Tag Archives: outbreaks

Francine Shaw, Savvy Food Safety, Inc.
FST Soapbox

Foodborne Illnesses and Recalls on the Rise

By Francine L. Shaw
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Francine Shaw, Savvy Food Safety, Inc.

The last word a manufacturer wants to hear is “recall”. During 2017, recalls involved everything from salad mix contaminated with a dead bat to hash browns infused with shredded golf balls.

Not all recalls are created equal. Both the USDA and the FDA have three classifications of recalls to indicate the relative degree of health hazard presented by the product being recalled:

  • Class I: A Class I recall is the most serious classification, involving a health hazard situation in which there is a reasonable probability that eating the food will cause health problems or death.
  • Class II: A Class II recall involves a potential health hazard situation in which there is a remote probability of adverse health consequences from eating the food.
  • Class III: A Class III recall involves a situation in which eating the food will not cause adverse health consequences.

During 2017, there were 456 recalls recorded in the United States. The number one reason for those recalls was undeclared allergens.

Identify the weak links in your supply chain: Attend the Food Safety Supply Chain Conference | June 12–13, 2018 | Rockville, MD | Learn moreFoodborne illnesses continue to be widespread, as well. In 2017, we saw Robin Hood flour contaminated with E.coli, Soygo yogurt with Listeria, tomatoes, cantaloupe, and ground turkey tainted with Salmonella, and even shredded coconut was responsible for causing a Salmonella outbreak in the United States and Canada. Foodborne illness outbreaks can happen at restaurants, corporate events, private parties, schools and cruise ships—anywhere and everywhere food is served.

Recalls and foodborne illnesses are 100% preventable. Incidents occur because of human error, and all it takes is one weak link to cause serious—and potentially fatal—problems. That’s it. One weak link can cause the traumatic deaths and/or illnesses of customers, and cost your company billions of dollars, loss of sales, plummeting stocks, negative media coverage and a severely damaged reputation.

When there’s a recall or a foodborne illness, products must be destroyed, which is lost revenue for manufacturers, retailers, restaurants, etc. Finding the source of the contamination can be a massive undertaking. The manufacturer may need to close all of their plants for cleaning until the source is identified, which adds up to a tremendous financial burden, and also requires significant time and effort. Class 1 recalls can cost hundreds of millions of dollars or more, to identify the source of contamination, recall products, sanitize facilities, and keep consumers safe.

It takes years for companies to establish a solid reputation, and food recalls and foodborne illness outbreaks can obliterate a brand’s reputation overnight. Consumers lose confidence much faster than they gain it, and bad news travels fast (especially in this time of social media where news spreads instantly and widely). And on top of that, there may be litigation as a result of the recall, incident or outbreak, which will result in attorney fees and potential settlements that could be very significant. If the risk of massive expense and bankruptcy isn’t enough, for the past few years, the U.S. District of Justice has been issuing fines and prison terms to company leaders involved in foodborne illnesses outbreaks and food recalls.

The government, media and general public are holding companies (and their leadership) accountable now, so you’d think that recalls and foodborne illness incidents would be on the decline but, unfortunately, that’s not the case. And with advancements in technology, why are we still having so many issues surrounding the safety of our food?

Many media outlets report that foodborne illnesses have been rising considerably in the past few years. However, according to the CDC, a study showed that the six most common foodborne illnesses have actually declined in frequency by 25% over the last two decades. Having said that, though, the severity of foodborne illness outbreaks seems to be increasing, and the number of outbreaks connected to produce has risen, as well. Some experts believe the increases may be due to better reporting processes rather than an actual increase in the number of foodborne illnesses.

There are various theories as to why foodborne illnesses may be getting worse. Some government agencies indicate it has to do with farming policies. The CDC disagrees. More widely accepted beliefs are the increase in popularity of organic produce—grown with manure rather than chemical fertilizer—which can transfer bacteria to the produce. Additionally, there’s debate that the use of antibiotics can cause bacteria that causes foodborne illnesses to become resistant.

Recalls may occur for a variety of reasons. Products may be pushed beyond their shelf life by the manufacturer, or maybe the design and development around the product was insufficient (equipment, building, etc.). Is the manufacturing facility designed in a manner that can prevent contamination—structurally and hygienically? Maybe the production quality control checks failed. Did the manufacturer conduct an adequate food safety risk assessment prior to launching the new product? Profit margins are often thin—did financial incentives prevent the company from implementing a thorough food safety program?

Getting back to the basics of food safety would reduce recalls and foodborne illnesses significantly. Manufacturers must be certain about food safety as well as the integrity of the ingredients they use. They need to be honest with themselves and understand the risks of the ingredients, processes and finished products that they are handling.

Human error is a given. It’s the corporation’s responsibility to minimize the risk. Implement ongoing food safety education and training for all employees, explaining the proper food safety protocols and processes. Develop internal auditing systems, using innovative digital tools. Get rid of the pen and paper forms, where it’s more likely for errors to occur and for pencil whipping to happen. Digital solutions provide more effective internal auditing, meticulousness in corrective action systems including root cause analysis, allergen management, and controls relating to packing product into the correct packaging format—all fundamental to keeping foods, consumers and businesses healthy and safe.

Martin Easter, Hygiena
In the Food Lab

The New Normal: Pinpointing Unusual Sources of Food Contamination

By Martin Easter, Ph.D.
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Martin Easter, Hygiena

Shiga toxin-producing E. coli in dry flour, and then romaine lettuce. E. coli O104 in fenugreek sprout seeds. Recent announcements of foodborne illness outbreaks have begun involving unusual combinations of bacteria and foods. These out-of-the-ordinary outbreaks and recalls are a small but growing part of the 600 million documented food poisonings that occur worldwide every year according to the World Health Organization. Preventing outbreaks from these new combinations of pathogen and food demand a range of accurate tests that can quickly identify these bacteria. Over the past several years, outbreaks from unusual sources included:

  • E. coli O121 (STEC) in flour: Last summer, at least 29 cases of a E. coli O121 infection were announced in six Canadian provinces. The source arose from uncooked flour, a rare source of such infections because typically flour is baked into final products. Eight people were hospitalized, and public health officials have now included raw, uncooked flour as well as raw batter and dough as a source of this type of infection.
  • E. coli O104:H4 in fenugreek sprouts: One of Europe’s biggest recent outbreaks (affecting more than 4,000 people in Germany in 2011, and killing more than 50 worldwide) was originally thought to be caused by a hemorrhagic (EHEC) E. coli strain that from cucumbers, but was but was later found to be from an enteroaggregative E. coli (EAEC) strain in imported fenugreek seeds—the strain had acquired the genes to produce Shiga toxins.
  • Mycoplasma in New Zealand dairy cows: While not unusual in cattle, the incident reported in August marks the pathogen’s first appearance in cows in New Zealand, a country known for strict standards on agricultural hygiene. The microorganism is not harmful to people, but can drastically impact livestock herds.
  • Listeria monocytogenes in food sources: Listeria monocytogenes causes fewer but more serious incidence of food poisoning due to a higher death rate compared to Salmonella and Campylobacter. Whereas Listeria has been historically associated with dairy and ready to eat cooked meat products, recent outbreaks have been associated with fruit, and the FDA, CDC and USDA are conducting a joint investigation of outbreaks in frozen as well as in fresh produce.
  • Listeria in cantaloupe: In 2011, one of the worst foodborne illnesses recorded in the United States killed 20 and sickened 147, from Listeria monocytogenes that was found in contaminated cantaloupes from a farm in Colorado. The outbreak bloomed when normal background levels of the bacteria grew to deadly concentrations in multiple locations, from transport trucks to a produce washer that was instead designed for potatoes.

The outbreaks underscore the fundamental need to have a robust food safety program. Bacteria can colonize many different locations and the opportunity is created by a change in processing methods and/or consumer use or misuse of products. So robust risk assessment and preventative QA procedures need to be frequently reviewed and supported by appropriate surveillance methods.

Food safety and public health agencies like the European Food Safety Authority (EFSA) or the CDC have employed a wide range of detection and identification tests, ranging from pulse field gel electrophoresis (PFGE), traditional cell culture, enzyme immunoassay, and the polymerase chain reaction (PCR). In the case of Germany’s fenugreek-based E. coli outbreak, the CDC and EFSA used all these techniques to verify the source of the contamination.

These tests have certain advantages and disadvantages. Cell culture can be very accurate, but it depends on good technique and usually takes a long time to present results. PFGE provides an accurate DNA fingerprint of a target bacteria, but cannot identify all strains of certain microorganisms. Enzyme immunoassays are precise, but can produce false-positive results in certain circumstances and require microbiological laboratory expertise. PCR is very quick and accurate, but doesn’t preserve an isolate for physicians to test further for pathogenic properties.

Identification of the pathogens behind foodborne contamination is crucial for determining treatment of victims of the outbreak, and helps public health officials decide what tools are necessary to pinpoint the outbreak’s cause and prevent a recurrence. Rapid methods such as the polymerase chain reaction (PCR), which can quickly and accurately amplify DNA from a pathogen and make specific detection easier, are powerful tools in our efforts to maintain a safe food supply.

Recently, scientists and a third-party laboratory showed that real-time PCR assays for STEC and E. coli O157:H7 could detect E. coli O121, O26 and O157:H7 in 25-g samples of flour at levels satisfying AOAC method validation requirements. The results of the study demonstrated that real-time PCR could accurately detect stx, eae and the appropriate E. coli serotype (O121, O26 or O157:H7) with no statistical difference from the FDA’s Bacteriological Analytical Manual (BAM) cell culture method.

Agencies like the World Health Organization and CDC have repeatedly stated that historical records of food poisoning represent a very small percentage of true incidents occurring every year worldwide. Many of today’s most common food pathogens, like Listeria monocytogenes, E. coli O157:H7 or Campylobacter jejuni, were unknown 30 years ago. It’s not clear yet if unusual sources of contamination arise from increasing vigilance and food safety testing, or from an increasingly interdependent, globally complex food supply. No matter the reason, food producers, processors, manufacturers, distributors and retailers need to keep their guard up, using the optimum combination of tools to protect the public and fend off food pathogens.

Tim Birmingham, Almond Board of California
In the Food Lab

10 Years, 0 Salmonella Outbreaks

By Tim Birmingham
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Tim Birmingham, Almond Board of California

Almond Board of California (ABC) tackled food safety head-on in the wake of emerging Salmonella concerns in the early 2000s. Conventional wisdom of the time suggested that low-moisture foods like almonds presented a minimal threat, but rather than simply accepting this, ABC engaged in research to better understand the risks. The resulting best practices and groundbreaking mandatory pasteurization program developed by ABC remain the gold standard for other sectors—and drive continued food safety and quality efforts for California Almonds.

In 2017, ABC marked the 10-year anniversary of its mandatory almond pasteurization program – and, most importantly, 10 years free of Salmonella recalls and outbreaks attributed to California Almonds. The almond industry is proud of its unified efforts over the last decade, as well as the food safety record we’ve been able to achieve. However, the work to protect and improve food safety and quality continues. Looking back at our initiatives and successes reminds us of how important this work is and drives our exploration of what’s next.

Understanding and Addressing the Risk

Outbreaks of Salmonella in 2001 and 2004 raised questions and concerns about food safety and quality across industries. For California Almonds, one of the biggest challenges was determining the true level of risk. The easy answer seemed to be that risk should be low, that, based on accepted conventions of the time, pathogens should not be able to grow in almonds and other low-moisture foods. However, ABC investigated further and quickly realized that the pathogen could present a problem. The organization decided to take action and tackle Salmonella and other potential threats.

In collaboration with food safety experts and research partners, ABC began research in 2001 to better understand the prevalence and concentration of contamination in almonds, conducted in tandem with efforts to develop strategies for contamination control. ABC was able to gather enough survey data over the course of several years to show that Salmonella was indeed present in about 1% of the almonds tested at very low concentrations. This data was fed into ABC’s risk assessment work, which enabled identification of appropriate performance criteria for ensuring consumer safety (>4-log reduction).

At the same time, ABC also worked to identify effective processing technologies and the best means of validating them. A technical expert review panel was assembled to help ABC develop a plan, assess research needs, establish standards and create guidelines for the industry. Extensive work went into determining how to validate equipment, including the determination of an appropriate surrogate (non-pathogenic microorganisms) that could be used in lieu of Salmonella in the plant. Concurrently, researchers worked to determine the specific time and temperature combinations needed for a >4-log (and 5-log) reduction for a range of pasteurization processes, including oil roasting, blanching and dry roasting, some steam processes and PPO processing. ABC and partners invested significant time and effort into this research, which culminated in the development of the groundbreaking mandatory pasteurization program for Salmonella reduction, and validation guidelines.

Process Implementation and Ongoing Education

Voluntary compliance with the pasteurization program began in 2004, well in advance of September 2007, when it became mandatory. By that time, pasteurization was established as the industry norm and laying the groundwork for ongoing food quality and safety efforts. Today, ABC has more than 1 billion pounds of validated pasteurization capacity for processes that maintain the raw characteristics of almonds, including steam, moist heat and propylene oxide (PPO). It also has close to 1 billion pounds of validated capacity for processes such as dry roasting, oil roasting and blanching. All reduce the level of potential contamination in almonds without diminishing the product’s quality, nutritional value or sensory qualities (taste and crunch).

ABC also developed a comprehensive round of updates to recommended food safety practices, creating a powerful program with tools that help growers and processors achieve their desired results. These tools include Good Agricultural Practices, Good Manufacturing Practices, HACCP guidelines and Pathogen Environmental Monitoring resources.

In total, ABC has made a $5 million investment in food quality and safety research and validated more than 200 treatment processes, to date. It remains committed to this mission, maintaining close connections with the scientific and regulatory communities to stay current on food safety in the broader context as well as issues specific to California Almonds. All relevant insights and information are disseminated to growers and processors in the form of clear, practical resources, including print publications and digital communications, and workshops and one-on-one field trainings.

What’s Next: Research, Tech and Regulatory Practices

The mandatory pasteurization program is now well established, but it isn’t static – ABC continues to stay on top of the latest methods, regulations and needs impacting California Almonds. Industry investment continues to increase, particularly in processes that maintain the raw characteristics of the product. And, while much information regarding processes and technologies are company-specific and confidential, equipment manufacturers continue evolving and growing their offerings, with a particular focus on maximizing almond quality and throughput.

On the regulatory side, FSMA continues to roll out for growers and processors. ABC helps growers and other stakeholders understand which rules apply, what actions to take to ensure compliance and when specific requirements come into effect for different operations, with FSMA-related resources, Preventative Controls and Produce Safety trainings and timely information available online. Many processors and non-farm huller/shellers started 2018 already meeting FSMA Preventive Control requirements, but the number of impacted orchards and huller/shellers expanded in January as the Produce Safety rule came into effect. At this point, the almond industry and the larger community of food and beverage industries have had time to assess the impact on their stakeholders and take action to ensure FSMA compliance.

FSMA reflects the evolving role of FDA in ensuring food safety. Traditionally, FDA has taken a reactive approach to food safety. The agency now has the authority to investigate farms and facilities regularly to ensure food safety regulations are followed. For the first time, growers and huller/shellers falling under the farm definition may be audited by FDA or FDA-designated agencies. While some growers may choose the exemption option, ABC encourages almond growers to understand the rule’s requirements and develop food safety plans appropriate to their farms. It will be new and uncertain territory for some, but with the FDA’s proactive approach, staying ahead of the curve on food safety and quality will be beneficial.

Currently, almonds are the only tree nut with a mandatory pasteurization program and defined performance criteria accepted by FDA. They have paved the way for validation of other tree nuts, and those industries should also consider implementing appropriate preventive controls for Salmonella. ABC’s work can be considered a road map for other nuts and low-moisture foods, but what works for almonds will not always work for other foods. Research specific to each type of nut needs to be conducted to uncover pathogen prevalence and concentration, as well as pathogen/surrogate resistance to various processes. We will continue to be proactive, as well, evaluating current practices and engaging in research to improve how we understand and control microbial contamination in almonds.

Even with a track record to take pride in, the responsibility and work of food quality and safety never end. We will continue to update and evolve programs, not only as a function of compliance, but to protect the almond customers who support us every day.

Listeria

Four Pathogens Cause Nearly 2 Million Foodborne Illness Cases a Year

By Food Safety Tech Staff
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Listeria

The CDC estimates that Salmonella, E. coli O157, Listeria monocytogenes and Campylobacter cause 1.9 million cases of foodborne illness in the United States. A report just released from the Interagency Food Safety Analytics Collaboration (IFSAC) analyzed data from more than 1000 foodborne disease outbreaks involving these pathogens from1998 through 2013.

The report found the following:

  • Salmonella illnesses came from a wide variety of foods (more than 75% came from the seven food categories of seeded vegetables, eggs, chicken, other produce, pork, beef and fruit.
  • More than 75% of E.coli O157 illnesses were linked to vegetable row crops, like leaf greens, and beef.
  • More than 75% of Listeria monocytogenes illnesses came from fruits and dairy products.
  • More than 80% of non-dairy Campylobacter illnesses were linked to chicken, other seafood (i.e., shellfish), seeded vegetables, vegetable row crops, and other meat and poultry (i.e., lamb or duck).

A copy of the report, “Foodborne illness source attribution estimates for 2013 for Salmonella, Escherichia coli O157, Listeria monocytogenes, and Campylobacter using multi-year outbreak surveillance data, United States”, is available on the CDC’s website.

Cara Pahoyo

5 Burning Questions About The Rise In Foodborne Illness

By Cara Pahoyo
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Cara Pahoyo

The food industry has been one of the most celebrated and fastest-growing industries over the last decade or so. Which is no surprise, considering how much food is now being consumed, or posted on Instagram, on a daily basis. Pop-up food carts and hole-in-the-wall food places have been a huge hit too and even inspired a number of Hollywood films about the tough competition and revolutionary marketing tactics that have taken over the food industry (see: Jon Favreau’s Chef and Bradley Cooper’s Burnt). It’s good times, for sure. Well, for the most part, I mean.

When did foodborne illness become a major concern in the US?

Unfortunately, it’s not just the revenue that’s on the rise, because food borne illnesses too are making the headlines as of late. Talk about spoiling (no pun intended) the fun, eh? Well, according to the US Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, the number of foodborne disease outbreaks resulting from imported foods increased during surveillance years 2005 to 2010.

Where are the numbers coming from?

Dr. L. Hannah Gould, Ph.D., a senior epidemiologist at the CDC, revealed those findings during an oral presentation here at the International Conference on Emerging Infectious Diseases in 2012. According to the CDC, 39 foodborne disease outbreaks were reported in which the implicated food had been imported into the United States. These outbreaks resulted in 2348 illnesses, 434 hospitalizations and 3 deaths.

How many are affected?

Though foodborne illnesses are often never formally reported, about 48 million Americans, or one in six, get sick each year from food, the CDC estimates, with 128,000 hospitalizations and 3,000 deaths. In fact, in 2014, 19,542 cases of infection were traced from 15% of the US population being surveyed by CDC.

Why is it on the rise?

The culprits? Chances are, you’ve been storing them somewhere inside your establishment: packaged caramel-coated apples, frozen ice cream sandwiches, fresh peaches and nectarines, frozen meet, etc. Not exactly the answers you were expecting, perhaps?

According to experts, the growing popularity of packaged foods such as pre-cut fruit and prepared sandwiches has heightened the risk of spreading foodborne illnesses. Furthermore, they have identified that contamination can occur between preparation and packaging, or in high-tech processing plants, after heating to destroy harmful bacteria and before packaging. Which means, somewhere in the last decade, we lost our way (or something like that).

What can we do to stop foodborne disease from spreading?

The whole fiasco regarding foodborne illness is a public safety concern and must be addressed by everyone. However, while adjusting individually may not be a problem for most of us, the same cannot be said for food places and restaurants. Just imagine the public relations horror for restaurant managers if any of their customers get sick while dining at their place?

Restaurants must be more strict and thorough when addressing food safety concerns. The entire crew must be trained when it comes to food handling and a food safety manager must also take charge in overseeing procedures in the kitchen. In fact, proper storage and disposal must also be adequately done at all times. With those safety measures in play, establishments will be able to showcase their commitment to adhere with local food standards and basic food handling procedures. That’s a step in the right direction, for sure.

Summing up, foodborne illness is definitely a manageable concern and will likely not become a factor that will hinder the overall growth of the food industry. However, the fact that it can be controlled and yet still recurring means that there’s still a fair amount of work needed to be done to improve the industry in other aspects—and that isn’t necessarily a bad thing (at least not yet).

Deirdre Schlunegger, CEO of STOP Foodborne Illness
Food Safety Culture Club

Telling the Story of Foodborne Illness

By Deirdre Schlunegger
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Deirdre Schlunegger, CEO of STOP Foodborne Illness

If you are looking for someone who has been ill or has had family members who were ill or died from a foodborne illness to come and speak at your food safety training, give Stanley Rutledge or myself a call, or send us an email. Individuals want to tell their stories, they want to make a difference, and they want to have an impact.   The stories are powerful and their stories are “the why” behind food safety. People who have attended the trainings tell us they never forget the people they meet and the stories told—they think about them everyday in their work and especially when making decisions that impact food and public safety.

Tauxe, STOP Foodborne Illness
Deirdre Schlunegger of STOP Foodborne Illness presents the Advancing Science for Food Safety Award to Robert Tauxe, M.D., MPH, deputy director of the CDC’s Division of Foodborne, Waterborne and Environmental Diseases at the National Center for Emerging and Zoonotic Infectious Diseases.

In the fall, I was on a phone call with a man from Smithfield Foods. We, along with a few others from the company, were planning an upcoming training and speaking engagement. He said that he would never forget listening to Nancy Donley talk about her son, Alex. Dr. Robert Tauxe told me a similar story about hearing Nancy in a public forum talk about her son. Rylee Gustafson, recently through STOP Foodborne Illness, spoke at The Partnership for Food Safety Education and told her story. Now a college student, she spoke about the long-term impacts of her illness—the diabetes, the damaged pancreas, the voice and vision problems, and the high blood pressure. The room was silent and so many people came up to her afterwards to thank her for sharing.

These stories illustrate that this is real: It does happen and when the person who was involved is standing before you reliving their story, you Will remember! Of course, we have fact sheets and a lot of other information on our website for your use, but there is nothing that is more direct, thought provoking and memorable than listening. If you want to read some of the stories, visit our website.  You can contact Stanley at srutledge@stopfoodborneillness.org or me at dschlunegger@stopfoodborneillness.org

Thanks for all that you do for food safety!

Pursuit of Clarity for WGS in Food Production Environments

By Joseph Heinzelmann
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Anyone who has attended a food safety conference in the last few years has experienced some type of whole genome sequencing (WGS) presentation. WGS is the next big thing for food safety. The technology has been adopted by regulatory agencies, academics, and some food companies. A lot has been said, but there are still some questions regarding the implementation and ramifications of WGS in the food processing environment.

There are a few key acronyms to understand the aspects of genomics in food safety (See Table I below).

PFGE Pulse Field Gel Electrophoresis Technique using restriction enzymes and DNA fragment separation via an electronic field for creation of a bacterial isolate DNA fingerprint; PFGE is being replaced by WGS at CDC and other public health laboratories
WGS Whole Genome Sequencing The general term used for sequencing—a misnomer—the entirety of the genome is not used, and depends on the analytical methodology implemented
NGS Next Generation Sequencing NGS is the next set of technology to do WGS and other genomic applications
SNP Single Nucleotide Polymorphisms A variation in a single nucleotide that occurs in specific position of an organism’s genome; Used in WGS as a methodology for determining genetic sameness between organisms
MLST Multilocus sequence typing A methodology for determining genetic sameness between organisms; Compares internal fragment DNA sequences from multiple housekeeping genes
16S 16s RNA sequencing A highly conserved region of the bacterial genome used for species and strain identification

Joseph Heinzelmann will be presenting: Listeria Testing Platforms: Old School Technology vs New Innovative Technology during the 2016 Food Safety Consortium | LEARN MOREIn 1996, the CDC established the PulseNet program for investigating potential foodborne illness outbreaks.  PulseNet has relied on using bacterial DNA fingerprints generated via PFGE as comparisons for mapping potential sources and spread of the outbreaks.  Due to a number of advantages over PFGE, WGS is quickly becoming the preferred method for organism identification and comparison. Moving to WGS has two critical improvements over PFGE: accuracy and relatedness interpretation. Like PFGE there are nuances when defining the difference between two very closely related organisms. However, instead of defining restriction enzymes and comparing the number of bands, the language changes to either single nucleotide polymorphisms (SNP) or the number of alleles. The other important aspect WGS improves is the ability to determine and interpret the relatedness of organisms more broadly. The frequent Listeria outbreaks and incidence from 1983-2015 provide an insight to what the future might hold with WGS implementation.1 The incidence report shows the increased ability to quickly and more accurately define relatedness between clinical cases creates a link of potential cases much faster.

WGS also provides key practical changes for outbreaks and recalls in the food industry. Sequencing provides a much faster response time and therefore means the outbreaks of foodborne illness decrease, as does the number of cases in each outbreak. As the resolution of the outbreaks increases, the number of outbreaks identified increases. The actual number of outbreaks has likely not increased, but the reported number of outbreaks will increase due increased resolution of the analytical method.

wgs_listeria
Figure 1: (Permission for use of slide from Patricia M. Griffin, M.D. – Center for Disease Control and Prevention)

WGS continues to establish itself as the go-to technology for the food safety agencies. For example, the USDA food safety inspection service recently published the FY2017–2021 goals. The first bullet point under modernizing inspection systems, policies and the use of scientific approaches is the implementation of in-field screening and whole genome sequencing for outbreak expediency.

Agencies and Adoption

The success of FDA and CDC Listeria project provides a foundation for implementation of WGS for outbreak investigations. The three agencies adopting WGS for outbreak investigations and as replacement for PulseNet are the CDC, FDA and USDA. However, there are still questions on the part of the FDA for when WGS is utilized, including under what circumstances and instances the data will be used.

In recent public forums, the FDA has acknowledged that there are situations when a recall would be a potential solution based on WGS results in the absence of any clinical cases.2 One critical question that still exists in spite of the public presentations and published articles is a clear definitions of when WGS surveillance data will be used for recall purposes, and what type of supporting documentation a facility would need to provide to prove that it had adequate controls in place.

A key element is the definition between agencies for sameness or genetic distance. The FDA and FSIS are using a SNP approach. A sequence is generated from a bacterial isolate, then compared with a known clinical case, or a suspected strain, and the number of different SNPs determines if the strains are identical. The CDC is using the Multilocus sequence typing (MLST) approach.

Simple sequence comparisons are unfortunately not alone sufficient for sameness determination, as various metabolic, taxa specific and environmental parameters must also be considered.  Stressful environments and growth rates have significant impact on how quickly SNPs can occur. The three primary pathogens being examined by WGS have very different genetic makeups. Listeria monocytogenes has a relatively conserved genomic taxa, typically associated with cooler environments, and is gram positive. Listeria monocytogenes has a doubling time of 45–60 minutes under enrichment conditions.3 These are contrasted with E. coli O157:H7, a gram negative bacteria, associated with higher growth rates and higher horizontal gene transfer mechanisms. For example, in an examination of E. coli O104, and in research conducted by the University in Madurai, it showed 38 horizontal gene elements.4

These two contrasting examples demonstrate the complexity of the genetic distance question. It demonstrates a need for specific definitions for sameness within a microbiological taxa, and with potential qualifiers based on the environment and potential genetic event triggers. The definitions around SNPs and alleles that define how closely related a Listeria monocytogenes in a cold facility should be vastly different from an E. coli from a warm environment, under more suitable growth conditions. Another element of interest, but largely unexplored is convergent evolution. In a given environment, with similar conditions, what is the probability of two different organisms converging on a nearly identical genome, and how long would it take?

MLST vs. SNP

As previously stated, the three agencies have chosen different approaches for the analytical methodology: MLST for CDC and SNP of the FDA and USDA. For clarity, both analytical approaches have demonstrated superiority over the incumbent PFGE mythology. MLST does rely on an existing database for allele comparison. A SNP based approach is supported by a database, but is often used in defining genetic distance specifically between two isolates. Both approaches can help build phylogenetic trees.

There are tradeoffs with both approaches. There is a higher requirement for processing and bioinformatics capabilities when using a SNP based approach. However, the resolution between organisms and large groups of organisms is meaningful using SNP comparison. The key take away is MLST uses a gene-to-gene comparison, and the SNP approach is gene agnostic. As mentioned in Table 1, both approaches do not use every A, T, C, and G in the analytical comparisons. Whole genome sequencing in this context is a misnomer, because not every gene is used in either analysis.

Commercial Applications

Utilizing WGS for companies as a preventive measure is still being developed. GenomeTrakr has been established as the data repository for sequenced isolates from the FDA, USDA, CDC and public health labs. The data is housed at the National Center for Biotechnology Information (NCBI).  The database contains more than 71,000 isolates and has been used in surveillance and outbreak investigations. There is a current gap between on premise bioinformatics and using GenomeTrakr.

The FDA has stated there are examples where isolates found in a processing facility would help support a recall in the absence of epidemiological evidence, and companies are waiting on clarification before adopting GenomeTrakr as a routine analysis tool. However, services like NeoSeek, a genomic test service by Neogen Corp. are an alternative to public gene databases like GenomeTrakr. In addition to trouble shooting events with WGS, NeoSeek provides services such as spoilage microorganism ID and source tracking, pathogen point source tracking. Using next generation sequencing, a private database, and applications such as 16s metagenomic analysis, phylogenetic tree generation, and identification programs with NeoSeek, companies can answer critical food safety and food quality questions.

References

  1. Carleton, H.A. and Gerner-Smidt, P. (2016). Whole-Genome Sequencing Is Taking over Foodborne Disease Surveillance. Microbe. Retrieved from https://www.cdc.gov/pulsenet/pdf/wgs-in-public-health-carleton-microbe-2016.pdf.
  2. Institute for Food Safety and Health. IFSH Whole Genome Sequencing for Food Safety Symposium. September 28­–30, 2016. Retrieved from https://www.ifsh.iit.edu/sites/ifsh/files/departments/ifsh/pdfs/wgs_symposium_agenda_071416.pdf.
  3. Jones, G.S. and D’Orazio, S.E.F. (2013). Listeria monocytogenes: Cultivation and Laboratory Maintenance. Curr Proto Microbiol. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920655/.
  4. Inderscience Publishers. “Horizontal gene transfer in E. coli.” ScienceDaily, 19 May 2015.
  5. Gerner-Smidt, P. (2016). Public Health Food Safety Applications for Whole Genome Sequencing. 4th Asia-Pacific International Food Safety Conference. Retrieved from http://ilsisea-region.org/wp-content/uploads/sites/21/2016/10/Session-2_2-Peter-Gerner-Smidt.pdf.

New Whole Genome Sequencing Test Monitors Threat of Pathogens

By Maria Fontanazza
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Today food companies will have access to a new whole genome sequencing (WGS) test that could help them prevent dangerous pathogens from getting into their products. Released by Clear Labs, the test takes a detailed approach to identifying pathogen strains in samples, providing information about their geography and from which food groups they originate.

In an exclusive interview with Food Safety Tech, Mahni Ghorashi, co-founder of Clear Labs, explains how he expects the company’s new test, which has a five- to seven-day turnaround time, will offer companies with a more accurate yet less expensive alternative to protecting consumers by actively monitoring their supply chain for emerging pathogens.

Food Safety Tech: What differentiates this WGS test from current available solutions?

Mahni Ghorashi: No one has been able to provide the food industry with modern whole genome sequencing techniques for food safety. What we’re releasing is a quantum leap in terms of what’s been available on the market today. Whole genome sequencing has been largely siloed to regulatory bodies like FDA and CDC to trace outbreaks and inform investigations—the technologies and techniques that they’re using are actually fairly old; they’re some of the original WGS techniques that emerged on the next-gen sequencing platform. We’ve taken the most advanced techniques on the NGS platform for human disease exploration and personalized medicine and adapted them for food industry.

What gives our WGS test a competitive advantage over legacy-based methods is two fold:

1. Clear Labs has a 2-million+ entry-curated database of genomic information and sequences for the accurate ID of food ingredients (pathogenic organisms and microbiomes). Its accuracy and the confidence level that comes behind our matching is a huge step above anything that’s available in the public domain today.

2. Being able to place pathogenic strain information in the context of overall food ingredients and samples. The whole genome sequencing test we developed has been specifically catered for the food industry, and for food samples in particular, [versus] FDA’s GenomeTrakr, CDC’s PulseNet, or other food safety labs that are offering full genomic sequencing of pathogen strains—they’re using some of the earliest methods to do this. On the NGS platform, we’re able to put those strains in the context of food ingredients and suppliers: Specifically, [matching] bacterial strains with food ingredients [and] suppliers.

Clear Labs, whole genome sequencing

FST: Does this test target specific foods?

Ghorashi: Our platform particularly shines in complex foods. The value of next-gen sequencing and DNA barcoding over PCR-based technologies, which is the gold standard in food safety, is its stability to break down complex food ingredients into all of their known parts, and to look in a universal and unbiased way into food samples. It’s untargeted, so you don’t have know what it is that you’re looking for—and that’s the real power.

FST: What impact do you anticipate for this test, especially in the context of FSMA?

Ghorashi: Our customers are using [the test] for monitoring ingredient supplies and the effectiveness of preventive and sanitary controls [and] to match specific pathogen strains to specific food ingredients. They are using it for proactive testing for FSMA compliance—there’s a lot of movement in this direction and hefty budgets are being allocated to put new preventive controls in place in response to FSMA; whole-genome sequencing will play a big role, and we anticipate large-scale partnerships with agencies and private industry on that front. And the most obvious use case is that it’s being used for techniques to mitigate or reduce the risk of product recall and outbreak.

We’ve been able to significantly reduce the price point on whole-genome sequencing, and all of our tests across the board, because we’re intimately familiar with how the inner workings of these platforms and how to best optimize them for scale and cost efficiency. We think the test will be more accurate and leaps and bounds ahead of what’s available, as well as cost competitive. We’re excited about the work we’re doing and its impact on food safety. I don’t think the food industry—retailers and manufacturers—have ever had access to these kind of tools and they’re being made available just in time for FSMA, as the industry moves towards a more proactive approach to food safety and [takes] preventive measures in their supply chains.  Hopefully we’ll soon be living in a world where outbreaks, illness and the financial toll are a thing of a past.

Clear Labs also just released a microbiome test that helps companies associate microbiomes with specific food ingredients.

Mahni Ghorashi: The microbiome test we’ve developed is able to sequence samples from the human gut and from food, and look at how the microorganisms are interacting. Our customers for this test have been large brands that have advanced R&D departments and academic research centers that are looking for how diet research and the microbiome interact together and how new product development can help us move toward personalized diets when it comes to prebiotic and probiotic diets.”

The impact of the microbiome and the correlations between bacteria of the human gut and the bacteria in the food we eat. The prevailing thesis at the moment is that the microbiome has a significant impact on our health when it comes to disease risk and diet, inflammation and mood disorders. We’re seeing very forward thinking brands like Nestle, ConAgra and Mars putting a lot of attention on the impact of the microbiome when it comes the development of new products, [such as] prebiotics and probiotics, or even specific food products as it pertains to the microbiome. We believe that this intersection— nutrigenomics and the personalized diet—is going to be a massive market, and we’re at the early stages of that.

Pathogen

IBM Research Uses Data to Accelerate Source of Contamination During Outbreaks

By Food Safety Tech Staff
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Pathogen

Using electronic retail scanner data from grocery stores, IBM Research scientists may have found a faster way to narrow down the potential source food contamination during an outbreak. Researchers from the firm conducted a study in which they were able to show that, using just 10 medical exam reports of foodborne illness, it is possible to pinpoint an investigation to 12 food products of interest in a only a few hours. A typically investigation ranges from weeks to months.

The study, “From Farm to Fork: How Spatial-Temporal Data can Accelerate Foodborne Illness Investigation in a Global Food Supply Chain”, demonstrated a new way to accelerate an outbreak investigation. Researchers reviewed the spatio-temporal data (i.e., geographic location and potential time of consumption) of hundreds of grocery products, and analyzed each product for shelf life, consumption location and the probability that the product harbored a pathogen. This information was then mapped to the known location of outbreaks.

“When there’s an outbreak of foodborne illness, the biggest challenge facing public health officials is the speed at which they can identify the contaminated food source and alert the public,” said Kun Hu, public health research scientist, IBM Research – Almaden in a press release. Rsearchers created a system to devise a list that ranked products based on likelihood of contamination, which would allow health officials to test the top 12 suspected foods. “While traditional methods like interviews and surveys are still necessary, analyzing big data from retail grocery scanners can significantly narrow down the list of contaminants in hours for further lab testing. Our study shows that big data and analytics can profoundly reduce investigation time and human error and have a huge impact on public health,” said Hu.

The researchers point of out their method isn’t a substitute for proven outbreak investigation tools but rather serves as a faster way to identify contaminated product(s). According to the study, researchers assert that their methodology could significantly reduce the costs associated with foodborne illness, outbreaks and recalls. Thus far IBM Research’s approach has been applied to a Norweigan E. coli outbreak in which there were 17 confirmed cases of infection. Public health officials used the method to devise a list of 10 potential contaminants from the grocery scanner data of more than 2600 products. From there, lab analysis traced the contamination source to batch and lot numbers of sausage.

The study was published in the Association for Computing Machinery’s Sigspatial Journal.

FDA, CDC

Study Makes Connection Between Outbreak Data and Foodborne Illnesses

By Food Safety Tech Staff
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FDA, CDC

Outbreak illnesses and sporadic illnesses have similar traits. In addition, outbreak data can be used to assess the foods that are most frequently connected to particular foodborne illnesses. This analysis, all according to a recent study by the Interagency Food Safety Analytics Collaboration (IFSAC), could aid in improving the progression of science as well as provide a better understanding of the role of sporadic foodborne illnesses and their relation to an outbreak.

Scientists from IFSAC published the paper, “Comparing Characteristics of Sporadic and Outbreak-Associated Foodborne Illnesses, United States, 2004-2011”, in a July 2016 issue of Emerging Infectious Diseases. They collected data from the CDC’s Foodborne Diseases Active Surveillance Network (FoodNet) and compared outbreak illnesses with sporadic illnesses.

Available on the CDC’s website, key findings of IFSAC’s analysis include:

  • Campylobacter, Listeria monocytogenes, and E. coli O157 outbreak illnesses are not significantly different from sporadic illnesses with respect to patients’ illness severity, gender, and age.
  • Salmonella outbreak illnesses are not significantly different from sporadic illnesses with respect to illness severity and gender. For age, the percentages of outbreak and sporadic illnesses that occur among older children and adults are also similar. The percentage of outbreak illnesses in the youngest age category (0-3 years) was significantly lower compared to other age groups.