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

How Do We Incentivize Behavior Change?

By Deirdre Schlunegger
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Deirdre Schlunegger, CEO of STOP Foodborne Illness

In March, I presented and participated in a session regarding produce safety at The Global Food Safety Conference in Houston. In April, I was the keynote speaker at the BRC conference in Orlando, Florida. I asked: What incentivizes the human spirit and how do we draw on people’s creativity and their ability to have empathy and to solve problems?  Which interventions are more or less likely to stimulate one’s ability to care about food safety as it relates to human beings? Knowledge alone seldom changes behavior. The imagination benefits from stimulation—for example, listening to personal stories. For change to happen, there must be an emotional connection to the idea of achievable outcomes.

This past year we spoke at a large food company. During a pre-call to discuss what the presentation might look like, one man said that nearly 20 years ago, he heard Nancy Donley speak about her son Alex, who died at the age of six from a foodborne illness. He said since that time, he has never looked at food safety the same way, and he takes every single infraction dealing with food safety as a possible consequence for someone’s life. A rational understanding of what a better outcome might look like will often involve a deeper understanding and a connection with an issue and with the individuals related to that issue. Change is difficult. We often don’t learn until we risk collapse or fail. In a moment of crisis, we are presented with a unique opportunity for change. This idea could stand to be finely calibrated, as there are moments that are too painful to activate learning as one struggles with a deep sense of hopelessness, and there are moments when change lies outside the realm of possibilities. An analytic perspective without access to emotional content is unlikely to provide the conditions for change, but a link between the head and the heart may initiate transformation.

I met Will Daniels, formerly of Earthbound Farms after an emotional presentation he made at a conference. He spoke about a young boy who died from the spinach outbreak and he referred to his children of nearly the same age. He also presented the sequence of events that led to and followed the outbreak in a very factual and logical way. This link between his head and his heart delivered a presentation that was impactful, emotional, factual and sincere. A cold analysis of a problem is seldom sufficient, nor is the condition of people when they are stuck in an overwhelming emotional state. The challenge is to find middle ground and put together thinking and feeling in a context where a coherent narrative will be created. For individuals to change their behavior, we must influence not only their environment, but their hearts and their minds. What we do know about change and people’s readiness to change is that it has much to do with timing and ripeness. The crucial question is whether issues are close enough to the surface to break into the public discourse or to have an impact on a system. As a protective mechanism, people resist the pain of engagement and hold onto old assumptions, often adopting a deluded narrative. People may find that blaming others, scapegoating, externalizing the other party, denying the problem, jumping to conclusions, or launching a distracting issue might restore stability and feel less stressful than facing and taking responsibility for a complex challenge.

We often see change in companies and their policies after they have experienced an outbreak, not before. Over the years we have seen this with several companies whose confidence was high prior to an outbreak, as they had never had a problem before and felt as if they were immune. The challenge is to allow for conditions in that there is sufficient pressure to change but there is also a safety net in place. There is a real tension between the pressure to change and the conditions that allow for necessary creativity, flexibility and imagination to get us through a crisis.   Businesses that are transparent in their admittance to a problem often are better able to create change in a safe environment. In other words, “yes, we have a problem and what are we going to do to change course?” Crisis isn’t necessary but in reality, catastrophic events often precede modifications in policy and practice. Creating a head/heart connection during planning and training may deliver a sense of urgency to help individuals remember “the why” behind food safety.

Until we prepare for a future with a sense of urgency and commitment and fully integrate “the why behind food safety”, we will merely repeat errors of the past. It takes courage and true leadership to carry out a vision, a future that doesn’t deny or divorce itself from the past but uses it in such a way that opens the door to progress. We have improved our narratives and are better at risk analysis and detection, and I believe we will continue to improve.

Nur Hasan, CosmosID
Food Genomics

Metagenomes and Their Utility

By Gregory Siragusa, Douglas Marshall, Ph.D., Nur A. Hasan
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Nur Hasan, CosmosID

Recall that in article one of this series we wrote that there are two main techniques to obtain a microbiome, a targeted (e.g., bacteria or fungi) or a metagenome (in which all DNA in a sample is sequenced, not just specific targets like bacteria or fungi).  In this column we will now explore metagenomes and some applications to food safety and quality.

We have invited Dr. Nur Hasan of CosmosID, Inc., an expert in the field of microbial metagenomics, to share his deep knowledge of metagenomics. Our format will be an interview style.

Safe food production and preservation is a balancing act between food enzymes and microbes. We will start with some general questions about the microbial world, and then proceed deeper into why and how tools such as metagenomics are advancing our ability to explore this universe. Finally, we will ask Dr. Hasan how he sees all of this applying to food microbiology and safe food production.

Greg Siragusa/Doug Marshall: Thank you for joining us. Dr. Hasan, please give us a brief statement of your background and current position.

Nur Hasan: Thanks for having me. I am a molecular biologist by training. I did my bachelor and masters in microbiology, M.B.A in marketing, and Ph.D. in molecular biology. My current position is vice president and head of research and development at CosmosID, Inc., where I am leading the effort on developing the world’s largest curated genome databases and ultra rapid bioinformatics tools to build the most comprehensive, actionable and user-friendly metagenomic analysis platform for both pathogen detection and microbiome characterization.

Siragusa/Marshall: The slogan for CosmosID is “Exploring the Universe of Microbes”. What is your estimate of the numbers of bacterial genera and species that have not yet been cultured in the lab?

Hasan: Estimating the number of uncultured bacteria on earth is an ongoing challenge in biology. The widely accepted notion is more than 99% of bacteria from environmental samples remain ‘unculturable’ in the laboratory; however, with improvements in media design, adjustment of nutrient compositions and optimization of growth conditions based on the ecosystem these bacteria are naturally inhabiting, scientists are now able to grow more bacteria in the lab than we anticipated. Yet, our understanding is very scant on culturable species diversity across diverse ecosystems on earth. With more investigators using metagenomics tools, many ecosystems are being repeatedly sampled, with ever more microbial diversity revealed. Other ecosystems remain ignored, so we only have a skewed understanding of species diversity and what portion of such diversity is actually culturable. A report from Schloss & Handelsman highlighted the limitations of sampling and the fact that it is not possible to estimate the total number of bacterial species on Earth.1 Despite the limitation, they took a stab at the question and predicted minimum bacterial species richness to be 35,498. A more recent report by Hugenholtz estimated that there are currently 61 distinct bacterial phyla, of which 31 have no cultivable representatives.2 Currently NCBI has about 16,757 bacterial species listed, which represent less than 50% of minimum species richness as predicted by Schloss & Handelsman and only a fraction of all global species richness of about 107 to 109 estimated by Curtis and Dykhuizen.3,4

Siragusa/Marshall: In generic terms what exactly is a metagenome? Also, please explain the meaning of the terms “shotgun sequencing”, “shotgun metagenomes”, and “metagenomes”.  How are they equivalent, similar or different?

Hasan: Metagenome is actually an umbrella term. It refers to the collection of genetic content of all organisms present in a given sample. It is studied by a method called metagenomics that involves direct sequencing of a heterogeneous population of DNA molecules from a biological sample all at once. Although in most applications, metagenome is often used to refer to microbial metagenome (the genes and genomes of microbial communities of given sample), in a broader sense, it actually represents total genetic makeup of a sample including genomes and gene sequences of other materials in the sample, such as nucleic acids contributed by other food ingredients of plant and animal origin. The metagenome provides an in-depth understanding of the composition, structure, functional and metabolic activities of food, agricultural and human communities.

Shotgun sequencing is a method where long strands of DNA (such as an entire genome of a bacterium) are randomly shredded (“shotgunning”) into smaller DNA fragments, so that they can be sequenced individually. Once sequenced, these small fragments are then assembled together into contigs by computer programs that find overlaps in the genetic code, and the complete sequence of the bacterial genome is generated. Now, instead of one genome, if you directly sequence entire assemblage of genomes from a metagenome using such shotgun approach, it’s called shotgun metagenomics and resulting output is termed a shotgun metagenome. By this method, you are literally sequencing thousands of genomes simultaneously from a given metagenome in one assay and get the opportunity to reconstruct individual genomes or genome fragments for investigation and comparison of the genetic consortia and taxonomic composition of complete communities and their predicted functions. Whereas targeted 16S rRNA or targeted 16S amplicon sequencing relies on amplification and sequencing of one target region, the 16S gene region, shotgun metagenomics is actually target free, it is aimed at sequencing entire genomes of every organism present in a sample and gives a more accurate, and unbiased biological representation of a sample. As an analogy of shotgun metagenomics, lets think about your library where you may have multiple books (like as different organisms present in a metagenome). You can imagine shotgun metagenomics as a process whereby all books from your library are shredded, mixed up, and then you will assemble the small shredded pieces to find text overlap and piecing the cover of all books together to reassemble each of your favorite books. Shotgun metagenomics approximates this analogy.

Metagenome and metagenomics are often used interchangeably. Where metagenome is the total collection of all genetic material from a given samples, metagenomics is the method to obtain a metagenome that utilizes a shotgun sequencing approach to sequence all these genetic material at once.

Shotgun sequencing and shotgun metagenomics are also used interchangeably. Shotgun sequencing is a technique where you fragment large DNA strands into small pieces and sequence all small fragments. Now, if you apply such techniques to sequence a metagenome, than we call it shotgun metagenomics.

Go to page 2 of the interview below.

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Zia Siddiqi, Orkin
Bug Bytes

Stored Product Pests May Be Lurking in Your Facility

By Zia Siddiqi, Ph.D.
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Zia Siddiqi, Orkin

Pests can be sneaky. Many can compromise food products without anyone realizing they’re present. This is bad news for food processing facilities where an abundance of food products can translate into high pest pressure.

Beetles and moths are two of the main offenders in this environment and are referred to as stored product pests. These creatures can cause safety and legal concerns if they find their way into products, as they are quite adept at doing. They can damage packaging and cause product contamination or alter the taste of products when they secrete chemicals from their bodies, as many do.

This is not only a concern for your business’s reputation and bottom line, but could cost you major points on your next audit. Especially under the new FSMA regulations, prevention must be the emphasis in all U.S. facilities. This represents a shift from previous regulations as the new ones require risk-based preventive controls.

Integrate pest management
Does your company have an integrated pest management plan? Image courtesy of Orkin

The best way to prevent stored product pests and adhere to FSMA regulations is by implementing an integrated pest management (IPM) program. IPM programs focus on proactively preventing pests by inspection, monitoring and eliminating conditions that attract or harbor them using tactics like exclusion and sanitation, using chemicals only as a last resort. Under FSMA, you need to identify potential roadblocks and actively work to remove them. Showing constant improvement over time is an absolute must.

These programs also call for comprehensive documentation to monitor pest issues and ensure improvements are made over time. Auditors love to see documentation, as it shows that you are consciously working to strengthen your pest management efforts with continual improvement. If your facility doesn’t have an IPM program, it’s time to make a change sooner rather than later.

To successfully prevent stored product pests, you need to understand what they are and why they are attracted to your facility.

Types of Stored Product Pests

There are many different species of stored product pests, but they can be classified by four main categories based on their biology and habits:

  1. Scavengers: Eat just about anything, even if other pests have been there first. Pests in this category include the red flour beetle and sawtoothed grain beetle.
  2. External feeders: Feed on the exterior of cereal (grain) and kernel products and work their way inside. Pests in this category include Indian meal moths and cigarette beetles.
  3. Internal feeders: Lay eggs in the grain and feed on kernels from inside. Pests in this category include granary weevils, lesser grain borers and Angoumois grain moths.
  4. Secondary feeders: Eat from the outside in and consume moldy and damp food products. Pests in this category include spider beetles and fungus beetles.

How do you know if you have stored product pests? An infestation becomes apparent when the pests can be observed crawling or flying around. At this point, it’s important to identify the specific species that is plaguing your facility, as this will dictate the appropriate treatment method.  A trained professional can help correctly identify the species and recommend the best course of action to resolve the problem. Stored product pests reproduce quickly, so it’s critical to address any infestations before they have time to multiply and contaminate additional product.

The most common stored product pests are:

  • Sawtoothed Grain Beetle. Can burrow directly through boxes and packaging, so even sealed foods are at risk. They prefer processed food products like bran, chocolate, oatmeal, sugar and macaroni.
  • Indian Meal Moths. One of the most common pests for food processing facilities, the larva feeds on a large variety of different products. Some distinctive signs of an infestation are silk webbing and frass near the surface of the product.
  • Cigarette and Drugstore Beetles. Also able to chew through packaging, these beetles prefer pet food, spices, tobacco and any packaged food.
  • Granary and Rice Weevils. Prefer whole grains or seed products like popcorn, birdseed and nuts. They are recognizable by a snout protruding from their head and their reddish-brown bodies. Grains infested by weevils will be hollow and have small holes.
  • Spider Beetles. Similar to small spiders in appearance, they prefer grains, seeds, dried fruits and meats. They often accompany a rodent infestation because they prefer grain products that are old and moist.

Prevention Tactics

To help prevent stored product pests, incorporate the following tactics as part of your IPM program:

  • Closely inspect incoming shipments and packages. Look for the signs of stored product pests, like webbing, larvae and live adult insects. Check for signs of damage, especially for holes that can be caused by boring pests. To monitor for pests entering in this way, a quality assurance sample should be placed in a closed, labeled plastic container for later observations to see if any activity is noticed. This will give you a better idea if pests are present and what types may be being introduced via the incoming shipment.
  • Use of pheromone traps. These are the best tool to monitor the pest activity. These traps can also be placed in transportation vehicles to see if the trucks have a resident stored product pest population.
  • Use temperature as a repellant. Most stored product pests cannot live in extreme temperatures. If storage rooms can be maintained at 60°F or lower, stored product pests won’t be able to establish themselves inside.
  • Practice the first-in, first-out (FIFO) approach for products. Deteriorating products are an invitation to stored product pests, so make sure that older products go first and remove any with damages. It is also best to store products off the floor and more than 18 inches from walls, as it makes it easier to clean the surrounding area.
  • Create a sanitation schedule. Keeping a facility free of food debris will go a long way in eliminating attractants for pests. Clean up product spills immediately, and vacuum and wipe down everything on a regular basis. Don’t forget the cracks and crevices!

Keep in mind that being proactive is an important part of this entire process. If you see something, say something. Resolving pest issues as quickly as possible will be beneficial in the long run, as infestations are naturally more difficult to remove and could cost your facility dearly during an audit. A pest management professional will be able to point out the hot spots around a facility and can help to ensure that proactive prevention tactics are in place before anything gets out of hand. If any products are compromised, discard them immediately.

Pest Management: A Team Effort

The stakes are high in the food processing environment, which means pest control must be a priority. The most successful pest control programs are a team effort. Form a strong partnership with your pest management provider and work closely with them throughout the year to proactively prevent pest problems. Reach out to them early and often if you suspect any issues.

It’s also important that your entire staff is aware of pest management initiatives and tactics, which is why many pest management providers offer free staff training courses upon request. Take advantage of the resources available through your provider.

Working with a pest management provider to create a customized, IPM plan will help prevent pests and in turn protect the quality of your products and your business.

Shawn K. Stevens, Food Industry Counsel
Food Safety Attorney

Five Things to Look for in a Trading Partner

By Shawn K. Stevens
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Shawn K. Stevens, Food Industry Counsel

Any ready-to-eat food product is only going to be as safe as the ingredients used to manufacture it. Unfortunately, most companies spend most of their money and time focused on broadening their customer base at the expense of properly screening new or existing suppliers. These companies fail to recognize that the single most significant threat to their company is failing to avert a potentially disastrous supplier problem that is lurking just outside of view. Whether your supplier has an inadequate food safety system or a poor food safety culture, such failures can cause your supplier’s products to become contaminated with deadly pathogens. In turn, if you are sourcing any products from that supplier, its food safety problems will inevitably become your own.

So, what should you do to ensure that your supplier’s food safety problems do not become your own?  Over the past two decades, I have witnessed countless food safety failures cause countless more outbreaks and recalls. Most of these outbreaks and recalls could have been avoided by the companies that were affected simply by taking a few extra precautions. Thus, throughout the years, I have developed the following recommendations that all companies who manufacture or sell ready-to-eat products should follow when they are screening new or existing suppliers.

First, visit each of your suppliers’ facilities and make sure that they are producing your products in a clean and sanitary environment. If the facility is old, worn and has significant maintenance issues, consider moving to a different supplier. Poor facility construction, or the failure to maintain a cleanable and sanitary environment in weathered facilities, remains one of the most significant causes of product contamination. Microorganisms can take hold and easily find residence in older facilities that are not being appropriately maintained. In turn, once harmful pathogens become entrenched in environments that are difficult to clean and sanitize, it becomes extremely difficult to root them out.

Second, make certain that each of your suppliers have a robust environmental monitoring program. The only way for your supplier to prove to you that its sanitation program is effectively controlling microorganisms in the environment is to test and to test often. Unfortunately, many suppliers’ testing programs are woefully inadequate because the suppliers test too infrequently or only after cleaning and sanitation. As a result, in addition to requiring that each of your suppliers implement a robust sampling program, you should also require each of your suppliers to sample their food processing environments at least three to four hours into production. This way, they will always have an accurate picture of the sanitary conditions of the processing area during production.

Third, be sure to only partner with suppliers who are willing to test their finished products before selling them to you. If a supplier has confidence in its sanitation and monitoring programs, then that supplier should be willing to test the products it is selling you. If, however, your supplier refuses to test its finished products, it signals that the supplier does not believe it is able to produce a ready-to-eat product that is consistently free from contamination. Thus, if you ask your supplier to test its ready-to-eat products for the presence of harmful pathogens, and it refuses, immediately take your business elsewhere.

Fourth, inquire about your supplier’s suppliers. Remember, a platoon is only as fast as its slowest runner. If any supplier in the distribution chain has a problem, that problem will affect every company located downstream from the failure. Thus, be sure to get a commitment from each one of your suppliers that it will impose the same requirements on each of its own suppliers, and then verify that your supplier is actually doing what is promised.

Fifth, make sure only to do business with those suppliers that can demonstrate they have a strong food safety culture. The best way to judge the strength of a supplier’s food safety culture is by inquiring about the structure and credentials of the supplier’s food safety team. If the person in charge of food safety for the supplier is well credentialed, has deep experience, and is supported by a well-qualified team, that demonstrates that the supplier takes food safety seriously. If, however, the supplier does not have a food safety director, his or her resume is weak, and he or she does not appear to have adequate support, then the company likely lacks any food safety culture whatsoever. In this case, it would be advisable to find an alternative supplier that has invested in the right people and put them in the right positions.

In the end, the best way to protect your products and brand is to only use suppliers that are appropriately vetted and screened. If you commit to only using suppliers that have invested in clean and sanitary facilities, robust environmental and finished product testing programs, and strong food safety cultures, then you will likely be able to virtually eliminate the chances that your products will be associated with an outbreak or recall. If, however, you choose to leave your suppliers’ food safety performance to chance, your suppliers problems (and, they will have problems) will inevitably become your own.

Shawn Stevens will be speaking during a webinar on this topic, Contracting With a New Trading Partner? Here’s Your Risk-Reduction Checklist, May 2, 2017, 1–2pm ET. Register now.

Phil Moyer, Unyson
FST Soapbox

Six Considerations When Choosing Your 3PL Provider

By Phil Moyer
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Phil Moyer, Unyson

The third-party logistics provider  (3PL) market is expected grow at a compound annual growth rate of more than 5% through at least 2024, according to Hexa Research. In addition, Aberdeen Research reports that industry leaders have increased the number of 3PLs they work with by more than 20% since 2013. Clearly, companies are outsourcing more of their logistics activities, and there are many factors to consider when choosing a 3PL, especially in the food industry. This article discusses a few essentials to take into account before betting your company reputation on a new 3PL relationship.

1. Experience

Transporting food is a serious and complex business, and it’s one place you don’t want to be a trailblazer. If the 3PL you’re considering doesn’t have extensive experience with products similar to yours, you are better off looking elsewhere. After all, it’s your reputation that will take the hit if things go wrong. This is one area where it pays to check references.

A company’s supply chain can be the weakest link in its food safety program. Learn how to mitigate these risks at the Food Safety Supply Chain conference | June 5-6, 20172. Familiarity With Food Safety

First and foremost, ensure your 3PL understands the ramifications of the latest legislation regarding food handling — including FSMA and HACCP. It should be able to point to material handling data sheets for every item of food it handles. Give the 3PL bonus points if it can personalize the handling instructions to each shipper.

Make sure the 3PL understands the rules in all the geographic areas where you ship, since local regulations can vary.

3. Certified Processes

FSMA requires specific documentation. The 3PL you choose should already be aware of the rules and have processes in place for compliance. It should have taken the initiative to have its processes audited for compliance. After all, compliance with regulations is part of the service it provides for you.

Ask the provider to show you its method for conveying handling instructions to carriers, and how it ensures that carriers follow the instructions. The burden of proof for cold-chain integrity or HACCP compliance falls to you, so don’t entrust your business to a 3PL that doesn’t understand it.

4. Track and Trace, Lot and Expiration Controls

Recalls happen. Your 3PL should have technology in place to provide visibility throughout the supply chain, including the ability to track and trace from end to end. Ask to see its picking process, and how it ensures first-in-first-out (FIFO) lot picking so you minimize spoilage. How does it handle expired or soon-to-expire lots? Can it segregate the goods so it doesn’t actually ship them? How does it notify you of upcoming expirations? Proactive alerting is the ideal mechanism.

5. Size and Locations

Once the 3PL you are considering has proven it understands how to handle food products safely and legally, the next step is to ensure it can provide the coverage you require. It should have offices in or near your distribution points. Ask to see the 3PL’s customer list. You don’t want to be much larger than its current largest customer because it may not be equipped to deal with your volumes. You also don’t want to be among its smallest shippers, because you may not get the attention you deserve.

Make sure the provider is fiscally sound, especially if you are entering this relationship for the long term.

6. Technology

Technology is fast becoming the biggest differentiator for a 3PL. Ask about the systems it uses for collaboration and visibility. Does it have automated picking capabilities? Are your business systems easily compatible if you want to integrate, or does it provide a shipper portal for 24/7 access? What are its future technology plans? A good 3PL should be excited to talk about its technology because it would know it’s a key differentiator. If the provider is reluctant to talk about it or lagging in the technology arena, it will not be a good long-term partner.

Your business depends on a great 3PL, and your customer’s health and safety may rely on it as well. Take the time to thoroughly vet any 3PL you are considering before signing on the dotted line.

Bryan Armentrout, Food Leadership Group
FST Soapbox

Tips on Handling an FDA Audit

By Bryan Armentrout
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Bryan Armentrout, Food Leadership Group

Here’s a typical scenario.

You are the QA Manager for a dairy manufacturing facility in the Midwest. It’s been a long week and you decide to come in a little earlier than normal to catch up on paperwork. You find out when you arrive that product is on hold because the filling line is down. Maintenance is all over the machines, and orders are piling up; the paperwork will have to wait. You head out to the line to see what you can do to help.

This only happens when the plant manager is on vacation, you think to yourself.

As you walk out to the floor, your ears perk up as you hear your name paged over the intercom. The receptionist needs you in the front office—immediately.

What now?

You can’t think of anyone who is scheduled to visit today. You heart sinks a little. You don’t like surprises and this could be a bad one.

You come around the corner to the lobby to see exactly who you were hoping you wouldn’t see: An FDA investigator.

“My name is Investigator Brown,” he says as he flashes a badge. “We’ve had an allegation of an illness from your product. I am here to look into it.”

You smile politely and nod. He does not smile. You motion for him to follow you to a conference room.

Your day just got a whole lot longer.

How will this go?

The answer to that question is, in many ways, up to you.

FDA investigators are people and they take their job as seriously as you do. They are there because they need answers. Their boss expects answers. If people are getting sick, they need to find out quickly and take action. If this is truly the case, you need to know as well. So does your boss. No one wants people to get sick.

The absolute wrong thing to do in this situation is to not have a plan. You need to know how to handle a regulatory inspection. You need a plan to prevent a misunderstanding or create a situation where something minor gets blown out of proportion.

This is not the time to play it by ear. You need training and you need a plan.

An important point to remember is that your product may not have caused the illness. People often assume the last food they ate is the one that made them sick. In reality, incubation times may take significantly longer for symptoms to manifest. Samples of the product in question are rarely available to test. Dosage, health of the person, and other factors also come into play. You need to work with facts and not supposition—as does the FDA.

Tips for an FDA Inspection

  1. You are guilty until proven innocent
  2. You are not alone
  3. You are the company spokesperson
  4. Take lots of notes
  5. Seek first to understand, then to be understood
  6. Answer the question being asked
  7. Know what is in scope and what is out of scope
  8. Don’t sign or initial anything

1. You are guilty until proven innocent

In general, you can assume that FDA thinks you are at fault; that is why they are there. You will have a hole to dig yourself out of before you can convince them otherwise. Don’t let that rattle you, they are only doing their job, and your job is to show them all the great food safety programs you have in place to prevent what they are concerned about. Keep this in mind as you go through the visit. If you are doing a good job, you should see their demeanor soften as they gain confidence in what you do.

2. You are not alone

Don’t be a hero, you need a team to help you in this situation. You need the people in the plant and you need people at corporate ready to back you up. You most likely also need access to outside counsel that specializes in food regulations. Your role in the room is to facilitate and work with FDA to get them what they need. You and FDA are on the same side of the table in this respect. Both of you are working to find out if the illness is real.

If you are not sure of an answer, say so! Call corporate QA and your legal counsel and discuss it. Find out what the answer is from someone who does know. If you still don’t have an answer, it’s better to admit it than to make something up. Tell them when they can expect an answer, even if it may be after the audit concludes. Never make stuff up.

3. You are the company spokesperson

The company should have only one voice (most likely, you) responding during the inspection. This avoids confusion and keeps you in control over the message being delivered. Other agencies, such as OSHA, have the right under the law to interview employees during an investigation. It is not that clear cut with FDA. Make sure you explain to FDA that you are the designated spokesperson for this inspection and that all questions need to be routed through you. The personnel in the facility need to understand this as well and defer to you if FDA questions them. If the question is out of the ordinary, it may need to be in writing. When on the floor, never leave the investigator alone, accompany them at all times (don’t go crazy, they can use the bathroom by themselves).

4. Take lots of notes

Have someone who can tag along with you to take written notes of the visit. Train them on what you expect. Time stamp the notes and use a stream of consciousness approach. Write down everything, more notes are preferred. You may need them in the future. Never take the notes yourself, you are going to be too busy to do that. Mark the notes confidential and do not give a copy to FDA. Also, make sure that you have a clear and explicit ‘no photography’ policy in place. Train your people and enforce it. FDA may want to take pictures and they will tell you that they have the right to do so. That is open to debate and the issue has yet to be resolved in court. In the meantime, your policy is clear, so insist that they do not take pictures. This is your plant and your proprietary process; even with the best care, your competitors might find out more than they should about what you do.

5. Seek First to Understand, then to be Understood

This rule applies everywhere in life, and especially during an FDA inspection. Gather all the information you can. Are they going to take samples? If so, you need to prepare for that. Ask for the purpose of the visit and any supporting information you can get. Seek to first meet the needs to the investigator and to understand the exact context of the inquiry. The better you understand the purpose, the easier the day will be. Just like the investigator, you have a boss. You have limits to what you can and cannot do. Make sure the FDA understands that you are the representative, but the answer may need to come from other sources. Company policies are not written by you and cannot be altered. You are both on the same side of the table and rules need to be followed. They will understand and respect that.

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Erika Miller
FST Soapbox

When Worlds Collide

By Erika Miller
2 Comments
Erika Miller

The Foreign Supplier Verification requirements of FSMA have perhaps been less well advertised than those of the Preventive Controls rules, but the compliance dates are fast approaching nevertheless. On May 30, 2017, a new field will appear in Ace, the software system wherein importers declare their imports and, in so doing, fulfill the requirements of many different U.S. regulations. This seemingly innocuous event will have serious and wide-reaching implications for all entities involved in the importation of food intended for consumption in the United States, but perhaps no one will be more affected than brokers and distributors, for they have long relied on the protection of their sources to ensure a share of the profits on their imports.

Exchange knowledge about managing your supply chain at the Best Practices in Food Safety Supply Chain conference | June 5–6, 2017 | LEARN MORE

Brokers and distributors often provide an important service by taking care of the legal requirements to bring a product into the country, and by purchasing large quantities of product that can then be broken down into more manageable quantities for their customers. Nowadays, information that was used to be transmitted to Customs and Border Protection (CBP) on paper forms is entered in Ace, which is a one-stop-shop software system that aggregates data on all imports. This data can then be accessed by several government agencies, including the FDA. Anyone wishing to bring food into the United States for consumption on our shores will be required to declare a Foreign Supplier Verification Program (FSVP) Importer for the food, and the names entered as FSVP Importers will then form a database from which the FDA will work to ensure enforcement of this program.

This FSVP Importer may or may not be the same as the Importer of Record (IOR). Large companies are already re-writing their import contracts to include this requirement, for it’s quite clear already that communication of expectations will be vital to the success of this program. The FDA recognizes that it is possible that unscrupulous parties may enter the name of a party as the FSVP Importer who does not realize their name has been entered; however, the main recourse for the injured party is to better communicate with their supply chain to ensure the issue does not arise again.

Although these technicalities are important to understand, it is perhaps even more interesting to consider the implications of all the FSMA requirements surrounding this rule. For example, FDA’s requirements for records are very clear, and each record must include the name and address of the facility at which it was created, in addition to other information. The rules of FSMA are also quite clear in stating that brokers or distributors cannot provide the necessary food safety paperwork on their own; rather, this documentation must come from the grower, manufacturer, processor—for a true farm-to-fork implementation, in keeping with the spirit of the rule.

What does this mean for the broker who sells to a large company that is perfectly capable of purchasing the large quantities required to “go direct”? Will they be cut out of their livelihoods by being forced to give this information to their customers? This is a question that has been raised in all the FSVP Importer classes held to date, and in reading the rule, it appears clear that the broker is expected to disclose their source. How else is it possible for them to follow the law, and assure their customer that the food was produced with the same level of food safety as if it were made here in the United States?

Foreign Supplier Verification, TraceGains A Comprehensive Guide to the Who, What & How to FSMA’s FSVP Rule

Have confusion regarding some of the specifics to FSMA’s Foreign Supplier Verification Program rule? You’re not alone… Are you the importer? What if you’re a broker? What are the actual contents of a verification program? This comprehensive guide can help answer some of these lingering questions, and will provide you with a couple real examples of FSVP in action.

This is a particularly interesting conundrum because at its heart, this is an issue of information exchange between private companies. Although the FDA does expect that some entity will keep the records to satisfy the requirements of the FSVP, they will not expect this paperwork to be transmitted to any government agency prior to approval of a load for import. Rather, the FDA will send electronic records requests to the entities declared as FSVP Importers later, wherein they will ask for the records related to previous shipments. Should the FSVP Importer declared at import not produce the required documentation at the time of this request, enforcement activities are expected to result (eventually, once the rule has gone into effect and regulation has begun).

It stands to reason that some entities may continue to operate in a fool’s paradise for some length of time, thinking nothing has really changed. This is incredibly dangerous for the business, its reputation and indeed, for the consumer. Times are obviously changing across the globe, and the FDA is doing its best to keep up with the demands of an increasingly complex global society. The broker who enters his own name without understanding the implications of what that means may find himself on the receiving end of a number of records requests from the FDA, with no records on hand with which to fulfill them. This is not an enviable position, and will likely result in an in-person visit from an investigator if the food imported is considered high-risk.

There are, of course, many brokers and distributors who are proactive and concerned about food safety. These are the companies that are sending multiple individuals to FSVP training to stay informed about the changing face of import regulations. Many of these brokers and distributors already gather paperwork such as third-party audit reports and letters of guarantee from their suppliers, but they do not transmit this information to their customers. Should these proactive companies be essentially punished for following the letter of the law? Even if a purchasing department has a warm personal relationship with their broker or distributor, if the C-suite sees an opportunity to save a substantial sum on their commodity of choice while increasing transparency in the supply chain, certainly those decisions will be made without regard for hurt feelings.

What about redaction? Can the brokers or distributors redact the sensitive information from the documents, and transmit them in that way? Perhaps, but after consultation with a brilliant and experienced legal mind, redaction may not be the panacea it first appears. For example, redaction of documents is a boring and redundant task, frequently relegated to the intern or other low-paid office worker due to its repetitive nature. These workers may perform the redaction lackadaisically, or use CTRL-F to find all appearances of the information to be redacted. In doing this, they often miss important information that appears in an image or is misspelled. Additionally, anyone who has spent much time in the food industry understands that this is a small world, and it is often easy to recognize a document simply from the style in which a particular company presents all its documentation. Clues such as colors, partial logos and incomplete redaction can lead to a shrewd individual deducing the original author of the documents quite easily.

Although there are no answers to be had at this juncture, especially considering that the compliance date for these requirements has not yet passed, it is important to think about all these implications, along with many others that are being brought to the forefront through the Importer workshops approved by the Food Safety Preventive Controls Alliance. The FDA readily admits they are learning right alongside industry, and they have every intention of continuing to educate while they regulate. If these issues cannot be hammered out between industry representatives and the FDA directly, it stands to reason the issue will eventually be brought before the courts, where the demands of capitalism will be weighed against those of regulation for food safety. Is there a legal precedent for this situation? If you know of one (or several), please leave the information in the comments below to continue the discussion.

Sean Crossey, arc-net
FST Soapbox

5 Problems Facing the Global Food Supply Chain

By Sean Crossey
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Sean Crossey, arc-net

The food we eat is a lot less secure than we would like to imagine. According to PricewaterhouseCoopers, food fraud is estimated to be a $40 billion a year problem, with instances of fraud becoming worryingly frequent—from wood shavings discovered in our parmesan to the 2013 horsemeat scandal in the UK.1-3 Not only do these incidents damage the faith consumers have in their food, but as seen in the 2009 salmonella peanut butter outbreak, which resulted in the death of 9 Americans and sickening of 714, they can have fatal consequences.4 Indeed, the World Health Organization estimates that nearly 1 in 10 people become ill every year from eating contaminated food.5

While it may be uncomfortable to imagine our food supply can be susceptible to such high profile attacks, what is more unsettling is that our food supply chain has grown so complex that it has become almost impossible for food producers to guarantee the provenance of their products—meaning consumers can never entirely trust in the food they eat. In this article I will identify five main issues the global food supply chain faces, and what steps can be taken to address them.

Exchange knowledge about managing your supply chain at the Best Practices in Food Safety Supply Chain conference | June 5–6, 2017 | LEARN MORE1. Consumer demand for traceability

Traceability is no longer a request from consumers, but a demand, and one that is only growing stronger. A recent transparency survey found that consumers want to see everything from a complete ingredient breakdown to sourcing information, with 94% of respondents saying they are likely to be more loyal to a brand that offers complete transparency.6 While a new study discovered that more than half of Canadians are concerned about food fraud.7

If we take seafood products as an example, almost half (46%) of respondents to an independent research survey conducted by the Marine Stewardship Council (MSC) agreed that they trust brands that use ecolabels (a form of third-party certification) more than those that do not.8 The survey also found that 66% of respondents felt that traceability of the product was the primary factor determining seafood purchasing decisions.

This kind of consumer driven, high-quality information opens up a world of possibilities for companies that recognize the significance of its demand. Brand protection, demand forecasting and consumer loyalty all becomes possible for early adapters who show themselves to be taking practical steps to guarantee the authenticity of their products.

2. Lack of communication between actors

One of the biggest challenges preventing full traceability of our food is the fragmented nature of the supply chain. For even the most seemingly simple of food items there can be a huge number of actors involved that are spread around the globe with little to no knowledge of one another’s actions.

For instance, to trace your hamburger from farm to fork may involve tracing your lettuce back to the farm in which it was grown (but not what happens to it before it reaches your supermarkets shelves), tracing the beef back to the cattle (with no guarantee, as seen with the horsemeat scandal, that the end product is 100% beef) and any number of logistical barriers.

It is vital then that stakeholders within the chain prioritize communication with their suppliers, either through the implementation of traceability solutions, or the commitment to engage only with suppliers they know they can trust. Not only is this beneficial to the end consumer, but to the food producers themselves, allowing them to ensure that their organizational reputation remains solely their responsibility and not left in the hands of unknown and uncontrollable third parties.

3. Influence of organized crime

When one thinks of the Mafia, it’s rare that olive oil is the first thing that comes to mind. Currently, however, it is the fraudulent manufacture of this and many other Italian exports (cheese, wine, etc.) that is fueling organized crime and ending up on our shelves.9

High-scale food fraud is not a naturally occurring phenomenon but rather exists as a result of highly organized criminal activity. In his 2014 UK government report, Professor Chris Elliot notes that “food fraud becomes food crime when it no longer involves random acts by “rogues” within the food industry, but becomes an organized activity by groups that knowingly set out to deceive and or injure, those purchasing food”.10

This is not just a problem for Italy; counterfeit food and drink occurs on a massive scale throughout the whole of Europe. A joint initiative by EUROPOL and INTERPOL last year led to the largest ever seizure of fake and adulterated projects. This project, known as OPSON V resulted in 11,000 tons and 1,440,000 liters of hazardous fake food and drink seized across 57 countries.11

In order to combat the growing threat organized crime has on our food supply, it is vital that governments devote resources to organizations with the sole responsibility of identifying food crime. In response to the horsemeat scandal, the UK government launched its National Food Crime Unit within the Food Standards Agency in London, while the FDA has a special focus on food defense.

The establishment of these organizations is important, as police forces traditionally have struggled to combat food fraud, either through a lack of time, resources, or simply understanding of the complexities of how fraud affects the supply chain. The creation of specialist taskforces not only legitimizes the fight against food fraud, but allows for easier intelligence share.

4. Lack of transparency throughout the supply chain

In her work on trust for the digital age, Racheal Botsman tells us that trust has evolved from an institutional based system to a distributed system. Nowhere has this more potential than with our food supply.

In such a complex system it becomes necessary to consider how the food industry can begin to move away from traditional systems of centralized trust. As Botsman points out, “institutional trust is not designed for the digital age”, the emergence of new technologies, most notably the blockchain, highlights the potential to introduce more trust in our food.12

Originally the technology underpinning Bitcoin, the blockchain has wide ranging applications beyond the world of FinTech. Blockchain is a transformative tool in the fight against food fraud, allowing an open and transparent ledger of our food products journey. This allows unalterable trust to be introduced into an untrustworthy system, ensuring every actor in the chain records and shares their interactions with our food.

This represents a huge opportunity for those companies who see the advantage of early adoption of blockchain infused traceability systems. Indeed by 2022, Gartner estimates an innovative business built on a blockchain will be worth $10 billion.13

5. Need for strong legislation

Steps have already been made in legislation to allow for earlier prevention of food safety incidents occurring, such as FSMA. While it is important that lawmakers are proactive in their response, the focus has primarily been on food safety, and there is still a difficulty in treating food fraud as its own separate entity.

Legislation regarding food labelling could also be more stringent, especially in Europe. At present only olive oil, fish (unless it’s canned or prepared), beef (fresh, chilled, frozen or minced), fresh or frozen poultry of non-EU origin, wine, most fresh fruit and vegetables, honey and eggs are required to be labelled. This means that origin information is largely missing on foods such as meat products (e.g., ham and sausages), yogurts and cheese, kitchen staples (e.g., oil, flour, sugar and pasta), biscuits and confectionery, or ready-meals.

Tighter legislation, leading to significant punitive measures taken against actors found to be committing fraud, would be a vital catalyst in ensuring that food in our supply chain is as secure as possible.

Conclusion

The growth of the global food supply chain may bring with it complexity and challenges, but also great opportunities. If actors can interject their processes with the kind of joined up thinking outlined above, with the help of technological tools that are becoming more and more accessible, the benefits will be significant, not just for them, but for all of us.

Resources

  1. PWC. (2016). Fighting $40bn food fraud to protect food supply [Press Release]. Retrieved from http://press.pwc.com/News-releases/fighting–40bn-food-fraud-to-protect-food-supply/s/44fd6210-10f7-46c7-8431-e55983286e22
  2. Mulvany, L. (February 16, 2016). The Parmesan Cheese You Sprinkle on Your Penne Could Be Wood. Retrieved from https://www.bloomberg.com/news/articles/2016-02-16/the-parmesan-cheese-you-sprinkle-on-your-penne-could-be-wood
  3. Grierson, J. (August 26, 2016). Three men charged over UK horsemeat scandal. Retrieved from https://www.theguardian.com/uk-news/2016/aug/26/three-men-charged-over-uk-horsemeat-scandal
  4. Andrews, J. (April 16, 2016). 2009 Peanut Butter Outbreak: Three Years On, Still No Resolution for Some. Retrieved from http://www.foodsafetynews.com/2012/04/2009-peanut-butter-outbreak-three-years-on-still-no-resolution-for-some/#.WD7tE6KLTpJ
  5. World Health Organization. (2015). WHO’s first ever global estimates of foodborne diseases find children under 5 account for almost one third of deaths [Press Release] Retrieved from http://www.who.int/mediacentre/news/releases/2015/foodborne-disease-estimates/en/
  6. Label Insight (2016). The 2016 Label Insight Transparency ROI Study. Retrieved from https://www.labelinsight.com/hubf /2016_Transparency_ROI_Study_Label_Insight.pdf?t=1486676060862
  7. Sagan, A. (February 21, 2017). Study finds 63 per cent of Canadians are concerned about food fraud. Retrieved from http://www.theglobeandmail.com/news/national/study-finds-63-per-cent-of-canadians-are-concerned-about-food-fraud/article34094664/
  8. MSC (2014). MSC Consumer Survey 2014. Retrieved from https://www.msc.org/newsroom/news/new-research-shows-increasing-appetite-for-sustainable-seafood
    Bacchi, U. (February 21, 2017). Italian police break mafia ring exporting fake olive oil to U.S. Retrieved from http://www.reuters.com/article/us-italy-crime-food-idUSKBN1602BD
  9. HM Government (2015) Elliot Review into Integrity and Assurance of Food Supply Networks. Retrieved from https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/350726/elliot-review-final-report-july2014.pdf
    EUROPOL (2016) largest ever seizures of fake food and drink in INTERPOL-EUROPOL operation [Press Release]. Retrieved from https://www.europol.europa.eu/newsroom/news/largest-ever-seizures-of-fake-food-and-drink-in-interpol-europol-operation
  10. Botsman, R. (October 20, 2015). The Changing Rules of Trust in the Digital Age. Retrieved from https://hbr.org/2015/10/the-changing-rules-of-trust-in-the-digital-age
  11. Panetta, K. (October 18, 2016) Gartner’s Top 10 Strategic Technology Trends for 2017. Retrieved from http://linkis.com/www.econotimes.com/Zk8mh
Tim Daniels, Autoscribe Informatics
In the Food Lab

Using LIMS to Get In Shape for FDA’s Visit

By Tim Daniels
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Tim Daniels, Autoscribe Informatics

FSMA is a major reform of the U.S. food safety laws. It shifts the emphasis for food safety to preventing contamination during manufacture instead of just responding to it. As part of the implementation process, the FDA will enforce these new rules during routine random inspections at food manufacturing sites. With such a significant change in emphasis, Shawn K. Stevens of Food Industry Counsel LLC, released an FDA Inspection Checklist. The checklist is designed to help food and beverage manufacturers to prepare for an agency inspection and to ensure they have the required controls and checks in place. Before we look in more detail at the checklist, it is worth reviewing some of the underlying requirements.

Some Basic Requirements

One of the fundamental requirements of FSMA is the establishment of an environmental monitoring program at each facility. It defines the testing protocols for appropriate microorganisms and verifies that the preventative measures undertaken are effective. Clear procedures and systems are required to identify the test microorganisms most suited to the risks in their systems. They need procedures to identify the locations from which samples will be collected and the number of sites to be sampled, since the number and location must be adequate to determine whether the preventative controls are effective. They also need to identify the timing and frequency for collecting and testing samples. The tests to be conducted must be specified, including the analytical methods used and the corrective action procedures in the event that testing detects an environmental pathogen or an indicating organism. Just as importantly, all of the data associated with this testing program needs to both be recorded and accessible for audit purposes.

Acquiring and Managing Environmental Monitoring Data

Any environmental monitoring program will come at a cost to the food manufacturer. While the program itself will need to be set up by experts in the field, much of the implementation can be carried out by lesser-qualified technicians. So a key aspect is having the tools to implement a program where the most effective use is made of each resource available, as this keeps costs down. In principle, one such tool is a Laboratory Information Management System (LIMS).  The use of a LIMS is commonplace in QA Labs to record and monitor laboratory samples, tests and results in order to simplify and automate processes and procedures. There is a variety of ways in which a LIMS could facilitate the environmental monitoring process to enable best practice even by non-specialist staff. For example, analysis can be simplified if each set of test results can be automatically linked to respective sampling points in the facility. Out-of-specification test results could be linked to corrective and preventive actions (CAPA). Test failures at a particular sampling point could be used to trigger more frequent testing at that point according to pre-set criteria.

  • The data management capabilities within a LIMS make it possible to:
  • Implement data management strategies that increase security and availability of data
  • Eliminate manual assembly of data for analysis and audit
  • Make data more useful with easy retrieval/visibility

Perhaps most importantly, a properly configured LIMS can provide a suitable framework for set-up and adjustment by the environmental monitoring expert, while reducing the expertise required to operate it on a daily basis.

Laboratory Information Management Systems
The Matrix Gemini Environmental monitoring solution is an example of an information management system that uses the capabilities of a LIMS to record and monitor laboratory samples, tests and results to simplify and automate environmental monitoring in QA Labs. Image courtesy of Autoscribe Informatics

FDA Inspection Checklist

This comprehensive document highlights the steps that companies need to take to prepare for the inspection process, navigate the inspection itself and respond to any criticisms arising from the inspection.

There are three main areas in the checklist where a LIMS could help satisfy FSMA requirements:

  1. Finalizing written food safety systems and making sure certain employees know the plans. LIMS provides the framework to set up documented food safety sampling requirements and track microbial test results over time. This facilitates recall and more detailed investigation should a sample fail.
  2. Well organized and maintained data, and ease of records access. LIMS should be capable of date and time stamping every entry and since it will contain all the test data over time, this can be easily recalled should the need arise. Typically a standard operating procedure would be developed, which will increase testing and start “out-of-specification” actions if abnormal microbial contamination is detected. LIMS can provide a full audit trail for all test data and produce reports showing result trends over time, highlighting variance and peaks in data.
  3. Proper documentation of corrective actions. In the event of failures, investigators will want to focus on the particular sample points and the “out-of-specification” actions that were initiated to investigate and resolve these failures. Typically three months of data is requested around these sample points, although up to two years’ worth of data could be requested. LIMS should allow data to be instantly pulled from the database as a report for further investigation.

FDA investigators will be most interested in what happens in the event of a failure and what learning gets incorporated into your regular regime. What happens when an out-of-specification result is obtained is the crux of preventive testing regimes. Actions might include changing sanitation methods, increasing test frequency or locations in areas of concern, segregating traffic patterns, re-training staff and so forth. Some of these actions, such as increasing test frequency, can be automated. All actions must be clearly documented, which can be done by adding appropriate records directly into the LIMS. This captures the actions that each quality improvement cycle needs in order to discover the likely root cause of any problems and how they may be avoided in the future.

All corrective actions should identify the root cause of the deviation, actions taken to prevent recurrence and, if product safety is not affected, a written conclusion (supported by factual and scientific data) that the deviation “does not create an immediate food safety issue.”

The emphasis should always be on preventive actions to remove potential points of failure before issues get into the final delivered products causing stock loss and costly recalls.

Configuring a LIMS for Environmental Monitoring

While most LIMS in principle provide the capability to handle the requirements of environmental monitoring, the system will need to be configured to do so, and this may not be a trivial exercise. The software will need to be configured to represent user requirements in terms of workflows, screen designs, menu designs, terminology, numbering schemes, report designs and much more. For many LIMS, full configuration for specific applications requires custom coding, which will require re-validation.

Once configured, LIMS can offer a practical way for food and beverage companies to document their sanitation/safety programs and instantly show written evidence of both testing and corrective actions when the FDA comes knocking.

Sanjay Singh, Eurofins
Food Genomics

How is DNA Sequenced?

By Sanjay K. Singh, Douglas Marshall, Ph.D., Gregory Siragusa, Ph.D.
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Sanjay Singh, Eurofins

Here is a prediction. Within the next year or years, at some time in your daily work life as a food safety professional you will be called upon to either use genomic tools or to understand and relay information based on genomic tools for making important decisions about food safety and quality. Molecular biologists love to use what often seems like a foreign or secret language. Rest assured dear reader, these are mostly just vernacular and are easily understood once you get comfortable with a bit of the vocabulary. In this the fourth installment of our column we progress to give you another tool for your food genomics tool kit. We have called upon a colleague and sequencing expert, Dr. Sanjay Singh, to be a guest co-author for this topic on sequencing and guide us through the genomics language barrier.

The first report of the annotated (labeled) sequence of the human genome occurred in 2003, 50 years after the discovery of the structure of DNA. In this genome document all the genetic information required to create and sustain a human being was provided. The discovery of the structure of DNA has provided a foundation for a deeper understanding of all life forms, with DNA as a core molecule of genetic information. Of course that includes our food and our tiny friends of the microbial world. Further molecular technological advances in the fields of agriculture, food science, forensics, epidemiology, comparative genomics, medicine, diagnostics and therapeutics are providing stunning examples of the power of genomics in our daily lives.  We are only now beginning to harvest the fruits of sequencing and using that knowledge routinely in our respective professions.

In our first column we wrote, “DNA sequencing can be used to determine the names, types, and proportions of microorganisms, the component species in a food sample, and track foodborne diseases agents.” In this month’s column, we present a basic guide to how DNA sequencing chemistry works.

Image courtesy of US Human Genome Project Knowledge base
Image courtesy of US Human Genome Project Knowledge base

DNA sequencing is the process of determining the precise order of four nucleotide bases, adenine or A, cytosine or C, guanine or G, and thymine or T in a DNA molecule. By knowing the linear sequence of A, C, G, and T in a DNA molecule, the genetic information carried in that particular DNA molecule can be determined.

DNA sequencing happened from the intersections of different fields including biology, chemistry, mathematics, and physics.1,2 The critical breakthrough was provided in 1953 by James Watson, Francis Crick, Maurice Wlkins and Rosalind Franklin when they resolved the now familiar double helix structure of DNA.3 Each helical strand was a polynucleotide, which consists of repeating monomeric units called nucleotides. A nucleotide consists of a sugar (deoxyribose), a phosphate moiety, and one of the four nitrogenous bases—the aforementioned A, C, G, and T. In the double helix, the strands run opposite to each other, commonly referred as anti-parallel. Repeating units of base-pairs (bp), where A always pairs with T and C always pairs with G, are arranged within the double helix so that they are slightly offset from each other like steps in a winding staircase. On a piece of paper, the double helix is often represented by scientists as a flat ladder-like structure, where the base pairs (bp) form the rungs of the ladder while the sugar-phosphate backbone form the antiparallel rails (see Figure 1).

DNA Double Helix
Artistic representation of DNA Double Helix. Source: Eurofins

The two ends of each polynucleotide strand are called 5′ or 3′-end, a nomenclature that represents the chemical structure of the deoxyribose sugar at that terminus. The lengths of a single- or double-stranded DNA are often measured in bases (b) or bases pairs (bp), respectively. The two polynucleotide strands can be readily unzipped by heating, and on cooling, the initial double-helix structure is re-formed or re-annealed. The ability to rezip the initial ladder-like structure can be attributed to the phenomenon of base pairing, which merits repetition—the base A always pairs with T and the base G always with C. This rather innocuous phenomenon of base pairing is the basis for the mechanism by which DNA is copied when cells divide and is also the theoretical basis on which most traditional and modern DNA sequencing methodologies have been developed.

Other biological advancements also paved the way towards the development of sequencing technologies. Prominent amongst these were the discovery of enzymes that allowed a scientist to manipulate the DNA. For example, restriction enzymes that recognize and cleave DNA at specific short nucleotide sequences can be used to fragment a long duplex strand of DNA.4 The DNA polymerase enzyme, in the presence of the deoxyribose nucleotide triphosphates (dNTPs: Chemically reactive forms of the nucleotide monomers), can use a single DNA strand to fill in the complementary bases and extend a shorter rail strand (primer extension) of a partial DNA ladder.5 A critical part of the primer extension is the ‘primer’, which are short single-stranded DNA pieces (15 to 30 bases long) that are complementary to a segment of the target DNA. These primers are made using automated high-throughput synthesizer machines. Today, such primers can be rapidly manufactured and delivered on the following day. When the primer and the target DNA are combined through a process called annealing (heat and then cool), they form a structure that shows a ladder-like head and a long single-stranded tail. In 1983, Kary Mullis developed an enzyme-based process called Polymerase Chain Reaction (PCR). Using this protocol, one can pick a single copy of DNA and amplify the same sequence an enormous number of times. One can think of PCR as molecular photocopier in which a single piece of DNA is amplified up to approximately 30 billion copies!

The other critical event that changed the course of DNA sequencing efforts was the publication of the ‘dideoxy chain termination’ method by Dr. Frederick Sanger in December 1977.6 This marked the beginning of the first generation of DNA sequencing techniques. Most next-generation sequencing methods are refinements of the chain termination, or “Sanger method” of sequencing.

Frederick Sanger chemically modified each base so that when it was incorporated into a growing DNA chain, the chain was forcibly terminated. By setting up a primer extension reaction where in one of the chemically modified ‘inactive’ base in smaller quantity is mixed with four active bases, Sanger obtained a series of DNA strands, which when separated based on their size indicated the positions of that particular base in the DNA sequence. By analyzing the results from four such reactions run in parallel, each containing a different ‘inactive’ base, Sanger could piece together the complete sequence of the DNA. Subsequent modifications to the method allowed for the determination of the sequence using dye-labeled termination bases in a single reaction. Since, a sequence of less than <1000 bases can be determined from a single such reaction, the sequence of longer DNA molecules have to be pieced together from many such reads.

Using technologies available in the mid-1990’s, as many as 1 million bases of sequence could be determined per day. However, at this rate, determining the sequence of the 3 billion bp human genome required years of sequencing work. By analogy, this is equivalent to reading the Sunday issue of The New York Times, about 300,000 words, at a pace of 100 words per day. The cost of sequencing the human genome was a whopping  $70 million. The human genome project clearly brought forth a need for technologies that could deliver fast, inexpensive and accurate genome sequences.  In response, the field initially exploded with modifications to the Sanger method. The impetus for these modifications was provided by advances in enzymology, fluorescent detection dyes and capillary-array electrophoresis. Using the Sanger method of sequencing, one can read up to ~1,000 bp in a single reaction, and either 96 or 384 such reactions (in a 96 or 384 well plate) can be performed in parallel using DNA sequencers. More recently a new wave of technological sequencing advances, termed NGS or next-generation sequencing, have been commercialized. NGS is fast, automated, massively parallel and highly reproducible. NGS platforms can read more than 4 billion DNA strands and generate about a terabyte of sequence data in about six days! The whole 3 billion base pairs of the human genome can be sequenced and annotated in a mere month or less.

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