Deirdre Schlunegger, CEO of STOP Foodborne Illness

By Deirdre Schlunegger

Hello everyone, Happy New Year! STOP Foodborne Illness had a busy 2016, and we are busy planning details for 2017. The ultimate goal is to work with all stakeholders to reduce foodborne illness. We are fortunate to have wonderful partners around the country and beyond who support our efforts and are interested in furthering the cause. There are too many people still dying from food poisoning.

We will continue to work with individuals, families, folks in the food industry and businesses related to solving the problem of foodborne illness. We are very interested in continuing our participation with food safety training including working with companies to create videos for training. Hearing a story and the consequences of foodborne illness makes a difference when one is trying to drive the importance home. We are leaning hard into our work as usual. If we can help you in any way, please give us a call or send us an email.

In the meantime, thanks to everyone who has helped us with our work in 2016, including our board members, our donors, our volunteers to those who helped with the webinar (Food Safety Culture: We Know Why, Let’s Talk About How), Mike Taylor, Frank Yiannas and Steve Schluneger, and to Food Safety Tech for hosting our annual event again in 2016 There are many more people to thank but not enough space here.

Please take a look at some of our 2016 efforts and successes!

Enjoy the year, enjoy your successes, learn from mistakes and stay safe in every way.

January 23, 2017

Retail Food Safety Forum

IoT a Key Ingredient for Food Safety

By Jeff Rieger

2 Comments

The Internet of Things (IoT) is the concept that everything will one day be connected, similar to when computers became networked and connected with the internet. A sensor in a walk-in freezer is now smart enough to communicate directly with the smartphone in your pocket and a computer at the office, all in real-time. This is what IoT is all about, bringing more information to our fingertips in order to make faster, more informed decisions.

These new technologies are beginning to intersect and create new solutions to old problems, such as periodically monitoring the temperature of equipment in a restaurant or the trailer of a refrigerated truck. Savvy operators who understand changing food safety regulatory demands are driving the adoption of these technologies that ease the transition towards ongoing compliance. Food safety technology is changing, and what follows are a few of the driving forces.

Smartphones, Tablets and Cloud Computing Create Ready-made Environment

Apple launched the first iPhone in 2007 and within six years, 50% of the U.S. population was using a smartphone and/or tablet. Another market event that helped create the foundation for IoT was the growth of the “cloud” model where organizations could “rent” hardware, software and data storage. When coupled with new affordable wireless networking capabilities (WiFi, Bluetooth) and expanded cellular coverage at decreased cost rates for data, it became economically viable for nearly any size company operating in the foodservice industry to collect, store and access data.

Over the course of the last decade, we’ve become more comfortable living in a connected world and, as the technology has matured, businesses started to look at how smart devices could be used to improve operational efficiency and outdated food safety protocols. Instead of manually checking equipment temperatures, wireless sensors are now connecting refrigerators and other temperature controlled environments to the cloud. Any operator with a smartphone is now able to view these temperatures (or receive alerts) in real-time to ensure equipment and product temperatures meet company standards and local regulatory requirements.

Heightened Diligence by Oversight Agencies, Increased Consumer Activism and Brand Protection Concern

The responsibility for food safety spans both national (FDA/USDA/CDC) and local (state and county health department) organizations. FSMA has widened these responsibilities across the cold chain. With limited resources, operators are being asked to adopt new regulations and do their part to ensure the integrity of the product that is being stored and/or transported.

In addition, consumers have become increasingly self-aware regarding various food-related issues, including oversight and traceability (i.e. labeling, processing, etc.). This same general trend can be seen where consumers are now expecting ongoing food safety inspections and access to inspection results online. This puts more pressure on operators to ensure guidelines are met and inspections are passed.

Finally, restaurants are becoming more proactive in protecting their brand. The idea of keeping any incidents limited to the awareness of only the few that were involved is a thing of the past. Forward-thinking restaurants realize that social media has changed the landscape, and what was once a single-store minor infraction can now cause franchise-wide problems. Additionally, food safety is just good business. Restaurants have moved beyond following procedures as a necessary hurdle to now actively following and implementing best practices and policies in order to achieve operational efficiency and elevate their brand reputation.

IoT the Enabler of a Data-driven Business

Simply put, the internet has reshaped all businesses, so why not restaurants and the cold chain? With the availability of “ready-made tech”, sensors can connect to front-of-house and back-of-house environments to monitor temperature (frozen, refrigerated, ambient, hot-holding) in all types of equipment (walk-in refrigerators and freezers, under-counter coolers, showcase units and sandwich lines) to continuously and wirelessly monitor temperature and send alerts if the proper temperature is not maintained.

Data gathering can also be extended to incorporate digital task management capabilities to replace traditional Hazard Analysis and Critical Control Points (HACCP) manual logbooks and simplify daily restaurant tasks. Organizations can streamline manual operational checklists and provide insight to managers on how well their teams are adhering to restaurant guidelines.

Restaurants now have an important tool to address the two sides of food safety—prevention and traceability. Additionally, through capturing larger data sets, restaurants can move from anecdotal guesswork to implementing data-based best practices. The ingredients are now in place for restaurants to offer the highest levels of food safety and quality that the industry has ever enjoyed.

January 10, 2017

FST Soapbox

Is Food-Grade always Food-Safe?

By Lance Roberie

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What? Why would food-grade not be food-safe? What is the difference between food-grade and food-safe? Doesn’t it mean the same thing? These may be some of your initial thoughts. So, what is the difference between food-grade and food-safe? Food-grade means that the material is fit for human consumption or permitted to come in contact with food. 21 CFR 174-178 for example, can be used to verify if a component is an appropriately regulated indirect additive and considered GRAS (Generally Recognized as Safe) for its intended use. But are food contact materials sometimes utilized for something other than its intended use? You bet your 483 they are. This is an important component that is often overlooked. Just because that material is permitted to come in contact with food, it doesn’t necessarily mean it is food-safe. Food-safe means that the food-grade material is also fit for purpose for its intended use and will not create a food-safety hazard. For example, it may be fit for purpose to use a food-grade container to hold a dry ingredient but that same container may not be fit for purpose to be used to hold a hot liquid. Section 117.40 in Subpart B of FSMA states: “Food-contact surfaces must be made of nontoxic materials and designed to withstand the environment of their intended use and the action of food, and, if applicable, cleaning compounds, sanitizing agents, and cleaning procedures”. Processors will be called upon more than ever to prove that food contact materials are indeed safe and “fit for purpose” or safe for its intended use. The practice of simply having a certificate of conformance stating that your food contact materials are food-grade will likely no longer be good enough. If you are familiar with GFSI and its standards, you already know that simply having a certificate of conformance for food contact materials is unacceptable if the manufacturer/supplier doesn’t acknowledge that the material is safe to use under the conditions in which you will use them (i.e., for its intended use). So, asking your supplier a few more questions about your food contact materials can go a long way when conducting an in-depth hazard analysis and a food-safety risk assessment. Some common questions are:

What is the recommended safe temperature range for this material?
Is this material safe for the type of food that it is contacting (i.e., fat percentage, pH, moisture percentage, etc.)?
Will the material physically hold up to the manufacturing environment for which it is being used?

You also need to think about how the material is constructed. Does it have pieces/parts that can be accidently removed during use, such as a pail with an attached handle that often falls apart and can potentially make its way into the product stream? Or maybe a cleaning brush that often loses its bristles. Does the material/equipment have seams, and are those seams smooth and cleanable? When evaluating equipment, always make sure it is designed for the intended use. If equipment is not designed for its intended use, it can often render it ineffective and depending on how critical the process, significantly increase a food-safety risk. Choosing materials that are “food-safe” can be just as important as choosing materials that are “food-grade”.

Have you ever heard someone say “it’s only a trash can if you put trash in it”? What does that mean exactly? It usually means that containers designed for trash may be used to hold food ingredients or products intended for human consumption. What is the potential risk in that situation? Is that container safe for food contact? It is obviously not the intended use and adulterated product may be the end result. So how does someone determine if the food contact material is “food-safe”? There are several third-party certification companies that verify food equipment and/or food contact materials are indeed “food-safe”, including HACCP International, NSF and 3A. If the material or product that you are evaluating does not have one of these certifications, then the burden is on you to properly risk assess the potential hazards of your operation and to prove to your customers and regulatory bodies that your process is food-safe. So, during your next food-safety team meeting, challenge your team members to take a good, hard look at everything that comes in contact with the food stream and ask, “is this truly ‘food-safe’?”

January 3, 2017

Food Genomics

Microbiomes Move Standard Plate Count One Step Forward

By Gregory Siragusa, Douglas Marshall, Ph.D.

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Last month we introduced several food genomics terms including the microbiome. Recall that a microbiome is the community or population of microorganisms that inhabit a particular environment or sample. Recall that there are two broad types of microbiomes, 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). This month we would like to introduce the reader to uses of microbiomes and how they augment standard plate counts and move us into a new era in food microbiology. Before providing examples, it might be useful to review a diagram explaining the general flow of the process of determining a microbiome (See Figure 1).

By analogy, if one thinks of cultural microbiology and plate counts as a process of counting colonies of microbes that come from a food or environmental sample, microbiome analysis can be thought of as identifying and counting signature genes, such as the bacterial specific 16S gene, from the microbes in a food or environmental sample. Plate counts have been and remain a food microbiologist most powerful indicator tool in the tool kit; however, we know there are some limitations in their use. One limitation is that not all bacterial or fungal cells are capable of outgrowth and colony formation on specific media under a set of incubation conditions (temperature, time, media pH, storage atmosphere, etc.). Individual plate count methods cannot cover the nearly infinite number of variations of growth atmospheres and nutrients. Because of these limitations microbiologists understand that we have not cultured but many different types of bacteria on the planet (this led to the term “The Great Plate Count Anomaly” (Staley & Konopka, 1985). Think of a holiday party where guests were handed nametags on which was printed: “Hello, I grow on Standard Methods Agar” or “Hello, I grow at 15°C”, etc. We can group the partygoers by ability to grow on certain media; we can also count partygoers, but they still do not have names. As effective as our selective and differential media have become, bacterial colonies still do not come with their own “Hello, My Name Is XYZ” name tags. Therefore, in the lab, once a plate is counted it is generally tossed into the autoclave bag, along with unnamed colonies and all they represent. Microbiomes can provide a nametag of sorts as well as what proportion of people at that party share a certain name. For instance: “Hello, My Name is Pseudomonas” or “Hello, My Name is Lactobacillus”, etc. The host can then say “Now we are going to count you; would all Pseudomonas pleased gather in this corner?” or “All Lactobacillus please meet at the punch bowl”.

A somewhat overly simplified analogy, but it makes the point that microbiome technology gives names and proportions. Microbiomes too have limitations. First, with current technologies microbiomes need a relatively large threshold of organisms of a specific group to appear in the microbiome pie chart— approximately 103. In theory, a colony on a plate of agar medium can be derived from a single cell or colony-forming unit (CFU). Not all amplified genes in a microbiome are necessarily from viable cells (A topic that will be covered later in this series of articles). Forming a colony on an agar surface on the other hand requires cell viability. Finally, the specificity of a microorganism name assigned to a group in a microbiome depends on the size of the sequenced amplicon (an amplicon is a segment of DNA, in this case the 16S gene DNA, resulting from amplification by PCR before sequencing) and how well our microbial databases cover different subtypes in a species. Targeted microbiomes can reliably name the genus of an organism, however resolution to the species and subspecies is not guaranteed. (Later in this series we will discuss metagenomes and how they have the potential to identify to a species or even subspecies level). Readers can find very informative reviews on microbiome specificity in the following cited references: Bokulich, Lewis, Boundy-Mills, & Mills, 2016; de Boer et al., 2015; Ercolini, 2013; Kergourlay, Taminiau, Daube, & Champomier Vergès, 2015.

When we consider the power of using cultural microbiology for quantitative functional indicators of microbial quality together with microbiomic analysis, with limitations and all for both, microbiomes have opened a door to the vast and varied biosphere of our food’s microbiology to a depth never before observed. This all sounds great, but how will we benefit and use this information? We have constructed Table 1 with examples and links of microbiome applications to problems that would have required years to study by cultural microbiology techniques alone. Please note this is by no means an exhaustive list, but it serves to illustrate the very broad and deep potential of microbiomics to food microbiology. We encourage the reader to email the editors or authors with questions regarding any reference. Using PubMed and the search terms “Food AND microbiome” will provide abstracts and a large variety of applications of this technology.

Foodstuff	Reference
Ale	(Bokulich, Bamforth, & Mills, 2012)
Beef Burgers	(Ferrocino et al., 2015)
Beefsteak	(De Filippis, La Storia, Villani, & Ercolini, 2013)
Brewhouse and Ingredients	(Bokulich et al., 2012)
Cheese	(Wolfe, Button, Santarelli, & Dutton, 2014)
Cheese and Listeria growth	(Callon, Retureau, Didienne, & Montel, 2014)
Cherries, Hydrostatic Pressure	(del Árbol et al., n.d.)
Cocoa	(Illeghems, De Vuyst, Papalexandratou, & Weckx, 2012)
Dairy Starters and Spoilage Bacteria	(Stellato, De Filippis, La Storia, & Ercolini, 2015)
Drinking Water Biofilms	(Chao, Mao, Wang, & Zhang, 2015)
Fermented Foods	(Tamang, Watanabe, & Holzapfel, 2016)
Foodservice Surfaces	(Stellato, La Storia, Cirillo, & Ercolini, 2015)
Fruit and Vegetables	(Leff & Fierer, 2013)
Insect Protein	(Garofalo et al., 2017)
Kitchen surfaces	(Flores et al., 2013)
Lamb	(Wang et al., 2016)
Lobster	(Tirloni, Stella, Gennari, Colombo, & Bernardi, 2016)
Meat and storage atmosphere	(Säde, Penttinen, Björkroth, & Hultman, 2017)
Meat spoilage and processing plant	(Pothakos, Stellato, Ercolini, & Devlieghere, 2015)
Meat Spoilage Volatiles	(Casaburi, Piombino, Nychas, Villani, & Ercolini, 2015)
Meat Stored in Different Atmospheres	(Ercolini et al., 2011)
Milk	(Quigley et al., 2011)
Milk and Cow Diet	(Giello et al., n.d.)
Milk and Mastitis	(Bhatt et al., 2012)
Milk and Teat Preparation	(Doyle, Gleeson, O’Toole, & Cotter, 2016)
Natural starter cultures	(Parente et al., 2016)
Olives	(Abriouel, Benomar, Lucas, & Gálvez, 2011)
Pork Sausage	(Benson et al., 2014)
Spores in complex foods	(de Boer et al., 2015)
Tomato Plants	(Ottesen et al., 2013)
Winemaking	(Marzano et al., 2016)
Table 1. Examples of microbiome analysis of different foods and surfaces.

See page 2 for references

Pages: 1 2

December 12, 2016

Retail Food Safety Forum

Supply Chain Logistics: 4 Reasons You Need a Retail Strategy

By Michael Link

5 Comments

Attend the Food Safety Supply Chain Conference, June 5–6, 2017 in Rockville, MD | LEARN MORERetailers demand peak supply chain performance, and suppliers who fail to provide on-time, accurate deliveries face costly penalties. Further to peak performance, retailers also require a high level of supply chain visibility and transparency to ensure the quality and safety of the food they’re selling. The many moving parts of the supply network require a fine-tuned logistical approach, and a big piece of this is having a retail strategy that optimizes and consolidates your food shipments. This helps suppliers in a myriad of ways, which we’ll delve into here.

Before we do that, let’s set the stage a bit: Compliance programs are the norm within today’s retail supply chain. These programs outline appointment times and delivery standards to ensure quality of goods—among other things—along with the penalties for not meeting the terms. Retailers’ compliance programs vary, but the theme is consistent: Non-compliance results in major costs that add up over time and cause the risk of loss of business.

To gain a competitive advantage, shippers are focusing more on retail consolidation programs that optimize and consolidate shipments while focusing on customer service to help shippers get ahead. These programs can provide complete visibility, enhance control, capture critical business intelligence, create efficiencies, decrease costs, reduce mileage, improve speed to market, and decrease over, short and damage (OS&D) claims—among other benefits.

Let’s take a closer look at some of these:

1. Enhanced Inventory Management

Inventory control is critical in the retail sector. Retailers try to keep their inventories low and have just-in-time deliveries from vendors. This helps to ensure goods are delivered and sold at the highest quality, which, for certain foods like fresh produce or refrigerated items, can often have a narrow window of freshness. At the same time, retailers want to make sure the product they need is going to be available. This is especially the case when seasonal demand for certain food items ebbs-and-flows, such as during the holidays.

As part of a retail optimization program, supply chain service providers can help retailers and suppliers manage inventory by analyzing data and making proactive, rather than reactive, inventory and transportation decisions.

2. Reduced Transit Times

The growth of the omni-channel sector—including in the grocery business—means customers want and expect things at the click of a button, and lead time has a major impact on the cost, quality control and continuity of ordering patterns. In fact, a recent report from Internet Retailer, 2016 Online Food Report, details how the online grocery sector is suddenly a booming market, and is expected to grow by 157% to $42.1 billion this year alone, according to Morgan Stanley.

Proactive communication and continual analysis of transit time data can help suppliers plan and execute an effective transportation strategy as the omni-channel food retail market continues to tick up. Namely, by combining potentially inefficient partial loads into fully utilized truckloads, suppliers can achieve shorter, more predictable transit times. With proper pre-planning, loads can be consolidated, which then allows zone skipping and more direct transportation routes. Zone skipping also reduces the number of times freight is handled, which reduces the risk of damage and errors.

3. Network Optimization

A comprehensive network analysis and optimization effort can drive significant reductions in landed costs while maintaining, or even improving, transit times by considering production, warehousing and inventory needs in addition to transportation. Warehouse location is a critical decision; however, growth projections and potential new markets must be included in forward planning to ensure that today’s appropriate solution does not become tomorrow’s barrier to scalability.

The decision to work with a single national warehouse provider or multiple regional warehouse providers is driven not solely by cost, but also by the consideration of utilizing a single or multiple warehouse management systems. This analysis complements a mode optimization effort, allowing shippers to control costs, ensure product safety and quality and enhance service through the optimum blend of intermodal, truckload and LTL services.

4. Better Visibility and Collaboration

Supply chain performance is critical to controlling costs, improving service, and when it comes to the food supply chain, ensuring quality of perishable goods. According to a survey by ECR McKinsey, successful collaboration on average resulted in a 4.4% decrease in out-of-stocks and a cost reduction of 5.4%.

Collaboration can begin early in the supply chain. Shippers’ supply chain providers can provide an analysis of the entire supply chain and break down the invisible barriers that exist between different divisions within a supplier. Often, suppliers don’t realize they are operating in silos, are unaware of what others within the business may be doing and are unaware of the implications of those actions. They can also become so focused on meeting their immediate goals, they lose sight of the big picture.

Early planning also helps providers offer a custom solution. For food service companies with multiple distribution facilities, retail consolidation becomes an important piece in the supply chain strategy and a critical method for improving profitability.

Implementing an Effective Retail Optimization Program

There are several elements of an effective retail optimization program, including:

Increased visibility
Network optimization
Mode optimization
Consolidation
Pool pointing

The right retail consolidation programs allow the entire supply network to comply with retailers’ requirements while also increasing visibility, reliability and quality of product. Overall, this creates value for the shipper and their end-customers through improved service. It’s a win-win situation for all parties involved.

December 5, 2016

FST Soapbox

Mitigating Supply Chain Risk with Transparency and Traceability

By Katy Jones

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Attend the Food Safety Supply Chain Conference, June 5–6, 2017 in Rockville, MD | LEARN MOREA recent study from The Hartman Group on the topic of transparency found that consumers are becoming more concerned about imports and the safety standards behind companies producing food and beverage products beyond U.S. borders.

So with the drastic rise in consumer expectations for food quality and safety in the past few years, how can companies ensure they’re mitigating risks in the supply chain while fostering transparency to meet consumer expectations?

To our benefit, the focus of the broader food industry and the government, as well as innovations in technology, are making it easier than ever to comprehensively track the supply chain.

Another Day, Another Food Recall, Another Listeria Scare

In today’s reality, whether we like it or not, food recalls are an inevitable part of the food industry, and adulteration in the supply chain is a key safety issue. With the wellbeing of consumers at stake, if a contamination finds its way into a brand’s supply chain, the best possible course of action is to take action on a recall using impeccable supply chain records and monitor the affected product moving throughout the chain.

With recalls being here to stay in the food industry, companies need to be prepared to handle these issues quickly and effectively. By implementing supplier management and whole-chain traceability software, allergens and impurities can be pinpointed to a specific lot of product as opposed to being limited to processing/issue date, and not knowing the source or country of origin of every ingredient (as many suppliers can contribute to one product) within the supply chain.

Additionally, with these technologies, brands can keep their supply chain transparent and compliant with growing industry regulations. With consumer standards on the line, proactive transparency can ensure that a company has a plan of attack when the inevitable hits.

A Targeted and Precise Plan

Companies and brands need to broaden their definition of food safety in order to manage and satisfy an expanded set of consumer expectations. The traditional, linear “one-up and one-back” (OUOB) approach to supply chain is no longer acceptable when it comes to comprehensive supply chain transparency.

Consumers need a targeted and precise plan when dealing with the safety of their food—it’s no longer just about whether the food safe to eat. The definition has expanded to include safety around ingredients and country of origin. Awareness of where a product came from and where it is going next is not an acceptable method if a company wishes to foster transparency with customers and effectively manage recalls. In addition, these standards are emphasized by federal regulations like the FSMA and FSVP—the industry is now shifting towards preventative approaches to safety matters, as opposed to reactive. FSMA requires food manufacturers to increase focus on prevention rather than response to contamination incidents, which will require a comprehensive view of the entire supply chain.

Brands will need to develop strong food safety plans with streamlined audits and compliance records, verifying supply chain partners and executing corrective actions for suppliers that are not in compliance with the process and food safety plan set in place. In establishing this process, having the technology to support it is paramount in ensuring that suppliers are sticking to the food safety practices necessary to follow industry regulation and exceed consumer expectation.

Transparency in Today’s Complex Food Paradigm

As the global food supply continues to grow in volume and complexity, brands have an opportunity and an obligation to adapt to the food paradigm. According to a Label Insight study, 94% of consumers say transparency from food brands is the #1 factor that impacts purchase. Brands are no longer able to blame a supplier’s lack of transparency or unreliable records for exposing consumers to unsafe products but instead, the brand is solely held accountable.

Transparency and proactivity were optional in the past, but are now established as fundamental components of a brand’s safety plan if they are to adapt to the changing industry landscape as well as consumer demand. As recalls are bound to happen, proactivity and transparency can ensure that a company is one step ahead of an outbreak at all times.

The fact is, adapting to this shifting environment and aligning with these best practices and the technologies that enable them is critical to the success of the supplier, distributor and across the whole supply chain. Food companies must look to utilize big data analytics and intelligent supply chain mapping technologies in order to improve transparency and increase traceability. With the ability to track ingredients back and forth across the supply chain, these technologies enable a safer consumer experience as well as provide tremendous business value in eliminating inefficiencies, managing supply chain issues, and effectively protecting the brand with the insights offered.

December 2, 2016

Bug Bytes

Rodents: The Winter Invaders

By Zia Siddiqi, Ph.D.

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As temperatures plummet throughout the United States, rodents become more active in seeking out a warm shelter for the winter. Unfortunately, food processing facilities are perfect for rodents because they have everything that rodents need to survive.

Rodents are scavengers, and as a result they like to have all of their survival needs in close proximity at all times. Once they enter your facility, their three main needs are food, water and shelter, so it’s easy to see why food processing facilities are an appealing target.

Before anything else, you’ll want to work with your pest management professional to make sure that your facility has an Integrated Pest Management (IPM) program to help keep pests out. An IPM program is tailor-made for each facility and focuses on environmentally friendly prevention and exclusion tactics to protect your facility, using chemicals only as a last resort. A strong program can help prevent a number of different pests from getting into your facility, even rodents. This preventive approach also compliments the HARPC under FSMA.

Adaptable and clever, rodents can be a pain if they are able to get inside. Rats can fit through a hole the size of a quarter, while mice can fit through a hole the size of a dime. Rodents are also known to chew on openings around a facility in order to make them large enough to squeeze through. Even the smallest of cracks and gaps can become a pathway inside to a wandering rodent.

There are significant health and safety risks associated with rodents that should make you carefully consider your current pest management program and its tactics for keeping them out. Rodents are known carriers of more than 35 different diseases including Hantavirus, salmonellosis, jaundice and plague. All of these are incredibly dangerous to have anywhere near your product, so the best solution is to prevent rodents from getting inside in the first place.

Also, rodents have tiny bladders and frequent bowel movements, so they leave behind a trail of urination and defecation everywhere they go. They’ll expend their waste, which naturally contains pathogens that spread disease, dozens of times a day.

Because of their roaming nature and constant waste expulsion, there are some telltale signs of rodents that can help you detect them before it becomes a major issue. It’s important that you educate your staff about these signs and contact your pest management professional to resolve the problem as quickly as possible.

Signs of Rodent Activity

Urine marks and droppings. These can be found nearly anywhere that a rodent has been. Look for little brown pellets and yellowish discoloring, which will show best under UV light. A black light inspection can help determine if there is an infestation.
Noises in the walls, basement or ceiling. Gnawing, clawing and scratching noises can be a sign that a rodent might be running around, especially if heard at night. Rodents prefer to stay out of sight when hunting for food, so you won’t often notice them during times of high activity around a facility.
Rub marks around corners and baseboards. As they look for food and try to remain unseen, rodents will most often stick close to walls and corners. When they do skitter around, they’ll leave behind brownish marks that can be seen if closely inspected.
Musky odors. When rodents congregate in a certain area, their nesting sites will begin to give off a detectable odor especially if the rodents are reproducing.

Issues with rodents can get out of hand quickly as rodents reproduce rapidly. As soon as a rodent feels safe and has warmth and shelter, it will start the reproduction process. Mice produce about eight litters every year with between four and seven pups in a litter, while rats produce about six litters every year with between eight and twelve pups in a litter. Some rodents can then reach sexual maturity in as little as 35 days after birth, which shows how quickly rodents can multiply within a facility.

Make sure to educate staff on your IPM program, and be sure to establish the proper protocol in the case of a pest sighting. It’s important to note when, where and how many pests were spotted, as this information is valuable when working to resolve a problem.

The key is to stop rodents before a problem becomes an infestation, but trying to catch and remove rodents yourself can make them wise to trapping and baiting techniques. Remember that rodents are quite clever and learn from past experiences. To avoid making things worse in the long run, contact a pest management professional if you think that you have a rodent problem, especially if it might be an infestation.

If you are looking for some ways to make a difference on your own, there are certainly some things that you can do. Treat your facility like a fortress, and every good fortress needs to be as impenetrable as possible. Below are some exclusion and prevention tactics that you can start doing immediately to make your facility as strong as possible.

Rodent Prevention Tips

Seal the exterior. Walk around the exterior of your facility and check for any holes or cracks the size of a dime or larger. Pay especially close attention to pipes and other penetrations that may have open spaces around where they enter the building.
Remove clutter. Rodents use a variety of materials to build their nests, so areas fraught with clutter will look appealing to them, especially if it’s materials like cardboard boxes and paper.
Store food effectively. Keep all food products tightly sealed and off of the floor, as rodents have an easier time detecting and getting into food if it isn’t elevated. Also, containers made of plastic or metal are preferable so that they won’t get chewed through.
Clean up. Food and drink particles from spills or waste bins will attract rodents, so clean up and take out the trash regularly. Regular sweeping and mopping is an absolute must, especially around trash receptacles.
Trim vegetation. Plants need to be cut back at least two feet from the outside of your building and grass needs to be kept short. Vegetation gives rodents a place to hide, so if not trimmed back it can serve as a “jumping off” point to help rodents get indoors.

It’s also important to consider the environment surrounding your facility, as this can be a major factor in the amount of pest pressure that you experience. For rodents, cities are often hot spots, as other factors like construction and greater waste output from a higher concentration of people can increase pest pressure on a facility.

If you’re worried that your facility might be at risk of a rodent infestation, contact your pest management provider and get an assessment. It’s always better to be prepared with an IPM program ahead of time, as these critters aren’t going to be easy to remove from your facility once they’ve settled inside.

November 29, 2016

Food Genomics

Introducing a New Column: Food Genomics

By Gregory Siragusa, Douglas Marshall, Ph.D.

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DNA sequencing can be used to determine the names, types, and proportions of microorganisms, the component species in a food sample, and track foodborne disease agents. Here we introduce a column exploring aspects and applications of these new techniques, known collectively as food genomics. Each month we will provide take-home knowledge in which every food safety scientist should be familiar.

We live in an exciting time of great change in all of biological and food sciences. In fact, it is not an overstatement to claim that a large portion of the fields of food science, biology, agriculture and medicine will be reformed in what has been called the post-genomics era or simply the genomics era. Food science and food microbiology are major players in this pack and moving in the fast track of these changes. This game-changing technology is fueled by the convergence of two rapidly evolving fields: DNA sequencing and the analysis of that sequencing data (i.e., bioinformatics).

The common jargon uses the acronym NGS for Next Generation Sequencing. NGS refers to the most updated automated DNA sequencing technology available. In several ways, sequencing can be considered a commodity service; hence its price has dropped and its availability is now widespread. What does this mean? A useful analogy is the following: Think of trying to publish a book you wrote. Would you go out, buy a printing press, paper, ink, binding machinery, and produce thousands of copies of your book, or, would you go to a professional printer and get them to print and manufacture copies? For most, the simplicity and experience of the professional print master trumps the do-it-yourself route. Once sequence data is obtained, what is next in the process of using that data? Analysis of sequence data is a specialized field called bioinformatics and has its own expert practitioners. It is a field of study that is a hybrid combination of mathematics, statistics, computer science, and biology. Bioinformatics analyzes the very large datasets produced by NGS and will be increasingly dependent on the internet cloud for its utility to be fully realized.

How will food genomics impact food safety and quality? How will it help in identifying the sources of outbreaks in a fraction of the time it once took? What will this mean for zero-tolerance, for pathogen control, and for responsibilities and liabilities of food producers and processors? There is a growing body of examples and literature that begins to apply genomics and microbiomics to the quality of food and sources of its microbial populations.^5-7

Over the course of this column, we will be exploring several examples to alert the reader to the myriad of uses of genomics for solving food production issues.

Genomics (NGS and Bioinformatics) are the basis of the US-FDA GenomeTrakr program.¹ Genomics offers an alternative means to serotype Salmonella isolates using DNA sequencing.² There are several examples of using sequencing of solving the epidemiological source of foodborne microbial outbreaks by comparing the entire bacterial genomes of clinical and food isolates.^3,4

One powerful application of genomics is to conduct the census of microbial communities to identify the microbial members and their relative proportions, an outcome called a microbiome, all from a single tube! The technique itself is termed microbiomics. Just think, we can now identify all bacteria in a complex mixture without isolating what will grow, as well as the many microorganisms we have not yet learned to culture or require unusual temperatures, nutrients, and atmospheres! Can you feel the excitement? Hopefully with knowledge of the power of food genomics you will begin to see the true utility of this technology and begin to appreciate its awesome power. Most importantly, you will begin to see how food genomics is a useful tool for the food science professional.

The microbiome field is changing as of this writing and moving toward using a technique known as whole shotgun metagenome (WSM) analysis in which all of the DNA in a sample is sequenced and not just bacterial, fungal, or specific genes; i.e., a metagenome approach vs. a targeted approach to determining the microbiome of a sample.^8,9 The whole genome shotgun approach is also a powerful tool not only for creating food microbiomes, but can help in the identification of the plant and animal species used as ingredients in foods. WSM requires relatively advanced and sophisticated bioinformatics tools and at the same time sequencing chemistry is advancing, so is bioinformatics. For example, there is an online tool suite known as NEPHELE, which offers publically available online programs, software, and data handling capacity for sequence analysis.^10,11

So here we are with some brand new shiny tools in the kit. Now the question is, how can the food safety professional begin to use these tools? More to the point is to understand when food genomic data is called for. The first step is to grasp some of the terminology and basic processes. Table 1 lists a few starter terms to become familiar with as well as some web resources that might be helpful to you in understanding these immensely powerful tools.^12,13

Table 1. Starter Terms in Food Genomics
Annotated Whole Bacterial Genome	High-quality, low-error, gap-free DNA sequence of an entire genome of an organism, in this case, an isolated bacterium, indicating genes and their locations. This can be considered a complete road map of an organism’s genetic makeup as expressed in the nucleotides Adenine, Thymine, Cytosine, and Guanine (ATCG’s). Can be referred to as WGS or Whole Genome Sequencing.
Bioinformatics	The science of managing and analyzing biological data using advanced computing techniques. Especially important in analyzing genomic research data.
Metagenomes or Whole Shotgun Sequencing	Sequences of Genetic material recovered directly from food, animal, plant, or environmental samples with no foreknowledge of the source of living materials therein. For instance, the metagenome of a yogurt sample will harbor DNA sequences characteristic of starter culture bacteria and bovine DNA (assuming it is bovine milk yogurt). This is another approach to obtaining a microbiome.⁶
Microbiome	A community of microorganisms that inhabit a particular environment or sample. For example, a plant microbiome includes all the microorganisms that colonize a plant’s surfaces and internal passages. This can be a Targeted (Amplicon Sequencing Based) or a Metagenome (Whole Shotgun Metagenome based) microbiome.⁶
Microbiomics	The process of determining a microbiome.
Microbiota	The ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share a space or are within a sample. Formerly the term ‘microflora’ was used, but this term is waning in usage.¹⁴
NGS (Next Generation Sequencing)	High throughput automated sequencing of nucleic acids DNA or RNA.

Finally, in the reference section we have tried to provide you with some useful online reference sources. The U.S. Department of Energy has perhaps the most intuitive, user-friendly and informative sites we have encountered as of late (“Genome Glossary,” 2016). The same source also published a talking glossary (“Talking Glossary of Genetic Terms,” 2016). The reader should be advised that genomic terminology and nomenclature is still not fully mature. In fact, the number of vague meanings, cross references, and acronyms can sometimes be frustrating; but fear not, as one reads and discusses the terms, they will become clearer. As a start we recommend downloading a helpful reference that follows.¹⁵ There are many other sites you will locate by performing a single web-search. If you would like to share your favorite genomics sites, please drop a line to either author and we will try to compile them into a single electronic document.

We hope this first column will find you coming back for more as we explore this burgeoning field and learn how it is being linked to food safety. Look for future articles on specific food applications, methods, and hot topics in food genomics. Goodbye for now.

References

Allard, M. W., Strain, E., Melka, D., Bunning, K., Musser, S. M., Brown, E. W., & Timme, R. (2016). Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database. Journal of Clinical Microbiology, 54(8), 1975–1983. https://doi.org/10.1128/JCM.00081-16
Zhang, S., Yin, Y., Jones, M. B., Zhang, Z., Deatherage Kaiser, B. L., Dinsmore, B. A., … Deng, X. (2015). Salmonella serotype determination utilizing high-throughput genome sequencing data. Journal of Clinical Microbiology, 53(5), 1685–1692. https://doi.org/10.1128/JCM.00323-15
Burall, L. S., Grim, C. J., Mammel, M. K., & Datta, A. R. (2016). Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks. PloS One, 11(3), e0150797. https://doi.org/10.1371/journal.pone.0150797
Chen, Y., Burall, L. S., Luo, Y., Timme, R., Melka, D., Muruvanda, T., Brown, E. W. (2016). Isolation, enumeration and whole genome sequencing of Listeria monocytogenes in stone fruits linked to a multistate outbreak. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.01486-16
Bokulich, N. A., Lewis, Z. T., Boundy-Mills, K., & Mills, D. A. (2016). A new perspective on microbial landscapes within food production. Current Opinion in Biotechnology, 37, 182–189. https://doi.org/10.1016/j.copbio.2015.12.008
Bokulich, N. A., & Mills, D. A. (2012). Next-generation approaches to the microbial ecology of food fermentations. BMB Reports, 45(7), 377–389.
Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., … Gilbert, J. A. (2015). The soil microbiome influences grapevine-associated microbiota. mBio, 6(2). https://doi.org/10.1128/mBio.02527-14
Microbial Foods – The Science Of Fermented Foods. (n.d.). Retrieved November 21, 2016, from http://microbialfoods.org/
Ranjan, R., Rani, A., Metwally, A., McGee, H. S., & Perkins, D. L. (2016). Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochemical and Biophysical Research Communications, 469(4), 967–977. https://doi.org/10.1016/j.bbrc.2015.12.083
Colosimo, M. E., Peterson, M. W., Mardis, S., & Hirschman, L. (2011). Nephele: genotyping via complete composition vectors and MapReduce. Source Code for Biology and Medicine, 6, 13. https://doi.org/10.1186/1751-0473-6-13
Weber, N. (n.d.). Cloud Computing for Scientific Research The NIH Nephele Project for Microbiome Analysis. Accessed November 21, 2016. Retrieved from https://www.google.com/url?q=http://casc.org/meetings/14sep/CASC-NIH-Microbiome-Cloud-Project-20140917.pdf&sa=U&ved=0ahUKEwj2mvTt1LrQAhXMC8AKHUiCBLsQFggHMAE&client=internal-uds-cse&usg=AFQjCNGt_lx2zw4qLNcHuYwZvSg10ivp5Aabout:blank
Genome Glossary. (n.d.). Accessed November 21, 2016. Retrieved from http://doegenomestolife.org/glossary/index.shtml
Talking Glossary of Genetic Terms. (n.d.). Accessed November 21, 2016. Retrieved from https://www.genome.gov/glossary/
Microbiota. (2016, November 14). In Wikipedia. Retrieved from https://en.wikipedia.org/w/index.php?title=Microbiota&oldid=749454552
Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3, 31. https://doi.org/10.1186/s40168-015-0094-5

Resource

Nutrition, C. for F. S. and A. (n.d.). Whole Genome Sequencing (WGS) Program – GenomeTrakr Network [WebContent]. Accessed November 21, 2016. Retrieved from http://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/ucm363134.htm

November 21, 2016

Retail Food Safety Forum

The Fresh Food Supply Chain and Product Safety

By Randy Fields

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Attend the Food Safety Supply Chain Conference, June 5–6, 2017 in Rockville, MD | LEARN MOREFresh foods are critically important to grocery retailers because these categories help create a point of differentiation from competitors. Store operators highlight the fresh sections in ads, promote the categories with in-store signage and now support the departments digitally and through social media. This isn’t to say the center store dry grocery items aren’t marketed, but they don’t get the advertising and promotional love that the produce, meat, dairy, deli, bakery and floral areas receive.

Given this focus, retailers and their suppliers work diligently to ensure the safety of the fresh products offered. They know that one slipup in produce or the deli can wreck the company’s reputation for months or longer. This is particularly true for the many fresh products that don’t have a brand standing behind them to share the impact (or blame).

Ask retail food safety directors where they spend most of their time and the answer 90+ times out of 100 is in the fresh areas. There are simply more things that can potentially go wrong in fresh and less that can go wrong with dry grocery. Sure there is the occasional ingredient issue, but the center store doesn’t have to worry about spoilage or even packaging problems now that nearly everything is tamper proof.

The bioterrorism act mandates that each link in the supply chain knows where their ingredients or product came from and where it was distributed. Recently, much effort has gone into developing traceability technologies and processes with the produce supply chain taking the lead. Growers and their trading partners are piecing together systems that allow practitioners to follow each batch of product through to the retail store, but the operative phrase is “piecing together.” Very few technologies can provide complete farm-to-fork traceability without standard product identification codes used by all participants in the supply chain. When a participant does not use the standard product identifier, visibility to the path of a product ends.

On the regulation front, the seven FSMA rules move the emphasis of the FDA from detection and response to prevention, which impacts both fresh and shelf-stable products. On a practical level, however, compliance with the rules is often more challenging for fresh products because of their limited shelf life. Also, some of the rules apply specifically to produce, meaning retailers and their produce suppliers need to pay special attention to preventing foodborne illness in the department.

At the recent Produce Marketing Association’s Fresh Summit in Orlando, Bob Whitaker, Ph.D., the trade group’s chief science & technology officer, and Jim Gorny, Ph.D., vice president, Food Safety & Technology, both emphasized the importance of communicating each retailer’s and supplier’s compliance with the FSMA regulations to the consumer. The North American Meat Institute, International Dairy-Deli-Bakery Association and other trade groups representing the marketers of fresh products have also been very active in helping both retailers and suppliers comply with the new regulations.

Beyond FSMA, retailers and their fresh foods suppliers need to do more work to not only ensure a safer supply chain, but to let consumers know they are working on food safety every day. Transparency needs to extend throughout the supply chain so suppliers and carriers can report on any potential safety issue from the farm to the checkout stand, because retailers are requiring more support from suppliers and more documentation for each load received. And, audits need to be periodically conducted to ensure accepted industry best practices are being followed.

Technology is helping the food safety process, especially in the fresh area, by organizing documentation for FSMA compliance and by providing supply chain transparency. The systems now available integrate all product and vendor information into a retailer’s ordering systems to ensure every requirement is met before a purchase is completed. They also send out alerts when additional details are required and they confirm that each lot shipped adheres to accepted best practices for food safety.

At the end of the day, all items sold in a supermarket or online must be safe for the consumer. The challenge is somewhat bigger with fresh foods than it is with dry grocery, so retailers and their suppliers must work that much harder to ensure the safety of products sold to their customers. A combination of accurate document management, compliance audits and traceability technology is now the most likely scenario to accomplish this goal.

November 11, 2016

In the Food Lab

Rapid Detection of Spoilage Organisms: The Forgotten Bad Guys?

By Phil Coombs, Ph.D.

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As rapid microbiology methods have been increasingly adopted by the food industry during the past 30 years, much emphasis has been placed on the detection of foodborne pathogens and reducing test times as much as possible. Novel methods such as PCR, along with other molecular approaches, have done much to find these organisms more quickly and identify the source of an outbreak. Quite rightly so: We all have to eat, and we all prefer to eat safe food.

What is often forgotten, however, and what has been less fashionable in the development of novel methods, is the impact of spoilage organisms on the economics of food production and the lack of more sophisticated methods to detect them. While media headlines may scream “Salmonella outbreak affects hundreds!”, the same outlets are less likely to report how much food is thrown away on any given day because of mold growth. “Penicillium spoils bread” is hardly an attention grabber on the 6 o’clock news.

A closely–related issue is that of food wastage, which together with spoilage accounts for billions of dollars of food that is thrown away. Estimates are in the region of $29–35 billion per year, and that doesn’t take into account the billions of dollars of wasted produce because of cosmetic imperfections—the so-called “ugly” fruit and vegetables that are still safe and nutritious to eat. In other estimates, it is suggested that in U.S. landfills, 21% of the contents are comprised of wasted food.

Another source of the problem is the confusion created by date labels–“best by”, “use by”, “sell by”. What do they really mean? This has become such an issue that Walmart is leading an effort, spearheaded by Walmart’s VP of Food Safety, Frank Yiannas, to rationalize date labels so that consumers are far less likely to throw away perfectly wholesome food. In this aspect, he has worked closely with the Institute of Food Technologists, the Grocery Manufacturers Association and the Food Marketing Institute to address the problem.

The amount of waste and spoilage has reached almost scandalous proportions and the issue must be addressed, as the planet’s human population is estimated to grow to 9–10 billion by the year 2050. Improved agricultural practices and biotechnology will help to improve yields and increase the food supply, but greater efforts must be made to reduce wasting the food that is produced.

The PCR Yeast and Mold Qualitative test is distributed by Weber Scientific in North America.

In the overall context of facing these challenges, new technologies are being developed. One such technology is a four-hour PCR Yeast and Mold Qualitative test, manufactured by Germany-based Biotecon, for use in dairy products. Genetic methods are typically associated with identifying bacterial and viral pathogens. But the same approach may be taken with groups of microbes responsible for spoilage, if there is a unique gene sequence common to the target organisms.

Typical test times for yeast/molds are historically five days, although more recently incubation times have been reduced to three days with some new “rapid” plating media. Still, this is a relatively long time compared to four hours. And it is worth noting that the PCR Yeast and Mold test is a “true” four-hour test, as it does not require any pre-enrichment.

The protocol follows a standard PCR protocol for DNA extraction and amplification with an important inclusion—a treatment step that allows discrimination between viable and non-viable organisms. Another important aspect is the inclusion of UNG (Uracil-N-Glycosylase), which greatly reduces the chance of cross-contamination between one sample and the next.

The method is remarkably robust. 100% specificity has been demonstrated with more than 300 strains of yeasts and molds representing 260 species covering all the phylogenetic groups. Conversely, 100% exclusivity has been shown against 60 strains of non-targets—comprised of microbes typically found in similar ecological niches; plant DNA; and animal DNA from human, mouse and canine sources. Sensitivity of the method for yeasts/molds is 101 – 102 cfu/g.

The method is also quantitative, and PCR cycle threshold times can be very closely correlated with plate counts on agar media. Thus, once a standard curve is generated, subsequent samples need only be tested by this new PCR method. Equivalent counts are then determined from the standard curve.

The rapid detection of yeast and molds is a much-needed analytical technique for the dairy industry. For producers of yogurt and similar fermented milk product with a typical shelf-life of 60 days, having the ability to release product to market four days earlier will help with operational efficiency. More importantly, knowing early on of any possibility of product spoilage will help deliver superior product to consumers. The method won the Institute for Food Technologists’ Innovation Award, with one of the judges commenting, “a four-test versus five days for spoilage organisms is a major breakthrough.”

In view of the level of wastage and spoilage that currently occurs, this new PCR method is a step along the way to using more sophisticated methods for the detection of the organisms responsible. Guardians of the food supply should see this as an important development.

A New Year

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