DNA sequencing

Whole Sample Next-Generation DNA Sequencing Method: An Alternative to DNA Barcoding

By Casey Schlenker, Jenna Brooks, Kent Oostra, Ryan McLaughlin
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DNA sequencing

This article discusses a non-targeted method for whole sample next generation DNA sequencing (NGS) that does not rely on DNA barcoding. DNA barcoding requires amplification of a specific gene region, which introduces bias. Our non-targeted method removes this bias by eliminating the amplification step. The applications of this method are broad and we have begun optimizing workflows for numerous materials, both processed and unprocessed. Some of the materials we have been able to successfully identify at the species level are fish tissue, fish meal, unrefined fish oil, unrefined plant-based oils (nuts, seeds, and fruits), specific components of cooked and processed products such as cookies and powders, and processed meats. Non-targeted NGS is also a very powerful tool to comprehensively identify constituents of microbial communities in probiotics and fermented products like kombucha. Additionally, this non-targeted technique is applicable to detection and identification of microbial contamination at various levels of manufacturing including equipment surfaces, processing water and assaying intermediate processing steps. In this communication we briefly review a current issue in the botanicals industry, discuss the methods that have been used in the past to tackle that problem, and present preliminary results from a pilot study we performed to determine the utility of non-targeted NGS in high-throughput identification of botanical raw materials.

The value of the global herbal dietary supplement (botanical) market was estimated to be greater than $90 billion in 2016, with a projected compound annual growth rate of 5-6%. Currently, regulators and manufacturers in this rapidly expanding market seek to confirm the veracity of label claims, investigate fraud, identify adulterants and ensure product quality.1 These products are often dried and ground, making visual identification difficult, time consuming and sometimes impossible.2 It is critical to this market that botanical identification be high-throughput, accurate and cost effective. Historically, various chromatography techniques have been used to meet this need, but those techniques rely on identification of molecules that can vary significantly due to storage conditions, which has led to the use of DNA barcoding as an analytical technique. However, DNA barcoding is not without significant challenges.1

For quite some time, scientists have had the ability to identify biological samples by sequencing their DNA.3 Currently DNA sequencing-based identification methods rely heavily on a technique called DNA barcoding, which functions analogously to the barcodes found on products in a grocery store. DNA barcoding amplifies a distinct small gene region that serves as a unique identifier and “scans” it by DNA sequencing.4 The advantages of this amplification are high sensitivity and simplification of data analysis. However, this amplification is not completely reliable and in practice can create biases and false positives.5 There is also the possibility that the amplification may fail, causing false negatives.6 When using DNA barcoding to identify botanical raw materials, numerous labs have observed notably high levels of apparent contamination.7 While it is certainly likely that some or even many botanical raw material samples contain contamination, it is also possible that the amplification-based method of DNA barcoding is itself contributing to the levels of contamination that are being observed.

We have partnered with Practical Informatics and Pacific Northwest Genomics to develop comprehensive whole sample DNA screening methods that don’t rely on amplification. To achieve this we are utilizing a non-targeted metagenomics workflow. Non-targeted metagenomic analysis is a powerful tool for examining the entire genetic content of a sample, instead of just one particular gene region (if a gene is a word or phrase, then a genome is the entire book, and the metagenome is the library). Unlike DNA barcoding, which requires PCR amplification, non-targeted metagenomic analysis requires no prior knowledge of a sample’s source and does not introduce the biases that plague PCR initiated methods. All of the DNA extracted from a sample is analyzed without targeting any particular gene region, relying instead on complex data analysis to identify the constituents (Figure 1). This is accomplished with the use of advanced molecular biology techniques and sophisticated computational methods, combined with a highly-curated database of species-identifying DNA sequences. Our research and development team has completed several experiments demonstrating the utility of a non-targeted DNA sequencing method.

DNA sequencing
Figure 1. The traditional targeted method, or DNA barcoding uses a PCR amplification step prior to sequencing. Non-target whole sample sequencing skips the amplification step and all present DNA is sequenced and used in analysis.

Our research endeavors to solve the issues of DNA sequence analysis that originate with the PCR step by simply eliminating amplification from our process entirely. PCR amplification as a prelude to DNA sequencing traces to traditional technologies that were lower throughput and required large amounts of material. Current generation high-throughput DNA sequencing technologies do not require large amounts of starting material, and therefore amplification can be avoided. Many DNA barcoding methods require universal primers, which, during PCR, can amplify some products but not others, leading to false negatives. A solution to that issue is to use specific primers, however this is also inherently problematic as a certain foreknowledge of the sample identity is required. What is the advantage to our non-targeted sequencing method? There is no need to direct the analysis to any particular identification before sequencing, decreasing the introduction of bias and false negatives. As an added bonus, we don’t need to know what the sample is prior to analysis—we can tell you what it is rather than you telling us.

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Reduce Foodborne Illness Causing Microorganisms through a Structured Food Safety Plan

By James Cook
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In 2011 three U.S. government agencies, the CDC, the FDA and the USDA’s Food Safety Inspection Service (FSIS) created the Interagency Food Safety Analytics Collaboration (IFSAC). The development of IFSAC allowed these agencies to combine their federal food safety efforts. The initial focus was to identify those foods and prioritize pathogens that were the most important sources of foodborne illnesses.

The priority pathogens are Salmonella, E. coli O157:H7, Listeria monocytogenes and Campylobacter. To research the most important product sources, the three agencies collaborated on the development of better data collection and developed methods for estimating the sources of foodborne illnesses. Some of this research was to evaluate whether the regulatory requirements already in effect were reducing the foodborne pathogens in a specific product matrix. The collection, sharing and use of this data is an important part of the collaboration. For example, when the FDA is in a facility for routine audit or targeted enforcement, they will generally take environmental swabs and samples of air, water and materials, as appropriate, which are then tested for the targeted pathogens. If a pathogen is found, then serotyping and pulsed-field gel electrophoresis (PFGE) fingerprinting is performed, and this is compared to the information in the database concerning outbreaks and illnesses. This data collection enables the agencies to more quickly react to pinpoint the source of foodborne illnesses and thereby reduce the number of foodborne illnesses.

The IFSAC strategic plan for 2017 to 2021 will enhance the collection of data. The industry must be prepared for more environmental and material sampling. Enhancement of data collection by both agencies can be seen through the FSIS notices and directives, and through the guidance information being produced by the FDA for FSMA. Some examples are the raw pork products exploratory sampling project and the FDA draft guidance for the control of Listeria monocytogenes in ready-to-eat foods.

Starting May 1 2017, the next phase of the raw pork products exploratory sampling project will begin. Samples will be collected and tested for Salmonella, Shiga-toxin producing E. coli (STECs), aerobic plate count and generic E. coli. In the previous phase, the FSIS analyzed 1200 samples for Salmonella for which results are published in their quarterly reports. This is part of the USDA FSIS Salmonella action plan published December 4, 2013 in an effort to establish pathogen reduction standards. In order to achieve any objective, establishing baseline data is essential in any program. Once the baseline data is established and the objective is determined, which in this situation is the Health People 2020 goal of reducing human illness from Salmonella by 25%, one can determine by assessment of the programs and data what interventions will need to take place.

The FDA has revised its draft guidance for the control of Listeria monocytogenes in ready-to-eat food, as per the requirement in 21 CFR 117 Current Good Manufacturing Practice, Hazard Analysis and Risk-Based Preventive Controls for Human Foods, which is one of the seven core FSMA regulations. Ready-to-eat foods that are exposed to the environment prior to packaging and have no Listeria monocytogenes control measure that significantly reduces the pathogen’s presence, will be required to perform testing of the environment and, if necessary, testing of the raw and finished materials. Implementing this guidance document helps the suppliers of these items to cover many sections of this FSMA regulation.

The purpose of any environmental program is to verify the effectiveness of control programs such as cleaning and sanitizing, and personnel hygiene, and to identify those locations in a facility where there are issues. Corrective actions to eliminate or reduce those problems can then be implemented. Environmental programs that never find any problems are poorly designed. The FDA has stated in its guidance that finding Listeria species is expected. They also recommend that instead of sampling after cleaning and/or sanitation, the sampling program be designed to look for contamination in the worst-case scenario by sampling several hours into production, and preferably, just before clean up. The suggestion on this type of sampling is to hold and test the product being produced and to perform some validated rapid test methodology in order to determine whether or not action must be taken. If the presence of a pathogen is confirmed, it is not always necessary to dispose of a product, as some materials can be further processed to eliminate it.

With this environmental and product/material testing data collected, it is possible to perform a trends analysis. This will help to improve sanitation conditions, the performance of both programs and personnel, and identity the need for corrective actions. The main points to this program are the data collection and then the use of this data to reduce the incidence of foodborne illness. Repeated problems require intervention and resolution. Changes in programs or training may be necessary, if they are shown to be the root cause of the problem. If a specific issue is discovered to be a supply source problem, then the determination of a suppliers’ program is the appropriate avenue to resolve that issue. Generally, this will mean performing an audit of the suppliers program or reviewing the audit, not just the certificate, and establishing whether they have a structured program to reduce or eliminate these pathogens.

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Vulnerability assessment

Protecting Food Against Intentional Adulteration: The Vulnerability Assessment (Part One)

By Debby L. Newslow
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Vulnerability assessment

FDA, as part of FSMA, released its rule titled “Protecting Food Against Intentional Adulteration” on May 27, 2016. This rule was proposed in 2013. FDA received and responded to 200+ comments prior to its final release.

FDA states that this rule “is aimed at preventing intentional adulteration from acts intended to cause wide-scale harm to public health, including acts of terrorism targeting the food supply. Such acts, while not likely to occur, could cause illness, death, [and] economic disruption of the food supply absent mitigation strategies.”1

The rule requires a documented “Food Defense Plan” that at a minimum includes the following:

  • Vulnerability assessment
  • Mitigation strategies
  • Procedures for food defense monitoring
  • Food defense corrective action procedures
  • Food defense verification procedures
  • Records confirming implementation, maintenance and conformance to the defined requirements
  • Evidence of effective training

As a food safety professional with more than 30 years in the industry, reviewing this rule brought back many memories. These memories combined with information gained from a recently completed Food Defense/ Crisis Management workshop presented by Rod Wheeler really set my brain into motion.2

Years ago, industry focused on crisis management and product recall. Requirements included having a crisis management team that was led by associates representing both upper and middle management. In addition, most programs included the following:

  • Posted identification of the crisis management team (i.e., pictures, phone numbers, etc.)
  • Specific training for receptionist and guards
  • Mock crisis exercises (i.e., fire drills)
  • Planned crisis calls to the operation’s direct incoming phone numbers (i.e., receptionist and guards)
  • Mock recalls (from supplier through finished product and distribution)
  • Security inspections which may now be considered the pre-cursor to today’s “Vulnerability Assessment”

With the introduction of the GFSI approved schemes (FSSC 22000, BRC, SQF, GlobalG.A.P., Primus, etc.), requirements for crisis management, emergency preparedness, security programs, food defense training and continuity planning gained an increase focus. Do any or all of these programs meet the requirement for a “vulnerability assessment”?

In the 2013 publication, Food Safety Management Programs, this subject-matter chapter was titled “Security, Food Defense, Biovigilance, and Bioterrorism (chapter 14)”.3 An organization must identify the focus/requirements that are necessary for its operation. This decision may relate to many different parameters, including the organization’s size, design, location, food sectors represented, basic GMPs, contractor and visitor communication/access, traceability, receiving, and any other PRP programs related to ensuring the safety of your product and your facility. Requirements must be defined and associates educated to ensure that everyone has a strong and effective understanding of the requirements and what to do if a situation or event happens.

Confirming the security of a facility has always been a critical operational requirement. Many audits have been performed that included the following management statement: “Yes, of course, all the doors are locked. Security is achieved through key cards or limited distribution of door keys, thus no unwanted intruder can access our building.” This statement reminds me of a preliminary assessment that I did not too long after the shootings at a Pennsylvania manufacturer in September of 2010. The organization’s representor and myself were walking the external parameter of a food manufacturer at approximately 7:30 PM (still daylight). We found two doors (one in shipping and one accessing the main office), with the inside door latch taped so that the doors were not secure. The tape was not readily evident. The doorknob itself was locked, but a simple pull on knob opened the door. Our investigation found that a shipping office associate was waiting for his significant other to bring his dinner and was afraid that he would not be at his desk when she arrived. An office associate admitted that that door had been fixed to pull open without requiring a key several months earlier because associates frequently forgot their keys and could not gain access to start work.

Debby Newslow Debby Newslow will present ” Sanitary Transportation for Human & Animal Food – Meeting the new FDA Requirements” at the Food Safety Supply Chain Conference  | June 5–6, 2017 | Attend in Rockville, MD or via webcast | LEARN MORE

We also observed a large overhead door adjacent to the boiler room along the street side of the facility open, allowing direct access to the processing area by passing through the boiler room and then the maintenance shop. It was stated that the door had been opened earlier in the day waiting for the delivery of new equipment. No one at the time knew the status of the shipment or why the door was still open.

Finding open access to facilities is becoming more and more common. A formal vulnerability assessment is not necessary to identify unsecured doors (24/7) in our facilities. Education and due diligence are excellent tools for this purpose.

Another frequently identified weakness is with organization’s visitor and contractor sign-in prerequisite programs. What type of “vulnerability” are we creating for ourselves (false confidence) with these programs? Frequently these programs provide more questions than answers:

  • Does everyone really sign in?
  • What does signing the visitor log mean?
  • Are visitors required to show identification?
  • Are the IDs actually reviewed and if so, what does this review include?
  • Who is monitoring visitors and contractors and are they trained?
  • Do all contractors have to sign the log or are they allowed to access the building at different locations?
  • Do those contractors who make frequent or regular trips have their own badges and/or keys (keycards) so they don’t have to take the time to sign-in (i.e., pest control, uniform supplier vending services)?
  • How are contractor badges controlled?
  • Are visitors required to be accompanied during the visit or does it depend on the visitor and whom they are visiting?
  • Are visitors and contractors trained in company requirements?
  • Do visitors and contractors have an identifying item to alert your associates of their status (i.e., visitor badge, visitor name badge, specifically colored bump cap, colored smock, etc.)?
  • How are truck drivers monitored? Do they have a secured room for them or do they have complete access to the facility to access the restrooms and breakroom?
  • How are terminated associates or associates that have voluntarily left the company controlled?
    • Can these associates continue to access the facility with keys, access cards, or just through other associates (i.e., friends or associates that did not know that they were no longer an employee)?
  • How many more questions can there be?

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Best Practices for ISO 17025 Accreditation: Preparing for Your Food Laboratory Audit (Part II)

By Joy Dell’Aringa
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In Part I of this article, we explored the considerations a laboratory should initially evaluate when pursuing accreditation, as well as guidance from leading industry experts on how to prepare for an ISO 17025 audit. Here we will review what comes after the on-site assessment and provide practical user-based advice for preparing a response, common areas of non-conformance, and future changes to the ISO 17025 Standard.

The Response

Once the assessor has completed the audit, they will typically hold a closing meeting on-site where they present their findings, also referred to as deficiencies or non-conformances. For each finding they will document a specific reference to the standard as evidence and provide opportunity for questions and discussion. Most assessors will be open and conversational during this final portion of the assessment; laboratories are well suited to take advantage of this time. Some assessors will even brainstorm possible responses and corrective actions while onsite; this is valuable insight for the laboratories quality team and can help them get a jump on the response.

Depending on the accrediting body, the laboratory will have a certain amount of time to respond to the findings, usually 30–60 days. The anatomy of a well-assembled response will include a full corrective action report, complete with root cause analysis. Often, the assessor will also request supporting documents and records to show the effectiveness of a corrective action. Most laboratories will have forms to help guide users through the corrective action and root cause process. It is important to have a systematic approach to ensure your corrective action is thorough and balanced.

Determining root cause is a critical part of this exercise. Erin Crowley, CSO of Q Laboratories shares their approach. “We use a variety of root cause analysis techniques, but have found for our operation the principle of the ‘5 Why’s’ is very effective,” she says. “Don’t simply answer the singular deficiency. Accrediting bodies will want to know that you have addressed all variables that might be associated with a finding. For example, if a specific incubator was out of range on a specific date, don’t just indicate that someone fixed it and move on. Assess how they addressed the issue, any impact on data, what they did to react to it, and how they are putting systems in place to prevent it from happening in the future on any other incubator. You have to show the full process.”

Implementing procedures as an outcome of a corrective action can also bring challenges to an operation. As a national multi-site reference lab, Eurofins Quality Manager Peter Dragasakis must work with other departments and locations to deploy new or changed systems for compliance. “Sometimes the most challenging part of the entire audit process is coordinating internal stakeholders across other departments such as IT or complimentary analytical departments,” he says. “Coordinating a response in a timely manner takes full organizational cooperation and support.” Communication throughout the quality and operational arms of an organization is critical to a successful response. Often, accrediting bodies and laboratories may shuttle a response back and forth a few times before everyone is satisfied with the outcome.

Common Areas of Non-Conformance: Pro-Tips

While all areas of the standard are important to a conformant operation, there are a few key areas that are frequently the focus of assessments and often bare the most findings.

Measurement Uncertainty. Depending on the laboratories Field of Testing (FOT), Measurement Uncertainty (MU) can be captured in a multitude of ways. The process aims to systematically and quantifiably capture variability in a process. For chemical analysis this is typically well defined and straightforward. For microbiological analysis the approach is more challenging. A2LA’s General Manager, Accreditation Services, Adam Gouker says the reason many labs find themselves deficient in this area is “they don’t consider all of the contributors that impact the measurement, or they don’t know where to begin or what they need to do.” Fortunately, A2LA offers categorical guidance in documents P103a and P103b (for the life sciences laboratories, two of the of many guidance documents aimed at helping laboratories devise systems and protocols for conformance.

Traceability. There are several requirements in the ISO 17025 standard around traceability. In terms of calibration conformance, which accrediting bodies seem to have emphasized in the last few years, Dragasakis offers this tip: “When requesting [calibration] services from a vendor, make sure you’re requesting 17025 accredited service. You must specify this, as several levels of service may be available, and “NIST Traceable” certificates are usually no longer sufficient.” He also advises that calibration certificates be scrutinized for all elements of compliance closely. “Some companies will simply state that it is ‘ISO 17025 compliant’, [and] this does not mean it is necessarily certified. Look for a specific reference to the accrediting body and the accreditation certificate number. Buyer beware, there is often a price difference between the different levels of calibration. Always practice due diligence when evaluating your calibration vendor and their services, and contact the calibration service if you have any questions.”

Validation vs. Verification. One of the more nuanced areas of the standard lies in determining when a test requires validation, verification, or an extension, specifically when there is a modification to a method or a sample type not previously validated by an internationally recognized organization (AOAC, AFNOR, etc.). Certified Laboratories Director Benjamin Howard reminds us, “think of validation and verification as existing on a spectrum. The more you stray away from an existing validation, the more validation work is required by the analyzing laboratory.” For example, analyzing Swiss cheese for Salmonella by a method that has already been validated for soft queso cheese may require only minimal verification or matrix extension. However, a laboratory that is altering a validated incubation time or temperature would require a much more robust and rigid validation process. Howard cautions, “Accredited laboratories must be transparent about modifications, not only on their scope of accreditation but on their reports [or CofA’s] as well. Under FSMA, companies are now accountable to the data that their laboratories generate. If you see a “modification” note on your report, perform due diligence and discuss this with your laboratory. Ensure a proper validation of the modification was performed. “Additionally, the ISO 17025 standard and accrediting bodies do not mandate how a validation or verification should be done. Laboratories should have a standalone SOP that outlines these procedures using scientifically supported justification for their approach.

CAPA / Root Cause. A good corrective action / preventive action (CAPA) and root cause (RC) analysis program is at the heart of every sound quality system. “Corrective and preventive action (CAPA) processes can either add value or steal time away from the organization according the quality of the root cause analysis,” says Vanessa Cook, quality systems manager at Tyson Foods Safety & Laboratory Services. “CAPA might be the single greatest influence on an organization’s ability to continuously improve and adapt to change if diligence is given to this activity.” Investing in resources such as ongoing training in CAPA/RC programs and techniques are key components to ensuring a robust and effective CAPA / RC program.

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Best Practices for ISO 17025 Accreditation: Preparing for a Food Laboratory Audit (Part I)

By Joy Dell’Aringa
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An increasing number of food testing laboratories are seeking accreditation to the ISO/IEC 17025:2005 standard. This growth is chiefly due to regulatory implications, customer requirements, and trade organization recommendations and is seen across laboratory segments: third-party contract laboratories, private in-house laboratories, and government laboratories. ISO 17025 is the most common standard in the food testing industry and sets the guideline for “Laboratories Performing Microbiological and Chemical Analysis of Food and Pharmaceuticals”. Accreditation is known generally as a third-party attestation related to a laboratory, which conveys formal demonstration of competency that implies a reliable and consistent level of quality across an operation for a well-defined parameter of tests, often referred to as the “Field of Testing”. There are several qualified organizations that accredit laboratories to the standard; these organizations are referred to as Accrediting Bodies and are responsible for assessing facilities for conformity to a given ISO standard.

Audit Preparation Guidance

Initial Accreditation: Considerations & Preparation

When a laboratory initially entertains applying for accreditation, several factors should be considered. The cost and time commitment required to become initially conformant, and the on-going resources required to maintain conformity should be thoroughly examined in an overall benefit analysis prior to applying for accreditation. Management should be fully aware of the investment and perpetual commitment of becoming an accredited facility. Accrediting Bodies (ABs) provide resources and literature that can help guide laboratories through the initial audit-preparation phase. However, creating the systematic application of these guidelines that balances the quality and operational objectives of the organization are unique from laboratory to laboratory. Simply put: There is no cookie-cutter approach to accreditation.

Consultant Considerations

Q Laboratories in Cincinnati, OH first embarked on the path to ISO 17025 accreditation in 2009. James Agin, director of regulatory compliance at Q Laboratories and member of the A2LA Laboratory Accreditation Council took the lead on preparing for the initial assessment eight years ago. Q Laboratories was initially unfamiliar with the process, so they hired a consultant who was also an assessor to walk them through the process. “We took about four to five months with a consultant,” says Agin,. “In addition to creating the necessary systems, we gathered the troops and did a deep training on what ISO 17025 is, why we were pursuing it, and why it was important to our business.” The Q Laboratory team created a deep sense of ownership during the education and training process from the supervisors to the bench analysts, which they credit to their ongoing success years later. Erin Crowley, chief scientific officer at Q Laboratories suggests new labs consider hiring a consultant to ease them through the process and get them audit-ready. “If you’re not accustomed to having certain systems in place, a consultant can provide clarity and help initiate processes,” says Crowley. “Having an open forum with an expert helped give our entire team confidence.”

A consultant can streamline the initial process and help avoid some of the pitfalls in creating a robust quality management system for the first time. Tim Osborne, senior director of training services at A2LA offers advice for organizations when vetting a consultant. “While certainly not required, a qualified consultant may be a good asset to have in your quiver,” says Osborne. “Look for industry references and pay close attention to involvement in the industry outside of its own laboratory. Does this person work for an accrediting body? What are the areas of analytical expertise? Does this person also provide training for an accrediting body? If so, it is likely the consultant will offer the quality of services you need to be successful.” It is important to note that assessors and consultants should be upfront with the accrediting body to avoid conflict of interest issues during the actual assessment. Impartiality is critical within the assessment process.

Application Process

Accrediting bodies publish their own “readiness” documents. Laboratories seeking accreditation should request an itemized guide that walks the organization through each phase of the process. The following is a general outline:

  • Obtain copy of ISO standard (17025, 17065, 17020, etc.). Review any specific requirements relevant to your field; these are generally available in a checklist format allowing the laboratory to prepare through an internal audit process.
  • Determine estimated costs with the accrediting body
  • Obtain a copy of the accrediting body s assessor checklist. This usually has to be completed as part of application process
  • Prepare the intended draft scope of accreditation (outlining, specific tests/test methods, calibration parameters/ranges, certification schemes)
  • Implement the management system, and ensure personnel are aware and accept the content
  • Perform an internal audit to verify compliance with the conformity assessment standard requirements, accrediting body requirements, your own management system requirements, and applicable technical requirements
  • Perform a management review
  • Foreign applicants may need to translate supporting application documents to English
  • Identify one specific individual to be responsible for accreditation efforts and interactions with the accrediting body. Identify the “quality manager” who is in charge of the management system
  • Obtain, prepare, and submit the application for accreditation to the accrediting body

Once the initial assessment is complete and the final response and corrections to any deficiencies is in, the laboratory will be reviewed and considered for accreditation through the accrediting body. When the decision is made in favor of accreditation, the laboratory will receive their accreditation certificate, which will correspond to a specific location and set of tests (commonly referred to as a Scope of Accreditation (“Scope”) for the Field of Testing (“FOT”) for which they were assessed). Depending on the accrediting body, the certificate may be valid for one to two years, and will require re-assessment and surveillance at defined frequencies. The laboratory is responsible to maintain conformance to the ISO 17025 standard in between assessments.

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barcode

How Digital Technology Streamlines Supply Chain Management

By Alex Bromage
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barcode

Today’s food and beverage producers must deliver to exact requirements and provide safe products of the highest quality. In an increasingly global and connected world, the emergence of new business models, such as Amazon Food and the offer of direct deliveries to consumers, is creating ever more complex supply chains for manufacturers. The number of steps between the raw ingredients and the consumer is increasing, creating new and more numerous challenges inside the production process for food and beverage manufacturers. Thus it is important to remain committed to constantly innovating and developing new services and technologies to support customers with increasing supply chain complexities. This includes systems to help track products as they enter the factory environment, when they leave the factory, and when they enter the retail distribution chain. The digitalization of management processes and services, alongside basic management processes, is playing an important role in helping food and beverage manufacturers to manage these complexities.

Learn more about keeping track of your suppliers at the Food Safety Supply Chain Conference | June 5–6, 2017 | Rockville, MD | Attend in-person or virtuallySupplier Base

The first step to keeping food safe starts before the raw ingredients enter the processing facility. The safety of raw material is so important because it impacts the end quality of the product. Pasteurization and heat treatment can only improve the product so much, and therefore the higher quality the raw ingredients, the better the final product.

Basic management processes must be in place at this stage of the supply chain, ensuring the good management of the supplier base. Working closely with customers to implement supplier framework audits that allow them to benchmark their suppliers’ performance is crucial. Through this supplier framework customers to collaborate transparently with their suppliers, encouraging the open sharing of information and traceability in the supply chain.

Production Process and Entering the Retail Distribution Chain

Increased sophistication of tools in the industry is also enabling high-level traceability at the packaging stage. This means that food and beverage manufacturers are tracking and tracing products right the way through to the consumer. One such available tool can enable food and beverage manufacturers to program their entire plant through a single data management system, and improve product traceability internally. Specifically designed for the food and beverage industry, specific software provides a user-friendly interface through which customers can control their entire operations—from raw material reception to finished packaged and palletized products. Streamlines data collection facilitates accurate data analysis to ensure that safety standards are maintained throughout the production process.

Using unique package identification technology, such as a 2-D barcode on packages, information can be processed this information and the product(s) tracked throughout the supply chain. For example, if a manufacturer were to experience a food safety issue in a certain production batch, the tool would be able to track all products in that batch and support making a recall. In addition to improving functions on a reactive basis, a reporting function, is designed to provide data to help prevent issues from happening again in the future, mitigating against food safety risks.

As new business models continue to emerge and more parties become involved in the production process, the complexity of the supply chain will only increase. Digital strategies alongside basic management processes have an increasingly important role to play in helping food and beverage manufacturers manage these complexities to ensure that their food is safe for the end consumer.

High processing pas

HPP: Achieve High Standards of Food Safety Without Compromising Food Quality

By Mark Duffy
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High processing pas

As food companies analyze and modify their production processes to ensure FSMA compliance, many are finding that traditional food processing technologies aren’t ideally suiting their needs. Conventional pasteurization technologies like heat pasteurization have been relied on to protect the safety of the food supply over the years, but they aren’t without their downsides. For example, sometimes they negatively impact the flavor, texture, nutrients and color of food products. Additionally, many traditional food processing methods require chemical additives to be integrated to preserve quality and taste. In a market where consumers are more frequently appreciating, if not demanding, cleaner labels with simple ingredients, these solutions are often becoming less attractive options for some companies.

This new demand for a higher level of food safety combined with an emphasis on food quality has led some producers of refrigerated foods to turn to an increasingly popular alternative: High pressure processing.

How HPP Works

High pressure processing, or HPP, is an effective technique that uses pressure rather than heat or chemicals to disable pathogens in food. After packaging, food products composed of some degree of water activity (Aw) are placed into a machine that applies incredibly intense water pressure to food—sometimes as much as 87,000 psi.

High pressure processing
How high pressure processing works. Graphic courtesy of Universal Pasteurization & Universal Cold Storage

This process interrupts the cellular function of the microorganisms both on the surface and deep within the food and can serve as a critical control point (CCP) in a HACCP program. Research studies on a wide range of refrigerated food products and categories confirm that HPP technology inactivates vegetative bacteria like Listeria monocytogenes, Salmonella, E. coli 0157:H7, and Campylobacter as well as yeasts and molds. Additionally, because pressure is applied after the food is packaged, HPP drastically reduces any chance of recontamination.

Besides its food safety benefits, HPP offers food producers added benefits over traditional methods. Because the pressure inactivates spoilage organisms along with pathogens, many foods see a substantial increase in shelf life after undergoing HPP, sometimes even twice as long. Processors use this shelf-life extension to increase their distribution reach and reduce food waste.

In a recent survey, 57% of respondents in the food and beverage industry characterized their companies’ use of HPP as substantial or growing. Survey respondents also scored HPP’s ability to make food safer by eliminating pathogens above a 4 on a 5-point scale, one of the highest of any food processing technology.

However, HPP isn’t right for every product. It isn’t effective on some enzymes and bacterial spores, like Clostridium botulinum. Producers need to tap into other techniques to address concerns not affected by HPP. The process also requires foods to be packaged in fairly flexible packaging to allow for an even application of pressure. Glass bottles or particularly hard plastics will not be suitable.

HPP can also be daunting to implement for some companies. Purchasing an HPP machine is a major investment, typically seven-figures, without factoring in specific facility requirements or staffing needs. In the same survey of food and beverage producers, the most commonly cited concerns had nothing to do with the efficacy or value of the technology, but rather with the cost of purchasing and staffing the equipment.

For businesses that don’t want to make that kind of capital expenditure commitment but want to take advantage of high pressure processing, HPP outsourcing providers offer a more affordable solution. These companies own and operate HPP machines on behalf of clients. That way, food brands don’t have to purchase expensive HPP machines and regularly maintain their own equipment.

Is HPP right for you? The answer and the nuances are highly variable, but HPP is a fast-growing food preservation technology offering many benefits, including food safety benefits, across a broad product spectrum.

Listeria

How One Company Eliminated Listeria Using Chlorine Dioxide Gas

By Kevin Lorcheim
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Listeria

The previous article discussed the various decontamination options available to eliminate Listeria. It was explained why the physical properties of gaseous chlorine dioxide make it so effective. This article focuses on one company’s use of chlorine dioxide gas decontamination for both contamination response and for preventive control.

The summer of 2015 saw multiple ice cream manufacturers affected by Listeria monocytogenes. The ice cream facility detailed in this article never had a supply outage, but ceased production for a short amount of time in order to investigate and correct their contamination. After a plant-wide review of procedures, workflows, equipment design and product testing, multiple corrective actions were put into place to eliminate Listeria from the facility and help prevent it from returning. One such corrective action was to decontaminate the production area and cold storage rooms using chlorine dioxide gas. This process took place after the rest of the corrective actions, so as to decontaminate the entire facility immediately before production was set to resume.

Responsive Decontamination

The initial decontamination was in response to the Listeria monocytogenes found at various locations throughout the facility. A food safety investigation and microbiological review took place to find the source of the contamination within the facility in order to create a corrective action plan in place. Listeria was found in a number of locations including the dairy brick flooring that ran throughout the production area. A decision was made to replace the flooring, among other equipment upgrades and procedural changes in order to provide a safer food manufacturing environment once production resumed. Once the lengthy repair and upgrade list was completed, the chlorine dioxide gas decontamination was initiated.

The facility in question was approximately 620,000 cubic feet in volume, spanning multiple rooms as well as a tank alley located on a different floor. The timeline to complete the decontamination was 2.5 days. The first half-day consisted of safety training, a plant orientation tour, a meeting with plant supervisors, and the unpacking of equipment. The second day involved the setup of all equipment, which included chlorine dioxide gas generators, air distribution blowers, and a chlorine dioxide gas concentration monitor. Gas injection tubing was run from the chlorine dioxide gas generators throughout the facility to approximately 30 locations within the production area. The injection points were selected to aid its natural gaseous distribution by placing them apart from one another. Gas sample tubing was run to various points throughout the facility in locations away from the injection locations to sample gas concentrations furthest away from injection points where concentrations would be higher. Sample locations were also placed in locations known to be positive for Listeria monocytogenes to provide a more complete record of treatment for those locations. In total, 14 sample locations were selected between plant supervisors and the decontamination team. Throughout the entire decontamination, the gas concentration monitor would be used to continuously pull samples from those locations to monitor the concentration of chlorine dioxide gas and ensure that the proper dosage is reached.

As a final means of process control, 61 biological indicators were brought to validate that the decontamination process was effective at achieving a 6-log sporicidal reduction. 60 would be placed at various challenging locations within the facility, while one would be randomly selected to act as a positive control that would not be exposed to chlorine dioxide gas. Biological indicators provide a reliable method to validate decontamination, as they are produced in a laboratory to be highly consistent and contain more than a million bacterial spores impregnated on a paper substrate and wrapped in a Tyvek pouch. Bacterial spores are considered to be the hardest microorganism to kill, so validating that the process was able to kill all million spores on the biological indicator in effect also proves the process was able to eliminate Listeria from surfaces. The biological indicators were placed at locations known to be positive for Listeria, as well as other hard-to-reach locations such as the interior of production equipment, underneath equipment and inside some piping systems.

In order to prepare the facility for decontamination, all doors, air handling systems, and penetrations into the space were sealed off to keep the gas within the production area. After a safety sweep for personnel, the decontamination was performed to eliminate Listeria from all locations within the production area.

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Gears

Three Practices for Supply Chain Management in the Food Industry

By Kevin Hill
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Gears

While building an effective logistics strategy, the end goal of supply chain management (SCM) needs to be kept in mind (i.e., allowing each member of the supply chain to achieve efficient inventory management as well as reach its customer service goals). To this end, it’s important to share information that will help each member achieve success. This includes data relating to demand forecasts, anticipated lead times and safety stock quantities. Let’s look at SCM best practices for food manufacturing and supply, and how this information plays a role.

Effective SCM: Best Practices for the Food Industry

Here’s an overview of SCM best practices in food supply and manufacturing:

Learn more about managing your supply chain at the Best Practices in Food Safety Supply Chain conference | June 5–6, 2017 | LEARN MOREDemand Forecasts. This is generally based on demand, sales or usage patterns in the past. However, future demand can be affected by changing situations such as:

  • Gaining/losing customers
  • Increased/decreased product popularity
  • Introduction of new products
  • Short-term increase in demand through promotions, etc.

Better estimates can be achieved with an effective derived demand or a CPFR (collaborative planning, forecasting and replenishment) system. This can be done through automated data collection, or by the following process:

  • Identifying customers who can predict future demand (i.e., what they may use or sell in the future)
  • Collecting demand forecasts about specific products from them
  • Comparing these forecasts against their actual purchases on a monthly basis
  • Helping them improve future predictions by sharing this data with them

Customers may overestimate demand, but you might consider offering a discount based on accurate forecasts to encourage better results. In addition, you should also consider these five elements:

  • Usage patterns in the past, not including CPFR data
  • Increasing/decreasing product popularity trends
  • Higher/lower seasonal usage or demand
  • Events/promotions in the near future
  • Market and industry data from sources such as management, sales, etc.
Organic, NonGMO, Natural, Labeling

Achieving Transparency in Organic and Natural Product Claims

By Lori Carlson
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Organic, NonGMO, Natural, Labeling

Consumer preference for organic and “all natural” foods remains on the rise, according to market trend research and retailer sales.1,2 The Organic Trade Association (OTA) recorded $40 billion in U.S. organic food sales for 2015, stating that sales have nearly doubled since 2008.3 Pair this with $21 billion in sales for Q1 2016 for non-GMO labeled foods and $1.6 billion in 2015 gluten-free sales and, it is hard to ignore this thriving market sector, which seeks to support consumers in their quest for fresh, healthy and transparently-labeled foods.4,5

As a result of these trends, the industry is experiencing a surge in natural food and beverage start-up companies as well as the acquisition of organic and natural product companies by manufacturing giants such as Campbell Soup Co., Danone and General Mills, Inc. But in complex—and especially global—supply chains, achieving transparency comes with hurdles for verifying product claims  such as “all-natural”, non-GMO, antibiotic-free, and other nutrient content or functional claims.

Organic and other natural food manufacturers are under increasing regulatory and consumer scrutiny for tracing claims back to the source for all ingredients. Failing to verify the authenticity or identity preservation (IP) status of materials, maintain chain of custody and ensure the accuracy of labels can have devastating consequences for a manufacturer, including regulatory action and consumer fraud class action law suits.6 It’s not just consumers demanding the “right to know” where food comes from, but manufacturers must also push this sentiment back through their supply chain to drive transparency for ensuring safety, brand protection and verifying product claims.

With the goal of meeting consumer demands for healthy food products, improved transparency in food production and clean labels, how can organic, non-GMO and natural food manufacturers stay ahead of the curve when it comes to ensuring that product claims provide the value consumers seek?

Consider the following tasks for achieving transparency in organic and natural product claims.

Analyze Your Ingredients for Risk

Get to know the pitfalls, which can affect the integrity of product claims. Many of these stem from cross contamination, authenticity or mislabeling issues for sourced materials. To prevent these pitfalls, analyze each ingredient for supply chain risks. Identifying potential risks, which may affect the integrity of claims creating liability for misbranding, is a critical step in achieving transparency.

For example, is there a potential for cross contamination from a non-organic source? This is a common risk where a supplier engages in the co-production of organic and non-organic materials. A lack of segregation and clear product identification during transportation, storage and processing activities can lead to commingling or cross-contamination, which affects material integrity and thus, any downstream product claims. Ensuring suppliers and the manufacturer have clear measures in place for segregation is an important consideration when determining risk.

Or, consider adulteration from a non-authentic material, which can affect the integrity of the claim. Identifying vulnerabilities within the supply chain is necessary to reduce opportunities for perpetrating food fraud. Materials such as organic products and some natural ingredients are at greater risk for fraud where limited availability is an issue and/or the material is a high-value commodity or product. Mislabeling, counterfeit production or economically motivated adulteration, such as the substitution or dilution of ingredients in a sourced material, has a significant impact on downstream product claims.

Unverified packaging and labels are other sources of risk with the potential to affect the integrity of product claims. Ensure your supplier’s labeling practices include controls to verify the correct packaging and labels when producing IP materials or other ingredients with nutrient content or functional claims.

With a clear understanding of material risks, what attributes of an ingredient should be prioritized, tested and/or verified when considering the integrity of finished product claims?

Once material risks are analyzed, establish clear specifications for raw materials, which are agreed upon between the supplier and manufacturer. This serves as the basis for verifying material claims and subsequently, downstream product claims. Where specifications are in place, material verification may be performed through a variety methods including: testing, mass balance, COA review and audits. Verifying materials against agreed upon specifications not only supports due diligence in product claims but also brings manufacturers closer to their suppliers, steering us towards the next task.

Get to Know Your Suppliers

At the heart of food production transparency is the relationship a manufacturer has with its suppliers. Even the simplest of manufactured foods have a handful of ingredients, which are typically sourced through a global supply chain network. Due to the seasonality of produce or supply chain risks such as market fluctuations, business disruptions, natural disasters, or transportation failures; manufacturers can’t rely on a single supplier for the sourcing of a particular ingredient.

This leads to reliance on multiple suppliers, which may be geographically dispersed. Sourcing from multiple suppliers—especially when this occurs for multiple ingredients across multiple products—can create hurdles to relationship building for enhanced transparency due to time and resource constraints for acquiring first-hand knowledge of a supplier’s operation. Thus, proactive supply chain management, which enables a manufacturer to learn about the supplier’s history and operation, is essential for transparency.

This can be accomplished by establishing supplier approval criteria to provide a baseline for getting to know your supplier and establish minimum criteria for sourcing. Building upon this, is the use of approved suppliers to solidify the relationship and develop out a stable supply chain network. And finally, it is best practice to visit the supplier’s site to learn more about operational practices and the people responsible for ensuring material specifications and identity status are consistently achieved.

Apply Supply Chain Management Best Practices

Effective management of suppliers to prevent or reduce risks, which can lead to mislabeling and false claims, relies on the risk assessment conducted for materials and suppliers, applied controls (e.g., segregation) and verification that the supplier’s controls consistently ensure material integrity.

GFSI benchmarked schemes paved the way for enhanced supply chain management and risk mitigation when it comes to sourcing materials to ensure food safety and legal status. Some schemes additionally require controls and verification activities such as the validation of health claims or verification of nutrient content to provide a framework for helping manufacturers develop a system, which ensures product integrity. For food sold in the United States, a GFSI-based system is now reinforced by the  FSMA Preventive Controls rule, which requires supply chain-applied controls to mitigate material risks along with additional controls to ensure that food is not adulterated or misbranded under the U.S. Food, Drug and Cosmetic (FD&C) Act.

It is important to note that while the FSMA Preventive Controls rule regulates most processors and manufacturers, organic raw agricultural commodities (RAC’s), dietary supplements and unprocessed meats are not covered by the rule as they are covered by other U.S. food regulations. Since these products may be included in organic and natural product formulations, manufacturers may want to consider applying a Preventive Controls methodology to their supply chain or pursue certification to a recognized food safety standard such as a GFSI benchmarked scheme where this is not already in place.

Simplify Your Supply Chain

Complex supply chains reduce visibility, add latency into monitoring, and increase opportunities for contamination or fraud.7,8

Simplifying your supply chain can take a variety of forms such as the sourcing of local or domestic materials.

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