Tag Archives: pathogen detection

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

 

 

Tyler Williams
FST Soapbox

A Nugget of Welcome News: USDA Adds Salmonella as a Chicken Adulterant

By Tyler Williams
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Tyler Williams

Chicken producers and processors must always pay close attention to listeria and E. coli. Their regulated to-market protocols incorporate intense testing and cleaning standards that help ensure the people who buy chicken sandwiches at fast casual restaurants, chicken fingers at sporting arenas and trays of fresh chicken legs at supermarkets don’t get sick.

The companies stay on top of listeria and E. coli because the USDA Food Safety and Inspection Service (FSIS) has considered them “adulterants,” or substances that should not be found in meat products, for decades. The federal agency banned listeria in 1987, and in 1994 listed E. coli as an adulterant in the wake of an E. coli outbreak at Jack in the Box restaurants that sickened 700 people in four states, and led to 171 hospitalizations and four deaths.

All along, however, another prominent bacteria, Salmonella, remained unregulated, despite its proclivity for making people ill—more than a 1.3 million cases of salmonellosis appear in the U.S. every year, leading to about 26,500 hospitalizations and roughly 400 deaths. It is the No. 1 cause for foodborne illness in the U.S., and most cases stem from chicken products.

But earlier this year the USDA announced that it now plans to consider Salmonella an adulterant in some chicken products. The matter is out for public comment now; if the USDA doesn’t change its clear intention to regulate Salmonella, federal food inspectors soon will be testing for it in select chicken products.

The chicken industry opposes the measure. In a news release issued shortly after the FSIS’ August announcement, the National Chicken Council (NCC) pointed toward the 1957 Poultry Products Inspection Act, which did not include Salmonella as an adulterant, as a set of standards worth upholding today.

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Well, a lot has changed in industrial agriculture during the past 65 years, and that includes a dramatic expansion of chicken farming and consumption across the country. In the 1950s, the average American ate about 16 pounds of chicken a year, compared to 56 pounds of beef and 50 pounds of pork. But by this year, Americans were eating close to 112 pounds of chicken a year, along with 56 pounds of beef and 50 pounds of pork. In terms of meat consumption, chicken now rules the roost. Regulating it might not have been necessary back when Dwight D. Eisenhower was president. But today I believe it most definitely is.

As a professional in the food safety industry, I champion the FSIS’ decision. It’s about time the agency added Salmonella to its list of adulterants; the bacteria causes far too much illness and death in the U.S. every year. Many of those cases could have been prevented through regulatory oversight.

Addressing Poultry Industry Concerns

It is true, as opponents of the proposed regulation argue, that Salmonella doesn’t always emerge in the processing plant; humans can inadvertently introduce the bacteria in their own kitchens. Why, the industry asks, should it be penalized for conditions outside of its control? In addition, proper cooking methods will kill Salmonella. If people don’t follow cooking directions on the packages of chicken they buy, and get sick from Salmonella as a result, the chicken industry believes it should not be held accountable.

On the first issue, it is unlikely that cases revolving around individual consumers introducing Salmonella to their chicken products would ever lead to penalties. Federal regulators scrutinize public health data for clusters of outbreaks, which often point toward entire product lines being infected with bacteria; isolated one-off cases, many of which indeed could be the result of human error, do not concern them.

For the second point, yes, people should read labels and closely follow cooking directions. But in my opinion, that is irrelevant; dangerous levels of Salmonella simply should not dwell in foods, and it’s the job of regulators to make sure food is safe.

Toy manufacturers, for example, must eliminate choking hazards from products designed for kids under 3 years, thanks to federal regulations. It shouldn’t be up to parents to constantly monitor their toddlers while they play with toys, to ensure they don’t gag on something potentially dangerous found on the stuffed giraffe.

Should the rule become policy, the FSIS will focus on just one category: stuffed, breaded and raw chicken products. These products, including dishes like chicken Kiev and chicken cordon bleu, often are heat-treated to set the batter or breading, but are not fully cooked. They have been associated with 14 outbreaks and about 200 illnesses since 1998.

This represents a solid start. Next, I’d like to see the FSIS pursue regulating Salmonella in other chicken products. Even if the agency doesn’t, however, many processors will have to implement new practices and testing procedures for all of their products anyway, as in many cases it won’t make sense to just incorporate new protocols within a few discrete product lines. Among other things, I would anticipate boosted commitments among producers and processors to cleaning and sanitation processes, environmental monitoring (probably the most important pursuit) and overall facility food safety measures.

Will this action by the FSIS completely eliminate Salmonella from the targeted products? Absolutely not. The rule sets a maximum threshold for Salmonella in the food the agency tests; in many cases, chicken products that contain negligible amounts of the bacteria will still make it to market. It’s just products containing dangerous amounts of Salmonella that will be subject to penalties.

Food safety serves as one of the foundations of a healthy society. It also reinforces and bolsters public trust in the products consumers buy, which nurtures and strengthens the entire food industry. With this proposed Salmonella rule by the USDA, the U.S. takes another important step toward ensuring the health of its citizens, and further enhancing consumer trust in the chicken products they buy.

Raj Rajagopal, 3M Food Safety
In the Food Lab

Pathogen Detection Guidance in 2020

By Raj Rajagopal
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Raj Rajagopal, 3M Food Safety

Food production managers have a critical role in ensuring that the products they make are safe and uncontaminated with dangerous pathogens. Health and wellness are in sharp focus for consumers in every aspect of their lives right now, and food safety is no exception. As food safety becomes a continually greater focus for consumers and regulators, the technologies used to monitor for and detect pathogens in a production plant have become more advanced.

It’s no secret that pathogen testing is performed for numerous reasons: To confirm the adequacy of processing control and to ensure foods and beverages have been properly stored or cooked, to name some. Accomplishing these objectives can be very different, and depending on their situations, processors rely on different tools to provide varying degrees of testing simplicity, speed, cost, efficiency and accuracy. It’s common today to leverage multiple pathogen diagnostics, ranging from traditional culture-based methods to molecular technologies.

And unfortunately, pathogen detection is more than just subjecting finished products to examination. It’s become increasingly clear to the industry that the environment in which food is processed can cross-contaminate products, requiring food manufacturers to be ever-vigilant in cleaning, sanitizing, sampling and testing their sites.

For these reasons and others, it’s important to have an understanding and appreciation for the newer tests and techniques used in the fight against deadly pathogens, and where and how they might be fit for purpose throughout the operation. This article sheds light on the key features of one fast-growing DNA-based technology that detects pathogens and explains how culture methods for index and indicator organisms continue to play crucial roles in executing broad-based pathogen management programs.

LAMP’s Emergence in Molecular Pathogen Detection

Molecular pathogen detection has been a staple technology for food producers since the adoption of polymerase chain reaction (PCR) tests decades ago. However, the USDA FSIS revised its Microbiology Laboratory Guidebook, the official guide to the preferred methods the agency uses when testing samples collected from audits and inspections, last year to include new technologies that utilize loop-mediated isothermal amplification (LAMP) methods for Salmonella and Listeria detection.

LAMP methods differ from traditional PCR-based testing methods in four noteworthy ways.

First, LAMP eliminates the need for thermal cycling. Fundamentally, PCR tests require thermocyclers with the ability to alter the temperature of a sample to facilitate the PCR. The thermocyclers used for real-time PCR tests that allow detection in closed tubes can be expensive and include multiple moving parts that require regular maintenance and calibration. For every food, beverage or environmental surface sample tested, PCR systems will undergo multiple cycles of heating up to 95oC to break open DNA strands and cooling down to 60oC to extend the new DNA chain in every cycle. All of these temperature variations generally require more run time and the enzyme, Taq polymerase, used in PCR can be subjected to interferences from other inhibiting substances that are native to a sample and co-extracted with the DNA.

LAMP amplifies DNA isothermally at a steady and stable temperature range—right around 60oC. The Bst polymerase allows continuous amplification and better tolerates the sample matrix inhibitors known to trip up PCR. The detection schemes used for LAMP detection frees LAMP’s instrumentation from the constraints of numerous moving pieces.

Secondly, it doubles the number of DNA primers. Traditional PCR tests recognize two separate regions of the target genetic material. They rely on two primers to anneal to the subject’s separated DNA strands and copy and amplify that target DNA.

By contrast, LAMP technology uses four to six primers, which can recognize six to eight distinct regions from the sample’s DNA. These primers and polymerase used not only cause the DNA strand to displace, they actually loop the end of the strands together before initiating amplification cycling. This unique looped structure both accelerates the reaction and increases test result sensitivity by allowing for an exponential accumulation of target DNA.

Third of all, it removes steps from the workflow. Before any genetic amplification can happen, technicians must enrich their samples to deliberately grow microorganisms to detectable levels. Technicians using PCR tests have to pre-dispense lysis buffers or reagent mixes and take other careful actions to extract and purify their DNA samples.

Commercialized LAMP assay kits, on the other hand, offer more of a ready-to-use approach as they offer ready to use lysis buffer and simplified workflow to prepare DNA samples. By only requiring two transfer steps, it can significantly reduces the risk of false negatives caused by erroneous laboratory preparation.

Finally, it simplifies multiple test protocols into one. Food safety lab professionals using PCR technology have historically been required to perform different test protocols for each individual pathogen, whether that be Salmonella, Listeria, E. coli O157:H7 or other. Not surprisingly, this can increase the chances of error. Oftentimes, labs are resource-challenged and pressure-packed environments. Having to keep multiple testing steps straight all of the time has proven to be a recipe for trouble.

LAMP brings the benefit of a single assay protocol for testing all pathogens, enabling technicians to use the same protocol for all pathogen tests. This streamlined workflow involving minimal steps simplifies the process and reduces risk of human-caused error.

Index and Indicator Testing

LAMP technology has streamlined and advanced pathogen detection, but it’s impractical and unfeasible for producers to molecularly test every single product they produce and every nook and cranny in their production environments. Here is where an increasing number of companies are utilizing index and indicator tests as part of more comprehensive pathogen environmental programs. Rather than testing for specific pathogenic organisms, these tools give a microbiological warning sign that conditions may be breeding undesirable food safety or quality outcomes.

Index tests are culture-based tests that detect microorganisms whose presence (or detection above a threshold) suggest an increased risk for the presence of an ecologically similar pathogen. Listeria spp. Is the best-known index organism, as its presence can also mark the presence of deadly pathogen Listeria monocytogenes. However, there is considerable skepticism among many in the research community if there are any organisms outside of Listeria spp. that can be given this classification.

Indicator tests, on the other hand, detect the presence of organisms reflecting the general microbiological condition of a food or the environment. The presence of indicator organisms can not provide any information on the potential presence or absence of a specific pathogen or an assessment of potential public health risk, but their levels above acceptable limits can indicate insufficient cleaning and sanitation or operating conditions.

Should indicator test results exceed the established control limits, facilities are expected to take appropriate corrective action and to document the actions taken and results obtained. Utilizing cost-effective, fast indicator tests as benchmark to catch and identify problem areas can suggest that more precise, molecular methods need to be used to verify that the products are uncontaminated.

Process Matters

As discussed, technology plays a large role in pathogen detection, and advances like LAMP molecular detection methods combined with strategic use of index and indicator tests can provide food producers with powerful tools to safeguard their consumers from foodborne illnesses. However, whether a producer is testing environmental samples, ingredients or finished product, a test is only as useful as the comprehensive pathogen management plan around it.

The entire food industry is striving to meet the highest safety standards and the best course of action is to adopt a solution that combines the best technologies available with best practices in terms of processes as well –from sample collection and preparation to monitoring and detection.

Food Labs Conference

Food Labs / Cannabis Labs 2020 Agenda Announced

By Food Safety Tech Staff
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Food Labs Conference

The agenda for the 2020 Food Labs / Cannabis Labs conference has been announced. The event, which will address regulatory, compliance and risk management issues that companies face in the area of testing and food laboratory management, is scheduled to take place on June 3–4 in Rockville, MD.

Some agenda highlights include a special morning session on June 3 that discusses the proposed FSMA rule on lab accreditation: “FSMA and the Impact on Laboratories and Laboratory Data Users” and “FSMA Proposed Rule on Laboratory Accreditation: What it says and what it should say” presented by Reinaldo Figueiredo of ANSI and Robin Stombler of Auburn Health Strategies, respectively. FDA has also been invited to speak on the proposed rule. Sessions will also cover the role of labs as it relates to pathogens, with presentations from Benjamin Katchman, Ph.D. (PathogenDx) about a novel DNA microarray assay used for detecting and speciating multiple Listeria species and Dave Evanson (Merieux Nutrisciences) on pathogen detection and control. The full agenda is listed on the Food Labs / Cannabis Labs website.

The early bird discount of $395 expires on March 31.

Innovative Publishing Company, Inc., the organizer of the conference, is fully taking into considerations the travel concerns related to the coronavirus. Should any
disruption that may prevent the production of this live event at its physical location in Rockville, MD due to COVID-19, all sessions will be converted to a virtual conference on the already planned dates. More information is available on the event website.

Michael Bartholomeusz, TruTag
In the Food Lab

Intelligent Imaging and the Future of Food Safety

By Michael Bartholomeusz, Ph.D.
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Michael Bartholomeusz, TruTag

Traditional approaches to food safety no longer make the grade. It seems that stories of contaminated produce or foodborne illnesses dominate the headlines increasingly often. Some of the current safeguards set in place to protect consumers and ensure that companies are providing the freshest, safest food possible continue to fail across the world. Poorly regulated supply chains and food quality assurance breakdowns often sicken customers and result in recalls or lawsuits that cost money and damage reputations. The question is: What can be done to prevent these types of problems from occurring?

While outdated machinery and human vigilance continue to be the go-to solutions for these problems, cutting-edge intelligent imaging technology promises to eliminate the issues caused by old-fashioned processes that jeopardize consumer safety. This next generation of imaging will increase safety and quality by quickly and accurately detecting problems with food throughout the supply chain.

How Intelligent Imaging Works

In broad terms, intelligent imaging is hyperspectral imaging that uses cutting-edge hardware and software to help users establish better quality assurance markers. The hardware captures the image, and the software processes it to provide actionable data for users by combining the power of conventional spectroscopy with digital imaging.

Conventional machine vision systems generally lack the ability to effectively capture and relay details and nuances to users. Conversely, intelligent imaging technology utilizes superior capabilities in two major areas: Spectral and spatial resolution. Essentially, intelligent imaging systems employ a level of detail far beyond current industry-standard machinery. For example, an RGB camera can see only three colors: Red, green and blue. Hyperspectral imaging can detect between 300 and 600 real colors—that’s 100–200 times more colors than detected by standard RGB cameras.

Intelligent imaging can also be extended into the ultraviolet or infrared spectrum, providing additional details of the chemical and structural composition of food not observable in the visible spectrum. Hyperspectral imaging cameras do this by generating “data cubes.” These are pixels collected within an image that show subtle reflected color differences not observable by humans or conventional cameras. Once generated, these data cubes are classified, labeled and optimized using machine learning to better process information in the future.

Beyond spectral and spatial data, other rudimentary quality assurance systems pose their own distinct limitations. X-rays can be prohibitively expensive and are only focused on catching foreign objects. They are also difficult to calibrate and maintain. Metal detectors are more affordable, but generally only catch metals with strong magnetic fields like iron. Metals including copper and aluminum can slip through, as well as non-metal objects like plastics, wood and feces.

Finally, current quality assurance systems have a weakness that can change day-to-day: Human subjectivity. The people put in charge of monitoring in-line quality and food safety are indeed doing their best. However, the naked eye and human brain can be notoriously inconsistent. Perhaps a tired person at the end of a long shift misses a contaminant, or those working two separate shifts judge quality in slightly different ways, leading to divergent standards unbeknownst to both the food processor and the public.

Hyperspectral imaging can immediately provide tangible benefits for users, especially within the following quality assurance categories in the food supply chain:

Pathogen Detection

Pathogen detection is perhaps the biggest concern for both consumers and the food industry overall. Identifying and eliminating Salmonella, Listeria, and E.coli throughout the supply chain is a necessity. Obviously, failure to detect pathogens seriously compromises consumer safety. It also gravely damages the reputations of food brands while leading to recalls and lawsuits.

Current pathogen detection processes, including polymerase chain reaction (PCR), immunoassays and plating, involve complicated and costly sample preparation techniques that can take days to complete and create bottlenecks in the supply chain. These delays adversely impact operating cycles and increase inventory management costs. This is particularly significant for products with a short shelf life. Intelligent imaging technology provides a quick and accurate alternative, saving time and money while keeping customers healthy.

Characterizing Food Freshness

Consumers expect freshness, quality and consistency in their foods. As supply chains lengthen and become more complicated around the world, food spoilage has more opportunity to occur at any point throughout the production process, manifesting in reduced nutrient content and an overall loss of food freshness. Tainted meat products may also sicken consumers. All of these factors significantly affect market prices.

Sensory evaluation, chromatography and spectroscopy have all been used to assess food freshness. However, many spatial and spectral anomalies are missed by conventional tristimulus filter-based systems and each of these approaches has severe limitations from a reliability, cost or speed perspective. Additionally, none is capable of providing an economical inline measurement of freshness, and financial pressure to reduce costs can result in cut corners when these systems are in place. By harnessing meticulous data and providing real-time analysis, hyperspectral imaging mitigates or erases the above limiting factors by simultaneously evaluating color, moisture (dehydration) levels, fat content and protein levels, providing a reliable standardization of these measures.

Foreign Object Detection

The presence of plastics, metals, stones, allergens, glass, rubber, fecal matter, rodents, insect infestation and other foreign objects is a big quality assurance challenge for food processors. Failure to identify foreign objects can lead to major added costs including recalls, litigation and brand damage. As detailed above, automated options like X-rays and metal detectors can only identify certain foreign objects, leaving the rest to pass through untouched. Using superior spectral and spatial recognition capabilities, intelligent imaging technology can catch these objects and alert the appropriate employees or kickstart automated processes to fix the issue.

Mechanical Damage

Though it may not be put on the same level as pathogen detection, food freshness and foreign object detection, consumers put a premium on food uniformity, demanding high levels of consistency in everything from their apples to their zucchini. This can be especially difficult to ensure with agricultural products, where 10–40% of produce undergoes mechanical damage during processing. Increasingly complicated supply chains and progressively more automated production environments make delivering consistent quality more complicated than ever before.

Historically, machine vision systems and spectroscopy have been implemented to assist with damage detection, including bruising and cuts, in sorting facilities. However, these systems lack the spectral differentiation to effectively evaluate food and agricultural products in the stringent manner customers expect. Methods like spot spectroscopy require over-sampling to ensure that any detected aberrations are representative of the whole item. It’s a time-consuming process.

Intelligent imaging uses superior technology and machine learning to identify mechanical damage that’s not visible to humans or conventional machinery. For example, a potato may appear fine on the outside, but have extensive bruising beneath its skin. Hyperspectral imaging can find this bruising and decide whether the potato is too compromised to sell or within the parameters of acceptability.

Intelligent imaging can “see” what humans and older technology simply cannot. With the ability to be deployed at a number of locations within the food supply chain, it’s an adaptable technology with far-reaching applications. From drones measuring crop health in the field to inline or end-of-line positioning in processing facilities, there is the potential to take this beyond factory floors.

In the world of quality assurance, where a misdiagnosis can literally result in death, the additional spectral and spatial information provided by hyperspectral imaging can be utilized by food processors to provide important details regarding chemical and structural composition previously not discernible with rudimentary systems. When companies begin using intelligent imaging, it will yield important insights and add value as the food industry searches for reliable solutions to its most serious challenges. Intelligent imaging removes the subjectivity from food quality assurance, turning it into an objective endeavor.

Food Labs Conference Announced for Spring 2020

By Food Safety Tech Staff
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— UPDATE — March 9, 2020 – IPC and the Food Labs/Cannabis Labs Conference want to reassure you, that in case of any disruption that may prevent the production of this live event at its physical location in Rockville, MD due to COVID-19, all sessions will be converted to a virtual conference on the already planned dates. Please note that if you initially register as a virtual participant (meaning you have no intentions of traveling to the event regardless) and the on-site event is not cancelled, you will ONLY be able to listen to the General Sessions and the Cannabis Sessions. You will have not have access to the Food Labs Sessions and there will be NO recording of these sessions. If you have any questions, please contact Veronica Allen, Event Manager.

–END UPDATE —

EDGARTOWN, MA, Jan. 22, 2020 – Innovative Publishing Co., the publisher of Food Safety Tech and organizer of the Food Safety Consortium Conference & Expo is announcing the launch of the Food Labs Conference. The event will address regulatory, compliance and risk management issues that companies face in the area of testing and food laboratory management. It will take place on June 3–4 in Rockville, MD.

Some of the critical topics include discussion of FDA’s proposed FSMA rule, Laboratory Accreditation Program for Food Testing; considerations in laboratory design; pathogen testing and detection; food fraud; advances in testing and lab technology; allergen testing, control and management; validation and proficiency testing; and much more.

The event is co-located with the Cannabis Labs Conference, which will focus on science, technology, regulatory compliance and quality management. More information about this event is available on Cannabis Industry Journal.

“By presenting two industry conferences under one roof, we can provide attendees with technology, regulatory compliance and best practices that cannabis and food might share but also focused topics that are unique to cannabis or food laboratory industry needs,” said Rick Biros, president of Innovative Publishing Co., Inc. and director of the Food Labs Conference.

The call for abstracts is open until February 28.

The agenda and speakers will be announced in early March.

About Food Safety Tech
Food Safety Tech publishes news, technology, trends, regulations, and expert opinions on food safety, food quality, food business and food sustainability. We also offer educational, career advancement and networking opportunities to the global food industry. This information exchange is facilitated through ePublishing, digital and live events.

Sasan Amini, Clear Labs
FST Soapbox

Beyond the Results: What Can Testing Teach Us?

By Sasan Amini
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Sasan Amini, Clear Labs

The microbiology lab will increasingly be understood as the gravitational center of big data in the food industry. Brands that understand how to leverage the data microbiology labs are producing in ever larger quantities will be in the best position to positively impact their bottom line—and even transform the lab from a cost center to a margin contributor.

The global rapid microbiology testing market continues to grow at a steady pace. The market is projected to reach $5.09 billion by 2023, up from $3.45 billion in 2018. Increased demand for food microbiology testing—and pathogen detection in particular—continues to drive the overall growth of this sector. The volume of food microbiology tests totaled 1.14 billion tests in 2016—up 15% from 2013. In 2018 that number is estimated to have risen to 1.3 billion tests, accounting for nearly half the overall volume of industrial microbiology tests performed worldwide.

The food industry is well aware that food safety testing programs are a necessary and 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.

We are going through a unique transition where food safety tests are evolving from binary tests to data engines that are capable of generating orders of magnitude of more information. This creates a unique opportunity where many applications for big data collected from routine pathogen testing can help go beyond stopping an outbreak. Paired with machine learning and other data platforms, these data have the opportunity to become valuable, actionable insights for the industry.

While some of these applications will have an impact on fundamental research, I expect that big data analytics and bioinformatics will have significant opportunity to push the utilities of these tests from being merely a diagnostic test to a vehicle for driving actions and offering recommendations. Two examples of such transformations include product development and environmental testing.

Food-Safety Testing Data and Product Development

Next-generation-sequencing (NGS) technologies demonstrate a great deal of potential for product development, particularly when it comes to better understanding shelf life and generating more accurate shelf-life estimates.

Storage conditions, packaging, pH, temperature, and water activity can influence food quality and shelf life among other factors. Shelf-life estimates, however, have traditionally been based on rudimentary statistical models incapable of accounting for the complexity of factors that impact food freshness, more specifically not being able to take into consideration the composition and quantity of all microbial communities present on any food sample. These limitations have long been recognized by food scientists and have led them to look for cost-effective alternatives.

By using NGS technologies, scientists can gain a more complete picture of the microbial composition of foods and how those microbial communities are influenced by intrinsic and extrinsic factors.

It’s unlikely that analyzing the microbiome of every food product or unit of product will ever be a cost-effective strategy. However, over time, as individual manufacturers and the industry as a whole analyze more and more samples and generate more data, we should be able to develop increasingly accurate predictive models. The data generation cost and logistics could be significantly streamlined if existing food safety tests evolve to broader vehicles that can create insights on both safety and quality indications of food product simultaneously. By comparing the observed (or expected) microbiome profile of a fresh product with the models we develop, we could greatly improve our estimates of a given product’s remaining shelf life.

This will open a number of new opportunities for food producers and consumers. Better shelf-life estimates will create efficiencies up and down the food supply chain. The impact on product development can hardly be underestimated. As we better understand the precise variables that impact food freshness for particular products, we can devise food production and packaging technologies that enhance food safety and food quality.

As our predictive models improve, an entire market for these models will emerge, much as it has in other industries that rely on machine learning models to draw predictive insights from big data.

Data Visualization for Environmental Monitoring

In the past one to two years, NGS technologies have matured to the point that they can now be leveraged for high-volume pathogen and environmental testing.

Just as it has in other industries, big data coupled with data visualization approaches can play a mainstream role in food safety and quality applications.

Data visualization techniques are not new to food safety programs and have proven particularly useful when analyzing the results of environmental testing. The full potential of data visualizations has yet to be realized, however. Visualizations can be used to better understand harborage sites, identifying patterns that need attention, and visualize how specific strains of a pathogen are migrating through a facility.

Some of this is happening in food production facilities already, but it’s important to note that visualizations are only as useful as the underlying data is accurate. That’s where technologies like NGS come in. NGS provides the option for deeper characterization of pathogenic microorganisms when needed (down to the strain). The depth of information from NGS platforms enables more reliable and detailed characterization of pathogenic strains compared to existing methods.

Beyond basic identification, there are other potential use cases for environmental mapping, including tracking pathogens as they move through the supply chain. It’s my prediction that as the food industry more broadly adopts NGS technologies that unify testing and bioinformatics in a single platform, data visualization techniques will rapidly advance, so long as we keep asking ourselves: What can the data teach us?

The Food Data Revolution and Market Consolidation

Unlike most PCR and immunoassay-based testing techniques, which in most cases can only generate binary answers, NGS platforms generate millions of data points for each sample for up to tens to hundreds of samples. As NGS technologies are adopted and the data we collect increases exponentially, the food safety system will become the data engine upon which new products and technologies are built.

Just as we have seen in any number of industries, companies with access to data and the means to make sense of it will be in the best position to capitalize on new revenue opportunities and economies of scale.

Companies that have adopted NGS technologies for food safety testing will have an obvious advantage in this emerging market. And they won’t have had to radically alter their business model to get there. They’ll be running the same robust programs they have long had in place, but collecting a much larger volume of data in doing so. Companies with a vision of how to best leverage this data will have the greatest edge.

magnifying glass

PCR or LAMP: Food Safety Considerations when Choosing Molecular Detection Methods

By Joy Dell’Aringa, Vikrant Dutta, Ph.D.
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magnifying glass

Food microbiology pathogen detection technology is constantly evolving and improving for fast, efficient and accurate analysis. Thanks to the wide commercialization of easy-to-use diagnostic kits, the end-user no longer needs a deep understanding of the intricacies of diagnostic chemistries to perform the analysis. However, when navigating the selection process in search of the technology that is best fit-for-purpose, it is critical to understand the key differences in principle of detection and how they can impact both operations and risk. Here, we will explore the difference between two broad categories of molecular pathogen detection: PCR and isothermal technologies such as LAMP.

PCR & LAMP Detection Chemistries: An Overview

PCR detection chemistries have come a long way from non-specific DNA-binding dyes like SYBR Green, to highly precise sequence-specific molecular probes. The efficiency of the real-time PCR reaction today allows for the use of a variety of detection probes, the most popular being Dual-Labeled Fluorescent Probes such as FRET, TaqMan probes, and Molecular Beacon probes.1 The precision of these probes is showcased in their ability to distinguish allelic single-nucleotide polymorphisms (SNPs).2,3 The most prevalent isothermal chemistry, Loop-Mediated Isothermal Amplification (LAMP), typically does not use molecular probes due to the lack of structure and formation consistency in its amplified products. As a result, LAMP mostly relies on detection through non-specific signal generation like ATP bioluminescence or non-specific dyes. In theory, this could come from specific and non-specific amplification events. This also makes LAMP inept to detect the allelic polymorphisms, which in some cases are critical to detecting crucial variations, like between close species, and within serotypes. In the end, the detection chemistries are only as good as the amplified products.

Key Takeaways:

  • PCR technology has improved greatly in detection efficiencies via target specific probes
  • LAMP technology typically does not utilize specific molecular probes, but instead relies on indirect signal generation
  • Target specific probes ensures signal from specific amplification events only
  • Indirect signal can come from specific and non-specific amplification events, which can lead to a reduced specificity and inability to detect in certain cases

PCR & LAMP: Amplification Strategies

Food safety pathogen detection protocols aim to find the single cell of a target organism lurking in a relatively large sample. In order to achieve detection, molecular technologies utilize amplification strategies to increase the concentration of target DNA to a detectable level. Nucleic acid amplifications in both PCR and isothermal technologies start by making a variety of amplified products. These products include non-specific amplifications (NSA), and specific (target) amplifications.4,5,6,7 Ideally, the concentration of the desired target amplified product increases over time to levels above NSA where the detection chemistries are able to provide a detectable signal from the desired amplified product (target). Various reaction components such as: Target DNA concentration, polymerase, buffers and primers play a defining role in maintaining the progressive amplification dynamics, and thereby act as core contributors to the robustness of the reaction. However, none play a more crucial contribution to the success of a reaction than temperature. Herein lies a key difference between the fundamentals of PCR and Isothermal amplification technologies.

Key Takeaways:

  • PCR and LAMP both make a variety of amplification products: Non-Specific (NSA) and Specific (target)
  • Ideally, target products increase above the levels of NSA to reach a reliable detectable signal
  • A variety of factors contribute to the overall robustness of the reaction

What Is the Difference between PCR and Isothermal Detection Technologies?

A key foundational difference between the two technologies lies in the utilization of the thermal profiles. PCR utilizes thermocycling, while isothermal does not. This difference is the tether around how the different amplification chemistries work. In PCR, the cyclical denaturation of DNA during thermocycling separates all dimers (specific and non-specific). As the reaction progresses, this leads to frequent correction of the amplification dynamics away from the NSA and favors amplification of the desired target amplifications. Isothermal chemistries do not have the ability to correct the NSA through thermocycling, so it must rely on alternate mechanisms to achieve the same result. For example, LAMP utilizes “nested” primers where the primer sequences outside the target region are used to create early amplification products. These are subsequently used as a template for the desired target amplifications. The presence of these extra primers, along with the diverse amplified structures formed during the LAMP reaction, creates many more opportunities for NSA production.5,8,9 This causes a less controlled and inefficient amplification, and is perhaps why the preheating of the DNA prior to the LAMP has shown to increase the LAMP sensitivity.10, 11 To the end user, this inefficiency can manifest itself in various ways such as restricted multiplexing, lack of internal amplification control, complex assay design, tedious sample prep methods, and increased chance for inaccurate results (i.e., false positives and false negatives).12 Scientific literature does provide a fair amount of evidence that, under controlled conditions, the isothermal amplification reaction can provide equivalent results to PCR. Isothermal chemistries also usually require simplified instruments and thereby can present interesting opportunities in non-conventional test environments with simple and predictable matrices. This likely explains the early footing of isothermal technologies in the clinical test environment as a “point of care test” (POCT) alternative. However, it must also be noted that recently PCR has also been adapted and successfully commercialized for the POCT format.13,14

Key Takeaways:

  • PCR utilizes thermocycling, Isothermal does not
  • In PCR, thermocycling allows for the reaction to favor the target amplification over the NSA
  • LAMP must rely on alternate mechanisms to correct for NSA and these mechanisms lead to a less controlled and therefore inefficient amplification
  • Under controlled conditions, isothermal technology can provide equivalent results to PCR
  • Low instrumentation requirements make isothermal technologies interesting for non-conventional test environments (i.e. POCT); however, PCR has also been recently adapted as a POCT

Internal Amplification Controls in Molecular Pathogen Detection Technologies: The Value & The Challenges

The purpose of an internal amplification control (IAC) is to provide an indication of the efficacy of the test reaction chemistry. The closer the IAC is to the target DNA sequence, the better view into the inner workings of each reaction. For food microbiology testing, the role of the IAC is more important now than ever. Driven by regulations, industry self-accountability and brand protection initiatives, more food laboratories are testing diverse product types with novel and innovative formulations and ingredients. IAC capability not only helps with troubleshooting, but it also allows for a more confident adoption of the technology for new and diverse food and environmental matrices.

Over the years, PCR has progressively developed into a robust and efficient technology that can provide a dynamic IAC, giving the end user a direct look into the compatibility of the test matrix within the PCR reaction. From a single reaction, we can now make a qualitative assessment of whether the crude DNA prep from a matrix undergoing testing is working with this PCR or if it is inhibiting the reaction. With legacy technologies, including the older generation PCR’s, we were limited to an “it-did-not-work” scenario, leaving the end user blind to any insights into the reason. Since isothermal chemistries typically do not have an IAC, the end user is vulnerable to false results. Even when isothermal chemistries such as nicking enzyme amplification reaction (NEAR) can provide IAC, they typically do not mimic the target reaction and, therefore, are not a direct indicator of the reaction dynamics. This limits the end user back to the “it-did-not-work” scenario. LAMP technology attempts to mitigate the absence of IAC by performing a separate and external reaction with each test matrix. This strategy leaves the final result vulnerable to a number of factors that are otherwise non-existent for IAC: Sampling variations, reagent and machine anomalies, and user error. External control approaches also have a notable impact to the end user, as the burden to demonstrate fit-for-purpose of the method for even the smallest matrix composition change increases both validation and verification activities, which can have a notable financial impact to the laboratory.

There are a few reasons why IAC incorporation is not always plausible for isothermal technologies such as LAMP. First, inefficient, less-controlled amplification reactions leave little room for reliable and meaningful supplementary reactions, like the ones required for IAC. Second, the lack of consistent amplified products make it much more difficult to pinpoint a DNA structure that can be dependably used as an IAC. Third, lack of specific detection mechanisms makes it hard to distinguish signal from the target versus the IAC reaction.

Key Takeaways:

  • Internal amplification controls (IAC) are critical for the food industry due to complex and ever-changing matrix formulations
  • IAC is useful for troubleshooting, optimizing assay performance, and adapting test for novel matrices
  • PCR has evolved to provide dynamic IAC, leading to increased confidence in results
  • LAMP is not able to utilize IAC due to the nature of the amplification products, reaction efficiency, and lack of specific detection mechanisms

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CERTUS system

CERTUS Achieves AOAC Performance Tested Certification

By Food Safety Tech Staff
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CERTUS system

This week CERTUS announced that it achieved AOAC Performance Tested certification for its rapid pathogen detection platform, the CERTUS System. The system uses SERS nanoparticle technology and real-time detection to provide users with faster results versus sending the samples to a third-party via mail.

AOAC validation gives small-to-mid size processing facilities an assurance on the reliability and efficiency of CERTUS’s in-house environmental Listeria monitoring process, according to CERTUS.. The company’s system has been certified for use on stainless steel, concrete, plastic and ceramic surfaces. The CERTUS system provides 98% accuracy by targeting organisms without destroying them and reducing the effect of substances commonly found in environmental food samples on assay results.

“We’re extremely proud and put tremendous value on achieving AOAC certification within two years of beginning our journey to help protect food production beyond a shadow of a doubt,” said CERTUS President John Coomes in a press release. “Recognition by AOAC, coupled with our robust R&D team and strong financial backing, demonstrates that we are moving quickly to bring unmatched, precise solutions to food processors across the industry.”

3M Molecular detection system

USDA FSIS Awards 3M Food Safety with Contract for Pathogen Testing

3M Molecular detection system
3M Molecular detection system
3M Molecular detection system

USDA FSIS has awarded a contract to 3M Food Safety for its pathogen detection instruments and kits. 3M’s molecular detection system will be the primary method used by the agency to detect Salmonella, Listeria monocytogenes and E. coli O157. The technology combines isothermal DNA amplification and bioluminescence detection for a fast, accurate and simple solution that also tackles some of the constraints of PCR methods. Users can concurrently run up to 96 different tests for many organisms across food and environmental samples.