Tag Archives: laboratories

LIMS, Laboratory information management system, food safety

How Advanced LIMS Brings Control, Consistency and Compliance to Food Safety

By Ed Ingalls
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LIMS, Laboratory information management system, food safety

Recent food scandals around the world have generated strong public concerns about the safety of the foods being consumed. Severe threats to food safety exist at all stages of the supply chain in the form of physical, chemical and biological contaminants. The current pandemic has escalated the public’s concern about cross contamination between people and food products and packaging. To eliminate food risks, manufacturers need robust technologies that allow for reliable monitoring of key contaminants, while also facilitating compliance with the ISO 17025 standard to prove the technical competence of food testing laboratories.

Without effective data and process management, manufacturers risk erroneous information, compromised product quality and regulatory noncompliance. In this article, we discuss how implementing a LIMS platform enables food manufacturers to meet regulatory requirements and ensure consumer confidence in their products.

Safeguarding Food Quality to Meet Industry Standards

Food testing laboratories are continually updated about foodborne illnesses making headlines. In addition to bacterial contamination in perishable foods and ingredient adulteration for economic gains, chemical contamination is also on the rise due to increased pesticide use. Whether it is Salmonella-contaminated peanut butter or undeclared horsemeat inside beef, each food-related scandal is a strong reminder of the importance of safeguarding food quality.

Food safety requires both preventive activities as well as food quality testing against set quality standards. Establishing standardized systems that address both food safety and quality makes it easier for manufacturers to comply with regulatory requirements, ultimately ensuring the food is safe for public consumption.

In response to food safety concerns, governing bodies have strengthened regulations. Food manufacturers are now required to ensure bacteria, drug residues and contaminant levels fall within published acceptable limits. In 2017, the ISO 17025 standard was updated to provide a risk-based approach, with an increased focus on information technology, such as the use of software systems and maintaining electronic records.

The FDA issued a notice that by February 2022, food testing, in certain circumstances, must be conducted in compliance with the ISO 17025 standard. This means that laboratories performing food safety testing will need to implement processes and systems to achieve and maintain compliance with the standard, confirming the competence, impartiality and consistent operation of the laboratory.

To meet the ISO 17025 standard, food testing laboratories will need a powerful LIMS platform that integrates into existing workflows and is built to drive and demonstrate compliance.

From Hazard Analysis to Record-Keeping: A Data-Led Approach

Incorporating LIMS into the entire workflow at a food manufacturing facility enables the standardization of processes across its laboratories. Laboratories can seamlessly integrate analytical and quality control workflows. Modern LIMS platforms provide out-of-the-box compliance options to set up food safety and quality control requirements as a preconfigured workflow.

The requirements set by the ISO 17025 standard build upon the critical points for food safety outlined in the Hazard Analysis and Critical Control Points (HACCP) methodology. HACCP, a risk-based safety management procedure, requires food manufacturers to identify, evaluate and address all risks associated with food safety.

LIMS, laboratory information management system
LIMS can be used to visualize control points for HACCP analysis according to set limits. Graphic courtesy of Thermo Fisher Scientific.

The systematic HACCP approach involves seven core principles to control food safety hazards. Each of the following seven principles can be directly addressed using LIMS:

  • Principle 1. Conduct a hazard analysis: Using current and previous data, food safety risks are thoroughly assessed.
  • Principle 2. Determine the critical control points (CCPs): Each CCP can be entered into LIMS with contamination grades assigned.
  • Principle 3. Establish critical limits: Based on each CCP specification, analytical critical limits can be set in LIMS.
  • Principle 4. Establish monitoring procedures: By defining sampling schedules in LIMS and setting other parameters, such as frequency and data visualization, procedures can be closely monitored.
  • Principle 5. Establish corrective actions: LIMS identifies and reports incidents to drive corrective action. It also enables traceability of contamination and maintains audit trails to review the process.
  • Principle 6. Establish verification procedures: LIMS verifies procedures and preventive measures at the defined CCPs.
  • Principle 7. Establish record-keeping and documentation procedures: All data, processes, instrument reports and user details remain secured in LIMS. This information can never be lost or misplaced.

As food manufacturers enforce the safety standards set by HACCP, the process can generate thousands of data points per day. The collected data is only as useful as the system that manages it. Having LIMS manage the laboratory data automates the flow of quality data and simplifies product release.

How LIMS Enable Clear Compliance and Optimal Control

Modern LIMS platforms are built to comply with ISO 17025. Preconfigured processes include instrument and equipment calibration and maintenance management, traceability, record-keeping, validation and reporting, and enable laboratories to achieve compliance, standardize workflows and streamline data management.

The workflow-based functionality in LIMS allows researchers to map laboratory processes, automate decisions and actions based on set criteria, and reduce user intervention. LIMS validate protocols and maintain traceable data records with a clear audit history to remain compliant. Data workflows in LIMS preserve data integrity and provide records, according to the ALCOA+ principles. This framework ensures the data is Attributable, Legible, Contemporaneous, Original and Accurate (ALCOA) as well as complete, consistent and enduring. While the FDA created ALCOA+ for pharmaceutical drug manufacturers, these same principles can be applied to food manufacturers.

Environmental monitoring and quality control (QC) samples can be managed using LIMS and associated with the final product. To plan environmental monitoring, CCPs can be set up in the LIMS for specific locations, such as plants, rooms and laboratories, and the related samples can then be added to the test schedule. Each sample entering the LIMS is associated with the CCP test limits defined in the specification.

Near real-time data visualization and reporting tools can simplify hazard analysis. Managers can display information in different formats to monitor critical points in a process, flag unexpected or out-of-trend numbers, and immediately take corrective action to mitigate the error, meeting the requirements of Principles 4 and 5 of HACCP. LIMS dashboards can be optimized by product and facility to provide visibility into the complete process.

Rules that control sampling procedures are preconfigured in the LIMS along with specific testing rules based on the supplier. If a process is trending out of control, the system will notify laboratory personnel before the product fails specification. If required, incidents can be raised in the LIMS software to track the investigation of the issue while key performance indicators are used to track the overall laboratory performance.

Tasks that were once performed manually, such as maintaining staff training records or equipment calibration schedules, can now be managed directly in LIMS. Using LIMS, analysts can manage instrument maintenance down to its individual component parts. System alerts also ensure timely recalibration and regular servicing to maintain compliance without system downtime or unplanned interruptions. The system can prevent users from executing tests without the proper training records or if the instrument is due for calibration or maintenance work. Operators can approve and sign documents electronically, maintaining a permanent record, according to Principle 7 of HACCP.

LIMS allow seamless collaboration between teams spread across different locations. For instance, users from any facility or even internationally can securely use system dashboards and generate reports. When final testing is complete, Certificates of Analysis (CoAs) can be autogenerated with final results and showing that the product met specifications. All activities in the system are tracked and stored in the audit trail.

With features designed to address the HACCP principles and meet the ISO 17025 compliance requirements, modern LIMS enable manufacturers to optimize workflows and maintain traceability from individual batches of raw materials all the way through to the finished product.

Conclusion

To maintain the highest food quality and safeguard consumer health, laboratories need reliable data management systems. By complying with the ISO 17025 standard before the upcoming mandate by the FDA, food testing laboratories can ensure data integrity and effective process management. LIMS platforms provide laboratories with integrated workflows, automated procedures and electronic record-keeping, making the whole process more efficient and productive.

With even the slightest oversight, food manufacturers not only risk product recalls and lost revenue, but also losing the consumers’ trust. By upholding data integrity, LIMS play an important role in ensuring food safety and quality.

Crop spraying, Ellutia

From Farm to Fork: The Importance of Nitrosamine Testing in Food Safety

By Andrew James
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Crop spraying, Ellutia

N-nitroso compounds (NOCs), or nitrosamines, have once again made headline news as their occurrence in some pharmaceuticals has led to high profile product recalls in the United States.1 Nitrosamines can be carcinogenic and genotoxic and, in the food industry, can compromise a food product’s quality and safety. One nitrosamine in particular, N-nitrosodimethylamine (NDMA), is a highly potent carcinogen, traces of which are commonly detected in foods and may be used as an indicator compound for the presence of nitrosamines.2

NOCs can potentially make their way into the food chain in a number of ways, including (but not limited to): Via the crop protection products used to maximize agricultural yields; via the sodium and/or potassium salt added to preserve certain meats from bacterial contamination; as a result of the direct-fire drying process in certain foods; and via consumption of nitrates in the diet (present in many vegetables due to natural mineral deposits in the soil), which react with bacteria and acids in the stomach to form nitrosamines.3

The crop protection and food manufacturing industries are focused on ensuring that levels of nitrosamines present in foods are minimal and safe. Detection technology for quantitating the amount of nitrosamines (ppm levels) in a sample had not advanced in nearly 40 years—until recently. Now, a thermal energy analyzer (TEA) —a sensitive and specific detector—is being relied on to provide fast and sensitive analysis for players throughout the food supply chain.

Regulatory Landscape

Both NDMA and the nitrosamine N-nitrososodiethylamine (NDEA) have been classified by national and international regulatory authorities as ‘probable human carcinogens’.3 NDMA in particular is by far the most commonly encountered member of this group of compounds.7

In the United States there are limits for NDMA or total nitrosamines in bacon, barley malt, ham and malt beverages, yet there are currently no regulatory limits for N-nitroso compounds (NOC) in foods in the EU.7

Developers of crop protection products are required to verify the absence of nitrosamines or quantify the amount at ppm levels to ensure they are within the accepted guidelines.

Crop Protection

The presence of nitrosamines must be traced and risk-managed along the food’s journey from farm to fork. The issue affects testing from the very beginning – particularly at the crop protection stage, which is one of the most highly regulated industries in the world. Without crop protection, food and drink expenditures could increase by up to £70 million per year and 40% of the world’s food would not exist.7

Development of a new crop protection product (herbicide, fungicide, insecticide or seed treatment) involves several steps: Discovery and formulation of the product, trials and field development, toxicology, environmental impacts and final registration. New product registration requires demonstration of safety for all aspects of the environment, the workers, the crops that are being protected and the food that is consumed. This involves comprehensive risk assessments being carried out, based on data from numerous safety studies and an understanding of Good Agricultural Practice (GAP).

One global producer of agrochemicals uses a custom version of the TEA to verify the absence of nitrosamines or quantitate the amount of nitrosamines (ppm levels) in its active ingredients. The LC-TEA enables high selectivity for nitro, nitroso and nitrogen (when operating in nitrogen mode), which allows only the compounds of interest to be seen. Additionally, it provides very high sensitivity (<2pg N/sec Signal to Noise 3:1), meaning it is able to detect compounds of interest at extremely low levels. To gain this high sensitivity and specificity, it relies on a selective thermal cleavage of N-NO bond and detection of the liberated NO radical by the chemiluminescent signal generated by its reaction with ozone.

The customized system also uses a different interface with a furnace, rather than the standard pyrolyser, to allow for the additional energy required and larger diameter tubing for working with a liquid sample rather than gas.

The system allows a company to run five to six times more samples with increased automation. As a direct result, significant productivity gains, reduced maintenance costs and more accurate results can be realized.

Food Analysis

Since nitrite was introduced in food preservation in the 1960s, its safety has been debated. The debate continues today, largely because of the benefits of nitrite in food products, particularly processed meats.6 In pork products, such as bacon and cured ham, nitrite is mostly present in the sodium and/or potassium salt added to preserve the meat from bacterial contamination. Although the meat curing process was designed to support preservation without refrigeration, a number of other benefits, such as enhancing color and taste, have since been recognized.

Analytical methods for the determination of N-nitrosamines in foods can differ between volatile and non-volatile compounds. Following extraction, volatile N-nitrosamines can be readily separated by GC using a capillary column and then detected by a TEA detector. The introduction of the TEA offered a new way to determine nitrosamine levels at a time when GC-MS could do so only with difficulty.

To identify and determine constituent amounts of NOCs in foods formed as a direct result of manufacturing and processing, the Food Standards Agency (FSA) approached Premier Analytical Services (PAS) to develop a screening method to identify and determine constituent amounts of NOCs in foods formed as a direct result of manufacturing and processing.

A rapid and selective apparent total nitrosamine content (ATNC) food screening method has been developed with a TEA. This has also been validated for the known dietary NOCs of concern. This method, however, is reliant on semi-selective chemical denitrosation reactions and can give false positives. The results can only be considered as a potential indicator rather than definitive proof of NOC presence.

In tests, approximately half (36 out of 63) samples returned a positive ATNC result. Further analysis of these samples by GC-MS/MS detected volatile nitrosamine contamination in two of 25 samples.

A key role of the TEA in this study was to validate the alternative analytical method of GC-MS/MS. After validation of the technique by TEA, GC-MS/MS has been proven to be highly sensitive and selective for this type of testing.

The Future of Nitrosamine Testing

Many countries have published data showing that toxicological risk from preformed NOCs was no longer considered an area for concern. Possible risks may come from the unintentional addition or contamination of foods with NOCs precursors such as nitrite and from endogenous formation of NOCs and more research is being done in this area.

Research and innovation are the foundations of a competitive food industry. Research in the plant protection industry is driven by farming and the food chain’s demand for greater efficiency and safer products. Because the amount of nitrosamines in food that results in health effects in humans is still unknown, there is scope for research into the chemical formation and transportation of nitrosamines, their occurrence and their impact on our health. Newer chromatographic techniques are only just being applied in this area and could greatly benefit the quantification of nitrosamines. It is essential that these new approaches to quality and validation are applied throughout the food chain.

References

  1. Christensen, J. (2020). More popular heartburn medications recalled due to impurity. CNN.
  2. Hamlet, C, Liang, L. (2017). An investigation to establish the types and levels of N-nitroso compounds (NOC) in UK consumed foods. Premier Analytical Services, 1-79.
  3. Woodcock, J. (2019). Statement alerting patients and health care professionals of NDMA found in samples of ranitidine. Center for Drug Evaluation and Research.
  4. Scanlan, RA. (1983). Formation and occurrence of nitrosamines in food. Cancer res, 43(5) 2435-2440.
  5.  Dowden, A. (2019). The truth about nitrates in your food. BBC Future.
  6.  Park, E. (2015). Distribution of Seven N-nitrosamines in Food. Toxicological research, 31(3) 279-288, doi: 10.5487/TR.2015.31.3.279.
  7.  Crews, C. (2019). The determination of N-nitrosamines in food. Quality Assurance and Safety of Crops & Foods, 1-11, doi: 10.1111/j.1757-837X.2010.00049.x
  8. (1989) Toxicological profile for n-Nitrosodimethylamine., Agency for Toxic substances and disease registry.
  9. Rickard, S. (2010). The value of crop protection, Crop Protection Association.
Food Labs Conference

Food Labs / Cannabis Labs 2020 Agenda Announced

By Food Safety Tech Staff
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Food Labs Conference

The agenda for the 2020 Food Labs / Cannabis Labs conference has been announced. The event, which will address regulatory, compliance and risk management issues that companies face in the area of testing and food laboratory management, is scheduled to take place on June 3–4 in Rockville, MD.

Some agenda highlights include a special morning session on June 3 that discusses the proposed FSMA rule on lab accreditation: “FSMA and the Impact on Laboratories and Laboratory Data Users” and “FSMA Proposed Rule on Laboratory Accreditation: What it says and what it should say” presented by Reinaldo Figueiredo of ANSI and Robin Stombler of Auburn Health Strategies, respectively. FDA has also been invited to speak on the proposed rule. Sessions will also cover the role of labs as it relates to pathogens, with presentations from Benjamin Katchman, Ph.D. (PathogenDx) about a novel DNA microarray assay used for detecting and speciating multiple Listeria species and Dave Evanson (Merieux Nutrisciences) on pathogen detection and control. The full agenda is listed on the Food Labs / Cannabis Labs website.

The early bird discount of $395 expires on March 31.

Innovative Publishing Company, Inc., the organizer of the conference, is fully taking into considerations the travel concerns related to the coronavirus. Should any
disruption that may prevent the production of this live event at its physical location in Rockville, MD due to COVID-19, all sessions will be converted to a virtual conference on the already planned dates. More information is available on the event website.

food safety tech

Next Week: Attend the ‘Drivers in Food Safety Testing’ Webinar

By Food Safety Tech Staff
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food safety tech
Angela Anandappa, Alliance for Advanced Sanitation
Angela Anandappa, Ph.D., founding director of the Alliance for Advanced Sanitation and member of the FST Advisory Board

Join Food Safety Tech next week for the first in a series of complimentary webinars, called Drivers in Food Safety Testing, about the important components and issues that encompass food safety testing. Angela Anandappa, Ph.D., founding director of the Alliance for Advanced Sanitation and member of the FST Advisory Board, will lead the discussion with a presentation about Technologies Leading the Way. The complimentary webinar is aimed at food safety professionals within quality assurance and control, compliance, food lab and contract lab management, and risk management. A technology spotlight given by Lyssa Sakaley, senior global product manager for molecular pathogen testing at MilliporeSigma will follow Anandappa’s presentation. The event will conclude with an interactive Q&A with attendees.

Drivers in Food Safety Testing: Technologies Leading the Way
Wednesday, March 18 at 1 pm ET
Register now!

Michele Pfannenstiel, Dirigo Food Safety
FST Soapbox

Quality Assurance and Food Safety in Cannabis-Infused Products

By Michele Pfannenstiel, DVM
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Michele Pfannenstiel, Dirigo Food Safety

The legal cannabis-infused products industry is growing with impressive and predictable rapidity. But because the rollout of new regulations occurs in an awkward and piecemeal fashion, with stark differences from one state to another, and sometimes even one county to another, uncertainty reigns.1 Many entrepreneurs are diving headlong into the nascent industry, hoping to take advantage of an uncertain regulatory environment where government audits and inspections are rare. These business owners will see quality assurance and product safety as burdens—costs to be avoided to the greatest extent possible.

I have seen this time and time again, even in the comparatively well-regulated food industry, and it is always a mistake.

If you find yourself thinking about quality assurance or food safety as a prohibitive cost, annoyance or distraction, I encourage you to change your thinking on this issue. The most successful businesses realize that product safety and quality assurance are inextricably linked with profitability. They are best thought of not as distractions, but as critical elements of an efficient and optimized process. Proper QA and safety are not costs, they are value.

Food safety and quality assurance should be seen as important elements of the process that you undertake to enforce the high standards and consistency that will win you repeat customers. The fact that they guard against costly recalls or satisfy meddlesome auditors is only a bonus. Realizing this will make your business smarter, faster and more profitable.

Learn more about the science, technology, regulatory compliance and quality management issues surrounding cannabis at the Food Labs / Cannabis Labs Conference | June 2–4, 2020If today you cannot clearly communicate your product standards to your employees and to your customers, then you have some work to do. That’s because quality assurance always begins with precise product specifications. (A good definition of “quality” is “conformance to specifications.”) How can you assess quality if you don’t have a definitive standard with which to evaluate it? My consulting firm works with food businesses both small and large, and this is where we begin every relationship. You might be surprised how often even a well-established business has a difficult time naming and describing every one of its products, let alone articulating objective standards for them.

This may be doubly difficult for fledgling businesses in the cannabis world. Because the market is so new, there are fewer agreed-upon standards to fall back on.

When we help businesses create specifications, we always look at the relevant regulations while keeping in mind customer expectations. In cannabis, the regulations just aren’t as comprehensive as they are for conventional food and agriculture. Laws and guidelines are still in flux, and different third-party standards are still competing for market dominance. Different states have entirely different standards, and don’t even agree, for example, whether cannabis edibles should be considered pharmaceuticals or food. To some extent, it’s the wild west of regulation, and as long as the federal government remains reluctant to impose national guidelines, it’s likely to remain so.

The wild west may be a good place for the unscrupulous, but it’s not good for business owners that care about the health of their customers and the long-term health of their brand. Don’t take advantage of confusing quality and safety standards by doing the least possible to get by. At some point there will be a scandal in this country when a novel cannabis product makes dozens of customers sick, or worse. You don’t want it to be yours.

With cannabis-infused products, there is a unique additional factor at play: The strength of THC and other psychoactive compounds. Again, there are few agreed-upon standards for potency testing, and relatively little oversight of the laboratories themselves. This allows labs to get sloppy, and even creates an incentive for them to return inflated THC counts; at the very least, results may hugely differ from one lab to another even for identical products.2 Some labs are ISO 17025 accredited, and some are not. Using an unaccredited laboratory may prevent your efforts to create consistent and homogeneous products.

Even in comparatively well-regulated states, such as Colorado, it is ultimately your responsibility to create products that are safe and consistent. And in the states where the politicians haven’t even figured out which department is regulating cannabis products, your standards should be tougher than whatever is officially required.

And so we look to the more established world of conventional food and agriculture as a guide for the best practices in the cannabis industry.

Hazards

The most constructive way to look at food safety, and the way your (eventual) auditors and regulators will view it, is to look at your product and process from the perspective of the potential hazards.

Some day, when regulation finally gets sorted out, you are likely to be asked to implement a Hazard Analysis and Critical Control Points (HACCP) safety system. HACCP framework recognizes three broad categories of hazards:

  • Physical hazards: Foreign material that is large enough to cause harm, such as glass or metal fragments.
  • Chemical hazards: Pesticides and herbicides, heavy metals, solvents and cleaning solutions.
  • Biological hazards: The pathogens that cause foodborne illness in your customers, such as E. coli, and other biological hazards, such as mycotoxins from molds.

All of these hazards are highly relevant to cannabis-infused product businesses.

The HACCP framework asks us to consider what steps in our process offer us the chance to definitively and objectively eliminate the risk of relevant hazards. In a cannabis cookie, for example, this might be a cooking step, a baking process that kills the Salmonella that could be lurking in your flour, eggs, chocolate or (just as likely!) the cannabis extracts themselves.

A good HACCP system is merely the capstone resting atop a larger foundational system of safety programs, including standard operating procedures, good manufacturing practices, and good agricultural practices. It’s important to use these agreed-upon practices and procedures in your own facility and to ensure that your suppliers and shippers are doing the same. Does your cultivator have a culture of safety and professionalism? Do they understand their own risks of hazards?

HACCP offers a rigorous perspective with which to look at a process, and to examine all of the places where it can go wrong. The safety system ultimately holds everything together because of its emphasis on scrupulous documentation. Every important step is written down, every time, and is always double-checked by a supervisor. It sounds like a lot of paperwork, but it is better viewed as an opportunity to enforce consistency and precision.

When you thoroughly document your process you’ll create a safer product, run a more efficient business, and make more money.

References

  1. Rough, L. (2016, March 4). Leafly’s State-by-State Guide to Cannabis Regulations. Retrieved from https://www.leafly.com/news/industry/leaflys-state-by-state-guide-to-cannabis-testing-regulations
  2. Jikomes, N. & Zoorob, M. (2018, March 14). The Cannabinoid Content of Legal Cannabis in Washington State Varies Systematically Across Testing Facilities and Popular Consumer Products. Retrieved from https://www.nature.com/articles/s41598-018-22755-2
Mahni Ghorashi, Clear Labs
In the Food Lab

The Food Safety Testing Lab as Profit Center

By Mahni Ghorashi
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Mahni Ghorashi, Clear Labs

It’s not that the industry has been more reluctant than others to embrace change; rather, the forces that will drive the food’s big data revolution have but recently come to bear.

Regulation is now playing a role. FSMA mandates that the industry embrace proactive food safety measures. That means higher testing volumes. Higher testing volumes means more data.

At the same time, new technologies like next-generation sequencing (NGS) are beginning to find wide-scale adoption in food-safety testing. And NGS technologies generate a lot of data—so much so that the food safety lab will soon emerge as the epicenter of the food industry’s big data revolution. As a result, the microbiology lab, a cost center, will soon emerge as one the industry’s most surprising profit centers.

A Familiar Trend

This shift may be unprecedented in food, but plenty of other industries touched by a technological transformation have undergone a similar change, flipping the switch from overhead to revenue generation.

Take the IT department, for instance. The debate about IT departments being a cost or profit center has been ongoing for many years. If data centers had simply kept doing what they have done in the past—data processing, enterprise resource planning, desktop applications, help desk—maintaining an IT department would have remained a cost center.

But things look quite different today. Companies in today’s fast-changing business environment depend on their IT departments to generate value. Now and for the foreseeable future, the IT department is on the hook to provide companies with a strategic advantage and to create new revenue opportunities.

Netflix, for example, recently estimated the value of their recommenders and personalization engines at $1 billion per year by quadrupling their effective catalog and dramatically increasing customer engagement and reducing churn.

Another great example are the call centers of customer support departments. For most of their history, call centers generated incredibly small margins or were outright cost centers.

Now, call centers armed with AI and chatbots are a source of valuable customer insights and are a treasure trove of many brands’ most valuable data. This data can be used to fuel upsells, inform future product development, enhance brand loyalty, and increase market share.

Take Amtrak as a prime example. When the commuter railway implemented natural language chatbots on their booking site, they generated 30% more revenue per booking, saved $1 million in customer service email costs, and experienced an 8X return on investment.

These types of returns are not out of reach for the food industry.

The Food Data Revolution Starts in the Lab

The microbiology lab will be the gravitational center of big data in the food industry. Millions of food samples flow in and out of these labs every hour and more and more samples are being tested each year. In 2016 the global food microbiology market totaled 1.14 billion tests—up 15% from 2013.1

I’d argue that the food-testing lab is the biggest data generator in the entire supply chain. These labs are not only collecting molecular data about raw and processed foods but also important inventory management information like lot numbers, brand names and supplier information, to name a few.

As technologies like NGS come online, the data these labs collect will increase exponentially.
NGS platforms have dramatically reduced turnaround times and achieve higher levels of accuracy and specificity than other sequencing platforms. Unlike most PCR and ELISA-based testing techniques, which can only generate binary answers, NGS platforms generate millions of data points with each run. Two hundred or more samples can be processed simultaneously at up to 25 million reads per sample.
With a single test, labs are able to gather information about a sample’s authenticity (is the food what the label says it is?); provenance (is the food from where it is supposed to be from?); adulterants (are there ingredients that aren’t supposed to be there?); and pathogen risk.

The food industry is well aware that food safety testing programs are already a worthwhile investment. Given the enormous human and financial costs of food recalls, a robust food-safety testing system is the best insurance policy any food brand can buy.

The brands that understand how to leverage the data that microbiology labs produce in ever larger quantities will be in a position to transform the cost of this insurance policy into new revenue streams.

Digitizing the Food Supply Chain

It’s clear that the food lab will generate massive amounts of data in the future, and it’s easy to see that this data will have value, but how, exactly, can food brands turn their data into revenue streams?

The real magic starts to happen when we can combine and correlate the trillions of data points we’re gathering from new forms of testing like NGS, with data already being collected, whether for inventory management, supply chain management, storage and environmental conditions, downstream sales data, or other forms of testing for additives and contaminant like pH, antibiotics, heavy metals and color additives.

When a food brand has all of this data at their fingertips, they can start to feed the data through an artificial intelligence platform that can find patterns and trends in the data. The possibilities are endless, but some insights you could imagine are:

  • When I procure raw ingredient A from supplier B and distributors X, Y, and Z, I consistently record higher-than-average rates of contamination.
  • Over the course of a fiscal year Supplier A’s product, while a higher cost per pound, actually increases my margin because, on average, it confers a greater nutritional value than the supplier B’s product.
  • A rare pathogen strain is emerging from suppliers who used the same manufacturing plant in Arizona.

Based on this information about suppliers, food brands can optimize their supplier relationships, decrease the risk associated with new suppliers, and prevent potential outbreaks from rare or emerging pathogen threats.

But clearly the real promise for revenue generation is in leveraging food data to inform R&D, and creating a tighter food safety testing and product development feedback loop.

The opportunity to develop new products based on insights generated in the microbiology lab are profound. This is where the upside lives.

For instance, brands could correlate shelf life with a particular ingredient or additive to find new ways of storing food longer. We can leverage data collected across a product line or multiple product lines to create new ingredient profiles that find substitutes for or eliminate unhealthy additives like corn syrup.

One of the areas I’m most excited about is personalized nutrition. With microbiome data collected during routine testing, we could develop probiotics and prebiotics that promote healthy gut flora, and eventually are even tailored to the unique genetic profile of individual shoppers. The holistic wellness crowd has always claimed that food is medicine; with predictive bioinformatic models and precise microbiome profiles, we can back up that claim scientifically for the first time.

Insights at Scale

Right now, much of the insight to be gained from unused food safety testing data requires the expertise of highly specialized bioinformaticians. We haven’t yet standardized bioinformatic algorithms and pipelines—that work is foundational to building the food genomics platforms of the future.

In the near future these food genomics platforms will leverage artificial intelligence and machine learning to automate bioinformatic workflows, dramatically increasing our ability to analyze enormous bodies of data and identify macro-level trends. Imagine the insights we could gain when we combine trillions of genomic data points from each phase in the food safety testing process—from routine pathogen testing to environmental monitoring to strain typing.

We’re not there yet, but the technology is not far off. And while the path to adoption will surely have its fair share of twists and turns, it’s clear that the business functions of food safety testing labs and R&D departments will grow to be more closely integrated than ever before.

In this respect the success of any food safety program will depend—as it always has—not just on the technology deployed in labs, but on how food brands operate. In the food industry, where low margins are the norm, brands have long depended on efficiently managed operations and superb leadership to remain competitive. I’m confident that given the quality and depth of its human resources, the food industry will be prove more successful than most in harnessing the power of big data in ways that truly benefit consumers.

The big data revolution in food will begin in the microbiology lab, but it will have its most profound impact at the kitchen table.

References

  1. Ferguson, B. (February/March 2017). “A Look at the Microbiology Testing Market.” Food Safety Magazine. Retrieved from https://www.foodsafetymagazine.com/magazine-archive1/februarymarch-2017/a-look-at-the-microbiology-testing-market/.
Dr. Douglass Marshall, Chief Scientific Officer – Eurofins Microbiology Laboratories
Food Genomics

Part II: Logistics of GenomeTrakr

By Douglas Marshall, Ph.D., Gregory Siragusa, Ph.D.
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Dr. Douglass Marshall, Chief Scientific Officer – Eurofins Microbiology Laboratories

Last month in Food Genomics we asked FDA scientists Drs. Marc Allard and Eric Brown to help the readers of Food Safety Tech understand the process used by GenomeTrakr. In part two we cover some logistical and more general questions.

Greg Siragusa/Douglas Marshall: Why should a food producer or processor submit its own pathogen isolates to GenomeTrakr? Are there any legal liabilities incurred by doing so?

Eric Brown/Marc Allard: The database is available publicly for any outside laboratory to be able to rapidly compare their new WGS data to all of the data in the database. The data is all publicly available so food industry members should carefully consider the strengths and weaknesses of sharing data. The main reason for sharing data is that if any matches arise then this would be immediately known for an investigation and corrective action. With knowledge, companies can better understand their risk and exposure to occasional contamination events.

Siragusa/Marshall: Are there private third-party providers who will perform the same method of sequence analysis for private companies that GenomeTrakr uses in the FDA?

Brown/Allard: Yes, as all of the FDA methods of data collection and analysis are fully transparent and publicly available, any expert third-party provider could easily set up and reproduce the GenomeTrakr methods. Third-party support may be an excellent mechanism for food industry partners that wish to examine the pathogens they have found connected to their products but do not wish to maintain an active WGS laboratory. An internet and reference search will uncover these private third-party providers, as this is a growing market with a diversity of services provided. The FDA works closely with the Institute for Food Safety and Health (IFSH) to share information that may be valuable to their industry partners.

Siragusa/Marshall: Will the FDA perform analysis of isolates for private parties and the sequence not made publicly available?

Brown/Allard: No. While we will sequence relevant strains from many different sources, as a matter of protocol we will submit all of these data to the GenomeTrakr database. That is, currently, the FDA sequences and uploads all available genomic strain data. All data are made publicly available through the GenomeTrakr and NCBI pathogen detection website. The metadata describing each isolate only includes species, date, state location and a general food description which could include the type of food (e.g., an egg) and/or the type of sample (e.g., environmental swab, surface water, sediment, etc.) as well as production date, pH, fat content and water activity. No trade or industry brand names are made publicly available, and the location is ambiguous down to the state level to allow for anonymity of specific farm names or processing centers. An example of metadata in the GenomeTrakr database might include Salmonella, from Washington State in spinach from 2015.

Siragusa/Marshall: Is the CDC tied into GenomeTrakr and if so, how?

Brown/Allard: CDC labels their clinical WGS data as PulseNet with the data uploaded to the NCBI Pathogen Detection website. USDA FSIS also uploads the isolates that they have collected and sequenced from foods that they regulate. All of this WGS data is housed in a centralized repository at NCBI Pathogen Detection website where NCBI conducts rapid analysis for QA/QC. The NCBI posts a daily tree for all species that recently have been uploaded. This way all of the data collected by these federal laboratories and their state and international partners are made publicly available for direct comparison. Numerous other international and academic laboratories also provide data to the NCBI centralized database. When isolates cluster together and appear to be closely related, the FDA works with CDC and USDA FSIS through the normal channels. The great benefit of combining food, environmental and clinical isolate genomes in a common database cannot be overstated.

Siragusa/Marshall: In the event of an outbreak, is it possible to obtain WGS’s from using a shotgun metagenome (a microbial and organismic profile obtain by sequencing all of the DNA in a sample, not just bacterial analysis of an enrichment thereby precluding isolation? (Refer to glossary; see Table 1)

Brown/Allard: Yes, preliminary research has documented the potential to obtain WGS data from cultural enrichments, saving the time it takes for full pure culture isolation, which potentially could provide time savings of two to five days depending on the pathogen. Having well characterized draft genomes such as those in the GenomeTrakr database will support rapid characterization from metagenomes after cultural enrichment. A future goal for the FDA is to transform and expand GenomeTrakr into metaGenomeTrakr to support either pure culture or enriched shotgun metagenomic samples.

Siragusa/Marshall: Is there any way that associated metadata tied to a strain (and hence its sequence) can be unmasked through legal action?

Brown/Allard: FDA protects confidential metadata collected during inspection just as it has always done with PFGE data. WGS data is protected at the same level as other types of subtyping information.

Siragusa/Marshall: Is the GenomeTrakr database associated with the GMI (Global Microbial Identifier)?

Brown/Allard: The GMI is a consortium of like-minded public health scientists who wish to collaborate to create a harmonized global system of DNA genome databases that is publicly available to promote a one-health approach. The GenomeTrakr is one of the databases that make up this larger effort that includes some data from members of the GMI.

Siragusa/Marshall: This column is meant to keep food safety professionals abreast of the latest knowledge, technology and uses of genomics for food safety and quality. Tell us your vision of how or which changes in technology (sequencing chemistry, bioinformatics, etc.) will be coming down the pike and how it might impact GenomeTrakr?

Brown/Allard: New technology has been constantly improving in WGS and in sequencing for the last 20 years, and there is no sign of this slowing down. Improvements continue to accrue in chemistry, equipment and software analysis. Likely future improvements will include more turnkey solutions for WGS from sample to report. This includes both DNA extraction and library preparation for sequencing, as well as data analysis pipelines (the system of analyzing the actual sequence data) that provide rapid, accurate and simple language results. Smaller mobile WGS devices are starting to show feasibility that would bring the lab to the samples and decrease the time to an answer (See: https://nanoporetech.com/products/minion) Metagenomics approaches appear to be maturing so that technology improvements are moving this out of a research phase and into direct applications. Currently MISeq (a commonly used workhorse nucleic acid sequencer made by the Illumina Co.) outputs are on the order of 300 base pair read lengths of nucleotides (i.e. A’s, T’s. C’s G’s), long read sequencing technologies, upwards of 1,500 base pairs may make analysis much easier so that more assembled and completed finished genomes are available in the databases. Cloud-based solutions of data analysis pipelines may provide simple solutions, giving wider access to rapid, validated data analysis and results. FDA researchers are working on all of these aspects of improvements in WGS technology as well as expanding the network to more global partners.

Siragusa/Marshall: Sequences deposited into GenBank (as part of GenomeTrakr) are accessible to anyone anywhere. Does this essentially usher in a whole new chapter in food microbiology especially at the pre-harvest level?

Brown/Allard: Yes, having well characterized reference genomes provided by GenomeTrakr partners will support microbial ecology and metagenomics studies. Metagenomics or microbiomes describing which species are present and what they may be doing in the ecology is providing new knowledge in all aspects of the farm to fork continuum. As the costs for these services decrease, we are seeing an increase in use to answer questions that have been impossible or extremely difficult in the past.

Siragusa/Marshall: GenomeTrakr is not a project per se; rather it is a program. How is it funded and will it continue on stable fiscal footing for the foreseeable future?

Brown/Allard: GenomeTrakr started as a research project in the Office of Regulatory Science in CFSAN, but much of this data collection is no longer research. Today, and for some time in the future, WGS at the FDA is collected as fully validated regulatory data to support outbreak and compliance investigations. As such, the FDA is in transition of moving WGS into a phase for more stable regulatory support. Research and development for future applications and technology exploration will always be a part of the FDA portfolio, although typically at lower funding levels than the regulatory offices. Public health funding is generally protected as everyone wants safe food.

Siragusa/Marshall: Are there any restrictions of isolate source? For instance, can isolates from poultry flocks or even wild birds be deposited?

Brown/Allard: The GenomeTrakr and NCBI pathogen detection databases are open to the public and thus there are no restrictions as long as the minimal metadata and QA and QC metrics are met. Current GenomeTrakr WGS foodborne pathogen data includes samples from both poultry and wild birds, as well as turtles, snakes and frogs. Members interested in what is in the database can go to the NCBI Pathogen Detection website and filter on simple words like avian, bird, gull, chicken, wheat, avocado, etc. An example is as follows for a snake.

Siragusa/Marshall: If a company deposits an isolate, will it have access to the GenomeTrakr derived sequence exclusively or at least initially for some period before that information becomes public?

Brown/Allard: No, currently the FDA does not hold WGS data. All data collected by the FDA is uploaded and released publicly at the GenomeTrakr bioprojects and at NCBI pathogen detection website with no delays. If companies wish to hold data then they need to look to third-party solutions for their needs. The reason that GenomeTrakr has been so successful is due to the real-time nature of the released information and that it is globally available.

Read on to page two below.

Food Safety is Key Initiative as FDA Develops Lab Testing Standards

When President Barack Obama in 2011 signed the Food Safety Modernization Act, the most sweeping reform of American food safety laws in more than 70 years, the Food and Drug Administration’s job got a lot tougher.

As the FDA’s Palmer Orlandi explained at Pittcon [on March 9], they might need your help to get that job done. Orlandi, who spoke as part of the two-day Food Safety Tech Food Labs Conference at Pittcon, is the agency’s  acting chief science officer in the office of food and veterinary medicine. The FDA traditionally has been very good at reacting to safety issues in our food supply as they arise and finding the source of the problem, Orlandi said. But, now the agency is charged with more of a preventive role, which means identifying the biggest risks before they become a threat to the public. That’s a big job, and the FDA can’t do it alone. “We’re looking for burden-sharing,” Orlandi said.

Partnerships with other federal agencies such as the Department of Agriculture and the Department of Homeland Security are part of the solution. They’re also working with state-level laboratories and even the private sector, he said. As an example, he cites the Food Emergency Response Network, which includes food-testing laboratories at the local, state, and federal levels. Initially formed to deal with bioterrorism threats, Orlandi said it has become a useful food safety network as well. FERN-affiliated labs recently tested 1,600 samples of avocados for salmonella and listeria, he said.

Much of the burden of this new preventive approach will fall on food producers. Orlandi said FDA is willing to work with private labs to develop standards. This can be tricky, however, because the agency doesn’t want to create the impression that it is somehow favoring one private sector entity over another. Meanwhile, private companies have their own trade secrets to protect. “Where is the middle ground where we can cooperate?” Orlandi asked rhetorically.

FDA has developed validation standards that field labs can use, he said. But, he concedes, the agency hasn’t done a good job compiling and publishing those standards into an accessible document or reaching out to stakeholders to make sure they’re up to speed. “That’s another thing on our to-do list,” he said.

Funding for these efforts is scarce. Joe Konschnik, a market research manager for Restek Chromatography Products who attended Orlandi’s presentation, helps to supply scientists working in College Park, MD to develop new procedures to analyze pesticides. Traditionally, once the research is published, the researchers’ jobs are over. Konschnik says now they’re trying to send the information out to other labs in the U.S. and overseas. That way, everyone can work from the same page to validate the work and create consistent standards.

One of the problems is that, for example, aerating seeds to run multilevel validation studies can cost $35,000, he said. But the FDA only has about $75,000 to fund such studies, which obviously would run out very quickly. “There’s no money to fund the back-end stuff,” Konschnik said. He said he works with the American Council of Independent Laboratories, which is willing to do the testing for free. But it still costs money for the FDA to make samples, send them to the labs, gather the data, and validate the data.

In short, the partnerships FDA is building remain a work in progress. But it has a new tool: the America Competes Act, which gives federal agencies the authority to award prizes for solving significant problems. The FDA has issued a “food safety challenge,” Orlandi said, looking for ways to reduce turnaround times on food safety tests, checking for salmonella, for example, from a few weeks to a day or two. The agency has a $500,000 prize pool, with $400,000 potentially going to the winner.

This article originally appeared in CEN media group’s Pittcon Today on Tuesday, March 10 and has been republished with permission. 

Sangita Viswanathan, Former Editor-in-Chief, FoodSafetyTech

The Value of Effective LIMS

By Sangita Viswanathan
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Sangita Viswanathan, Former Editor-in-Chief, FoodSafetyTech

With the announcement of proposed rules under the Food Safety Modernization Act (or FSMA), the burden of food safety testing and record keeping placed on smaller and medium size food companies and use of contract testing labs is growing tremendously. So how do these labs manage growing requests for testing, and increasing volumes of data and demand for records? 

Here is where Laboratory Information Management Systems or LIMS play an important role, in helping labs manage the testing requests, handle all the data and records, be better prepared for audits, and comply with changing regulations, says Anthony Uzzo, President & Co-Founder of Core Informatics.

Uzzo has extensive experience in software engineering, informatics, laboratory automation, project management and science. He co-founded Core Informatics in 2006, along with Jim Gregory (Executive VP of Customer Solutions). A biomedical engineer, Uzzo started his career as a pharmaceutical lab scientist, and in that role, realized that most LIMS solutions were rigid in their scope. 

“This exposed me to different labs having different data management requirements, and gave me a profound appreciation of the impact of data management and having effective LIMS in labs. When starting Core Informatics, my goal was to provide labs with the opportunity to tailor their data management system to their needs without having to change their workflow, systems, personnel etc.,” he describes. 

We present below some excerpts from an interview with Food Safety Tech (FST).

FST: Why are LIMS so important for food and beverage companies in the current environment?

Uzzo:The food and beverage industry faces increasing regulatory scrutiny, pressures to control costs, and the challenge of maintaining quality throughout a global supply chain. A LIMS solution needs to be a solution to aid companies in the delivery and discovery of products, while complying with industry and government regulations.

The LIMS need to identify hazards, determine and monitor critical control points, and establish corrective actions and verification procedures to ensure that standards are met and the system is functioning properly. Our HACCP compliant system helps companies in the F&B industry to monitor products and make sure they do not become contaminated with chemicals or food pathogens. 

FST: How can food companies and labs choose the ideal LIMS solution?

Uzzo: According to me, the top criteria for choosing a LIMS solution would be flexibility; being web-based (able to use the LIMS with smart devices for data entry and access and no antiquated client server technology); and total cost of ownership.

There are now all sorts of novel testing methodologies being applied for food safety, and as a result, the data management requirements are constantly changing. Solutions would need to facilitate administrators to use the LIMS without writing a new code, and easily and quickly enable multi-site collaboration. For instance, there are new rapid detection technologies, such as PCR technologies for Salmonella detection, now in the market. An ideal LIMS should be able to rapidly process these results and use that data analysis, come up with efficient reports and enable lab scientists to do their job in a cost-effective manner. 

Cloud-based solutions offer great advantages in providing the ability to auto-scale, handle any amount of data, send out samples to other labs, support multi-site collaboration etc. Core Informatics, for instance, is fully embracing the power of the cloud. 

An ideal LIMS solution should address chain of custody from registration to report. The final report needs to be mentioned and be able to track who had handled that sample and every derivative of it, how it has been handled, under which condition it has been stored and for how long, and if appropriate procedures have been followed for storage and handling. Downstream, if there’s any problem, we need to be able to go back upstream and identify the correct source material.

LIMS solutions need to be prepared as new laws come into play in the next few years. Industry trends are accelerating the use of contract food testing labs. How effectively companies are able to process their data management requirements such as automatically receiving and recording test requests, preparing for their audits and complying with their food safety management programs, will all become critical.