan Amini, Clear Labs

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.