Tag Archives: food production

Salim Al Babili, Ph.D., KAUST
Food Genomics

To Boost Crop Resilience, We Need to Read Our Plants’ Genetic Codes

By Salim Al Babili, Ph.D.
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Salim Al Babili, Ph.D., KAUST

In just 30 years, worldwide food production will need to nearly double to feed the projected population of 9 billion people. Challenges to achieving food security for the future include increasing pressures of global warming and shifting climatic belts, a lack of viable agricultural land, and the substantial burdens on freshwater resources. With the United Nations reporting nearly one billion people facing food insecurity today, our work must begin now.

A key research area to meet this crisis is in developing crops resilient enough to grow in a depleting environment. That’s why we need to search for ways to improve crop resilience, boost plant stress resistance and combat emerging diseases. Researchers around the world, including many of my colleagues at Saudi Arabia-based King Abdullah University of Science and Technology (KAUST), are exploring latest genome editing technologies to develop enough nutritious, high-quality food to feed the world’s growing population.1

Where We’ve Been, and Where We Need to Go

Farmers have been genetically selecting crop plants for thousands of years, choosing superior-looking plants (based on their appearance or phenotype) for breeding. From the early 20th century, following breakthroughs in understanding of genetic inheritance, plant breeders have deliberately cross-bred crop cultivars to make improvements. In fact, it was only a few decades ago that Dr. Norman Borlaug’s development of dwarf wheat saved a billion lives from starvation.

However, this phenotypic selection is time-consuming and often expensive—obstacles that today’s global environment and economy don’t have the luxury of withstanding.

Because phenotypic selection relies on traits that are already present within the crop’s genome, it misses the opportunity to introduce resilient features that may not be native to the plant. Features like salt tolerance for saltwater irrigation or disease resistance to protect against infections could yield far larger harvests to feed more people. This is why we need to explore genome editing methods like CRISPR, made popular in fighting human diseases, to understand its uses for agriculture.

What Our Research Shows

We can break down these issues into the specific challenges crops face. For instance, salt stress can have a huge impact on plant performance, ultimately affecting overall crop yields. An excess of salt can impede water uptake, reduce nutrient absorption and result in cellular imbalances in plant tissues. Plants have a systemic response to salt stress ranging from sensing and signaling to metabolic regulation. However, these responses differ widely within and between species, and so pinpointing associated genes and alleles is incredibly complex.2

Researchers must also disentangle other factors influencing genetic traits, such as local climate and different cultivation practices.

Genome-wide association studies, commonly used to scan genomes for genetic variants associated with specific traits, will help to determine the genes and mutations responsible for individual plant responses.3 Additionally, technology like drone-mounted cameras could capture and scan large areas of plants to measure their characteristics, reducing the time that manual phenotyping requires. All of these steps can help us systematically increase crops’ resilience to salt.

Real-world Examples

“Quinoa was the staple ‘Mother Grain’ that fueled the ancient Andean civilizations, but the crop was marginalized when the Spanish arrived in South America and has only recently been revived as a new crop of global interest,” says Mark Tester, a professor of plant science at KAUST and a colleague of mine at the Center for Desert Agriculture (CDA). “This means quinoa has never been fully domesticated or bred to its full potential even though it provides a more balanced source of nutrients for humans than cereals.”

In order to further understand how quinoa grows, matures and produces seeds, the KAUST team combined several methods, including cutting-edge sequencing technologies and genetic mapping, to piece together full chromosomes of C. quinoa. The resulting genome is the highest-quality quinoa sequence to date, and it is producing information about the plant’s traits and growth mechanisms.4,5

The accumulation of certain compounds in quinoa produces naturally bitter-tasting seeds. By pinpointing and inhibiting the genes that control the production of these compounds, we could produce a sweeter and more desirable crop to feed the world.

And so, complexity of science in food security increases when we consider that different threats affect different parts of the world. Another example is Striga, a parasitic purple witchweed, which threatens food security across sub-Saharan Africa due to its invasive spread. Scientists, including my team, are focused on expanding methods to protect the production of pearl millet, an essential food crop in Africa and India, through hormone-based strategies for cleansing soils infested with Striga.6

Other scientists with noteworthy work in the area of crop resilience include that of KAUST researchers Simon Krattinger, Rod Wing, Ikram Blilou and Heribert Hirt; with work spanning from leaf rust resistance in barley to global date fruit production.

Looking Ahead

Magdy Mahfouz, an associate professor of bioengineering at KAUST and another CDA colleague, is looking to accelerate and expand the scope of next-generation plant genome engineering, with a specific focus on crops and plant responses to abiotic stresses. His team recently developed a CRISPR platform that allows them to efficiently engineer traits of agricultural value across diverse crop species. Their primary goal is to breed crops that perform well under climate-related stresses.

“We also want to unlock the potential of wild plants, and we are working on CRISPR-guided domestication of wild plants that are tolerant of hostile environments, including arid regions and saline soils,” says Mahfouz.

As climate change and population growth drastically alters our approach to farming, no singular tool may meet the urgent need of feeding the world on its own. By employing a variety of scientific and agricultural approaches, we can make our crops more resilient, their cultivation more efficient, and their yield more plentiful for stomachs in need worldwide. Just as technology guided Dr. Bourlag to feed an entire population, technology will be the key to a food secure 21st century.

References

  1. Zaidi, SS. et al. (2019). New plant breeding technologies for food security. Science. 363:1390-91.
  2. Morton, M. et al. (2018). Salt stress under the scalpel – dissecting the genetics of salt tolerance. Plant J. 2018;97:148-63.
  3. Al-Tamimi, N. et al. (2016). Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communicat. 7:13342.
  4. Jarvis, D.E., et.al. (2017). The genome of Chenopodium quinoa. Nature. 542:307-12.
  5. Saade. S., et. al. (2016). Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Sci Reports. 6:32586.
  6. Kountche, B.A., et.al. (2019). Suicidal germination as a control strategy for Striga hermonthica (Benth.) in smallholder farms of sub‐Saharan Africa. Plants, People, Planet. 1: 107– 118. https://doi.org/10.1002/ppp3.32
Karen Everstine, Decernis
Food Fraud Quick Bites

COVID-19 and Food Fraud Risk

By Karen Everstine, Ph.D.
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Karen Everstine, Decernis

While foodborne transmission of the novel coronavirus is unlikely , the virus has significantly affected all aspects of food production, food manufacturing, retail sales, and foodservice. The food and agriculture sector has been designated as a “critical infrastructure,” meaning that everyone from farm workers to pest control companies to grocery store employees has been deemed essential during this public health crisis.* As a society, we need the food and agriculture sector to continue to operate during a time when severe illnesses, stay-at-home orders and widespread economic impacts are occurring. Reports of fraudulent COVID-19 test kits and healthcare scams reinforce that “crime tends to survive and prosper in a crisis.” What does all of this mean for food integrity? Let’s look at some of the major effects on food systems and what they can tell us about the risk of food fraud.

Supply chains have seen major disruptions. Primary food production has generally continued, but there have been challenges within the food supply chain that have led to empty store shelves. Recent reports have noted shortages of people to harvest crops, multiple large meat processing facilities shut down due to COVID-19 cases, and recommendations for employee distancing measures that reduce processing rates. One large U.S. meat processor warned of the need to depopulate millions of animals and stated “the food supply chain is breaking.” (An Executive Order was subsequently issued to keep meat processing plants open).

Equally concerning are reports of supply disruptions in commodities coming out of major producing regions. Rice exports out of India have been delayed or stopped due to labor shortages and lockdown measures. Vietnam, which had halted rice exports entirely in March, has now agreed to resume exports that are capped at much lower levels than last year. Other countries have enacted similar protectionist measures. One group has predicted possible food riots in countries like India, South Africa and Brazil that may experience major food disruption coupled with high population density and poverty.

Supply chain complexity, transparency and strong and established supplier relationships are key aspects to consider as part of a food fraud prevention program. Safety or authenticity problems in one ingredient shipment can have a huge effect on the market if they are not identified before products get to retail (see Figure 1). Widespread supply chain disruptions, and the inevitable supplier adjustments that will need to be made by producers, increase the overall risk of fraud.

Reconstructed supply chain
Figure 1. Reconstructed supply chain based on recall data following the identification of Sudan I in the chili powder supply chain in 2005. Data source: Food Standards Agency of the U.K. National Archives and The Guardian. Figure from: Everstine, K. Supply Chain Complexity and Economically Motivated Adulteration. In: Food Protection and Security – Preventing and Mitigating Contamination during Food Processing and Production. Shaun Kennedy (Ed.) Woodhead Publishing: 26th October 2016. Available at: https://www.elsevier.com/books/food-protection-and-security/kennedy/978-1-78242-251-8

Regulatory oversight and audit programs have been modified. The combination of the public health risk that COVID-19 presents with the fact that food and agriculture system workers have been deemed “critical” has led to adjustments on the part of government and regulatory agencies (and private food safety programs) with respect to inspections, labeling requirements, audits, and other routine activities. The FDA has taken measures including providing flexibility in labeling for certain menus and food products, temporarily conducting remote inspections of food importers, and generally limiting domestic inspections to those that are most critical. USDA FSIS has also indicated they are “exercising enforcement discretion” to provide labeling flexibilities. The Canadian Food Inspection Agency (CFIA) announced they are prioritizing certain regulatory activities and temporarily suspending those activities determined to be “low risk.” GFSI has also taken measures to allow Certification Program Owners to provide certificate extensions due to the inability to conduct in-person audits.

While these organizations have assured stakeholders and the public that food safety is of primary importance, the level of direct regulatory and auditing oversight has been reduced to reduce the risk of virus transmission during in-person activities. Strong auditing programs with an anti-fraud component are an important aspect of food fraud prevention. Adjustments to regulatory and auditing oversight, as necessary as they may be, increase the risk of fraud in the food system.

There is a focus on safety and sustainability of foods. The food industry and regulatory agencies are understandably focused on basic food safety and food sustainability and less focused on non-critical issues such as quality and labeling. However, there is a general sense among some in industry that the risk of food fraud is heightened right now. Many of the effects on the industry due to COVID-19 are factors that are known to increase fraud risk: Supply chain disruptions, changes in commodity prices, supplier relationships (which may need to be changed in response to shortages), and a lack of strong auditing and oversight. However, as of yet, we have not seen a sharp increase in public reports of food fraud.

This may be due to the fact that we are still in the relatively early stages of the supply chain disruptions. India reported recently that the Food Safety Department of Kerala seized thousands of kilograms of “stale” and “toxic” fish and shrimp illegally brought in to replace supply shortages resulting from the halt in fishing that occurred due to lockdown measures.

High-value products may be particularly at risk. Certain high-value products, such as botanical ingredients used in foods and dietary supplements, may be especially at risk due to supply chain disruptions. Historical data indicate that high-value products such as extra virgin olive oil, honey, spices, and liquors, are perpetual targets for fraudulent activity. Turmeric, which we have discussed previously, was particularly cited as being at high risk for fraud due to “‘exploding’ demand ‘amidst supply chain disruptions.’”

How can we ensure food sufficiency, safety, and integrity? FAO has recommended that food banks be mobilized, the health of workers in the food and agriculture sector be prioritized, that governments support small food producers, and that trade and tax policies keep global food trade open. They go on to say, “by keeping the gears of the supply chains moving and actively seeking international cooperation to keep trade open, countries can prevent food shortages and protect the most vulnerable populations.” FAO and WHO also published interim guidance for national food safety control systems, which noted the increased risk of food fraud. They stated “during this pandemic, competent authorities should investigate reported incidences involving food fraud and work closely with food businesses to assess the vulnerability of supply chains…”.

From a food industry perspective, some important considerations include whether businesses have multiple approved suppliers for essential ingredients and the availability of commodities that may affect your upstream suppliers. The Acheson Group recommends increasing supply chain surveillance during this time. The Food Chemicals Codex group recommends testing early and testing often and maintaining clear and accurate communication along the supply chain.1 The nonprofit American Botanical Council, in a memo from its Botanical Adulterants Prevention Program, stated “responsible buyers, even those with relatively robust quality control programs, may need to double- or even triple-down on QC measures that deal with ingredient identity and authenticity.”

Measures to ensure the sufficiency, sustainability, safety and integrity of foods are more closely linked than ever before. In this time when sufficiency is critical, it is important to avoid preventable food recalls due to authenticity concerns. We also need to stay alert for situations where illegal and possibly hazardous food products enter the market due to shortages created by secondary effects of the virus. The best practices industry uses to reduce the risk of food fraud are now important for also ensuring the sufficiency, sustainability and safety of the global food supply.

Reference

  1. Food Safety Tech. (April 24, 2020). “COVID-19 in the Food Industry: Mitigating and Preparing for Supply Chain Disruptions “. On-Demand Webinar. Registration page retrieved from https://register.gotowebinar.com/recording/1172058910950755596

*Foodborne transmission is, according to the Food Standards Agency in the U.K., “unlikely” and, according to the U.S. FDA, “currently there is no evidence of food or food packaging being associated with transmission of COVID-19.”

Food Safety & Environmental Monitoring in Food Production

This webinar will present a time saving, paperless, and cost-effective solution to manage an environmental monitoring program guided by ISO 22000. Attendees will learn how to identify critical control points for the testing process in food production laboratories and how implementing a LIMS can address food safety and quality industry trends and challenges.

Benjamin Katchman, PathogenDx
In the Food Lab

Revolutionary Rapid Testing for Listeria Monocytogenes and Salmonella

By Benjamin A. Katchman, Ph.D., Michael E. Hogan, Ph.D., Nathan Libbey, Patrick M. Bird
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Benjamin Katchman, PathogenDx

The Golden Age of Bacteriology: Discovering the Unknown in a Farm-to-Market Food Supply.

The last quarter of the 19th Century was both horrific and exciting. The world had just emerged from four decades of epidemic in cholera, typhoid fever and other enteric diseases for which no cause was known. Thus, the great scientific minds of Europe sought to find understanding. Robert Koch integrated Pasteur’s Germ Theory in 1861 with the high technology of the day: Mathematical optics and the first industrialized compound microscopes (Siebert, Leiss, 1877), heterocycle chemistry, high-purity solvents (i.e., formaldehyde), availability of engineered glass suitable as microscope slides and precision-molded parts such as tubes and plates in 1877, and industrialized agar production from seaweed in Japan in 1860. The enduring fruit of Koch’s technology integration tour de force is well known: Dye staining of bacteria for sub-micron microscopy, the invention of 13 cm x 1 cm culture tubes and the invention of the “Petri” dish coupled to agar-enriched culture media. Those technologies not only launched “The Golden Age of Bacteriology” but also guided the entire field of analytical microbiology for two lifetimes, becoming bedrock of 20th Century food safety regulation (the Federal Food, Drug and Cosmetic Act in 1938) and well into the 21st century with FSMA.

Learn more about technologies in food safety testing at the Food Labs / Cannabis Labs Conference | June 2–4, 2020 | Register now!Blockchain Microbiology: Managing the Known in an International Food Supply Chain.

If Koch were to reappear in 2020 and were presented with a manual of technical microbiology, he would have little difficulty recognizing the current practice of cell fixation, staining and microscopy, or the SOPs associated with fluid phase enrichment culture and agar plate culture on glass dishes (still named after his lab assistant). The point to be made is that the analytical plate culture technology developed by Koch was game changing then, in the “farm-to-market” supply chain in Koch’s hometown of Berlin. But today, plate culture still takes about 24 to 72 hours for broad class indicator identification and 48 to 96 hours for limited species level identification of common pathogens. In 1880, life was slow and that much time was needed to travel by train from Paris to Berlin. In 2020, that is the time needed to ship food to Berlin from any place on earth. While more rapid tests have been developed such as the ATP assay, they lack the speciation and analytical confidence necessary to provide actionable information to food safety professionals.

It can be argued that leading up to 2020, there has been an significant paradigm shift in the understanding of microbiology (genetics, systems based understanding of microbial function), which can now be coupled to new Third Industrial Age technologies, to make the 2020 international food supply chain safer.

We Are Not in 1880 Anymore: The Time has Come to Move Food Safety Testing into the 21st Century.

Each year, there are more than 48 million illnesses in the United States due to contaminated food.1 These illnesses place a heavy burden on consumers, food manufacturers, healthcare, and other ancillary parties, resulting in more than $75 billion in cost for the United States alone.2 This figure, while seemingly staggering, may increase in future years as reporting continues to increase. For Salmonella related illnesses alone, an estimated 97% of cases go unreported and Listeria monocytogenes is estimated to cause about 1,600 illnesses each year in the United States with more than 1,500 related hospitalizations and 260 related deaths.1,3 As reporting increases, food producers and regulatory bodies will feel an increased need to surveil all aspects of food production, from soil and air, to final product and packaging. The current standards for pathogenic agriculture and environmental testing, culture-based methods, qPCR and ATP assays are not able to meet the rapid, multiplexed and specificity required to meet the current and future demands of the industry.

At the DNA level, single cell level by PCR, high throughput sequencing, and microarrays provide the ability to identify multiple microbes in less than 24 hours with high levels of sensitivity and specificity (see Figure 1). With unique sample prep methods that obviate enrichment, DNA extraction and purification, these technologies will continue to rapidly reduce total test turnaround times into the single digit hours while simultaneously reducing the costs per test within the economics window of the food safety testing world. There are still growing pains as the industry begins to accept these new molecular approaches to microbiology such as advanced training, novel technology and integrated software analysis.

It is easy to envision that the digital data obtained from DNA-based microbial testing could become the next generation gold standard as a “system parameter” to the food supply chain. Imagine for instance that at time of shipping of a container, a data vector would be produced (i.e., time stamp out, location out, invoice, Listeria Speciation and/or Serovar discrimination, Salmonella Speciation and/or Serovar discrimination, refer toFigure 1) where the added microbial data would be treated as another important digital attribute of the load. Though it may seem far-fetched, such early prototyping through the CDC and USDA has already begun at sites in the U.S. trucking industry, based on DNA microarray and sequencing based microbial testing.

Given that “Third Industrial Revolution” technology can now be used to make microbial detection fast, digital, internet enabled and culture free, we argue here that molecular testing of the food chain (DNA or protein based) should, as soon as possible, be developed and validated to replace culture based analysis.

Broad Microbial Detection
Current microbiological diagnostic technology is only able to test for broad species of family identification of different pathogens. New and emerging molecular diagnostic technology offers a highly multiplexed, rapid, sensitive and specific platforms at increasingly affordable prices. Graphic courtesy of PathogenDx.

References.

  1. Scallan, E., Hoekstra, R. M., Angulo, F. J., Tauxe, R. V., Widdowson, M. A., Roy, S. L., … Griffin, P. M. (2011). Foodborne illness acquired in the United States–major pathogens. Emerging infectious diseases, 17(1), 7–15. doi:10.3201/eid1701.p11101
  2. Scharff, Robert. (2012). Economic Burden from Health Losses Due to Foodborne Illness in the United States. Journal of food protection. 75. 123-31. 10.4315/0362-028X.JFP-11-058.
  3. Mead, P. S., Slutsker, L., Dietz, V., McCaig, L. F., Bresee, J. S., Shapiro, C., … Tauxe, R. V. (1999). Food-related illness and death in the United States. Emerging infectious diseases, 5(5), 607–625. doi:10.3201/eid0505.990502
Ben Schreiber, ActiveSense
Bug Bytes

How ERM Can Simplify Pest Management

By Benjamin Schreiber
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Ben Schreiber, ActiveSense

Whether you work in food manufacturing, distribution or retail, pests are both a fact of life as well as a regulatory disruption. At the same time, pest management solutions aren’t always clear-cut: While there are a variety of effective strategies employed by pest management professionals (PMPs) servicing the food industry, industry challenges—shifting regulatory standards, a lack of proper documentation and more—can complicate the process. For these reasons, short-term rodent problems can become long-term logistical nightmares, leaving food manufacturers in an undesirable situation when a third-party food plant auditor arrives.

Fortunately, emerging technologies in pest management practices are helping facility managers streamline their food and beverage quality assurance processes, reducing the risk of product loss, regulatory action, improper brand management and more. Specifically, electronic remote monitoring (ERM) allows PMPs to detect and monitor rodents in real time, providing you with important information to help reduce risk and increase audit compliance. As such, the value of food safety pest management strategies that incorporate ERM systems is only growing. Seeking out PMPs who use ERM allows you to invest in technologies that protect your margins, ensure the quality of your product and, ultimately, safeguard your most important asset—your reputation.

Modernizing Pest Management With ERM

At first glance, it might seem like pest management practices haven’t drastically changed since they were first implemented in the food manufacturing industry. Many rodent trapping systems remain similar to their original design: Devices designed to trap or kill that must be individually inspected and serviced by professional technicians. Technicians must then relay any risks to facility managers, who have to determine if additional resources are needed to avoid product loss or audit-based infractions.

Upon closer examination, it’s clear that while pests themselves have not significantly changed, both the pest management industry and the modern food supply chain have become increasingly complex. Food facility managers must contend with increasingly stringent food safety standards, and PMPs must rise to meet these needs with evolving pest management strategies.

In many ways, ERM technologies are the structural pest control industry’s response to these challenges, providing technicians with real-time notifications about rodent behavior and allowing them to make risk-based assessments that identify and treat problems before infestations occur. Unlike pest control strategies that rely on periodic service visits from technicians, PMPs who utilize ERM technology can monitor pest activity around the clock, 24/7/365, in virtually any environment. Instead of monitoring individual traps, PMPs can use ERM technology to know exactly when and where pest activity occurs, including in hard-to-monitor areas such as drop ceilings, crawlspaces, shelving undersides and other traditionally overlooked spaces. Technicians then receive valuable analytics from each trap they install, as well as documentation and reporting, that help managers achieve audit and regulatory compliance.

FSMA and ERM

In 2015, the FDA issued the final component of preventative control for human food under FSMA, officially enacting legislation that requires food safety plants to focus on risk-based pest prevention instead of reactive pest control strategies. As a result, quality assurance professionals and facility managers are often tasked with reallocating personnel toward proactive pest control activities in addition to their day-to-day responsibilities.

In many ways, ERM systems go hand-in-hand with FSMA and GFSI regulations. While preparing for a situation that hasn’t yet occurred can be a costly and time-consuming process, ERM has helped PMPs develop custom pest management strategies that assess and control situations in accordance with FSMA and other auditing firm guidelines. In many ways, ERM can provide all parties—PMPs, in-house auditors and third-party regulators—with a track record of pest history that all parties can cross-reference when assessing a facility.

From Risk-Averse to Risk-Based

When it comes to food safety rules and regulations, the only constant is change. In the structural pest control industry, auditors have historically implemented strict guidelines about trap placement that are frequently changing: For instance, traps should be placed every 10, 15, or 20 feet, regardless of facility susceptibility to various pest conditions. Failure to comply with regulations can result in point deductions on audits, even if the conditions that might lead to an infestation are not present. As such, food processing plants often choose to abide by the most stringent audit guidelines imposed upon them by other parties, such as retailers. By utilizing ERM technologies, food safety and quality assurance professionals can use additional pest monitoring analytics to focus on specific compliance issues, rather than spending additional time and money on other strategies.

Additionally, ERM allows PMPs to focus their efforts not only on weekly service visits and station checks, but also on important tasks, including assessing facility vulnerabilities, tracking rodent access points, and providing consultation and additional management strategies to their client—you.

Approaching the Audit with ERM

Food plant managers and retailers alike know that auditor approval is everything. Because ERM is a fast-developing technology, many quality assurance managers and facility owners are curious to know if ERM is audit approved. In truth, there are many kinds of audits, each with different goals, assessment techniques and regulatory standards. When it comes to audits, the gold standard is not necessarily the assessment of the facility and production line itself, but rather how well the assessment matches records kept by the food production plant.

To this end, ERM might be the answer to a streamlined audit process. No matter what kind of audit a plant is currently undergoing, ERM allows PMPs to provide records auditors need to verify that all systems are working properly. ERM can mean the difference between a streamlined process and a laborious audit, acting as a documentation system that helps officials conduct a PMP-verified “second-check.” This kind of verification is invaluable in an industry where there are already more than enough regulatory categories to consider without having to further worry about potential pest infestations.

ERM-Oriented Solutions

Thanks to the many advantages they offer, ERM and other remote pest monitoring technologies are growing in popularity. Many facility managers appreciate that ERM allows them to assess pest activity, prevent infestations before they occur, gather data that helps them remain industry-compliant, and acquire and share information with additional parties. If you’re a facility manager, quality assurance professional or other food safety decision-maker interested in the opportunities ERM technologies provide, consider starting the conversation about your pest prevention system with your PMP and how ERM might help improve it.

Trust, But Verify

There is an overwhelming consensus in the pest control industry that technology should be developed to provide end-users with more information. ERM systems are a natural extension of this belief, providing each component of the food production and distribution supply chain—manufacturers, distributors, retailers, quality assurance officials, technicians and others—with more data about how pest control decisions are made. Without data, it can be difficult to ensure technician service visits end in greater transparency about the issues facility owners will face as they prepare for an audit.

Fortunately, ERM can help provide the level of trust and assurance plant managers need to feel confident in their day-to-day operations. ERM is an important step forward for manufacturer-regulator relations, which require a strong combination of data, trust and transparency to ensure that communication systems don’t break down. After all, there are many industries in which miscommunication can lead to catastrophic consequences, and food production is no exception.

While each manufacturing facility, processing plant, distribution center, storage warehouse and retail outlet is different, none are insusceptible to pest infestations, and none can avoid audits required to keep them compliant. Because rigorous oversight is crucial for food producers and consumers alike, working with your PMP to develop pest monitoring strategies that utilize ERM systems and other cutting-edge technologies should be part of your larger pest control consideration process.

In the end, the pest infestation that causes the least damage to your product, profit potential and industry reputation is the infestation that never occurs.

Gregory Siragusa, Eurofins
Food Genomics

Introducing a New Column: Food Genomics

By Gregory Siragusa, Douglas Marshall, Ph.D.
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Gregory Siragusa, Eurofins

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.

Gregory Siragusa, Eurofins
Gregory Siragusa will be presenting Microbiome Applications in Controlling Food Spoilage and Safety  during the 2016 Food Safety Consortium

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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Bokulich, N. A., & Mills, D. A. (2012). Next-generation approaches to the microbial ecology of food fermentations. BMB Reports, 45(7), 377–389.
  7. 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
  8. Microbial Foods – The Science Of Fermented Foods. (n.d.). Retrieved November 21, 2016, from http://microbialfoods.org/
  9. 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
  10. 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
  11. 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
  12. Genome Glossary. (n.d.). Accessed November 21, 2016. Retrieved from http://doegenomestolife.org/glossary/index.shtml
  13. Talking Glossary of Genetic Terms. (n.d.). Accessed November 21, 2016. Retrieved from https://www.genome.gov/glossary/
  14. Microbiota. (2016, November 14). In Wikipedia. Retrieved from https://en.wikipedia.org/w/index.php?title=Microbiota&oldid=749454552
  15. 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

 

Meritech Helps Companies Improve Employee Hygiene GMPs

Meritech, manufacturer of the world’s only fully-automated, touch-free handwashing systems will be exhibiting at the 2016 Food Safety Consortium in Schaumburg, Illinois — with one of its automated handwashers onsite for attendees to experience the technology-based approach to employee hand hygiene. Meritech offers a full line of automated handwashing and footwear sanitizing systems, designed to meet increasingly stringent food safety standards and regulations.

All CleanTech automated handwashing systems deliver a consistent 12-second wash and rinse cycle, removing 99.98% of dangerous pathogens from hands. Meritech products use 75% less water, require less soap/sanitizer, and reduce discharge waste, compared to equivalent manual handwashing.

Listeria and Salmonella outbreaks are some of the biggest fears throughout the food industry. Effective employee hygiene at critical control points is necessary and Meritech offers the best guaranteed preventative measures through its automated systems.  Effective, efficient footwear sanitizing, especially when  combined with simultaneous handwashing, can reduce or eliminate the spread of these and other pathogens. Meritech’s automated handwasher with an optional footwear sanitizing pan guarantees clean hands and sanitized shoes in 12 seconds.

Meritech helps companies in a wide variety of markets, including food production, food service, theme parks, cruise lines and hospitals. All Meritech products are designed and manufactured in Golden, Colorado. The company ensures that your equipment is always effective by delivering best-in-class, proprietary chemicals and providing no charge, onsite scheduled calibration by its team of Service Engineers. Visit www.meritech.com to learn more.

Kraft and Heinz Merger Forms World’s 5th Largest Food Company

By Food Safety Tech Staff
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The new Kraft Heniz Co. will house several iconic brands such as Oscar Meyer meats, Velveeta, Jell-O, Kool-Aid, Planters and Philadelphia. Eight of its combined brands will be worth more than $1 billion each, while five will be worth approximately $500 million to $1 billion each.

Kraft-Heinz-mergerKraft Foods Group, maker of macaroni-and-cheese products, announced Wednesday that it would merge with H.J. Heinz Co., maker of the ketchup, to become the fifth largest food-and-beverage company in the world and the third largest in the U.S.

The new company, the Kraft Heinz Co., will be co-headquartered in the Chicago and Pittsburgh areas and will have revenues of roughly $28 billion, the companies announced in a statement Wednesday.

The new company will house several iconic brands such as Oscar Meyer meats, Velveeta, Jell-O, Kool-Aid, Planters and Philadelphia. Eight of its combined brands will be worth more than $1 billion each, while five will be worth approximately $500 million to $1 billion each.

Berkshire Hathaway Inc. and Brazilian private-equity firm 3G Capital, which co-own Heinz, will invest an additional $10 billion into the merged company, of which current Heinz and Kraft shareholders will collectively own 51 percent and 49 percent respectively. Kraft shareholders will also receive special cash dividends of $16.50 per share.

According to some estimates the merge will help create $1.5 billion a year in savings due to combined efficiencies and shared resources.

Berkshire Hathaway chairman and CEO Warren Buffett said in a statement. “This is my kind of transaction, uniting two world-class organizations and delivering shareholder value. I’m excited by the opportunities for what this new combined organization will achieve.”