Deadly Outbreaks and the Role of Metagenomics

By Maria Fontanazza

Americans consume 350 billion pounds of food each year, with one out of six people falling victim to foodborne illness, and 3000 dying. The significant amount of Listeria outbreaks hitting the industry (most recently, the staggering number occurring in produce) has left many food safety and quality assurance professionals searching for better methods of prevention and detection. Using big data, specifically metagenomics, to improve food safety and detect potentially deadly outbreaks is indeed where the future is headed.

DID YOU KNOW? The estimated U.S. cost of one case of Listeriosis is $1.4 million. Listeria is a prime concern due to the high percentage of fatalities that occur as a result of contracting Listeriosis. And what’s worse is the fact that many of the cases are preventable.

During Food Safety Tech’s Listeria Detection & Control Workshop this week, John Besser, Ph.D., deputy chief of CDC’s Enteric Diseases Laboratory Branch, outlined how the agency is leveraging metagenomics to find unrecognized problems in the food supply. Perhaps the most important element of disease surveillance is that it enables the detection of new issues, especially those whose presence was previously unknown.

Pathogen-specific surveillance allows the detection of more outbreaks, which will in turn make the food supply safer, because it will enable industry to understand the root causes of outbreaks and help them address problems much sooner. The CDC is focused on genome-based outbreak detection because of its ability to achieve faster detection—and with greater precision in identifying the source. The method has also helped the agency solve outbreaks with fewer cases occurring, and it concurrently helps rule out sources.

PulseNet, a nationwide database (comprised of 87 labs in the United States) that links cases most likely to share a cause for illness, has prompted food safety improvements across a variety of products, including sprouts, peanut products, leafy greens, flour, melons, eggs and poultry. Combine this capability with the Listeria initiative, which was launched in the mid-2000s, and the CDC has been able to find more (and smaller) outbreaks than ever before. In fact, there’s been a dramatic increase in the number of outbreak cases that have been solved (with the food source being identified). During the pre-whole genome sequencing (WGS) stage (September 2012–August 2013), only one outbreak was solved; in year one of the WGS project (September 2013–August 2014), four cases were solved; in year 2 of the WGS project (September 2014–August 2015), nine outbreaks were solved. In these respective time periods, the median number of cases per cluster dropped from six to four to three. In addition, the number of cases linked to a food source jumped from 6 to 16 to 93 during this respective time period.

Besser also discussed the role of metagenomics, or the study of total genetic material recovered directly from environmental samples. A couple of years ago, this was science fiction and wasn’t possible, he said. But as we look to the future, metagenomics will become a lot cheaper as computers become more powerful—and at break-neck speed. He referenced IBM Research, who earlier this year announced a project being conducted in conjunction with Mars, Inc. and Biorad for sequencing the food supply chain (calling it the “largest-ever metagenomics study”).

Read Food Safety Tech’s interview with IBM Research about the next-generation sequencing project, “Preventing Outbreaks a Matter of How, Not When”

Metagenomics enables the profiling of communities of microbiomes anywhere in the food supply chain. And the method is fast—it can potentially shave weeks off the process of identifying clusters of interest. In addition, it can increase the value of interviews conducted with patients who have fallen ill (Think about it: Do you remember what you ate two weeks ago? What about a month ago?).

Currently there are several limiting factors surrounding metagenomics: Cost; sequencing read length and error rate; specific software (and pipelines); computing processing power and bandwidth; and the signal-to-noise factor. However, with the rapid rate in which technology has been improving in this space, the high likelihood of these issues being addressed and resolved in the not-so-distant future will present exciting opportunities in outbreak prevention and detection.

May 26, 2016

FSMA Webisode: Training for your PCQI vs. Qualified Individual

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Dr. Hilary Thesmar, VP FMI Food Safety Programs reviews the difference in responsibility and required training for each role for your checklist.

FSMA introduced two different types of identified individuals, the Preventive Controls Qualified Individual and the Qualified Individual. Specific training requirements are associated with each. Dr. Hilary Thesmar, VP FMI Food Safety Programs reviews the difference in responsibility and required training for each role for your checklist. Watch the webisode

May 26, 2016

FSMA Intentional Adulteration Rule Released

By Food Safety Tech Staff

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–UPDATE (5/27/2016)– The final rule has been published on the Federal Register‘s website. –END UPDATE–

FDA just released the final FSMA rule, “Mitigation Strategies to Protect Food Against Intentional Adulteration”. Under the rule, domestic and foreign food facilities must complete and maintain a written food defense plan that assesses their vulnerabilities to intentional contamination.

“Today’s final rule on intentional adulteration will further strengthen the safety of an increasingly global and complex food supply,” said Stephen Ostroff, M.D., incoming FDA deputy commissioner for foods and veterinary medicine in a press release. “The rule will work in concert with other components of FSMA by preventing food safety problems before they occur.”

The final rule will be published on the Federal Register tomorrow. To preview the PDF document, visit the Federal Register’s website.

May 25, 2016

FDA’s Annual Food Registry Report Finds Listeria and Allergens as Top Issues

By Food Safety Tech Staff

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Yesterday FDA released its Reportable Food Registry (RFR) and cited Listeria monocytogenes as generating the greatest number of reports (223), along with undeclared milk (27), in Year Five (from September 8, 2013–September 7, 2014).

FDA defines a reportable food as “an article of food/feed for which there is a reasonable probability that the use of, or exposure to, such article of food will cause serious adverse health consequences or death to humans or animals.” The purpose of the registry is to allow FDA to track patterns of food and feed adulteration in order to help the agency focus its already limited inspection resources.

Year Five saw 909 reportable food entries, including 201 primary reports regarding safety concerns with food or animal feed and 464 subsequent reports from suppliers or recipients of food or feed that was the subject of the primary reports, and 244 amended reports. The following food safety hazards were identified within the 201 primary reports in Year Five: Drug contamination, pathogenic E. coli, Listeria monocytogenes, nutrient imbalance, lead, Salmonella, undeclared allergens and undeclared sulfites. In addition, Salmonella, Listeria and undeclared allergens made up about 88% of the total primary entries for all five years of the RFR.

The report’s complete breakdown of the RFR submissions by year, along with identified commodities and hazards, is available on FDA’s website.

May 24, 2016

Health Canada Approves GMO Salmon, Sparks More Outcry

By Food Safety Tech Staff

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Following a “thorough and rigorous” scientific review process, Health Canada announced the approval of GMO salmon, also known as AquAdvantage Salmon, last week. The salmon is developed by Massachusetts-based AquaBounty Technologies, Inc. According to a release from Health Canada, the AquAdvantage Salmon underwent safety and nutrition assessments by both Health Canada for use as food and by the Canadian Food Inspection Agency for use as livestock feed. The assessments found the salmon to be “as safe and nutritious as” traditional salmon.

The approval was met with distain by several groups, including Friends of the Earth, which called the approval “irresponsible and disappointing” in a news release.

“This approval also comes despite the Canadian Department of Fisheries and Oceans draft risk assessment that questions the health and welfare of AquaBounty Technologies Inc.’s genetically modified salmon. The draft risk assessment concluded that AquaBounty’s GMO salmon are not only ‘more susceptible to Aeromonas salmonicida, a type of disease-causing bacteria,’ but exhibit ‘diminished growth rates’ and ‘widely varied performance.’” –Friends of the Earth news release

More than 60 grocery store chains have committed to keeping GMO salmon off their shelves, including Trader Joe’s, Costco, Whole Foods, Aldi, Target and Safeway.

May 23, 2016

Supplier Accountability Focus of Latest Protest Against Chipotle

By Food Safety Tech Staff

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The labor union International Brotherhood of Teamsters has been holding nationwide protests at Chipotle locations this month, taking issue with one of the restaurant chain’s suppliers. The supplier at the focus of the demonstrations is California-based produce company Taylor Farms, which supplies tomatoes and peppers to Chipotle, according to Teamsters.

“Over the past five years, Taylor Farms has had more than 20 food recalls for problems such as Listeria, Salmonella and E. coli. In November 2015, Taylor Farms products containing celery and sold at Costco and other retail outlets were recalled for possible E. coli 0157:H7 contamination,” according to a Teamster news release. “At Taylor Farms’ plant in Tracy, Calif., the company has also committed safety and health violations and violations of laws that protect workers’ rights. Recently, the company settled extensive labor rights violations that involved payments of $267,000 to illegally terminated workers and a required posting in which the company promises to never again violate a long list of employee rights.”

The Teamsters protested at 12 Chipotle locations across the country, following 30 previous protests at Chipotle over the past several months.

Teamster Vice President Rome Aloise points the finger at Chipotle for allowing Taylor Farms to “have a total disregard for consumers’ and workers’ health and safety, as well as workers’ rights,” he said. “Chipotle claims to serve ‘Food With Integrity’, but where’s the integrity when it turns a blind eye to its supplier’s behavior? Chipotle must not cut and run – which would hurt Taylor Farms workers – it must carry out its social responsibility and demand Taylor Farms treat workers fairly and with respect.”

Taylor Farms has not released a statement addressing the protests.

May 19, 2016

North American Meat Institute Fires Back at Burger Report Findings

By Food Safety Tech Staff

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As Clear Labs’ latest report on burger products, The Hamburger Report, has gained widespread media attention, the North American Meat Institute is sounding an alarm about the findings. Clear Labs is a “fledging company” that is “up to its same old tricks”, using burgers as its target just in time for the grilling season, said Betsy Booren, Ph.D., vice president, scientific affairs at the North American Meat Institute, in a statement from the organization.

Read the article on Food Safety Tech: Next-Gen Sequencing Exposes Problems with Burgers

“A review of the company’s procedures suggest[s] collection methods prone to mistakes and a range of errors throughout the analysis process. A look at the company’s own promotional video featuring shots of overpacked freezers and technicians testing products using plastic forks and knives with paper towels would suggest cross contamination in the lab is a very good possibility,” said Booren. “When a single cell can generate a finding, precise methods are crucial. It’s entirely possible that the human DNA found could be linked back to the company’s own staff—we just don’t know. Likewise, when the lab company suggests some products showed the presence of another species, like chicken in a beef product, this finding could also stem from a single cell and even result from the pulling samples from multiple packages in the same room, as the company appears to have done.”

Booren called Clear Labs’ report a marketing ploy and went on to assert that today’s ground beef is safer than ever, saying there have been significant reductions in pathogenic bacteria, which has been “further confirmed by this report [The Hamburger Report]”.

May 18, 2016

Packaging Technique Could Help Produce Last Longer

By Food Safety Tech Staff

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Michigan State University (MSU) may have come up with a way to make packaged vegetables last much longer. After conducting an extensive evaluation of current techniques, researchers at MSU found that combining a package’s atmosphere of elevated carbon dioxide and reduced oxygen with a sanitizing treatment of sodium hydrochlorite could help ready-to-use onions last two weeks in a package (meaning that they were acceptable for purchase at this point). The results of the research, which was partially funded by USDA, were featured in an issue of the International Journal of Food Microbiology.

“We focused on ready-to-use onions, which have grown to become one of the five most commonly sold vegetables in the last decade,” said Eva Almenar, MSU AgBioResearch scientist in a news release. “Of all the variations that we tested, this one reduced microbial growth, respiration and discoloration, and preserved the desired aroma.”

The packaging technique could have potential use with other vegetables as well. Almenar is also investigating gas composition packaging and containers made from renewable sources.

May 17, 2016

Next-Gen Genomic Sequencing Exposes Problems with Burgers

By Maria Fontanazza

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Burgers are the quintessential American food. But as prices continue to rise in the beef industry and U.S. consumers seek more health-conscious alternatives such as veggie and salmon burgers, some food companies may be cutting corners. Clear Labs used next-generation genomic sequencing (NGS) to conduct molecular analysis of 258 burger products (ground meat, frozen patties, fast food burgers and veggie burger products from 79 brands and 22 retailers) and found significant issues—instances of substitution, missing ingredients, pathogens or hygienic problems—in about 14% of samples. This is a red flag for industry, indicating a need to remain vigilant about vulnerabilities in the supply chain and the way in which products are tested.

Ironically, perhaps the biggest problems that The Hamburger Report revealed surrounded meat-alternative products. Out of 89 vegetarian samples, 23.6% were found to have issues, from ingredient substitutions to rat DNA to pathogens (see Figure 1). “We were surprised by the higher rate of problems in veggie burgers,” says Mahni Ghorashi, co-founder of Clear Labs. “There were nearly twice as many problems in those samples as their meat counterparts, which is surprising, because you normally think of a veggie product as perhaps a safer bet, but we actually found more cases of pathogen strains. And we found things like beef in veggie products, which isn’t acceptable. That was somewhat troubling.” Ghorashi suggests that manufacturers should be doing more to ensure consistency and adequate labeling of best-handling practices for consumers. “The message is that we need more awareness about the unknown risks and the potential need for more stringent safety measures,” he says. “We follow a great deal of these practices when it comes to meat-based products. Perhaps we’re not as sensitive toward veggie-based products.”

The Hamburger Report, Clear Labs — Figure 1. The Hamburger Report found a higher rate of issues with meat-alternative burger products. (Figure courtesy of Clear Labs)

The report also uncovered several high-risk pathogens in samples, but not the typical ones (i.e., Listeria, Salmonella, E. coli) that make news headlines. Out of the 258 samples, 4.3% contained pathogenic DNA, with vegetable products accounting for four of those instances. Pathogens found included Yersinia pseudotuberculosis, Yersinia enterocolitica, clostridium perfringens, and klebsiella pneumonia. Although these strains are often rare, they still have health implications and can cause tuberculosis-like symptoms, digestive issues and gastroenteritis. Typical methods such as polymerase chain reaction (PCR) are used to detect pathogenic strains such as Listeria, Salmonella and E. coli, but can potentially miss other strains. “The industry should take off their pathogen blinders and start to test for lesser known and potentially dangerous pathogens using these types of blind-testing techniques,” says Ghorashi. “It’s worth casting a wider net and filter in order to catch these [pathogens].”

Although the screening method that Clear Labs used is currently unable to determine whether a pathogen is dead or alive, nor the count, there are other benefits to using next-generation DNA sequencing, says Ghorashi, who thinks the method has the potential to become the technology of choice in the food industry. “The strength of this platform as it differentiates itself from existing solutions is its ability to look unbiasedly and universally into food samples and tell you everything that’s there,” he says. “It’s able to detect any type of DNA-based species within a sample as opposed to specific queries that you might be looking for. This technology can detect everything that’s there, so it often catches things that one might miss. Existing solutions look very focused on one particular item.”

What are the implications of The Hamburger Report in the context of FSMA?

Ghorashi: It’s very much in line with what FDA is rolling out with FSMA. This speaks back to where industry is headed in terms of rolling out more preventive measures versus responsive measures. It plays into economic adulteration and fraud. It also plays into the concept of proactive testing and measures, a better sense of the overall landscape of the supply chain and where the weaknesses are. These are all the areas that software-driven and data-driven platforms can help emphasize. We look at FDA as a forwarding-thinking organization and an ally in this initiative. Hopefully emerging companies, including ourselves, that have new disruptive technologies can help assist the food industry, whether producers, manufacturers, retailers or distributors, in building more air-tight safety programs and complying more closely with FSMA regulations.

Clear Labs is working towards building out its first product, Clear View. The software data analytics platform integrates NGS technology and is designed to aggregate test data in the cloud to provide food manufacturers, suppliers and retailers with insights about their supply chains. The company is also continually growing its internal database, which, according to Ghorashi, is currently the largest molecular food database in the world.

May 16, 2016

Supplier Documentation: To Automate or Not to Automate

By Maria Fontanazza

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Q&A Part I: Hiring and Training, Understanding FSMA Remain Big Industry ChallengesIn part two of Food Safety Tech’s Q&A with TraceGains, Anthony Arocha (customer success consultant), Rajan Gupta (vice president of customer success), and Jason Ulrich (customer success manager) explain the factors at play surrounding the lack of supplier documentation in the food industry.

Food Safety Tech: Just 44% of respondents said they automate supplier documents. What information can you glean from this? Why aren’t more companies automating?

Arocha: Companies understand that using technology is essential to manage the increasing demands on accurate food safety documentation and verification. For many companies, it is likely to be just a timing and resource issue as to why they have not yet adopted automation—timing as in they have not yet reached the pain threshold required to justify the new cost to implement and to have a resource to support or focus on it. As companies grow and new budgets get created, it is just a matter of time before they will have to include automation help if they have not already.

Gupta: I believe lack of internal respect for QA and thus lack of education and funding are key contributors to this area. Most of the quality staff is stuck doing daily activities with limited time to explore options to make their processes better. Lack of empowerment to make business process changes is also a large factor in not adopting technology. Marc states that the companies have silos as indicated by the transparency gains from technology—while that is true, the root cause of this may be that the various groups within an organization have never really paid attention to FSQA areas and thus never envisioned having access to information that can help the organization proactively manage risk and increase food safety awareness.

Ulrich: This is all about people money, and time. The industry as a whole doesn’t have enough in quality departments. The lack of qualified individuals available in QA departments has always been an issue. The money is usually used to improve production and other departments except quality. That leaves the limited resources in the department with very little time to review and implement new processes or software.

Food Safety ad Quality Assurance Survey, TraceGains — 2016 Annual TraceGains Food Safety & Quality Assurance (FSQA) Professional Survey (Figure courtesy of TraceGains)

FST: Regarding supplier documentation management, where are companies falling short?

Arocha: Supplier document management is not easy. You are at the mercy of your vendors. I think the biggest issue is trying to do everything too fast versus having a risk-based approach and focusing on the top priority items first. Build on success. If you try to do too much too fast, it is hard to pick out the success stories easily and can become overwhelming.

Gupta: Anthony is right but he is also stating the obvious problem – “mercy of vendors”. We believe that technology such as TraceGains Network can improve efficiency greatly in sharing documentation and risk-based data, but lack of education and rapid acceptance within the industry of new approaches hinders innovation and limits already stretched resources to take shortcuts that may not be the best course of action long-term.

Ulrich: In addition to what Marc, Anthony and Raj stated most are afraid to challenge the supplier. There is a fear of making them angry or asking for too much.

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