Tag Archives: PCR

Next-Generation Sequencing Targets GMOs

By Maria Fontanazza
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As the movement among consumers for more information about the products they’re purchasing and consuming continues to grow, the food industry will experience persistent pressure from both advocacy groups and the government on disclosure of product safety information and ingredients. Top of mind as of late has been the debate over GMOs. “Given all of the attention on GMOs on the legislative side, there is huge demand from consumers to have visibility and transparency into whether products have been genetically modified or not,” says Mahni Ghorashi, co-founder of Clear Labs.

Mahni Ghorashi, Clear Labs
Mahni Ghorashi, co-founder of Clear Labs

Today Clear Labs announced the availability of its comprehensive next-generation sequencing (NGS)-based GMO test. The release comes at an opportune time, as the GMO labeling bill, which was passed by the U.S. House of Representatives last week, heads to the desk of President Obama.

Clear Labs touts the technology as the first scalable, accurate and affordable GMO test. NGS enables the ability to simultaneously screen for multiple genes at one time, which could companies save time and money. “The advantage and novelty of this new test or assay is the ability to screen for all possible GMO genes in a single universal test, which is a huge change from the way GMO testing is conducted today,” says Ghorashi.

The PCR test method is currently the industry standard for GMO screening, according to the Non-GMO Project. “PCR tests narrowly target an individual gene, and they’re extremely costly—between $150–$275 per gene, per sample,” says Ghorashi. “Next-generation sequencing is leaps and bounds above PCR testing.” Although he won’t specify the cost of the Clear Labs assay (the company uses a tiered pricing structure based on sample volume), Ghorashi says it’s a fraction of the cost of traditional PCR tests.

The new assay screens for 85% of approved GMOs worldwide and targets four major genes used in manufacturing GMOs (detection based on methods of trait introduction and selection, and detection based on common plant traits), allowing companies to determine the presence and amount of GMOs within products or ingredient samples. “We see this test as a definitive scientific validation,” says Ghorashi. The company’s tests integrate software analytics to enable customers to verify GMO-free claims, screen suppliers, and rank suppliers based on risk.

Clear Labs, GMO, testing
Screenshot of the Clear Labs GMO test, which is based on next-generation sequencing technology.

Clear Labs isn’t targeting food manufacturers of a specific size or sector within the food industry but anticipates that a growing number of leading brands will be investing in GMO testing technology. “We expect to see adoption across the board in terms of company size, related more to what their stance is on food transparency and making that information readily available to their end consumers,” says Ghorashi.

PCR Test, weighing milk powder

Spoil No More: Rapid Test for Dairy Products Goes Beyond Detecting Microbes

By Maria Fontanazza
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PCR Test, weighing milk powder

Detecting yeast and mold is one of the most time consuming parts of the testing process for dairy products. With more pressure to move products that have a short shelf life out the door as quickly as possible, time really is money. Having a rapid, real-time test that enables companies to make immediate production decisions can provide a significant advantage. “[This technology] brings test time within the same timeframe as other microbiology tests, so a test for yeast and mold is no longer the outlier. That’s a huge savings right there,” says Phil Coombs, product specialist at Weber Scientific.

biotecon_diagnostics_starprep
Weber Scientific was one of three recipients of the Food Expo Innovation Award on July 17, 2016 at the IFT Annual Meeting in Chicago.

Coombs is referring to Weber Scientific’s recently released PCR Yeast and Mold Quantitative Test, which has been validated for finished dairy products. The company was asked by Germany-based Biotecon Diagnostics, the creator of the newly developed PCR method, to be its partner in introducing the test to the U.S. market. The technology reduces testing time for yeasts and molds from five days to four hours or less—from sample prep to the time-to-result, with no pre-enrichment required. “We make a big deal out of this, because sometimes [companies] with a pathogen test will say they have a four-hour test but it’s not truly, from start-to-finish, a four-hour test—you have to do some form of pre-enrichment, and so it’s a 24–48 hour test,” says Coombs. “When looking at fermented milk product like yogurt, it might have a shelf life of about 50 days. There’s much more time for the yeast and mold (because they’re typically slower growing organisms) to get busy and spoil the product. Yeast and mold can tolerate the lower pH, so that’s been the biggest sector of interest so far.”

One of the features of the technology is its ability to protect against false-negative results from non-viable DNA and false-positives from previous PCR test runs, which greatly reduces the chances of cross-contamination as well.

PCR Test for dairy products
The PCR Yeast and Mold Quantitative Test conducts analysis on milk powder. Image courtesy of Weber Scientific.

Achieving a shorter time-to-result means that if a company uncovers an issue, it can take immediate remedial action rather than waiting several days. This can have a big economic impact on production and warehousing, along with releasing product into commerce and distribution, especially when dealing with products that require refrigeration. In addition, the PCR test goes beyond detecting microbes that will spoil fermented milk products and offers advantages in the broader context of reducing food waste and spoilage. “It will be attractive to many companies that are developing a broad range of sustainability measures,” says Fred Weber, president of Weber Scientific. “And to cut down on food waste at the consumer level is a big deal.”

The company expects AOAC approval next year.

Mislabeled Salmon

Rapid Salmon ID Test the Latest in Fraud Prevention

By Food Safety Tech Staff
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Mislabeled Salmon

Two rapid test kits have been launched for the identification of salmon species: Chinook (Oncorhynchus tshawytscha) and Sockeye (Oncorhynchus nerka). The tool kits were developed in collaboration with the University of Guelph and allow distributors, food processors and government regulators to positively identify the salmon species in less than two hours. 

Recent studies have revealed that a significant amount of the salmon sold in the United States is mislabeled.

The test kits are used in conjunction with a portable, real-time PCR system that provides DNA detection. The tools are part of the Instant ID Species product line from InstantLabs, which include seafood identification tests for Atlantic (Salmo salar) and Coho Salmon (Oncorhynchus kisutch as well as Atlantic Blue Crab (Callinectes sapidus) and U.S. Catfish (Ictalurus species).

Ravi Ramadhar, Food Safety Business Director for Life Sciences Solutions, Thermo Fisher Scientific
In the Food Lab

Molecular Diagnostics – Generation 3: 2005 to Present

By Ravi Ramadhar
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Ravi Ramadhar, Food Safety Business Director for Life Sciences Solutions, Thermo Fisher Scientific

In my previous blog, I covered the first two generations of Molecular Diagnostics: Generation one, was the advent of these tests prior to 1995, while the second generation saw the evolution of molecular diagnostics with the emergence of standardized food molecular and method workflow.

The advent of automated DNA sequencing and use of multiple fluorescent dyes by companies like Applied Biosystems and Roche led to the development of multiple fluorescent dyes and real- time quantitative PCR systems (qPCR). At first these qPCR systems were only used in the research environment, but quickly found their way to the food industry.

Applications such as quantitation of GMOs and multiple pathogen targets became common. Real-time PCR systems permitted users to visualize amplification as it happened and enabled simultaneous detection of multiple targets. With the use of newer chemistries and improved enzymes, shorter amplification cycles – sometimes as low as 40 minutes – could be achieved. The real-time systems offered faster time-to-result with additional target probes and thus higher target specificity. As with most molecular methods, the workflow was sensitive to food matrix inhibition and required alternative sample preparation methods to meet the wide variety of food matrixes.

Within this generation of solutions, alternatives were introduced, that promised faster, easier or more sensitive results. These included alternative to either the detection method or enzymes utilized Iisothermal amplification, for example without need for multiplexing capability of qPCR or internal controls, as well as targeting alternative nucleic acid such as RNA were introduced to the food market. These incremental improvements did not lead to any significant new paradigms or improvements to the food testing workflow. Their emergence instead led to an explosion of additional and alternative molecular platforms for food, without any real innovation. Within this, solutions introduced to the food industry eventually brought us to where we are today.

Directly taking systems from the clinical diagnostics workflow and introducing these platforms and systems as food solutions. While these systems automate the entire workflow or automate the PCR setup it remains to be seen if with their higher complexity and high maintenance these systems can survive the food industry. The basic molecular workflow for food has remained intact since its introduction in the late 1990s with innovation more or less stagnant. What’s needed is for someone to truly develop a platform from the ground up with the food laboratory in mind.

Today’s landscape and what’s next

Today, there are some early signals of where innovations and changes for food labs will emerge. A recent poster by Nestle, for example, highlighted the uses of next-generation sequencing (NGS) and DNA sequencing to develop a DNA method to allow the identification of coffee varieties through the value chain, from the field to the finished product. The method is applied on routine basis to guarantee the purity and authenticity of raw material used by Nespresso.

Applications of NGS in outbreak response and trace back investigations are being used in parallel with existing technologies. Finally, availability of new sequencing data enables better assay design and development of adjacent technologies.

NGS was preceded by emulsion amplification and sequencing by synthesis. These developments led to the development and introduction of digital PCR. Within a digital PCR reaction, millions of simultaneous reactions from one sample occur. The advantages of dPCR include lower and absolute, not relative gene copy number. The data has high precision and has better tolerance to inhibitors. These characteristics can lead to better and more precise molecular tests in food. , Before dPCR wide spread adoption is seen, however, the limitations of high cost and limited dynamic range must be addressed.

It’s not only in the testing labs and adjacent technologies that NGS is having an impact. In the labs driving innovation in food and food ingredient development, applications of NGS are being used to develop targeted food ingredients.

Nestle is the leader in this convergence of food, health and nutrition and over the last three years, the company has acquired and formed partnerships targeting the space. In its formation of the Nestle Institute of Health Sciences, Emmanuel Baetge, head of NHIS, emphasized NHIS expertise and research capabilities using systems biology, next generation sequencing, and human genetics.

The world of food safety is as dynamic as the natural flora of food itself. Changing regulations, evolving organisms, technological change and consumers’ changing tastes require new solutions. The requirements of the food laboratory have not changed. They are the protectors of brands and the teams we trust to deliver safe and quality foods. However, how they do that has and will continue to change.

Next time… molecular serotyping.

References:

  1. Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: www.genome.gov/sequencingcosts. Accessed 1/13/2014 [DOA 1/13/12014].
  2. Beilei Ge and Jianghong Meng , 2009 14: 235 Advanced Technologies for Pathogen and Toxin Detection in Foods: Current Applications and Future Journal of Laboratory Automation DOI: 10.1016/j.jala.2008.12.012.
  3. Morisset D, Sˇ tebih D, Milavec M, Gruden K, Zˇ el J (2013) Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR. PLoS ONE 8(5):e62583. doi:10.1371/journal.pone.0062583.
  4. http://www.nestle-nespresso.com/asset-libraries/Related%20documents%20not%20indexed/Nespresso%20poster%20ASIC2012%20DNA%20traceability.pdf