Tag Archives: pathogen detection

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PCR or LAMP: Food Safety Considerations when Choosing Molecular Detection Methods

By Joy Dell’Aringa, Vikrant Dutta, Ph.D.
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Food microbiology pathogen detection technology is constantly evolving and improving for fast, efficient and accurate analysis. Thanks to the wide commercialization of easy-to-use diagnostic kits, the end-user no longer needs a deep understanding of the intricacies of diagnostic chemistries to perform the analysis. However, when navigating the selection process in search of the technology that is best fit-for-purpose, it is critical to understand the key differences in principle of detection and how they can impact both operations and risk. Here, we will explore the difference between two broad categories of molecular pathogen detection: PCR and isothermal technologies such as LAMP.

PCR & LAMP Detection Chemistries: An Overview

PCR detection chemistries have come a long way from non-specific DNA-binding dyes like SYBR Green, to highly precise sequence-specific molecular probes. The efficiency of the real-time PCR reaction today allows for the use of a variety of detection probes, the most popular being Dual-Labeled Fluorescent Probes such as FRET, TaqMan probes, and Molecular Beacon probes.1 The precision of these probes is showcased in their ability to distinguish allelic single-nucleotide polymorphisms (SNPs).2,3 The most prevalent isothermal chemistry, Loop-Mediated Isothermal Amplification (LAMP), typically does not use molecular probes due to the lack of structure and formation consistency in its amplified products. As a result, LAMP mostly relies on detection through non-specific signal generation like ATP bioluminescence or non-specific dyes. In theory, this could come from specific and non-specific amplification events. This also makes LAMP inept to detect the allelic polymorphisms, which in some cases are critical to detecting crucial variations, like between close species, and within serotypes. In the end, the detection chemistries are only as good as the amplified products.

Key Takeaways:

  • PCR technology has improved greatly in detection efficiencies via target specific probes
  • LAMP technology typically does not utilize specific molecular probes, but instead relies on indirect signal generation
  • Target specific probes ensures signal from specific amplification events only
  • Indirect signal can come from specific and non-specific amplification events, which can lead to a reduced specificity and inability to detect in certain cases

PCR & LAMP: Amplification Strategies

Food safety pathogen detection protocols aim to find the single cell of a target organism lurking in a relatively large sample. In order to achieve detection, molecular technologies utilize amplification strategies to increase the concentration of target DNA to a detectable level. Nucleic acid amplifications in both PCR and isothermal technologies start by making a variety of amplified products. These products include non-specific amplifications (NSA), and specific (target) amplifications.4,5,6,7 Ideally, the concentration of the desired target amplified product increases over time to levels above NSA where the detection chemistries are able to provide a detectable signal from the desired amplified product (target). Various reaction components such as: Target DNA concentration, polymerase, buffers and primers play a defining role in maintaining the progressive amplification dynamics, and thereby act as core contributors to the robustness of the reaction. However, none play a more crucial contribution to the success of a reaction than temperature. Herein lies a key difference between the fundamentals of PCR and Isothermal amplification technologies.

Key Takeaways:

  • PCR and LAMP both make a variety of amplification products: Non-Specific (NSA) and Specific (target)
  • Ideally, target products increase above the levels of NSA to reach a reliable detectable signal
  • A variety of factors contribute to the overall robustness of the reaction

What Is the Difference between PCR and Isothermal Detection Technologies?

A key foundational difference between the two technologies lies in the utilization of the thermal profiles. PCR utilizes thermocycling, while isothermal does not. This difference is the tether around how the different amplification chemistries work. In PCR, the cyclical denaturation of DNA during thermocycling separates all dimers (specific and non-specific). As the reaction progresses, this leads to frequent correction of the amplification dynamics away from the NSA and favors amplification of the desired target amplifications. Isothermal chemistries do not have the ability to correct the NSA through thermocycling, so it must rely on alternate mechanisms to achieve the same result. For example, LAMP utilizes “nested” primers where the primer sequences outside the target region are used to create early amplification products. These are subsequently used as a template for the desired target amplifications. The presence of these extra primers, along with the diverse amplified structures formed during the LAMP reaction, creates many more opportunities for NSA production.5,8,9 This causes a less controlled and inefficient amplification, and is perhaps why the preheating of the DNA prior to the LAMP has shown to increase the LAMP sensitivity.10, 11 To the end user, this inefficiency can manifest itself in various ways such as restricted multiplexing, lack of internal amplification control, complex assay design, tedious sample prep methods, and increased chance for inaccurate results (i.e., false positives and false negatives).12 Scientific literature does provide a fair amount of evidence that, under controlled conditions, the isothermal amplification reaction can provide equivalent results to PCR. Isothermal chemistries also usually require simplified instruments and thereby can present interesting opportunities in non-conventional test environments with simple and predictable matrices. This likely explains the early footing of isothermal technologies in the clinical test environment as a “point of care test” (POCT) alternative. However, it must also be noted that recently PCR has also been adapted and successfully commercialized for the POCT format.13,14

Key Takeaways:

  • PCR utilizes thermocycling, Isothermal does not
  • In PCR, thermocycling allows for the reaction to favor the target amplification over the NSA
  • LAMP must rely on alternate mechanisms to correct for NSA and these mechanisms lead to a less controlled and therefore inefficient amplification
  • Under controlled conditions, isothermal technology can provide equivalent results to PCR
  • Low instrumentation requirements make isothermal technologies interesting for non-conventional test environments (i.e. POCT); however, PCR has also been recently adapted as a POCT

Internal Amplification Controls in Molecular Pathogen Detection Technologies: The Value & The Challenges

The purpose of an internal amplification control (IAC) is to provide an indication of the efficacy of the test reaction chemistry. The closer the IAC is to the target DNA sequence, the better view into the inner workings of each reaction. For food microbiology testing, the role of the IAC is more important now than ever. Driven by regulations, industry self-accountability and brand protection initiatives, more food laboratories are testing diverse product types with novel and innovative formulations and ingredients. IAC capability not only helps with troubleshooting, but it also allows for a more confident adoption of the technology for new and diverse food and environmental matrices.

Over the years, PCR has progressively developed into a robust and efficient technology that can provide a dynamic IAC, giving the end user a direct look into the compatibility of the test matrix within the PCR reaction. From a single reaction, we can now make a qualitative assessment of whether the crude DNA prep from a matrix undergoing testing is working with this PCR or if it is inhibiting the reaction. With legacy technologies, including the older generation PCR’s, we were limited to an “it-did-not-work” scenario, leaving the end user blind to any insights into the reason. Since isothermal chemistries typically do not have an IAC, the end user is vulnerable to false results. Even when isothermal chemistries such as nicking enzyme amplification reaction (NEAR) can provide IAC, they typically do not mimic the target reaction and, therefore, are not a direct indicator of the reaction dynamics. This limits the end user back to the “it-did-not-work” scenario. LAMP technology attempts to mitigate the absence of IAC by performing a separate and external reaction with each test matrix. This strategy leaves the final result vulnerable to a number of factors that are otherwise non-existent for IAC: Sampling variations, reagent and machine anomalies, and user error. External control approaches also have a notable impact to the end user, as the burden to demonstrate fit-for-purpose of the method for even the smallest matrix composition change increases both validation and verification activities, which can have a notable financial impact to the laboratory.

There are a few reasons why IAC incorporation is not always plausible for isothermal technologies such as LAMP. First, inefficient, less-controlled amplification reactions leave little room for reliable and meaningful supplementary reactions, like the ones required for IAC. Second, the lack of consistent amplified products make it much more difficult to pinpoint a DNA structure that can be dependably used as an IAC. Third, lack of specific detection mechanisms makes it hard to distinguish signal from the target versus the IAC reaction.

Key Takeaways:

  • Internal amplification controls (IAC) are critical for the food industry due to complex and ever-changing matrix formulations
  • IAC is useful for troubleshooting, optimizing assay performance, and adapting test for novel matrices
  • PCR has evolved to provide dynamic IAC, leading to increased confidence in results
  • LAMP is not able to utilize IAC due to the nature of the amplification products, reaction efficiency, and lack of specific detection mechanisms

Follow the link to page 2 below.

CERTUS system

CERTUS Achieves AOAC Performance Tested Certification

By Food Safety Tech Staff
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CERTUS system

This week CERTUS announced that it achieved AOAC Performance Tested certification for its rapid pathogen detection platform, the CERTUS System. The system uses SERS nanoparticle technology and real-time detection to provide users with faster results versus sending the samples to a third-party via mail.

AOAC validation gives small-to-mid size processing facilities an assurance on the reliability and efficiency of CERTUS’s in-house environmental Listeria monitoring process, according to CERTUS.. The company’s system has been certified for use on stainless steel, concrete, plastic and ceramic surfaces. The CERTUS system provides 98% accuracy by targeting organisms without destroying them and reducing the effect of substances commonly found in environmental food samples on assay results.

“We’re extremely proud and put tremendous value on achieving AOAC certification within two years of beginning our journey to help protect food production beyond a shadow of a doubt,” said CERTUS President John Coomes in a press release. “Recognition by AOAC, coupled with our robust R&D team and strong financial backing, demonstrates that we are moving quickly to bring unmatched, precise solutions to food processors across the industry.”

3M Molecular detection system

USDA FSIS Awards 3M Food Safety with Contract for Pathogen Testing

3M Molecular detection system
3M Molecular detection system
3M Molecular detection system

USDA FSIS has awarded a contract to 3M Food Safety for its pathogen detection instruments and kits. 3M’s molecular detection system will be the primary method used by the agency to detect Salmonella, Listeria monocytogenes and E. coli O157. The technology combines isothermal DNA amplification and bioluminescence detection for a fast, accurate and simple solution that also tackles some of the constraints of PCR methods. Users can concurrently run up to 96 different tests for many organisms across food and environmental samples.

Mahni Ghorashi, Clear Labs
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The Future of Food Safety: A Q&A with Mars, Inc.

By Mahni Ghorashi
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Mahni Ghorashi, Clear Labs

Food safety professionals often work behind-the-scenes, developing the systems and processes that keep our food supply free of harm. While a vital job, it’s often thankless work—recognition only comes when there’s a recall or an outbreak.

And yet, the food safety industry is evolving rapidly. New threats are emerging, new technologies are being deployed, and new regulations are causing changes in our fundamental infrastructure. “Good enough” pathogen detection is no longer good enough. As a result of new pressures, the food safety lab is emerging as one of the most promising centers of innovation in the entire supply chain. It’s time that the people who are driving this wave of innovation and change receive the positive recognition for their work that they deserve.

That’s why we’re starting this Q&A series—to hear the success stories, the best practices, the hurdles and the achievements from the best in the industry. We will dive deep with the experts into some of the biggest challenges and opportunities our industry faces, focused particularly on new technology that is advancing the industry by leaps and bounds—from blockchain to NGS to machine learning. As this series evolves, we hope that readers will be informed and inspired by what the future holds.

For our first interview, I had the pleasure of interviewing Bob Baker, corporate food safety science and capability director at Mars, Inc.. Bob leads the corporate food safety science strategy for Mars, Incorporated and provides leadership and consultation on food safety capability development and current and future challenges impacting global food security. Prior to his current role, Bob was responsible for the design, construction and leadership of the Mars Global Food Safety Center in Beijing, China.

Mahni Ghorashi: What are the biggest risks to our food safety infrastructure in 2018? What’s keeping you up at night?

Bob Baker: Food safety risks are increasing at an unprecedented rate, with new threats and hazards constantly emerging, changes in agricultural practices and food production, and the environment. The globalization of trade means that an issue in one part of the world often impacts the global supply chain.

To ensure safer food for all, the identification and isolation of potential and developing issues needs to happen at a much faster pace. At Mars, we believe industry has a crucial role to play in helping all stakeholders in the food supply chain identify risks and solutions, but no entity can do this alone. That’s why we have advocated for a new approach to food safety, one rooted in knowledge sharing and collaboration. That’s why we launched our Global Food Safety Center (GFSC) in 2015.

GFSC is conducting original research and collaborating in a number of areas that we see as critical—mycotoxin management, rapid detection and identification of pathogens, raw material and product authenticity, operational food safety optimization and transforming food safety through data integration.

Although we see improvements in some areas, some of them are becoming more complex. Mycotoxins are a prime example of that. Food fraud is another area of growing concern, and addressing that is going to take a focus on technology, regulation and enforcement and a number of other areas to deliver transparency, to verify sourcing, and ultimately ensure that customers and consumers are purchasing and consuming safe food.

Ghorashi: What are you most excited about? What’s changing in a good way in the food safety sector?

Baker: What’s encouraging is we’re seeing is a willingness to share information. At Mars we often bring together world experts from across the globe to focus on food safety challenges. We continue to see great levels of knowledge sharing and collaboration.

There are also new tools and new technologies being developed and applied. Something we’re excited about is a trial of portable ‘in-field’ DNA sequencing technology on one of our production lines in China. This is an approach that could, with automated sampling, reduce test times.

We’re also excited about the IBM-Mars Consortium for Sequencing the Food Supply Chain—early signs have been very encouraging. This is an approach that could change the nature of food safety management, taking us from testing for a specific pathogen, to a situation where we could map the entire makeup of an environment and predict food safety issues based on changes within that environment.

Ghorashi: If you take a look at the homepage of any of the food safety trade publications, all you see is recall after recall. Are transparency and technological advancement bringing more risks to light, and are things generally trending towards improvement?

Baker: At Mars, quality is our first principle and we take it seriously—if we believe that a recall needs to be made in order to ensure the safety of our consumers then we will do it. We also share lessons from recalls across our business to ensure that we learn from every experience.

Unfortunately, there does not seem to be a safe place for businesses to share such insights with each other. So although we are seeing more collaboration in the field of food safety generally, critical knowledge and experience from recalls is not being shared more broadly which may be having an impact.

Regarding the role of technological advancement, the hope is that as better tools and more advanced technology become available, it will be easier to pinpoint issues in the food supply chain much more effectively and much earlier than before which can only be a good thing.

Ghorashi: Do you see 2018 as the year when NGS technologies will find widespread adoption for food-safety testing applications? What can government and industry do to help accelerate adoption?

Baker: Next-generation sequencing has a lot of potential, but it may take time to be adopted fully.

We are very pleased to see the U.S. government continue to view food safety as a priority. The FDA and the CDC are already moving from single-cell cultures and single genes to mixed genomics and metagenomics. At Mars, we see metagenomics as the future of food safety because it may help identify sentinels of food safety and predict potential issues through microbiome shifts.

The key to the development and adoption of any successful technology is sharing knowledge so that all parties from the government, industry and NGOs can build on it. Early results from the IBM-Mars Consortium for Sequencing the Food Supply Chain have been encouraging and we are actively sharing these initial insights via publications and scientific forums.

Ghorashi: What are some new technology processes on the horizon for 2018, and where should industry and government be investing its time and resources?

Baker: Food safety challenges are increasing, and we need to collaborate and share insights if we are to ensure safe food.

One major area is informatics and how we can enable better application of data mining, more applied bioinformatics and statistics. How can key players –regulators, industry, NGOs—get together and share data? How do you better mine data to move to a predictive model? This is an area that could benefit from a more focused approach between government and industry.

Ghorashi: What is your #1 goal for the industry in 2018? Fewer recalls? New tech implementation? Better regulatory oversight?

Baker: We’d like to see progress in all of the above, and we will continue to work with a range of stakeholders to move the needle on food safety.

That said, the food safety challenges facing us all are complex and evolving. Water and environmental contaminants are areas that industry and regulators are also looking at, but all of these challenges will take time to address. It’s about capturing and ensuring visibility to the right insights and prioritizing key challenges that we can tackle together through collaboration and knowledge sharing.

Dollar

Pathogens Drive More Than Half of $12 Billion Global Food Safety Testing Market

By Maria Fontanazza
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The importance of food safety testing technologies continues to grow, as companies are increasingly testing their products for GMOs and pesticides, and pathogens and contamination. Last year the global food safety testing market had an estimated value of $12 billion, according to a recent report by Esticast Research & Consulting. Driven by pathogen testing technologies, the global food safety testing market is expected to experience a 7.4% CAGR from 2017–2024, hitting $21.4 billion in revenue in 2024, said Vishal Rawat, research analyst with Esticast.

With a CAGR of 9.3% from 2017–2024, rapid testing technologies are anticipated to lead the market. Testing methods responsible for this growth include immunoassays (ELISA), latex agglutination, impedance microbiology, immune-magnetic separation, and luminescence and gene probes linked to the polymerase chain reaction, said Rawat, who shared further insights about the firm’s market projections with Food Safety Tech.

Food Safety Tech: With the GMO food product testing market expected to experience the highest growth in the upcoming future, can you estimate the projected growth?

Vishal Rawat: The GMO food product testing market is estimated to generate a revenue of approximately $5.2 billion in 2016. The market segment is expected to witness a compound annual growth rate of 8.3% during the forecast period of 2017–2024. This is a global market estimation.

FST: What innovations are occurring in product testing?

Rawat: Nanomaterials and nanobased technologies are attracting interest for rapid pathogen testing. Sustainable technologies such as edible coatings or edible pathogen detection composition can attain a trend in the near future. Also, new rapid allergen testing kits are now emerging out as the latest food testing technology in the market, which are portable and easy to use.

FST: Which rapid pathogen detection testing technologies will experience the most growth from 2017–2024?

Rawat: New and emerging optical, nano-technological, spectroscopic and electrochemical technologies for pathogen detection, including label-free and high-throughput methods would experience the highest growth.

FST: What pathogen testing technologies are leading the way for meat and poultry in the United States?

Rawat: The presence of a microbial hazard, such as pathogenic bacteria or a microbial toxin, in ready-to-eat (RTE) meat or poultry products is one basis on which these products may be found adulterated. The FSIS is especially concerned with the presence of Listeria monocytogenes, Salmonella, Escherichia coli O157: H7, and staphylococcal enterotoxins in RTE meat and poultry products. Rapid pathogen testing for E. coli O157:H7 and Salmonella, for ground beef, steak and pork sausages is going to lead the U.S. market.

An overview of the report, “Food Safety Testing Market By Contaminant Tested (Pathogens, GMOs, Pesticides, Toxins), By Technology (Conventional, Rapid), Industry Trends, Estimation & Forecast, 2015– 2024” is available on Esticast’s website.

3M Molecular Detection Assay 2

3M Receives Edison Award in Diagnostics

3M Molecular Detection Assay 2

3M has announced that its Molecular Detection Assay 2 has won the Gold Edison Award in the diagnostic tools category. The 2017 Edison Awards recognize innovators that have had a positive impact globally. The assay platform is a next-generation of tests, which also previously won an Edison award.

The technology is powered by isothermal DNA amplification and bioluminescience detection to provide a faster molecular detection of pathogens. Its single assay protocol enables batch processing of up to 96 different samples simultaneously and can provide same-day results.

The platform can be used to identify Salmonella, Listeria, Listeria monocytogenes, and E.coli O157 in food or environmental samples, and Cronobacter in powdered infant formula.

BAX-System_X5_Hero

Hygiena to Acquire DuPont’s Food Safety Diagnostics Business

By Food Safety Tech Staff
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BAX-System_X5_Hero

In an agreement expected to close in Q1 2017, Hygiena, a provider of rapid food safety and environmental sanitation testing, is acquiring Dupont’s global food safety diagnostics business. Financial terms of the deal were not disclosed.

The acquisition includes DuPont Diagnostics’ BAX system for pathogen detection (used globally by food manufacturers, quality labs and governments worldwide) and RiboPrinter Systems, the company’s globally and technically trained sales, R&D and manufacturing, and its in-house production capacity.

“The combination of DuPont Diagnostics and Hygiena will create a broad food safety diagnostics company that can better serve our customers, said Steve Nason, CEO of Hygiena in a press release. “The combined company’s microbiology products will cover the full manufacturing process, from in-process environmental tests to finished products tests.”

Hygiena is a portfolio company of private equity firm Warburg Pincus. Its products are distributed in 80 countries and include rapid hygiene monitoring systems, environmental collections systems, and its ATP testing system.

New Dipstick for Rapid Detection of Salmonella on the Farm

By Food Safety Tech Staff
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A new rapid assay may help growers make faster and more informed decisions right on the farm. Researchers from the University of Massachusetts and Cornell University are developing a test that addresses the challenge of sampling produce and assessing risk in a timely manner. The dipstick would enable rapid detection of Salmonella in agricultural samples in about three hours.

How It Works

“Users simply place a leaf sample in a small plastic bag that contains enzymes and incubate it for about 1.5 hours. Users would then squeeze a small liquid sample through a filter and place it in a tube with bacteriophages—viruses that are harmless to humans but infect specific bacterium, such as Salmonella or E. coli. Some phages are so specific they will only infect one bacterium serotype while others will infect a broader range of serotypes within an individual species. Phages also will only infect and replicate in viable bacteria, ensuring that non-viable organisms are not detected. This distinction is useful if prior mitigation steps, such as chlorination, have already been used. The phages used in the test were engineered to insert a particular gene into the bacteria.” – Center for Produce Safety

“We have been developing dipstick assays for ultra-low detection limits,” the technical abstract, Rapid bacterial testing for on-farm sampling, states. “Our preliminary data suggests that our fluorescent dipstick will have a detection limit of Salmonella spp. cells which makes the test ideal for on-farm use and appropriate federal requirements.”

Role Play: Be FDA for a Day

By Food Safety Tech Staff
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Mary Duseau, chief commercial officer at Roka, will review a self-auditing program that companies can use to essentially play FDA for a day—using technology that identifies hidden risks in a food processing facility.
During the webinar, Mary Duseau, chief commercial officer at Roka, will review a self-auditing program that companies can use to essentially play FDA for a day—using technology that identifies hidden risks in a food processing facility. REGISTER HERE

Food company executives are in a new world of criminal liability as they navigate a different regulatory environment. During a free webinar next month, attendees can learn how to Play FDA for a Day. Roka Bioscience, along with food safety attorney Shawn Stevens, will discuss:

  • How to navigate the regulatory environment
  • Impact of Whole Genome Sequencing
  • Using accurate pathogen detection technology
  • Self-auditing of food facilities to avoid regulatory or criminal exposure

“Ensuring your CEO stays out of prison is a great ROI. Food company executives and managers need to perform additional testing to see what FDA will find, and then correct it, before FDA arrives in their facility.” – Shawn K. Stevens

Shawn K. Stevens, Food Industry Counsel Check out the latest insights from Shawn K. Stevens in his column, Food Safety Attorney

During the 2016 Food Safety Consortium, Shawn Stevens will lead the following panel:

Thursday, 12/8

10:30–11:15 AM

Ask the Experts: Strategies to avoid FDA criminal liability
Round table discussion group lead by Shawn K. Stevens, Global Food Safety Attorney, Food Industry Counsel LLC

LEARN MORE

John Besser, Listeria conference

Deadly Outbreaks and the Role of Metagenomics

By Maria Fontanazza
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John Besser, Listeria conference

Americans consume 350 billion pounds of food each year, with one out of six people falling victim to foodborne illness, and 3000 dying. The significant amount of Listeria outbreaks hitting the industry (most recently, the staggering number occurring in produce) has left many food safety and quality assurance professionals searching for better methods of prevention and detection. Using big data, specifically metagenomics, to improve food safety and detect potentially deadly outbreaks is indeed where the future is headed.

DID YOU KNOW? The estimated U.S. cost of one case of Listeriosis is $1.4 million. Listeria is a prime concern due to the high percentage of fatalities that occur as a result of contracting Listeriosis. And what’s worse is the fact that many of the cases are preventable.

During Food Safety Tech’s Listeria Detection & Control Workshop this week, John Besser, Ph.D., deputy chief of CDC’s Enteric Diseases Laboratory Branch, outlined how the agency is leveraging metagenomics to find unrecognized problems in the food supply. Perhaps the most important element of disease surveillance is that it enables the detection of new issues, especially those whose presence was previously unknown.

John Besser, Listeria conference
CDC’s John Besser, Ph.D. discusses genome-based outbreak detection work at the agency. (Click to enlarge)

Pathogen-specific surveillance allows the detection of more outbreaks, which will in turn make the food supply safer, because it will enable industry to understand the root causes of outbreaks and help them address problems much sooner. The CDC is focused on genome-based outbreak detection because of its ability to achieve faster detection—and with greater precision in identifying the source. The method has also helped the agency solve outbreaks with fewer cases occurring, and it concurrently helps rule out sources.

PulseNet, a nationwide database (comprised of 87 labs in the United States) that links cases most likely to share a cause for illness, has prompted food safety improvements across a variety of products, including sprouts, peanut products, leafy greens, flour, melons, eggs and poultry. Combine this capability with the Listeria initiative, which was launched in the mid-2000s, and the CDC has been able to find more (and smaller) outbreaks than ever before. In fact, there’s been a dramatic increase in the number of outbreak cases that have been solved (with the food source being identified). During the pre-whole genome sequencing (WGS) stage (September 2012­–August 2013), only one outbreak was solved; in year one of the WGS project (September 2013–August 2014), four cases were solved; in year 2 of the WGS project (September 2014–August 2015), nine outbreaks were solved. In these respective time periods, the median number of cases per cluster dropped from six to four to three. In addition, the number of cases linked to a food source jumped from 6 to 16 to 93 during this respective time period.

Besser also discussed the role of metagenomics, or the study of total genetic material recovered directly from environmental samples. A couple of years ago, this was science fiction and wasn’t possible, he said. But as we look to the future, metagenomics will become a lot cheaper as computers become more powerful—and at break-neck speed. He referenced IBM Research, who earlier this year announced a project being conducted in conjunction with Mars, Inc. and Biorad for sequencing the food supply chain (calling it the “largest-ever metagenomics study”).

Read Food Safety Tech’s interview with IBM Research about the next-generation sequencing project, “Preventing Outbreaks a Matter of How, Not When”

Metagenomics enables the profiling of communities of microbiomes anywhere in the food supply chain. And the method is fast—it can potentially shave weeks off the process of identifying clusters of interest. In addition, it can increase the value of interviews conducted with patients who have fallen ill (Think about it: Do you remember what you ate two weeks ago? What about a month ago?).

Currently there are several limiting factors surrounding metagenomics: Cost; sequencing read length and error rate; specific software (and pipelines); computing processing power and bandwidth; and the signal-to-noise factor. However, with the rapid rate in which technology has been improving in this space, the high likelihood of these issues being addressed and resolved in the not-so-distant future will present exciting opportunities in outbreak prevention and detection.