Rizo-López Foods, a Modesto, Calif.-based dairy product manufacturer, has voluntarily recalled 61 of its products after a CDC investigation uncovered a link to an outbreak of Listeria monocytogenes infections.

As of February 12, there have been 26 illnesses, including 24 hospitalizations and two deaths, associated with the outbreak. The outbreak has spanned nearly a decade—from June 2014 to December 2023—and run through 11 states. Of the known cases, eight cases were reported in California, with other confirmed cases in Arizona, Colorado, Texas, Tennessee, Georgia, North Carolina, Florida, Oregon, Nevada, and Washington.

The recalled products include cheeses, crema, and yogurt sold under the brand names Tio Francisco, Don Francisco, Rizo Bros, Rio Grande, Food City, El Huache, La Ordena, San Carlos, Campesino, Santa Maria, Dos Ranchitos, Casa Cardenas, and 365 Whole Foods Market. Additionally, the products were sold at retail deli counters at El Super, Cardenas Market, Northgate Gonzalez, Superior Groceries, El Rancho, Vallarta, Food City, La Michoacana, and Numero Uno Markets. A full list of recalled products can be found on FDA’s website.

The CDC began investigating the listeria outbreak in 2017 and reopened the case in 2021, but both times even though evidence pointed to queso fresco and similar cheeses as the probable source of the outbreak, there wasn’t enough information to pinpoint any specific brand.

Since the revelation, FDA has initiated an on-site inspection at Rizo Lopez Foods, which is still on-going. The company has temporarily ceased the production and distribution of these products. while their investigation continues.

The post Dairy Recall Widens, Impacts National Food Chains appeared first on Food Quality & Safety.

In the food processing industry, the Listeria monocytogenes can be deadly to humans and is monitored closely. Not only can the pathogen make people extremely ill, it is now known to be developing resistance to various food safety measures across the world.

A study conducted in South Africa and recently published in the journal Microbiology Spectrum used whole-genome sequencing to provide insights into two species of presumed nonpathogenic Listeria—L. innocua and L. welshimeri—and found that they are developing a surprising number of characteristics that are potentially harmful to humans.

The researchers conclude that Listeria innocua strains are developing resistance to temperature, pH, dehydration, and other stresses, and the species is developing hypervirulence genetically identical to that of Listeria monocytogenes.

In fact, some strains of L. innocua and L. welshimeri examined in the study show three genes for resistance to a widely-used disinfectant, from the quaternary ammonium compound (QAC or QUAT) group of chemicals.

In total, 258 isolates from butcheries, abbatoirs, retail outlets, cold stores, and processing facilities all over South Africa were studied. Of these, 38 were found to be nonpathogenic L. innocua and another three isolates were found to be nonpathogenic L. welshimeri. Additionally, two strains of L. innocua that were analyzed in the study were shown to have developed three or more concerning pathogenic characteristics, including CRISPR CAS-type adaptive immune systems.

“The Listeria innocua that we tested has some of the genes that are also found in pathogenic Listeria monocytogenes,” says Thendo Mafuna, PhD, a lecturer at the University of Johannesburg, and co-author of the study. “These shared genes between L. innocua and L. monocytogenes are also responsible for disease in humans and stress tolerance such as resistance to the disinfectant Benzalkonium chloride.”

Each of the L. innocua strains tested in the study also showed the complete LIPI-4 hypervirulence gene sequence, which can cause disease in humans.

According to Dr. Mafuna, the study corroborates other research from around the world that shows growing resistance in nonpathogenic Listeria species. For instance, the LIPI-4 sequence, Dr. Mafuna says, is identical to that found in pathogenic L. monocytogenes, as recorded by the Pasteur Institute in Paris.

Dr. Mafuna adds that food processors should look out for these new strains of Listeria because they are becoming resistant to disinfectants. “Big industrial food processors may want to investigate how efficient BC or quat disinfectants are in their facilities,” Dr. Mafuna says. “This can be done by taking swabs before cleaning and again after cleaning [and] culturing those to see how well the disinfectant regimens are working.”

The post New Presumed Nonpathogenic <i>Listeria</i> Species are Developing Harmful Characteristics appeared first on Food Quality & Safety.

The CDC, public health and regulatory officials in several states, USDA’s Food Safety and Inspection Service (FSIS), and FDA are investigating a multistate outbreak of Listeria monocytogenes infections. The epidemiologic and laboratory data collected show that meat and cheese from deli counters contaminated with Listeria are making people sick. Investigators are still working to identify any specific products or delis that may be contaminated with the outbreak strain.

As of November 9, a total of 16 people infected with the outbreak strain of Listeria have been reported from six states—California, Illinois, Maryland, Massachusetts, New York, and New Jersey. The agencies collected samples from sick people from April 17, 2021 to September 29, 2022. CDC says that the true number of sick people in this outbreak is likely higher than the number reported, and the outbreak may not be limited to the states with known illnesses. Thirteen people have been hospitalized and one person became sick during their pregnancy, which resulted in pregnancy loss. Additionally, one death has been reported from Maryland.

State and local public health officials are interviewing people about the foods they ate in the month before they got sick. Of the 12 people interviewed, 11 reported eating meat or cheese from deli counters. Among seven sick people in New York, five bought sliced deli meat or cheese from at least one location of NetCost Market, a grocery store chain that sells international foods. Sick people from other states purchased deli meats or cheeses from other deli counters. The investigators do not believe that NetCost Market delis are the only source of illnesses because some sick people in the outbreak did not shop at a NetCost Market. A contaminated food likely introduced the outbreak strain of Listeria into delis in multiple states.

Symptoms from Listeria can take several days to two weeks to appear, contributing to the difficulty in determining the source of the contamination. Symptoms include neck stiffness, confusion, headache, fever, loss of balance, muscle aches, nausea, and intestinal distress.

CDC is advising that people at higher risk of severe Listeria illness—people who are pregnant, people who are 65 years of age and older, and people with a weakened immune system—to not eat meat or cheese from any deli counter unless it is reheated to an internal temperature of 165°F. Consumers should discard any deli meats or cheeses and thoroughly clean and sanitize any surfaces that came into contact with these products and wash hands after handling.

The post <em>Listeria</em> Outbreak Linked to Deli Meats and Cheese appeared first on Food Quality & Safety.

Because foodborne disease is a significant public health issue in the United States, FDA recently developed the Foodborne Outbreak Response Improvement Plan (FORIP) to help the agency and its partners enhance the speed, effectiveness, coordination, and communication of outbreak investigations. “Tackling foodborne illnesses faster and revealing their root cause is essential to the prevention of future outbreaks,” says Frank Yiannas, FDA’s deputy commissioner for food policy and response. “We are confident that these actions outlined in the plan will contribute to bending the curve of foodborne illness in this country by helping to prevent future outbreaks.”

The plan is a necessary component of the agency’s strategy to ensure that the most effective tools and procedures are being used to streamline outbreak investigations and alleviate the effects of foodborne illness.

Key Areas of the Outbreak Response Plan

FORIP focuses on four specific priority areas in which improvements will have the most impact on outbreaks associated with human food:

1. Tech-enabled product traceback,
2. Root cause investigations (RCIs);
3. Analysis and dissemination of outbreak data; and
4. Operational improvements within the agency.

Yiannas notes that the plan focuses specifically on reducing the time needed to identify contaminated product; gathering and sharing critical investigational findings and recommendations to prevent future outbreaks more quickly and fully; more rapidly identifying a source and providing earlier and more open communications with government partners, industry, and the public; and measuring, streamlining, and continuously improving FDA’s performance.

David Goldman, MD, MPH, chief medical officer in FDA’s Office of Food Policy and Response, notes that FDA learns something new with each outbreak that occurs and then tries to incorporate that knowledge into its response. “Metrics are being addressed across the entire foods program,” he says. “We’re looking at a combination of operational and public health metrics—which, together, we intend to translate into faster response, earlier action, and secondary prevention—that are preventing further illnesses during an outbreak.”

Craig W. Hedberg, PhD, professor in the division of environmental health sciences at the University of Minnesota in Minneapolis, who conducted an independent review of FDA’s foodborne outbreak response processes, notes that FORIP was necessary to address new food safety challenges that continue to emerge and to take better advantage of new developments in public health surveillance methods. “In particular, the development of whole-genome sequencing for bacterial pathogens such as Salmonella, Shigatoxin-producing E. coli, and Listeria provides more information to better identify outbreaks with small numbers of cases, to link cases to food or environmental isolates, and to identify recurring patterns over time that highlight persisting problems that may not have been adequately addressed,” he says.

Being able to rapidly assemble records for shipment of food products through the distribution system to the point of service will greatly increase the speed and reliability of traceback efforts and make it more feasible to incorporate traceback data into the epidemiologic investigations.—Craig W. Hedberg, PhD

Liz Sertl, senior director of community engagement for GS1 US, a nonprofit standards organization, notes that FORIP is an extension of the work that FDA already has in place with the Food Safety Modernization Act and its New Era of Smarter Food Safety. “FORIP is focused on multi-state outbreaks that require significant engagement coordinated by FDA’s Coordinated Outbreak Response and Evaluation (CORE) Network,” she says. “The plan seeks to enhance the speed, effectiveness, coordination, and communication of those outbreak investigations. Ultimately, the plan is intended to complement two of the blueprint’s core elements, “Tech-Enabled Traceability” and “Smarter Tools and Approaches for Prevention and Outbreak Response.”

The positive impact of this work is made possible, she adds, by using smarter ways of digitizing information to help get to the root cause of foodborne illness more quickly due to the speed of information available. “Data that’s identified, captured, and shared in a standardized, digitized manner is key for FORIP, as this enables trading partner collaboration and systems interoperability, and can help members meet the requirements of FDA regulations,” Sertl adds.

New Elements of the Plan

FORIP aligns closely with FDA’s existing New Era of Smarter Food Safety Blueprint, which was established in 2020. The blueprint includes four core elements, including tech-enabled traceability, smarter tools and approaches for prevention and outbreak response, new business models and retail modernization, and food safety culture.

FORIP includes actionable steps to implement the strategies and principles of the blueprint specifically related to foodborne illness outbreak response. Some of the key components of the plan include reducing the time needed to identify contaminated product, accelerating the gathering and sharing of findings and recommendations, disseminating pertinent information quickly, and—ultimately—raising the bar to continually improve performance in this area. “At the core of all three of these new factors will be technology that helps food manufacturers to determine exactly how to predict, identify, and stop foodborne illnesses from coming to fruition,” says Joe Scioscia, VP of Sales for VAI, an organization that offers software for tracking and traceability in the food industry. “FORIP’s new elements will work to cover all the bases of a potential foodborne illness process, including identifying its origins, detailed analysis, and determining areas of weakness so that distributors can better prevent another incident from occurring.”

FDA is also trying to improve tracebacks of food items during outbreak investigations by defining data elements that can be tracked electronically without requiring field staff to physically visit every establishment and review documents. Outbreak responses will be sped up by digitizing processes for collecting consumer purchase data and leveraging advanced analytics tools. “Being able to rapidly assemble records for shipment of food products through the distribution system to the point of service will greatly increase the speed and reliability of traceback efforts and make it more feasible to incorporate traceback data into the epidemiologic investigations,” Dr. Hedberg says. “Increasing the speed and efficiency of tracebacks and incorporation of traceback data into epidemiologic investigations are critical areas for improvement.”

In the plan, there are also detailed steps for systematizing the agency’s root RCIs and adopting a continuous improvement approach for food safety operations.

Additionally, FORIP facilitates a streamlined process for analyzing and disseminating outbreak data to the Centers for Disease Control and other regulatory partners. “Many of these additional efforts will increase the amount of information available from outbreak investigation partners and increase the timeliness of the information, so that contaminated food products can be more rapidly identified and removed from commerce,” Sertl says.

Measuring Success

FDA is using both performance and outcome metrics to identify the level of success it achieves in reaching its goal of enhancing the speed, effectiveness, coordination, and communication of outbreak investigations. While the individual metrics are important, the true progress indicators will be reduced cases of sickness, hospitalization, and death related to foodborne illness outbreaks.

Scioscia calls FORIP a necessary step forward, both for the safety of food suppliers and distributors working alongside the various touchpoints throughout the supply chain and for consumers at the receiving end. “Without food safety track and trace technologies and plans in place, food distributors cannot identify and remove contaminated food items in time,” he says. “The FORIP is necessary for suppliers to gain access to IoT technology and food [enterprise resource planning] ERP applications with AI and predictive analytics, that will help prevent contaminated foods from reaching restaurants and store shelves and getting into the hands of consumers.”

According to Yiannas, successfully implementing the series of actions outlined in FORIP will enable FDA to respond more quickly and more efficiently to foodborne outbreaks and reduce the number of foodborne outbreaks that go unsolved in the future.

Dr. Hedberg says that success of FDA’s plan will be measured by the increased speed and effectiveness of investigations to identify the source of outbreaks and by the improved ability to provide insights to industry on how they can develop preventive controls based on better understanding of the root causes of outbreaks. “For that to happen, we need time, continued investment in the public health system that supports these efforts, and the continued belief that these efforts matter.”

The post A Look at FDA’s Foodborne Outbreak Response Improvement Plan appeared first on Food Quality & Safety.

Listeria monocytogenes soon may become easier to track down in food recalls and other investigations, thanks to a new genomic and geological mapping tool created by Cornell University food scientists. The national atlas will tell scientists where Listeria and other related species reside within the contiguous United States. This could help trace and pinpoint sources of the pathogen found in ingredients, food processing facilities, and finished products, according to research published in Nature Microbiology.

Knowing that the pathogen occurs naturally in soil, the researchers asked hundreds of scientists across the country to collect soil samples from generally undisturbed places in the natural world, such as the off-trail areas of state and national parks. From these samples, the group developed a nationwide atlas of 1,854 listeria isolates, representing 594 strains, and 12 families of the bacteria, called phylogroups.

“As we’re trying to figure out the risk of getting Listeria from soil and different locations, our group created a more systematic way of assessing how frequently different Listeria are found in different locations,” says senior author Martin Wiedmann, PhD, a food safety and food science professor in the Cornell University College of Agriculture and Life Sciences in Ithaca, N.Y. “We’ve studied Listeria in places as diverse as New York, Colorado, and California, but before this atlas, [it] was difficult to make comparisons and assess Listeria diversity in different locations.”

Lead author Jingqiu Liao, PhD, who worked in Dr. Wiedmann’s laboratory as a graduate student, is now a post-doctoral researcher at Columbia University. She found Listeria present across a wide range of environmental circumstances. This bacterium is controlled mainly by soil moisture, salinity concentrations and molybdenum—a trace mineral found in milk, cheese, grains, legumes, leafy vegetables, and organ meats.

“The goal of this work was to systematically collect soil samples across the United States,” says Dr. Liao, “and to capture the true large-scale spatial distribution, genomic diversity, and population structure of Listeria species in the natural environment.

“With whole genome sequencing and comprehensive population genomics analyses,” Dr. Liao says, “we provided answers to the ecological and evolutionary drivers of bacterial genome flexibility—an important open question in the field of microbiology.”

Dr. Liao says that this work can serve as a reference for future population genomics studies and will likely benefit the food industry by locating Listeria contaminations that may have a natural origin.

If the pathogen is found in a processing facility in the western U.S., for example, and that facility had used ingredients from a distant state, Dr. Wiedmann says, “Knowing the genomic information of Listeria isolates and their possible locations across the U.S., we can better narrow the origins to a specific region. You can use this information almost like a traceback; it’s not always proof, but it leads you to evidence.”

The post Cornell Scientists Create National Genomic Atlas for <i>Listeria</i> appeared first on Food Quality & Safety.

Tyson Foods, Inc., based in Dexter, Mo., is voluntarily recalling approximately 8.5 million pounds of ready-to-eat chicken products that may be adulterated with Listeria monocytogenes, according to the USDA Food Safety and Inspection Service (FSIS). Tyson has been working closely with USDA on this recall, and while the company says there is no conclusive evidence that the products were contaminated at the time of shipment, the recall is being initiated out of an abundance of caution.

The frozen, fully cooked chicken products were produced between December 26, 2020, and April 13, 2021. The products that are subject to recall are listed here. View the labels here.

The products subject to recall bear establishment number “EST. P-7089” on the product bag or inside the USDA mark of inspection. These items were shipped nationwide to retailers and institutions, including hospitals, nursing facilities, restaurants, and schools.

On June 9, 2021, FSIS was notified of two people who were sick with listeriosis. Working in conjunction with the CDC and state public health partners, FSIS determined there is evidence linking the Listeria monocytogenes illnesses to precooked chicken produced at Tyson Foods.

The epidemiologic investigation identified three listeriosis illnesses, including one death, between April 6, 2021, and June 5, 2021. During routine sample collection, FSIS collected two precooked chicken samples from two establishments that are closely related genetically to Listeria monocytogenes from sick people. One of the samples was collected at Tyson Foods.

USDA is continuing to work with federal and state public health partners to determine if there are additional illnesses linked to these products.

The post Tyson Recalls 8.5 Million Pounds of RTE Chicken Due to Possible <i>Listeria</i> Contamination appeared first on Food Quality & Safety.

Cornell food scientists recently discovered five novel species of Listeria, and this has piqued the interest of food safety experts from around the globe.

The research was funded by the Center for Produce Safety and the Florida Department of Agriculture and Consumer Service (FDACS) Specialty Crop Block Grant Program, and was published in the International Journal of Systematic and Evolutionary Microbiology. The researchers studied different soil and agricultural water samples from the United States, which led to the identification of 27 Listeria isolates that could not be categorized. The research team conducted whole-genome sequence-based tests, which resulted in the discovery of the five novel species.

What does this breakthrough mean for food safety and food quality?

Revising Standards and Guidelines

Of the five species, L. immobilis, as the name suggests, is non-motile. This challenges one of the most common and traditional preliminary detection methods of the species—mobility. L. monocytogenes exhibits a distinct tumbling motion when viewed under a microscope. According to the publication’s lead author, Catherine R. Carlin, PhD, “This discovery effectively calls for a rewrite of the standard identification protocols issued by food safety regulators.” Researchers will now also have to study other parameters, such as the impact of temperature fluctuations on motility.

Updating Educational and Training Content

Great teachers are teachable too. Educators and trainers linked to the life science space understand the need to stay up to date on recent discoveries and advancements. This also means updating content within formal education and training systems, and informational systems such as marketing materials aimed at educating consumers.

When updates are made to scientific content, it is important to highlight not just what changed, but also why it changed. Using storytelling skills can help build a better narrative that your audience can comprehend. Clear, consistent, and easy-to-digest bits of information will encourage people to have more conversations around new scientific subjects, which, in turn, will impact how they approach food safety as a behavior.

Revisiting Risk Assessments

Listeriosis, though rare, is quite severe, as its effects can be long term. The recent multi-state Listeria outbreak that was linked to El Abuelito Cheese resulted in 12 hospitalizations, two pregnancy losses, one premature birth, and one death. While L. monocytogenes remains the species of focus, understanding how the other species of Listeria interact with one another may offer new insights. Food safety professionals may have to revisit how risks are assessed and categorized. Team leaders overseeing food safety management systems such as HACCP, FSSC 22000, etc., may have to reconsider how they develop their HACCP plans and operational manuals.

Updating Audits and Inspections Criteria

Making changes to standards and guidelines will also mean making changes to food inspection systems and audit strategies. Inspectors and auditors will have to develop a deeper understanding of these novel species before they can recommend necessary corrective actions, or cite areas of noncompliance.

Catalyzing Innovation

New challenges present new opportunities. The awareness of the biodiversity that exists within the Listeria species will enable developers to think of new opportunities for improvement. Improving supply chain safety protocols and extending the shelf lives of food products will help promote sustainability and reduce food wastage.

It’s an exciting time to be in the world of science and technology. It’s also encouraging to see subject matter experts remaining resilient and educated while navigating the changes brought about by the pandemic, which has forced us to rethink how we solve modern-day problems.

The post <i>FQ&S</i> Blog: How the Discovery of Novel <i>Listeria</i> Species May Impact Food Safety appeared first on Food Quality & Safety.

While examining the prevalence of Listeria in agricultural soil throughout the U.S., scientists at Cornell University in New York City have stumbled upon five previously unknown and novel relatives of the bacteria. The discovery, researchers say, will help food facilities identify potential growth niches that, until now, may have been overlooked, which could improve food safety.

The research was published May 17, 2021 in the International Journal of Systematic and Evolutionary Microbiology.

“This research increases the set of Listeria species monitored in food production environments,” says lead author Catharine R. Carlin, a doctoral student in food science. “Expanding the knowledge base to understand the diversity of Listeria will save the commercial food world confusion and errors, as well as prevent contamination, explain false positives, and thwart foodborne outbreaks.”

Detection Methods for Listeria May Need to Be Overhauled

One of the novel species, L. immobilis, lacked motility. Motility has previously been thought to be common among Listeria closely related to L. monocytogenes and used as a key test in detection methods. This discovery effectively calls for a rewrite of the standard identification protocols issued by food safety regulators, Carlin says.

As Listeria species are often found co-existing in environments that support the growth of L. monocytogenes, food facilities will monitor for all Listeria species to verify their sanitation practices.

L. monocytogenes can have profound pathogenic influence on food processing plants and those plants must be kept clean. Listeriosis has a mortality rate of 20% to 30%, even with a patient taking antibiotics, according to FDA. The Centers for Disease Control and Prevention estimate that 1,600 people in the U.S. get listeriosis annually and nearly 260 die.

“This paper describes some unique characteristics of Listeria species that are closely related to L. monocytogenes, which will be important from an evolutionary perspective and from a practical standpoint for the food industry,” says co-author Martin Wiedmann, PhD, a professor in food safety and food science. “Likely, some tests will need to be re-evaluated.”

Understanding the different Listeria species is key to comprehending their similarities. “This will help us to get better about identifying L. monocytogenes,” Dr. Wiedmann says, “and not misidentifying it as something else.”

Since 2010, Dr. Wiedmann’s research group has discovered 13 of the 26 species classified in the genus Listeria. “When you’re inspecting the environments of food processing plants or restaurants, you need to know the pathogenic Listeria from the non-pathogenic species,” he says. “You need to tell the good guys from the bad guys.”

The post Researchers Discover Five Novel Species of <em>Listeria</em> appeared first on Food Quality & Safety.

FDA and the Centers for Disease Control (CDC) are investigating a multistate outbreak of Listeria monocytogenes (Lm) infections that may be linked to certain fresh and soft cheeses.

CDC reports that seven people have been infected with the outbreak strain of Lm in Connecticut, Maryland, New York, and Virginia. Of four infected people interviewed by CDC, three report eating at least one type of Hispanic-style fresh and soft cheeses, and each of these three reported eating queso fresco, the agency says.

As part of this outbreak investigation, the Connecticut Department of Public Health collected product samples of El Abuelito-brand Hispanic-style fresh and soft cheeses from a store where a sick person bought cheeses. FDA says that an analysis showed the presence of Lm in samples of El Abuelito Queso Fresco sold in 10 oz packages, marked as Lot A027 with an expiration date of February 26, 2021. On February 19, whole genome sequencing (WGS) analysis conducted by the Connecticut State Laboratory determined that the Listeria monocytogenes found in the samples is a match to the outbreak strain.

El Abuelito Cheese, Inc. of Paterson, N.J. has now recalled all queso fresco products with “sell by” dates through March 28, 2021. The products include El Abuelito, Rio Grande, and Rio Lindo brand queso frescos, distributed in Connecticut, Maryland, North Carolina, New Jersey, New York, Pennsylvania and Virginia.

At press time, El Abuelito Cheese has ceased production and distribution of all products.

The post FDA, CDC Investigate <em>Listeria</em> Outbreak in Certain Fresh and Soft Cheeses appeared first on Food Quality & Safety.

Whole-genome sequencing (WGS) has proven to be very effective at identifying where resident Listeria strains may be found in a food facility. To date, however, it has also been proven to be equally effective at ensuring that only a few food companies want to use the technology.

Whole-Genome Sequencing as a Technology

For the most part, scientists, such as molecular biologists, and regulators, such as FDA, view whole-genome sequencing as an evolving state of the art. Using these methods has repeatedly helped regulators identify resident strains in a food facility before the strains can cause significant public health issues. If the strains end up on manufacturing equipment and/or in food, whole-genome sequencing is very useful at identifying the association between the original source, retail distribution, and public consumption of that food.

Whole-genome sequencing is, in essence, an upgrade from its precursor technologies such as pulse-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and multiple-locus VNTR analysis (MLVA).

As has been demonstrated in recent years, the science of identifying genes, bacteria, and food-related organisms keeps progressing, and always will. As many people have stated in published articles and speeches, WGS technology has probably outpaced the food industry’s ability to keep up with it at the moment. But surprisingly, industry has been reluctant to embrace the technology, in large part because of fear that their products will be linked to human illness and the potential resulting regulatory enforcement actions. 

Keeping Up with the Technology

Grabbing any new technology and putting it to work in a manufacturing plant is rarely straightforward, is difficult to mandate, and must be done with careful consideration. This is because new technologies come with baggage, some of which include significantly higher costs initially (compared with past/current technologies), longer lead times initially, and higher alpha- and beta-risks (i.e., chances of false results).

These are all good reasons why the food industry in general has not embraced WGS as a routine tool. And this is in spite of the fact that FDA will sequence any positive it finds during a “swab-a-thon.” In fact, the food industry has barely even embraced WGS as a problem-solving tool. 

Whole-Genome Sequencing as a Problem-Solving Tool

One of the best uses of WGS in a food production plant is increasing the odds of finding the root source of a strain of Listeria that is resident. For example, positive WGS findings (i.e., matching gene sequences with an extremely high probability) can help a company identify a regularly incoming raw material as the source of a Zone 3 recurring contamination (e.g., on pallets).

FDA takes this same approach in attempting to link a specific Listeria strain sequence found in a clinical isolate or food product with an identical strain found in a food plant.

FDA wants to encourage use of WGS to help minimize food safety risks to the public, but by its policy execution, it may be driving the industry away from a proven scientific tool that could achieve that very end.

Using WGS in this manner takes a lot of time (and money), and it is at the moment a best practice for identifying Listeria strains that have resided in given locations over time. This allows discovery of “hot spots” and certainly helps in identifying external sources (e.g., a supplier issue). Hence, a regular use of WGS testing of strategic samples around a food facility can pay huge dividends in identifying, and then eradicating, resident Listeria strains.

By contrast, WGS is a poor tool to use to identify transient strains of Listeria and/or when results are needed quickly to be able to respond to an issue or corrective action. This is primarily because of the fact that by the time the WGS results come back, the transient organism is long gone. And although the cost of WGS testing has dropped by orders of magnitude over the years (as happens with new technologies that become mainstream—look at wide-screen TVs), simply churning out WGS samples to try to locate Listeria in a food facility can become extraordinarily expensive.

Other techniques are far quicker and can be equally effective at the end game. For example, there is still value in using some of the older techniques such as PFGE and MLVA. Even easier and cheaper, although less informative, is using well-proven standard microbiological techniques to assay for Listeria (e.g., FDA BAM Chap 10). These standard micro tests have widespread proven use in environmental monitoring programs to “seek out and destroy” pathogens in a food facility, regardless of whether those organisms are transient or resident. WGS can then be used sparingly as a means of continued surveillance, ensuring that strains are or are not taking up residency.

The “time and cost” value equation of WGS, however, is still a reason why food companies do not routinely use WGS. Do note that over the past two years, turnaround time and costs have been significantly reduced (e.g., a five-business day turn for Listeria WGS is about $500). However, this value equation is either still not good enough, and/or companies are still saying that the tests are “too long and too costly” as a shield for not wanting to enter FDA’s territory.

FDA and Whole-Genome Sequencing

Clearly FDA sees WGS as a savior; euphemistically speaking, if use of the technology prevents even one illness, then its use is warranted. And, since the technology is available, an informed public would most likely want FDA to use it. So, it may be that as time progresses, public and political pressure may push WGS forward independent of food safety professionals wanting to do so or not.

Having WGS in its toolkit also allows FDA to trumpet what it is doing: WGS is a well-defined technology, and the public can understand it (especially when the public watches crime shows that use DNA testing, or consumers use DNA sequencing for ancestry determination purposes). FDA will continue to use these tools to find organisms, such as Listeria monocytogenes, which can cause significant adverse health consequences or death to the small populations that are highly susceptible to the organism’s effects.

This is also why FDA continues to maintain a “zero tolerance” policy for Listeria monocytogenes. This is not the case worldwide (e.g., Canada and Australia), but it is the position FDA has taken. Granted, the rationale for this is to protect the public health, but it also allows FDA to conduct deeper investigations into a food company’s practices and, when resident pathogens are detected and linked to human illness, initiate the enforcement actions the public would expect them to take.

Why FDA Is the Biggest Reason for Industry Not Using Whole-Genome Sequencing

Setting aside consideration of whether or not FDA should be spending so much time enforcing a zero-tolerance principle, one would surmise that if FDA allowed for some tolerance of Listeria, the food companies might begin using the technology much more widely. But, as everyone knows, they are not.

Why?

FDA has issued a Draft Guidance for Industry: Control of Listeria monocytogenes in Ready-To-Eat Foods. Although still in draft form, the document essentially offers a “three strikes and you’re out” approach for detection of Listeria species in a food production plant. In other words, if there is a new identification of Listeria on a non-food contact surface (for example), this is not the end of the world. Intensified sampling and/or cleaning might be mandated, but production does not necessarily need to halt.

Many people have praised this approach, and for good reason: The odds that an environmental sample is positive for Listeria monocytogenes are generally low, as are the odds of a consumer being exposed to a sufficient number of organisms to become compromised (since the vast majority of people eating the food are healthy). Moreover, many products require further preparation and heating by consumers prior to consumption. Thus, even when Listeria may be present, the risk to consumers is often generally low.

If FDA finds Listeria in a food facility or in its review of a company’s environmental monitoring records, then FDA often times responds aggressively. Sometimes, some would argue, too aggressively. It is likely that all food companies would likely test more frequently for Listeria in food facilities, and work harder to find Listeria, if FDA did not take such a critical view of zero-tolerance positive testing results.

This is a major reason why the approach of other countries might be better in the long run. Canada, Australia, and the European Union (via its laboratory Guidance Document), all use an allowable limit of <100 CFU/gm for Listeria monocytogenes.

While the focus of this article is FDA, it is important to note that for dual-jurisdiction plants, USDA quietly watches, and sometimes follows the lead of, FDA. USDA conducts its own environmental sampling for enforcement purposes, but for the most part the agency seems to keep an eye out for what action FDA is pursuing. USDA often asks companies for their FDA data with regard to Listeria, even if the company is not legally obliged to share the data with them.

Why Having Listeria Data Is Good—and Bad

It is also important to note that this article is not advocating a cavalier attitude toward Listeria. A company cannot get a “hit” or “two” and then think they can take some action to avoid the “third strike.” This is indeed a road to perdition, not only for the company but for public health. Rather, the company needs to have a scientifically justified corrective action plan in place, and a very active environmental monitoring program for the organism.

That said, FDA risk becomes even worse if a company has WGS data, and doubly worse should the company know that the sequence of their Listeria sample matches a sequence in FDA’s GenomeTrakr database. This would mean that the company knows of a linkage, and one which may or may not implicate the company. Should FDA be told, or should the company solve the problem and move on?

Let’s say that the company generated its data (and linked an environmental sample to a retail food or, worse, a clinical sample from a patient hospitalized in their immediate vicinity) under a protected status, e.g., attorney-client privilege. The company would seem justified in not sharing the data with FDA. But what if there is a public health problem down the road, and FDA uncovered that same data after the fact?

Almost no company wants to be in either pressure-cooker, i.e., having data that could escape into the public domain, or having data which could be discovered later. What is the result? The result is that few companies want to use WGS under these circumstances, no matter how helpful the data might be to public health protection.

Of course, this is the same reason food companies have their microbiology labs test only for Listeria spp. and not directly for Listeria monocytogenes (Lm). Again, as soon as the Lm notation appears, “zero tolerance” comes to mind. And, once that “Lm” designation is in the corporate files, it could be devastating for the company even if the company is taking all appropriate efforts to eradicate the bacteria from the premises.

The Sword: Double-Edged, or Damocles?

This clash of paradigms is clearly a double-edged sword. FDA wants to encourage use of WGS to help minimize food safety risks to the public, but by its policy execution, it may be driving the industry away from a proven scientific tool that could achieve that very end.

My call to action, then, is for FDA to allow a better path for companies to use WGS testing, without having to face the consequences of an initial positive result. Perhaps, human isolates could be stripped from a custom public database that could be accessed by food companies. If this were made available, it seems likely that a significant number of additional companies would begin using WGS to solve contamination challenges in their facilities.

If nothing changes in the near term, then the use of WGS will likely remain low. That would be a shame, not just from the perspective of trying to banish Listeria from food facilities, but also due to the opportunity cost of spending so much time being outmaneuvered by these elusive bacteria.

Lijana is a food safety technical consultant based in North Carolina. Reach him at boblijana@gmail.com.

The post Opinion: Whole-Genome Sequencing Is a Double-Edged Sword for the Food Industry appeared first on Food Quality & Safety.