Tag Archives: Testing

Sequencing pattern, pathogens

Build Stronger Food Safety Programs With Next-Generation Sequencing

By Akhila Vasan, Mahni Ghorashi
No Comments
Sequencing pattern, pathogens

According to a survey by retail consulting firm Daymon Worldwide, 50% of today’s consumers are more concerned about food safety and quality than they were five years ago. Their concerns are not unfounded. Recalls are on the rise, and consumer health is put at risk by undetected cases of food adulteration and contamination.

While consumers are concerned about the quality of the food they eat, buy and sell, the brands responsible for making and selling these products also face serious consequences if their food safety programs don’t safeguard against devastating recalls.

A key cause of recalls, food fraud, or the deliberate and intentional substitution, addition, tampering or misrepresentation of food, food ingredients or food packaging, continues to be an issue for the food safety industry. According to PricewaterhouseCoopers, food fraud is estimated to be a $10–15 billion a year problem.

Some of the more notorious examples include wood shavings in Parmesan cheese, the 2013 horsemeat scandal in the United Kingdom, and Oceana’s landmark 2013 study, which revealed that a whopping 33% of seafood sold in the United States is mislabeled. While international organizations like Interpol have stepped up to tackle food fraud, which is exacerbated by the complexity of globalization, academics estimate that 4% of all food is adulterated in some way.

High-profile outbreaks due to undetected pathogens are also a serious risk for consumers and the food industry alike. The United States’ economy alone loses about $55 billion each year due to food illnesses. The World Health Organization estimates that nearly 1 in 10 people become ill every year from eating contaminated food. In 2016 alone, several high-profile outbreaks rocked the industry, harming consumers and brands alike. From the E. coli O26 outbreak at Chipotle to Salmonella in live poultry to Hepatitis A in raw scallops to the Listeria monocytogenes outbreak at Blue Bell ice cream, the food industry has dealt with many challenges on this front.

What’s Being Done?

Both food fraud and undetected contamination can cause massive, expensive and damaging recalls for brands. Each recall can cost a brand about $10 million in direct costs, and that doesn’t include the cost of brand damage and lost sales.

Frustratingly, more recalls due to food fraud and contamination are happening at a time when regulation and policy is stronger than ever. As the global food system evolves, regulatory agencies around the world are fine-tuning or overhauling their food safety systems, taking a more preventive approach.

At the core of these changes is HACCP, the long implemented and well-understood method of evaluating and controlling food safety hazards. In the United States, while HACCP is still used in some sectors, the move to FSMA is apparent in others. In many ways, 2017 is dubbed the year of FSMA compliance.

There is also the Global Food Safety Initiative (GFSI), a private industry conformance standard for certification, which was established proactively by industry to improve food safety throughout the supply chain. It is important to note that all regulatory drivers, be they public or private, work together to ensure the common goal of delivering safe food for consumers. However, more is needed to ensure that nothing slips through the food safety programs.

Now, bolstered by regulatory efforts, advancements in technology make it easier than ever to update food safety programs to better safeguard against food safety risks and recalls and to explore what’s next in food.

Powering the Food Safety Programs of Tomorrow

Today, food safety programs are being bolstered by new technologies as well, including genomic sequencing techniques like NGS. NGS, which stands for next-generation sequencing, is an automated DNA sequencing technology that generates and analyzes millions of sequences per run, allowing researchers to sequence, re-sequence and compare data at a rate previously not possible.

The traditional methods of polymerase chain reaction (PCR) are quickly being replaced by faster and more accurate solutions. The benefit of NGS over PCR is that PCR is targeted, meaning you have to know what you’re looking for. It is also conducted one target at a time, meaning that each target you wish to test requires a separate run. This is costly and does not scale.

Next-generation sequencing, by contrast, is universal. A single test exposes all potential threats, both expected and unexpected. From bacteria and fungi to the precise composition of ingredients in a given sample, a single NGS test guarantees that hazards cannot slip through your supply chain.  In the not-too-distant future, the cost and speed of NGS will meet and then quickly surpass legacy technologies; you can expect the technology to be adopted with increasing speed the moment it becomes price-competitive with PCR.

Applications of NGS

Even today’s NGS technologies are deployment-ready for applications including food safety and supplier verification. With the bottom line protected, food brands are also able to leverage NGS to build the food chain of tomorrow, and focus funding and resources on research and development.

Safety Testing. Advances in NGS allow retailers and manufacturers to securely identify specific pathogens down to the strain level, test environmental samples, verify authenticity and ultimately reduce the risk of outbreaks or counterfeit incidents.

Compared to legacy PCR methods, brands leveraging NGS are able to test for multiple pathogens with a single test, at a lower cost and higher accuracy. This universality is key to protecting brands against all pathogens, not just the ones for which they know to look.

Supplier Verification. NGS technologies can be used to combat economically motivated food fraud and mislabeling, and verify supplier claims. Undeclared allergens are the number one reason for recalls.

As a result of FSMA, the FDA now requires food facilities to implement preventative controls to avoid food fraud, which today occurs in up to 10% of all food types. Traditional PCR-based tests cannot distinguish between closely related species and have high false-positive rates. NGS offers high-resolution, scalable testing so that you can verify suppliers and authenticate product claims, mitigating risk at every level.

R&D. NGS-based metagenomics analysis can be used in R&D and new product development to build the next-generation of health foods and nutritional products, as well as to perform competitive benchmarking and formulation consistency monitoring.

As the consumer takes more and more control over what goes into their food, brands have the opportunity to differentiate not only on transparency, but on personalization, novel approaches and better consistency.

A Brighter Future for Food Safety

With advances in genomic techniques and analysis, we are now better than ever equipped to safeguard against food safety risks, protect brands from having to issue costly recalls, and even explore the next frontier for food. As the technology gets better, faster and cheaper, we are going to experience a tectonic shift in the way we manage our food safety programs and supply chains at large.

We will be discussing this topic, “Building Stronger Food Safety Programs through Next-Generation Sequencing”, during a live conversation on June 7, 2017 at 2:00 pm ET. Microbiologists, testing personnel, food industry management, and anyone interested in how to leverage these new technologies to fortify their food safety programs will learn how NGS is going to transform the future of food safety.

Reduce Foodborne Illness Causing Microorganisms through a Structured Food Safety Plan

By James Cook
1 Comment

In 2011 three U.S. government agencies, the CDC, the FDA and the USDA’s Food Safety Inspection Service (FSIS) created the Interagency Food Safety Analytics Collaboration (IFSAC). The development of IFSAC allowed these agencies to combine their federal food safety efforts. The initial focus was to identify those foods and prioritize pathogens that were the most important sources of foodborne illnesses.

The priority pathogens are Salmonella, E. coli O157:H7, Listeria monocytogenes and Campylobacter. To research the most important product sources, the three agencies collaborated on the development of better data collection and developed methods for estimating the sources of foodborne illnesses. Some of this research was to evaluate whether the regulatory requirements already in effect were reducing the foodborne pathogens in a specific product matrix. The collection, sharing and use of this data is an important part of the collaboration. For example, when the FDA is in a facility for routine audit or targeted enforcement, they will generally take environmental swabs and samples of air, water and materials, as appropriate, which are then tested for the targeted pathogens. If a pathogen is found, then serotyping and pulsed-field gel electrophoresis (PFGE) fingerprinting is performed, and this is compared to the information in the database concerning outbreaks and illnesses. This data collection enables the agencies to more quickly react to pinpoint the source of foodborne illnesses and thereby reduce the number of foodborne illnesses.

The IFSAC strategic plan for 2017 to 2021 will enhance the collection of data. The industry must be prepared for more environmental and material sampling. Enhancement of data collection by both agencies can be seen through the FSIS notices and directives, and through the guidance information being produced by the FDA for FSMA. Some examples are the raw pork products exploratory sampling project and the FDA draft guidance for the control of Listeria monocytogenes in ready-to-eat foods.

Starting May 1 2017, the next phase of the raw pork products exploratory sampling project will begin. Samples will be collected and tested for Salmonella, Shiga-toxin producing E. coli (STECs), aerobic plate count and generic E. coli. In the previous phase, the FSIS analyzed 1200 samples for Salmonella for which results are published in their quarterly reports. This is part of the USDA FSIS Salmonella action plan published December 4, 2013 in an effort to establish pathogen reduction standards. In order to achieve any objective, establishing baseline data is essential in any program. Once the baseline data is established and the objective is determined, which in this situation is the Health People 2020 goal of reducing human illness from Salmonella by 25%, one can determine by assessment of the programs and data what interventions will need to take place.

The FDA has revised its draft guidance for the control of Listeria monocytogenes in ready-to-eat food, as per the requirement in 21 CFR 117 Current Good Manufacturing Practice, Hazard Analysis and Risk-Based Preventive Controls for Human Foods, which is one of the seven core FSMA regulations. Ready-to-eat foods that are exposed to the environment prior to packaging and have no Listeria monocytogenes control measure that significantly reduces the pathogen’s presence, will be required to perform testing of the environment and, if necessary, testing of the raw and finished materials. Implementing this guidance document helps the suppliers of these items to cover many sections of this FSMA regulation.

The purpose of any environmental program is to verify the effectiveness of control programs such as cleaning and sanitizing, and personnel hygiene, and to identify those locations in a facility where there are issues. Corrective actions to eliminate or reduce those problems can then be implemented. Environmental programs that never find any problems are poorly designed. The FDA has stated in its guidance that finding Listeria species is expected. They also recommend that instead of sampling after cleaning and/or sanitation, the sampling program be designed to look for contamination in the worst-case scenario by sampling several hours into production, and preferably, just before clean up. The suggestion on this type of sampling is to hold and test the product being produced and to perform some validated rapid test methodology in order to determine whether or not action must be taken. If the presence of a pathogen is confirmed, it is not always necessary to dispose of a product, as some materials can be further processed to eliminate it.

With this environmental and product/material testing data collected, it is possible to perform a trends analysis. This will help to improve sanitation conditions, the performance of both programs and personnel, and identity the need for corrective actions. The main points to this program are the data collection and then the use of this data to reduce the incidence of foodborne illness. Repeated problems require intervention and resolution. Changes in programs or training may be necessary, if they are shown to be the root cause of the problem. If a specific issue is discovered to be a supply source problem, then the determination of a suppliers’ program is the appropriate avenue to resolve that issue. Generally, this will mean performing an audit of the suppliers program or reviewing the audit, not just the certificate, and establishing whether they have a structured program to reduce or eliminate these pathogens.

Continue to page 2 below.

New Dipstick for Rapid Detection of Salmonella on the Farm

By Food Safety Tech Staff
No Comments

A new rapid assay may help growers make faster and more informed decisions right on the farm. Researchers from the University of Massachusetts and Cornell University are developing a test that addresses the challenge of sampling produce and assessing risk in a timely manner. The dipstick would enable rapid detection of Salmonella in agricultural samples in about three hours.

How It Works

“Users simply place a leaf sample in a small plastic bag that contains enzymes and incubate it for about 1.5 hours. Users would then squeeze a small liquid sample through a filter and place it in a tube with bacteriophages—viruses that are harmless to humans but infect specific bacterium, such as Salmonella or E. coli. Some phages are so specific they will only infect one bacterium serotype while others will infect a broader range of serotypes within an individual species. Phages also will only infect and replicate in viable bacteria, ensuring that non-viable organisms are not detected. This distinction is useful if prior mitigation steps, such as chlorination, have already been used. The phages used in the test were engineered to insert a particular gene into the bacteria.” – Center for Produce Safety

“We have been developing dipstick assays for ultra-low detection limits,” the technical abstract, Rapid bacterial testing for on-farm sampling, states. “Our preliminary data suggests that our fluorescent dipstick will have a detection limit of Salmonella spp. cells which makes the test ideal for on-farm use and appropriate federal requirements.”

Robert Ferguson, Strategic Consulting

Increased Testing for Pathogens and More Complex Tests Means More Outsourcing

By Maria Fontanazza
2 Comments
Robert Ferguson, Strategic Consulting

Companies are under more pressure to analyze food samples for pathogens, but not all of them have the expertise to handle the complexity involved in laboratory analysis. In addition, companies don’t want to risk contamination throughout their facility. As a result, many are outsourcing these services to contract labs.

Changing Landscape for Selecting a Food Safety Contract Laboratory

Strategic Consulting, Inc. recently conducted a study of food processors and the trends in outsourcing their laboratory testing work to food contract laboratories. The firm spoke with 100 food processors nationwide in 15 food processing categories, including protein, dairy, vegetables and packaged foods, inquiring about the types of samples they collect, how many are collected on a daily and monthly basis, their target analytes, and where they have the analysis performed (an in-plant lab, central company lab or an outsourced food contract laboratory); the firm also spoke with folks at leading food companies and a number of large food contract labs.

Bob Ferguson, managing director at Strategic Consulting, shared his insights with Food Safety Tech about the survey, the details of which will be presented at the Food Safety Consortium in December.

Food Safety Tech:  What were some of the major findings?

Bob Ferguson: Food processors continue to outsource more and more of their lab analysis.  This is a trend that we outlined in our Food-8 market report in 2014, and it is clearly continuing and growing. The impact is particularly acute in microbiology testing, especially when analysis is for pathogens.  Of the companies we surveyed, 87% did some amount of routine microbiology testing and 67% of those analyzed the samples at an in-house lab. But when asked about pathogens, 77% of the companies analyze samples for pathogens but only 34% analyze the samples at an in-house lab.  Clearly there is a higher level of concern in handling pathogens at in-house labs.

Food Safety Tech: What are the processors’ concerns regarding pathogens?

Ferguson: I would say that their concerns fall into two major categories: Technical and operational. From a technical perspective, there is always a risk when working with pathogens in a food processing facility. Microbiologists understand how easily bacteria can travel through a facility—being carried on employees, their clothing, or equipment, through air currents, or even through penetration connections such as drains. And most diagnostic tests not only require handling pathogen samples but also enriching the samples prior to analysis. The presence of food samples with high concentrations of pathogens can present a risk for the spread of contamination into production areas.

From an operational standpoint, running a food analysis lab is becoming increasingly more complex. Analytical methods continue to get more sensitive and sophisticated, and this requires more expertise and a greater focus on instrument service and calibrations.  Requirements for accreditation of food testing laboratories are also raising the bar for in-plant labs.  Finally, running a food lab requires recruiting and hiring skilled analysts. More food processors are coming to the conclusion that none of these functions are part of their core competencies and are electing to outsource that work to a contract lab.

Robert Ferguson, Strategic Consulting
Robert Ferguson, managing director, Strategic Consulting, Inc., will discuss the results of the survey at the 2016 Food Safety Consortium in December | LEARN MORE

Food Safety Tech:  What does this mean for food contract labs?

Ferguson: This could become a significant business growth opportunity for food contract laboratories.  As we indicated in our Food Contract Laboratory market report, microbiology is one of the largest business areas for most food contract laboratories, comprising, on average, approximately 52% of lab revenues and growing on average at 12% annually. The average lab also reports pathogen testing growth at more than 13%. This is remarkable in that the overall growth in sample volume is only growing 6%, so labs are clearly gaining a greater share of samples.

Food Safety Tech: Is this good news for the food contract laboratory companies?

Ferguson: Well, I would say that this will dramatically change the nature of competition and will be good news for some lab companies, namely those who can best adapt to the changing market conditions, but certainly not all.  Our analysis shows, for example, that about 70% of pathogen samples outsourced are sent to a lab within 100 miles of the food processing facility.   This bodes well for labs with a robust national network of locations. Single-location or limited-location labs may have trouble competing and will be acquired or otherwise may not survive. Also, as more samples get outsourced, the most efficient laboratories will have a competitive advantage. Our data also shows that outsourcing does not occur uniformly across all types and sizes of food processing companies, and laboratories may be at more or less risk depending on their customer mix or concentration in a particular food processing segment. Food contract laboratories that understand these factors will be in a better position to compete and thrive as the market changes.

Changing Landscape for Selecting a Food Safety Contract Laboratory

By Bob Ferguson, Thomas R. Weschler
No Comments

A recent study of more than 100 food processing customers of food contract laboratories examined the key factors that make a commercial food laboratory competitive in the eyes of their customers. The details of this study, which was conducted by Strategic Consulting, will be presented at the Food Safety Consortium in December.

The 2016 Food Safety Consortium takes place December 5–9 in Schaumburg, IL | LEARN MOREThe volume of microbiology testing worldwide is growing annually at 6%. The study data, however, shows that the growth of microbiology testing at food contract labs is growing at twice that rate—12%—annually. This means that every year food contract labs are taking a larger share of the micro-testing market. Specific to pathogen testing, the situation is more pronounced. Two-thirds of the food processors surveyed conduct routine microbiology testing at their in-house lab, but the number willing to conduct pathogen analysis in-house has dropped to one-third. With more and more companies becoming wary about the risks and costs of analyzing pathogens in a plant lab, outsourcing continues to grow and the volume of total pathogen tests conducted at food contract labs is growing at more than 13% per year. Based on the data generated from the study, it can be deduced that, for the first time in the United States, the number of pathogen tests conducted at food contract labs now exceeds 50% of all pathogen tests conducted in the country. This is not only changing the face of microbiology testing, but it is also creating a very competitive market for laboratory services.

With this test volume now going to food contract laboratories, anyone who needs microbiology analysis has already (at least once) checked the qualifications of a food contract laboratory and validated that it has the right scope of accreditations, specific experience with product type, and proof that they can reliably meet test specifications and detection limits.

These basic qualifications, however, are “table stakes” in today’s highly competitive food safety contract laboratory market.

In the study, the most common answers to the question of the top decision criteria used when selecting a food contract laboratory for microbiology testing were, in order of importance, price, turnaround time, and dependability. When asked about testing of pathogens, most respondents reported that “accreditations” was their number one decision criteria, followed in order by the three previous factors of price, turnaround time and dependability.

A key distinction to understand in this analysis is the term “accreditations” was certainly used to describe formal lab accreditations, but it was also commonly used interchangeably with “expertise.”  In detailed conversations with buyers, it was clear that specialization and competence in pathogen testing was of primary importance and, in many cases, specific experience with the specific pathogen in which they were interested, and in most cases, experience with their specific product type (e.g., meat, dairy, processed foods, etc.).

Interestingly, although proximity to the plant ranked last of the six most common selection criteria, greater than 70% of the plant personnel interviewed reported that they use a food contract lab for pathogen testing that is within 100 miles of their production location. Based on the interviews it was clear that proximity was very important (and linked to turnaround time), but it also revealed that all of the major customers reported that all of the labs they would even consider had locations within a 100-mile radius of their plant. Of these labs, 60% offered a courier service to collect samples at the plant and deliver them to the lab. It is clear that proximity and a sample collection service, while once a point of differentiation, is now seen less as key selection criteria and more of a “table stake” for being considered at all.

Food processors, of course, run samples for testing for parameters other than microbiology. In this study, 78% of the companies surveyed ran tests for nutritional chemistry and, of those, 42% used an in-plant lab. In addition, 81% of the companies test for contaminants (e.g., pesticides, drug residues, metals) and of those, 55% run the tests in an in-plant lab. Of the companies that use a food contract lab for either types of tests, 60–65% (depending on the parameter) report sending samples to a lab that is more than 100 miles from their plant.

It is clear from this data that food processors are far more comfortable analyzing samples for nutritional parameters, contaminants and routine microbiology in an in-plant lab, but fewer are comfortable running pathogen tests in-plant. And while proximity is important for pathogen tests, it was not a top qualifier for nutritional or contaminant testing. As more and more pathogen samples are outsourced to food contract labs, however, it remains to be seen if the samples will “drag” samples for these other parameters along with them to the closer proximate labs. But it is clear that the contract labs with a network of locations that place them close to their customer’s locations and who have expertise in pathogens as well as a full range of other analyses will likely have an advantage.

The role of food contract laboratories will continue to grow, creating great business opportunities. The dynamics of this market, however, are clearly changing the ground rules and presenting companies with new risks and opportunities. Understanding this changing landscape will be of paramount importance to food contract labs, and their  success or failure will depend on their strategic decisions and how well they navigate these changing conditions.

These business environment changes are also essential for food processors to understand. As market conditions change, pricing, turnaround times, and add-on services available from food contract labs will also change, presenting risks and opportunities for processors. Food processors that understand these changes will also be able to take advantage and improve their testing programs.

Next-Generation Sequencing Targets GMOs

By Maria Fontanazza
1 Comment

As the movement among consumers for more information about the products they’re purchasing and consuming continues to grow, the food industry will experience persistent pressure from both advocacy groups and the government on disclosure of product safety information and ingredients. Top of mind as of late has been the debate over GMOs. “Given all of the attention on GMOs on the legislative side, there is huge demand from consumers to have visibility and transparency into whether products have been genetically modified or not,” says Mahni Ghorashi, co-founder of Clear Labs.

Mahni Ghorashi, Clear Labs
Mahni Ghorashi, co-founder of Clear Labs

Today Clear Labs announced the availability of its comprehensive next-generation sequencing (NGS)-based GMO test. The release comes at an opportune time, as the GMO labeling bill, which was passed by the U.S. House of Representatives last week, heads to the desk of President Obama.

Clear Labs touts the technology as the first scalable, accurate and affordable GMO test. NGS enables the ability to simultaneously screen for multiple genes at one time, which could companies save time and money. “The advantage and novelty of this new test or assay is the ability to screen for all possible GMO genes in a single universal test, which is a huge change from the way GMO testing is conducted today,” says Ghorashi.

The PCR test method is currently the industry standard for GMO screening, according to the Non-GMO Project. “PCR tests narrowly target an individual gene, and they’re extremely costly—between $150–$275 per gene, per sample,” says Ghorashi. “Next-generation sequencing is leaps and bounds above PCR testing.” Although he won’t specify the cost of the Clear Labs assay (the company uses a tiered pricing structure based on sample volume), Ghorashi says it’s a fraction of the cost of traditional PCR tests.

The new assay screens for 85% of approved GMOs worldwide and targets four major genes used in manufacturing GMOs (detection based on methods of trait introduction and selection, and detection based on common plant traits), allowing companies to determine the presence and amount of GMOs within products or ingredient samples. “We see this test as a definitive scientific validation,” says Ghorashi. The company’s tests integrate software analytics to enable customers to verify GMO-free claims, screen suppliers, and rank suppliers based on risk.

Clear Labs, GMO, testing
Screenshot of the Clear Labs GMO test, which is based on next-generation sequencing technology.

Clear Labs isn’t targeting food manufacturers of a specific size or sector within the food industry but anticipates that a growing number of leading brands will be investing in GMO testing technology. “We expect to see adoption across the board in terms of company size, related more to what their stance is on food transparency and making that information readily available to their end consumers,” says Ghorashi.

David Chambliss, IBM Research
In the Food Lab

Scientific Breakthrough May Change Food Safety Forever

By David Chambliss
No Comments
David Chambliss, IBM Research

How safe is a raw diet? Could sterilizing our food actually make us more prone to sickness? Are vegans healthier than carnivores? In the last few decades, global food poisoning scares from beef to peanut butter have kept food scientists and researchers around the world asking these questions and searching for improved methods of handling and testing what we eat.

It’s been more than 150 years since Louis Pasteur introduced the idea of germ theory—that bacteria cause sickness—fundamentally changing the way we think about what makes our food safe to eat. While we’ve advanced in so many other industrial practices, we’re still using pasteurization as the standard for the global food industry today.

Although pasteurization effectively controls most organisms and keeps the food supply largely safe, we continue to have foodborne outbreaks despite additional testing and more sophisticated techniques. The potential health promise of genomics, and the gut microbiome genetics and bacterial ecosystems, could be the key to the next frontier in food safety.

The scientific community is once again at the cusp of a new era with the advent of metagenomics and its application to food safety.

What is metagenomics? Metagenomics is the study of the bacterial community using genetics by examining the entire DNA content at once. Whole genome sequencing of a single bacterium tells us about the DNA of a specific organism, whereas metagenomic testing tells us about the interaction of all the DNA of all the organisms within a sample or an environment. Think of the vast quantity of genetic material in the soil of a rice patty, a lettuce leaf, your hand, a chicken ready for cooking, or milk directly from a cow. All of them have thousands of bacteria that live together in a complex community called the microbiome that may contain bacteria that are sometimes harmful to humans—and possibly also other bacteria that help to keep the potentially harmful bacteria in check.

Metagenomics uses laboratory methods to break up cells and extract many millions of DNA molecular fragment, and sequencing instruments to measure the sequences of A’s, C’s, G’s, and T’s that represent the genetic information in each of those fragments. Then scientists use computer programs to take the information from millions or billions of fragments to determine from what bacteria they came. The process is a little like mixing up many jigsaws, grabbing some pieces from the mix, and figuring out what was in the original pictures. The “pictures” are the genomes of bacteria, which in some cases carry enough unique information to associate a given bacterium with a previously seen colony of the same species.

Genomics of single bacterial cultures, each from a single species, is well established as a way to connect samples of contaminated foods with reported cases of foodborne illnesses. With metagenomics, which essentially looks for all known species simultaneously, one hopes to do a better job of early detection and prevention. For example, if a machine malfunction causes pasteurization or cleaning to be incomplete, the metagenomics measurement will likely show compositional shifts in which bacterial phyla are abundant. This can make it possible to take remedial action even before there are signs of pathogens or spoilage that would have led to a costly recall.

Up until now, keeping food safe has meant limiting the amount of harmful bacteria in the community. That means using standard methods such as pasteurization, irradiation, sterilization, salt and cooking. To determine whether food is actually safe to eat, we test for the presence of a handful of specific dangerous organisms, including Listeria, E. coli, and Salmonella, to name a few. But what about all the “good” bacteria that is killed along with the “bad” bacteria in the process of making our food safe?

Nutritionists, doctors and food scientists understand that the human gut is well equipped to thrive unless threatened by particularly dangerous contaminants. The ability to determine the entire genetic makeup within a food could mean being able to know with certainty whether it contains any unwanted or unknown microbial hazards. Metagenomic testing of the food supply would usher in an entirely new approach to food safety—one in which we could detect the presence of all microbes in food, including previously unknown dangers. It could even mean less food processing that leaves more of the healthful bacteria intact.

More than 150 years ago, Pasteur pointed us in the right direction. Now the world’s brightest scientific minds are primed to take the food industry the next leap toward a safer food supply.

USDA Logo

USDA Touts Food Safety Progress Under Obama Administration

By Food Safety Tech Staff
1 Comment
USDA Logo

Between 2009 and 2015 there was a 12% reduction in foodborne illnesses associated with meat, poultry and processed egg products. “We’re better now at keeping unsafe food out of commerce, whether it’s made unsafe because of dangerous bacteria, or because of an allergen, like peanuts or wheat,” said Agriculture Secretary Tom Vilsack in a USDA release. “Over the course of [President Obama’s] Administration, we have tightened our regulatory requirements for the meat and poultry industry, enhanced consumer engagement around safe food handling practices, and made smart changes to our own operations, ultimately moving the needle on the number of foodborne illness cases attributed to products that we regulate.”

USDA’s Food Safety and Inspection Service (FSIS) has implemented a number of initiatives since 2009, including:

  1. Establishing a zero-tolerance policy for raw beef products that contain shiga-toxin producing E. coli: O26, O103, O45, O111, O121 and O145.
  2. Labeling mechanically tenderized meat. The blades or needles used to tenderize meat an introduce pathogens into the meat.
  3. First-ever pathogen reduction standards for poultry parts in order to reduce consumer exposure to Salmonella and Campylobacter. The standard is expected to prevent 50,000 cases of foodborne illness each year.
  4. Requiring that all poultry facilities create a plan to prevent contamination with Salmonella and Campylobacter, instead of addressing the problem after it occurs. Poultry companies must collect samples at two points in the production line and test them to show control of enteric pathogens.
  5. Requiring meat and poultry companies to hold all products that are undergoing lab analysis until USDA microbial and chemical tests for harmful hazards are complete.
In the Food Lab

New Dynamics in Environmental Testing

By Erin Dreyling, Ph.D
No Comments

Recent recalls and outbreaks associated with Listeria coupled with FDA’s finalization of the FSMA preventive controls rule have heightened the industry’s need to focus on environmental testing programs. The need for a preventive control program with higher resolution is especially highlighted by the government’s increasing use of whole genome sequencing data to more rapidly link human illness to food processing establishments. I work with many customers who simply do not recognize all of the factors that influence their ability to detect Listeria in environmental samples. For many, an environmental sample is collected, shipped to a third-party lab, results are received within two to four days, and few questions asked. Most companies have not invested the time and resources needed to truly understand how each component of an environmental sample impacts their ability to detect Listeria. So what factors should be considered to maximize Listeria detection in the plant environment?

Learn innovative ways to mitigate the threat of Listeria at the Listeria Detection & Control Workshop | May 31–June 1, 2016 | St. Paul, MN | LEARN MOREListeria is a True Survivor

Listeria is inherently a hearty organism that can withstand highly adverse conditions in the plant environment. It is able to survive and grow across a wide range of temperatures, including refrigeration, and it is more tolerant to heat than Salmonella and E. coli. Additionally, the organism survives across a wide pH range, including extended periods in highly acidic conditions, and can survive food processing and preservation with up to 25.5% salt. These traits may result in highly injured Listeria being collected in environmental samples, and requires optimization of the sample collection and analysis process in order for detection and culture confirmation to occur.

Sanitation Programs May Not Destroy Listeria

Sanitation practices are intended to destroy Listeria in the plant environment, but not all sanitizers will be 100% effective. In some cases, sanitizers may not fully kill Listeria, leaving highly injured Listeria that may require an extended lag phase in order for growth and detection during testing. Sub-lethally injured Listeria remains a food safety concern, as the bacteria maintain the ability to recover and flourish in a nutritive environment. Additionally, Listeria readily forms biofilms in the plant environment, which many traditional sanitizers do not effectively remove. Biofilms in the plant environment may maintain low levels of Listeria that may be challenging to detect without the use of a sensitive detection method.

Sample Collection: Choose the Right Tool for the Job

The neutralizing and nutritive capacity of the collection media used with the collection device can have a significant impact on the ability to resuscitate, detect and culture stressed Listeria. When selecting a collection media, it is important to ensure that the media will effectively neutralize the sanitizers used in the plant environment. For instance, peroxyacetic acid and quaterinary ammonia-based sanitizers will not be neutralized well by commonly used collection media such as Neutralizing Buffer or Letheen Broth. Neutralization of the sanitizer in environmental samples is important in order for resuscitation and growth of any Listeria present within the sample. Additionally, use of a collection media that contains nutrients to begin the resuscitation process for Listeria immediately upon collection is also important for detection and culture confirmation of Listeria in samples. Collection media such as Neutralizing Buffer contains monopatassium phosphate, sodium thiosulfate, and aryl sulfonate complex intended only to neutralize sanitizers. Conversely, D/E Broth and HiCap Broth have components to nourish Listeria and facilitate resuscitation in addition to neutralizing sanitizers.

Enrichment Media Determines Recovery & Growth

Enrichment media plays a major role in the speed of recovery and growth of Listeria in environmental samples. Medias that facilitate faster recovery of injured Listeria allow for shortened lag phases facilitating more rapid growth. Enrichment media that facilitate faster recovery and growth allow Listeria to reach the limit of detection for screening tools more quickly. When paired with a highly sensitive method, enrichment media, which foster greater Listeria growth and recovery, can allow for significant reductions in time to results for screening methods. Additionally, faster recovery and growth of Listeria due to enrichment media can increase the likelihood of culturally confirming Listeria found at low levels pre-enrichment.

Not All Detection Methods are the Same

The ability of a detection method to find Listeria in an environmental sample is impacted by two factors: 1) method sensitivity and 2) method robustness in the presence of sanitizers. The more sensitive a rapid test method, the greater the chance of finding low levels of Listeria in an environmental sample. Low levels of Listeria in environmental samples are likely due to the injured state of Listeria in the plant environment post sanitization. Immuno-based rapid methods have a sensitivity of 105–106, DNA-based methods have a sensitivity of 104–105 and RNA based methods have a sensitivity of 102–103. Using an RNA-based method offers 1 to 2 logs greater sensitivity and greatly increases the chance of finding low-level Listeria.1 This can be particularly true when sampling conditions such as collection media or enrichment media are less than optimal for the neutralization of sanitizers and growth and recovery of Listeria.

Another important factor that influences a test method’s ability to detect Listeria in an environmental sample is the method’s ability to amplify and detect the organism in the presence of sanitizers. Most molecular-based methods do not include a sample clean up step resulting in sanitizer being present during the amplification step. For some methods, sanitizers may inhibit amplification, resulting in indeterminate or false negative results.

Confirmation Requires Optimization of the Sampling Process

The ability to culturally confirm a Listeria sample that screens positive is influenced by the entire environmental sampling process. In order to culture confirm samples with highly injured, low-level Listeria, it is necessary to optimize the sample collection media, enrichment media, and confirmation process to provide the greatest likelihood of culture recovery. If Listeria is not adequately resuscitated and able to achieve sufficient growth, the level of Listeria present in the sample post-enrichment may be below the limit of detection for culture. The likelihood of culture confirmation can be increased by incorporating steps such as a secondary enrichment or concentration via IMS capture. Culture confirmation for samples that screen positive on a rapid method can be especially challenging if a highly sensitive test method is used for screening that may detect Listeria at lower levels than culture. Thus, optimizing the environmental sample program is especially important if confirmation of screening results for highly sensitive methods is desired.

Method Sensitivity and Increased Positivity

Employing a highly sensitive screening tool for environmental samples provides a better lens to view risk within the food safety processing environment. Many companies fear that a more sensitive method will result in significant increases in positivity and cost for increased sanitation. In working with customers who have moved from immune-based methods to a highly sensitivity molecular method, I’ve observed an initial increase in positivity followed by a leveling off of low-level positivity after enhanced interventions are taken in the plant. Companies that proactively seek out and destroy Listeria in their plants are then able to maintain low level rates of positivity with routine cleaning measures, while also maintaining the confidence that they are using the best tool available for Listeria monitoring.

Understand Your Risk & Establish a Culture of Food Safety

It is important for food safety professionals to fully consider the hidden risks that may exist in their plant environment due to the environmental sample process masking the true presence of Listeria. Each component of the environmental monitoring process, sanitizer, collection media, enrichment media, detection method and culture process plays an important role in a company’s ability to be able to detect and culture confirm Listeria in the plant environment. Optimizing each step within the environmental sample process allows a company to be proactive instead of reactive. This approach creates a company culture of food safety that can seek out, detect and destroy Listeria in the plant environment, can significantly mitigate risk. The good news is that by incorporating the right food safety culture and making data-driven choices, today’s manufacturer can achieve both short-term dividends of risk reduction as well as a long-term elevation of control of its process.

Reference

  1. Culture Shift: The New Dynamics of Listeria Environmental Control and Testing. Roka Bioscience, Webinar.
FST Soapbox

Intelligent Algorithms Shape Food Safety

By Steven Burton
No Comments

The North American food safety testing market is projected to reach $16 billion by 2020, according to a recent study by Markets and Markets. In just a few short years, it’s safe to say that purchasing a software solution to create and manage food safety programs will become ubiquitous, equivalent to that of employing any other software tool such as Microsoft Excel.

However, there is a broad range of capabilities for food safety software, and some solutions are much more complex than others. Many types of HACCP software operate as part of an ERP system, merely managing documents online under IT administration. But the technological capabilities of a food safety management system are endless in terms of value-driven innovation. Any competitive software on the market should go further, and be flexible and agile enough to meet and contain the challenges of a changing regulatory landscape and aggressive market space.

One of the ways food safety management can take things further is through the use of intelligent algorithms that can help food safety professionals get the most out of their software—and their HACCP plan. For example, instead of manually searching for all the physical, chemical and biological hazards (as well as radiological hazards under HARPC), intelligent algorithms can use data from other HACCP plans to suggest hazards. By comparing facility types, process flows, ingredients and more, a sophisticated algorithm can make smart suggestions that give food safety professionals a significant leg up, cutting down research time and providing a context of learning since it’s much easier to learn by example than starting from scratch. As such, suggestions can equip food safety professionals with the right mindset to discover potential hazards.

There are core benefits to searching for software technologies that have intelligent algorithms in place to analyze and retrieve data for those food businesses looking to get the most long-term value out of their vendor purchase.

Facilities with High-Risk Products and Complex Process Steps

High-risk foods are defined by the FDA as foods that “may contain pathogenic microorganisms and will normally support formation of toxins or growth of pathogenic microorganisms.” High-risk foods include raw meat, poultry, fish, dairy, fresh fruit, and vegetables, and processors working with these products handle more hazards and process steps in general than processors making low-risk foods. Instead of sorting through hundreds of hazards, facilities with high-risk products and complex process steps are able to skip much of the manual grunt work and simply select automatically generated hazards and process steps suggested to them at their fingertips.

Small Business Owners or Basic Food Safety Professionals

It’s common for small food businesses to put the bulk of their food safety duties on the shoulders of the owner. For many who have no previous background in food safety, there can be an unexpected and frustrating learning curve to overcome before you can pay the sweat equity required to develop a HACCP plan, and not for lack of trying. Similarly, junior food safety employees in new facilities can find established food safety practices challenging to navigate. Through intelligent algorithms, a software system can reinforce food safety hazards and process steps that might have been missed or forgotten by making them instantly available for retrieval and selection.

Giving Back Time

Recordkeeping is an essential component to an excellent food safety culture. In the grand scheme of things, managing resources to allocate time to high-level tasks that require human expertise on the production floor is a critical activity that most food safety professionals prioritize. Having more time to correct potential risk actions is crucial to ensuring the lowest possible likelihood of a recall. Smart software systems facilitate better employee time management practices so they can maximize their hours for meaningful, rather than menial, work. By taking back the time that would have been spent researching hazards, smart suggestions provide food safety professionals with a starting point that allows them to choose from a curated selection without delay.

Experimental Facilities with Changing Product Portfolio

Facilities that have a tendency to experiment with product development (i.e., food startups) are prone to using a significant amount of ingredients and formulas. When it comes time to present the right information for inspections and audits, this translates into a substantial amount of additional work in maintaining a HACCP plan. Intelligent algorithms enable a clear and organized focus, eliminating the minutiae surrounding information management of experimental product development.

New Regulations and International Compliance

Around the world new regulations surrounding acceptable food safety documentation are coming into effect; notably, FSMA even adds to the traditional hazards included under HACCP. For foreign exporters as well as American businesses, regulatory expectations for a more comprehensive approach to hazards and critical control points are higher than in the past. In the face of new regulatory demands, smart algorithms help food businesses lay out a common framework so that they can build internationally compliant programs

Extra Safeguard Check

Human error is inevitable. The beauty of technology is that it acts as a safeguard to ensure there are no glaring omissions that may have an impact on food safety duties. As a final once-over before sending in the HACCP plan, it makes good sense to have smart suggestions to cover all the bases.

Intelligent algorithms allow food safety professionals to do more with their time. By selecting from suggestions related to ingredients, materials, packing and process steps, a considerable amount of time is restored to the work day compared to the time-consuming exercise of manually assembling lists. The main benefit to a food safety software solution with intelligent algorithms is to reinforce the right mindset for listing physical, chemical and biological hazards for ingredients, material, processes and beyond. While smart suggestions should always be verified by a food safety professional familiar with the internal operations of a facility, for companies that aim to work smarter but not harder, smart algorithms are a key feature to keep in mind when researching software vendors.