Tag Archives: whole genome sequencing

Listeria

Adapting Food Safety Testing to meet Modern Demands

By Jani Holopainen
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Listeria

Confidence in food safety has hit an all-time low in the U.S., according to a recent Gallup poll[i]. Food recalls have dominated the news recently, ranging from harmful pathogens and allergy risks to non-food materials contaminating the food supply. There is a more general awareness of how our food impacts our overall physical and mental health and rising concerns over what ingredients may have the most significant effects. Now more than ever, food safety testing needs to evolve to meet current expectations—in our testing capabilities and thinking—to instill confidence in food safety testing again.

Why food safety testing needs to evolve

Like any industry, food safety trends and demands change over time, and the industry needs to evolve along with them. To keep pace with consistent threats, the industry must adapt to address emerging pathogens that pose risks to food safety. These pathogens have the potential to mutate to favorable conditions, much like any other pathogen. This means new strains of bacteria, like E. coli or Listeria, can sometimes affect the food supply but pass established food safety tests. As an industry, we must be able to quickly identify when there is a new strain of a pathogen and adapt testing methods to detect that new strain. Another way the industry needs to evolve is by keeping up with the increasing globalization of our food supply. Across industries, our world is becoming more reliant on a global supply chain. For food, this means that throughout the process of getting a specific food product to a consumer, there are several points where contamination can occur. Food safety testing needs to be able to account for these additional contamination opportunities.

Food safety testing for perishable products also presents a specific set of challenges. Testing for perishable food needs to be completed quickly due to the limited time frame in which it can be kept fresh and ready for sale in stores. Occasionally, delays in getting test results back on food samples could lead to perishable products being released before testing has been confirmed, running the risk of pathogens getting into the food supply. Food producers, particularly in produce, also need to be more vigilant against the food safety risks that come with fruits and vegetables, given they are often eaten raw. Irrigation water can contaminate produce if drawn from a source close to where livestock is being raised, and some wild animals can also contaminate the irrigation water. For other food producers, it is vital to remember that when antibiotics are used as a preventive measure in livestock, they eventually create bacterial strains resistant to a broad range of antibiotics, posing substantial human health risks.

In addition to being able to detect pathogens and biological contamination, the food safety industry also needs to be focused on combating food fraud and bad actors who intentionally adulterate food. Food fraud can happen when someone purposely leaves out, takes out, or replaces a valuable ingredient. It can also occur when someone adds something to food. For example, companies looking to save costs could mix in a cheaper substance or mislabel a food product, which could have harmful effects on consumers. Ensuring food safety relies on detecting any adulteration promptly to maintain quality standards and protect consumer health.

How we can evolve our food safety testing capabilities

While there are still critical issues that need to be addressed, we are seeing a massive shift in the technology used in food safety testing to respond to the evolving challenges. For example, qPCR-based technologies have evolved significantly and become the gold standard in food pathogen testing over the past 10 years. Next-generation sequencing (NGS) has also recently made its way into food safety and food authenticity testing. Because of its discriminatory power, NGS is a powerful tool, especially in food authenticity testing. It can also be used for microorganism strain typing, whole genome sequencing and metagenomics, all of which can help us learn more about the production environment and food we’re consuming.

Automation is also becoming more common in food safety testing. It can remove human error from the equation, improve repeatability and increase sample throughput, making it a lucrative option for mid- and large-size food safety laboratories. In the future, we can expect to see more artificial intelligence and machine learning (AI/ML) implemented into food safety workflows. AI may be able to help food safety specialists by quickly interpreting test results or identifying possible issues with tests and providing guidelines for how to correct anything that may be wrong. We may also see a world where AI can help fill knowledge gaps. It has the potential to help less experienced specialists be confident in operating the food safety workflows and in the accuracy of their results. Finally, testing on the production line, instead of sending it to internal or external labs, may become available. This “on-line” testing would shorten the time to results and mean production lines can more quickly adjust their operations if there is an issue.

How we can evolve our thinking around food safety

As we improve the technology implemented to help keep food safe, we must also ensure the food safety testing method fits the purpose. Not all tests are suitable for all processes or samples, and not all tests are identical. For example, food safety test suppliers often have certain external certifications on their workflows, like ISO 16140, AOAC PTM or AOAC OMA, and product claims to provide evidence of their methods’ performance and reliability. However, food producers should not solely rely on these certificates but verify the product claims internally to ensure the selected method performs accordingly in their own setting and, more importantly, with their samples. A sample matrix may vary by its background flora depending on the geographical region the sample originates from, which could substantially impact the target pathogen detection.

Consumers and customers are already more aware of when things go wrong, with recalls being a news focus. The U.S. Food and Drug Administration, the U.S. Department of Agriculture and other governmental organizations are very public about food recalls, and they should be. This means, however, that food safety in consumers’ minds can have negative connotations. One way food producers could address valid concerns from consumers is by becoming more visible about their food safety procedures and the efforts they undertake to improve the safety of their food.

While recalls and issues with quality control are never 100% avoidable, we can, as an industry, keep learning, continuously assess and improve testing procedures and methods, and share the best practices to ensure our food is as safe as possible. This learning must be done in real-time and at a fast pace. We can’t anticipate every new pathogen that will impact our food, but adapting quickly and effectively can help us safeguard our food supply and ensure customers’ confidence in the food they’re consuming.

[i] https://news.gallup.com/poll/650024/trust-government-assurance-food-safety-hits-record-low.aspx

Romaine Lettuce

Study Identifies Listeria Contamination Patterns in Produce Processing Facilities

By Food Safety Tech Staff
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Romaine Lettuce

A two-year study on Listeria monocytogenes (Lm) contamination patterns and related sanitation programs in produce processing facilities is already uncovering valuable insights. Ana Allende, Ph.D., and her team from the CEBAS-CSIC research institute in Spain, are hoping that their research, funded by the Center for Produce Safety, will yield practical data about produce facilities’ environmental monitoring plans as well as the efficacy of sanitation programs.

The researchers worked with three processing plants: one with a cut iceberg lettuce line, one with a cut fruit line, and one with a salad bowl line. Their first objective was to understand how different factors such as zoning, sanitary design, and connectivity affected the probability of contamination in different fresh produce processing facilities. In the case of salad bowls, the ingredients included not only leafy greens and other vegetables but also proteins from meat, fish and cheese, or pastas from different sources.

The researchers divided the processing areas into three zones based on their proximity to contact with the produce. Zone 1 involved areas with direct contact, such as knives and conveyor belts. Zone 2 included surfaces that did not contact food but were in close proximity, and zone 3 included more remote non-contact surfaces, such as drains, floors, and ceilings that could potentially lead to contaminating zones 1 and 2.

They conducted systematic sampling of the facilities at the end of the day before cleaning and sanitizing. They also resampled the three processing lines after the cleaning and disinfection activities. In addition to the more than 600 total samples from the three zones, the researchers collected 45 samples from raw ingredients and end products.

“By sampling the processing plants before and after cleaning and disinfection, we could understand which might be the entry points of the contamination,” said Allende.

Regardless of the facility, they had the highest number of positive Lm samples from zone 3. “One of the hypotheses we had was the raw material was introducing much of the Listeria,” said Allende. “This was before we did sampling and the whole genome sequencing to understand the isolates and that they were not all coming from the raw material. Some of the contamination was probably coming from zone 3 in the different processing facilities.”

The researchers also conducted whole genome sequencing on 100 samples to better understand whether the Lm was transient or persistent. What surprised them was that the same two serotypes of L. monocytogenes were found on the three processing lines after the two samplings, before and after cleaning. “This makes us understand that these serotypes are inherent and are moving from zone 3 to zone 1,” said Allende.

As part of the project, the researchers also evaluated the efficacy of biocides against resident Lm isolates. “We found, indeed, all of the isolates obtained from the environment after cleaning were sensitive to the biocides,” said Allende. This allayed concerns that the pathogens were becoming resistant to the sanitizers.

While the research aimed to provide relevant results for the three cooperating produce processors, it also has broader implications for the produce industry about how they should conduct environmental monitoring including sampling after processing just before cleaning. In addition, it should help processors better understand the main contamination points in zone 1 and how they relate to identical or similar Lm sequence types in zones 2 and 3.

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!