Tag Archives: rapid testing

Benjamin Katchman, PathogenDx
In the Food Lab

Revolutionary Rapid Testing for Listeria Monocytogenes and Salmonella

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

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

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

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

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

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

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

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

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

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

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

References.

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

Beyond the Results: What Can Testing Teach Us?

By Sasan Amini
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Sasan Amini, Clear Labs

The microbiology lab will increasingly be understood as the gravitational center of big data in the food industry. Brands that understand how to leverage the data microbiology labs are producing in ever larger quantities will be in the best position to positively impact their bottom line—and even transform the lab from a cost center to a margin contributor.

The global rapid microbiology testing market continues to grow at a steady pace. The market is projected to reach $5.09 billion by 2023, up from $3.45 billion in 2018. Increased demand for food microbiology testing—and pathogen detection in particular—continues to drive the overall growth of this sector. The volume of food microbiology tests totaled 1.14 billion tests in 2016—up 15% from 2013. In 2018 that number is estimated to have risen to 1.3 billion tests, accounting for nearly half the overall volume of industrial microbiology tests performed worldwide.

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

We are going through a unique transition where food safety tests are evolving from binary tests to data engines that are capable of generating orders of magnitude of more information. This creates a unique opportunity where many applications for big data collected from routine pathogen testing can help go beyond stopping an outbreak. Paired with machine learning and other data platforms, these data have the opportunity to become valuable, actionable insights for the industry.

While some of these applications will have an impact on fundamental research, I expect that big data analytics and bioinformatics will have significant opportunity to push the utilities of these tests from being merely a diagnostic test to a vehicle for driving actions and offering recommendations. Two examples of such transformations include product development and environmental testing.

Food-Safety Testing Data and Product Development

Next-generation-sequencing (NGS) technologies demonstrate a great deal of potential for product development, particularly when it comes to better understanding shelf life and generating more accurate shelf-life estimates.

Storage conditions, packaging, pH, temperature, and water activity can influence food quality and shelf life among other factors. Shelf-life estimates, however, have traditionally been based on rudimentary statistical models incapable of accounting for the complexity of factors that impact food freshness, more specifically not being able to take into consideration the composition and quantity of all microbial communities present on any food sample. These limitations have long been recognized by food scientists and have led them to look for cost-effective alternatives.

By using NGS technologies, scientists can gain a more complete picture of the microbial composition of foods and how those microbial communities are influenced by intrinsic and extrinsic factors.

It’s unlikely that analyzing the microbiome of every food product or unit of product will ever be a cost-effective strategy. However, over time, as individual manufacturers and the industry as a whole analyze more and more samples and generate more data, we should be able to develop increasingly accurate predictive models. The data generation cost and logistics could be significantly streamlined if existing food safety tests evolve to broader vehicles that can create insights on both safety and quality indications of food product simultaneously. By comparing the observed (or expected) microbiome profile of a fresh product with the models we develop, we could greatly improve our estimates of a given product’s remaining shelf life.

This will open a number of new opportunities for food producers and consumers. Better shelf-life estimates will create efficiencies up and down the food supply chain. The impact on product development can hardly be underestimated. As we better understand the precise variables that impact food freshness for particular products, we can devise food production and packaging technologies that enhance food safety and food quality.

As our predictive models improve, an entire market for these models will emerge, much as it has in other industries that rely on machine learning models to draw predictive insights from big data.

Data Visualization for Environmental Monitoring

In the past one to two years, NGS technologies have matured to the point that they can now be leveraged for high-volume pathogen and environmental testing.

Just as it has in other industries, big data coupled with data visualization approaches can play a mainstream role in food safety and quality applications.

Data visualization techniques are not new to food safety programs and have proven particularly useful when analyzing the results of environmental testing. The full potential of data visualizations has yet to be realized, however. Visualizations can be used to better understand harborage sites, identifying patterns that need attention, and visualize how specific strains of a pathogen are migrating through a facility.

Some of this is happening in food production facilities already, but it’s important to note that visualizations are only as useful as the underlying data is accurate. That’s where technologies like NGS come in. NGS provides the option for deeper characterization of pathogenic microorganisms when needed (down to the strain). The depth of information from NGS platforms enables more reliable and detailed characterization of pathogenic strains compared to existing methods.

Beyond basic identification, there are other potential use cases for environmental mapping, including tracking pathogens as they move through the supply chain. It’s my prediction that as the food industry more broadly adopts NGS technologies that unify testing and bioinformatics in a single platform, data visualization techniques will rapidly advance, so long as we keep asking ourselves: What can the data teach us?

The Food Data Revolution and Market Consolidation

Unlike most PCR and immunoassay-based testing techniques, which in most cases can only generate binary answers, NGS platforms generate millions of data points for each sample for up to tens to hundreds of samples. As NGS technologies are adopted and the data we collect increases exponentially, the food safety system will become the data engine upon which new products and technologies are built.

Just as we have seen in any number of industries, companies with access to data and the means to make sense of it will be in the best position to capitalize on new revenue opportunities and economies of scale.

Companies that have adopted NGS technologies for food safety testing will have an obvious advantage in this emerging market. And they won’t have had to radically alter their business model to get there. They’ll be running the same robust programs they have long had in place, but collecting a much larger volume of data in doing so. Companies with a vision of how to best leverage this data will have the greatest edge.

Dollar

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

By Maria Fontanazza
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Dollar

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.

Gina Kramer
Food Safety Think Tank

Rapid, On-site Pathogen Testing a Game Changer

By Gina R. Nicholson-Kramer
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Gina Kramer

Learn innovative ways to mitigate the threat of Listeria at the Listeria Detection & Control Workshop | May 31–June 1, 2016 | St. Paul, MN | LEARN MOREWaiting days for test sample results can be the difference between keeping consumers safe and allowing contaminated food to enter the supply chain. I recently spoke with Mark Byrne, president and CEO of start-up ProteoSense, about his company’s portable pathogen detection system, which can find foodborne pathogens in food and environmental samples in 15 minutes or less, with no incubation required. Licensed from Ohio State University, the technology, called RapidScan, has unique sensor technology that provides a sensitive and specific assay with very low noise to enable a direct measurement of the presence of a pathogen.

When I asked Mark what effect he thought this technology would have on the food industry, he said: “I think the effect is going to be very profound. First of all, anytime you can give management information quickly, it changes their ability to respond, to take action.”

The technology has the potential to help companies deliver food to consumers safer and faster, and with less waste. Samples can be tested at various parts of the food supply chain, from in the field to final packaging.

RapidScan has been demonstrated for Salmonella, and ProteoSense is working on a Listeria assay. If all goes as planned, we can expect to see the product on the market in 2017. Watch my discussion with Mark to learn more about this innovative technology and how it could help you mitigate risks in your supply chain.

 

InstantLabs Launches DNA-based Atlantic and Coho Salmon SpeciesID Test Kits to Combat Seafood Mislabeling

The company has broadened species identification product line created in partnership with University of Guelph and plans to release additional test kits during the year.

InstantLabs announced today the expansion of its SpeciesID product line by offering DNA-based tests for Atlantic and Coho salmon. InstantLabs SpeciesID™ tests provide accurate DNA verification in under two hours.

The launch of the salmon test kits highlights InstantLabs’ efforts to meet market demand by expanding the affordable, simple-to-use InstantID™ product line. The company already offers kits to identify Atlantic Blue Crab, pork and horse meat. The InstantLabs’ system gives food wholesalers, processors and inspectors a fast and reliable option for product tests.

The two new products were created in partnership with the University of Guelph, an international leader in agricultural and food science. The InstantID test kits for Atlantic (Salmo salar) and Coho salmon (Oncorhynchus kisutch) are the first of four salmon assays planned for release during 2015. InstantLabs will launch InstantID™ for Chinook (Oncorhynchus tshawytscha) and Sockeye (Oncorhynchus nerka) salmon later this year.

Expanding its presence in the high-demand seafood market, the Baltimore-based manufacturer of the Hunter® system expects to also release InstantID™ kits for snapper, catfish, grouper, and tilapia.

“Producers, wholesalers and government entities needs robust tools to combat seafood fraud,” said Steven Guterman, chief executive officer of InstantLabs. “InstantLabs’ real-time PCR testing systems and reagent kits can become an integral part in a testing program to verify labeling accuracy.”

InstantLabs’ Hunter® Real-Time PCR instrument combines accuracy, speed, and ease-of-operation into a compact portable system. The Hunter system is designed for use at points-of-need to detect and analyze a wide variety of food samples by targeting DNA. Results delivered quickly allow seamless integration into food industry firms’ processes and facilities.

Dr. Robert Hanner, Ph. D., has directed the University of Guelph’s research in conjunction with InstantLabs. “This collaboration has been essential in commercializing DNA-based food authentication tests for the seafood industry,” said Dr. Hanner, associate professor at the Center of Biodiversity Genomics. “This technology will help safeguard against existing supply chain vulnerabilities, protecting both businesses and consumers from food fraud.”

InstantLabs identification tests are designed for use on the Hunter, a real-time PCR system developed by the company, and are also available for use with other PCR instruments.

Seafood industry reports continue to highlight concerns about fraud, species substitution and consumer preferences to use sustainable fish stocks. Approximately one-third of all fish sold in the U.S. was mislabeled, reported a recent survey from Oceana. The U.S. Food and Drug Administration identifies a range of lower valued fish regularly substituted for 20 higher-priced species. InstantLabs will provide critical tool sets needed by the industry to ensure the integrity of the supply chain.

ABOUT INSTANTLABS:

InstantLabs, a molecular diagnostic device company, developed and markets the Hunter® Accelerated-PCR system, a fully-integrated, easy-to-use, portable and affordable real-time polymerase chain reaction (RT-PCR) platform for rapid, accurate pathogen detection. InstantLabs Medical Diagnostics Corp., the legal entity, offers the Hunter® system for use with several food-borne pathogen test kits for the global food industry. The Hunter® system is especially well suited for use at points-of-care and points-of-need to detect and analyze a wide variety of common and problematic pathogens. InstantLabs’ growing worldwide customer base includes some of the world’s leading food companies. InstantLabs is also developing products for additional markets, including medical diagnostics where gold-standard accuracy, combined with Ease-of-use and rapid results, are critical. Founded in 2008, InstantLabs is located in Baltimore, MD. For more information please visit www.instantlabs.com.

ABOUT THE UNIVERSITY OF GUELPH:

Acknowledged as one of the leading public research universities, the University has 39 Canada Research chairs in natural sciences, energy, health services and social sciences. With a commitment to student learning and innovative research, University leaders are dedicated to cultivating the essentials for our quality of life – water, food, environment, animal and human health, community, commerce, culture and learning. The University community also shares a profound sense of social responsibility, an obligation to address global issues and a concern for international development. Learn more at www.uoguelph.ca.

Additional resources on seafood fraud: