Tag Archives: DNA sequencing

Dollar

Developments in PCR Technology Boost Food Pathogen Testing Market Outlook

By Vinisha Joshi
No Comments
Dollar

In recent years, foodborne illness has ignited alarming concerns across the globe. Food products can become contaminated with pathogenic bacteria through exposure to inadequate processing controls, animal manure, improper storage or cooking, and cross contamination. The following is a look at some of the pivotal figures that illustrate the effects of food contamination:

  • • According to WHO, an estimated of 600 million people globally fall ill after consuming contaminated food, of which 420,000 succumb to death every year.
  • Children under 5 years of age carry 40% of the foodborne disease burden, with 125,000 fatalities recorded annually.
  • Regionally, CDC reports suggest that foodborne pathogens cause nearly 9.6 million illnesses, 57,500 hospital admissions, and 1,500 deaths yearly in the United States alone.
  • Considering the financial aspects, it is essential to note that about $110 billion is lost almost every year in productivity and medical expenses from unsafe food consumption in low-and middle-income economies.

With such daunting numbers taking over the globe, there stands an innate requirement of cost-effective, easy-to-use, and accurate testing methods that ensure the consumer is delivered nothing but the safest food.

It has been estimated that global food pathogen testing market size could potentially surge to $5.5 billion by 2024.

Why is pathogen testing necessary? Pathogen testing is generally carried out to decrease and remove foodborne illnesses. It is a technique implemented in the very nascent stage of food production to ensure proper sanitation and food safety. The testing can be done using conventional technologies or the cutting-edge methods, including Polymerase Chain Reaction (PCR) or an immunoassay test.

PCR technology: An ideal and convenient technology in use for pathogen detection in food industry

PCR is one of the most frequently used technologies. The test enables the detection of a single bacterial pathogen, including E. Coli, Salmonella and Listeria, present in food by detecting a specific target DNA sequence. Aiding to such advantages, various business conglomerates that are involved in the food pathogen testing industry are taking strategic measures to bring forth novel innovations and practices in the space. The following is a brief snapshot of some developments in the PCR based pathogen testing technology landscape:

  • Sanigen, Ilumina partnership for development of NGS panel
    Owing to the escalating demand for PCR testing technology for detecting the presence of food pathogens, South Korea-based Sanigen, recently announced standing as a channel partner in the region for Illumina. Both the companies, in unison, are expected to work towards the development of NGS panels that can robustly detect 16 types of foodborne pathogen from around 400 samples.
  • Thermo Scientific’s 2020 launch of SureTest PCR Assays
    Last year Thermo Scientific expanded its portfolio of foodborne pathogen detection with the launch of the SureTest PCR Assays. The testing technology is poised to offer various food producers an access to a more holistic range of tests for every step of the analysis process.

A look at one sector: How is the expanding dairy sector complementing the growth structure of food pathogen testing market?

The dairy production industry is rapidly expanding in various developing and developed economies, marking a significant contribution to health, environment, nutrition and livelihoods. According to a National Farmers Union report, the U.S. dairy industry accounts for 1% of the GDP, generating an economic impact of $628 billion, as of 2019. However, dairy products, although deemed healthy, can contribute to severe human diseases in umpteen ways, with dairy-borne diseases likely to top the list.

Milk and products extracted from the milk of dairy cows can house a variety of microorganisms, emerging as a source of foodborne pathogens. This has pushed the need for appropriate testing methods and technologies, which can eliminate the presence of dairy-borne bacteria, like Salmonella.

Today, various rapid pathogen testing solutions that are suitable for detecting the presence of distinct bacteria and organisms are available for dairy-based food companies. For instance, PCR-based solutions are available to test for mastitis in dairy, which is a common rudder infection caused by microorganisms in dairy cattle, affecting the quality of milk. Apparently, Thermo Fisher offers VetMAX MastiType qPCR kits for relatively faster, efficient and easier mastitis diagnostics. In fact, the kits are deemed to be reliable tools that would accurately detect all mastitis causing bacteria in frozen, fresh and preserved milk samples.

Meat Products

Consumption of raw or undercooked meat is also expected to generate a significant food pathogen testing kits demand in the coming years. Common contaminants found in these products are E. coli and Salmonella. One of the strains of E. coli, Shiga Toxin-producing E. coli (STEC), is expected to emerge as a fatal contaminant present in the meat products. Consider the following:

  • WHO reports estimate that up to 10% of patients with STEC infection are vulnerable to developing haemolytic uraemic syndrome (HUS), with a case-mortality rate ranging from 3 to 5%.
  • Moreover, it has the ability to cause neurological complication in 25% of HUS patients and chronic renal sequelae, in around 50% of survivors.

Under such circumstances, the demand for pathogen testing in meat products, for detecting E. coli and other contaminants is gradually expanding worldwide. In January this year, PerkinElmer introduced its new tool for detection of E. coli O157 in food products. The kit has been developed for generating rapid results while simultaneously putting them forth to support food safety efforts related to beef and its self-life.

The global food and beverage sector is subject to stringent safety requirements and a considerable part of the responsibility lies with food producers. As such, access to rapid testing technologies will enable the producers to fulfill their safety obligations without compromising on productivity and bottom lines. The consistent development of PCR-based tools will certainly outline the gradual progress of food pathogen testing industry, keeping in mind the high penetration of dairy and processed meat products worldwide.

Megan Nichols
FST Soapbox

Technology Tools Improving Food Safety

By Megan Ray Nichols
No Comments
Megan Nichols

To cap off a tumultuous year for foodborne illnesses, the end of 2018 saw a rather large E. coli outbreak that affected several different types of lettuce. In all, about 62 people got sick in the United States, with another 29 affected in Canada. The outbreak was traced back to a farm in California thanks to a specific DNA fingerprint in the E. coli. It started in a water reservoir and spread to the nearby crops.

Unfortunately, the event was only one of two separate incidents involving romaine lettuce last year. Another E.coli outbreak was traced back to a source in Arizona. Are these outbreaks more common than we realize? The CDC estimates that 48 million Americans fall ill each year from foodborne pathogens. Of those who get sick, 128,000 have to be hospitalized, and about 3,000 perish.

It’s clear that the industry as a whole needs to buckle down and find more effective solutions, not just for preventing outbreaks but also for mitigating damage when they happen. A new level of safety and management can be achieved with the help of many new, innovative technologies.

The following are some of the technology tools shaping the future of food safety and quality management fields.

Blockchain

As a result of the E. coli outbreak, Walmart implemented blockchain technology to track leafy greens and boost supply chain transparency. The systems and infrastructure is anticipated to be in place by the end of 2019.

Blockchain is a secure, digital ledger. It holds information about various transactions and data, all of which are carried out on the network. It’s called a blockchain because each data set within the network is a chunk or “block,” and they’re all linked to one another—hence the chain portion of the name. What this allows for is complete transparency throughout the supply chain, because you can track goods from their origin all the way to distribution and sale.

Each block is essentially a chunk of information, and when it’s entered into the chain, it cannot be altered, modified or manipulated. It’s simply there for viewing publicly. You cannot alter information contained within a single block without modifying the entire chain—which operates much like a peer-to-peer network and is split across many devices and servers.
This unique form of security establishes trust, accuracy and a clear representation of what’s happening. It allows a company to track contaminated foods along their journey, stopping them before they contaminate other goods or reach customers.

Infrared Heating

Thanks to the rising popularity of ready-to-eat meals, the industry is under pressure to adopt preservation and pasteurization methods. Particularly, they must be able to sanitize foods and package them with minimal exposure and bacteria levels. This practice allows them to stay fresh for longer and protects customers from potential foodborne illness.

Infrared heating is a method of surface pasteurization, and has been used for meats such as ham. Infrared lamps radiate heat at low temperatures, effectively killing surface bacteria and contaminants. The idea is to decontaminate or sanitize the surface of foods before final packaging occurs.

Industrial IoT and Smart Sensors

The food and beverage industry has a rather unique challenge with regard to supply chain operations. Food may be clean and correctly handled at the source with no traces of contamination, but it’s then passed on to a third party, which changes the game. Maybe a refrigerated transport breaks down, and the food within is thawed out. Perhaps a distributor doesn’t appropriately store perishable goods, resulting in serious contamination.

This transportation stage can be more effectively tracked and optimized with the help of modern IoT and smart, connected sensors. RFID tags, for instance, can be embedded in the packaging of foods to track their movements and various stats. Additional sensors can monitor storage temps, travel times, unexpected exposure, package tears and more.

More importantly, they’re often connected to a central data processing system where AI and machine learning platforms or human laborers can identify problematic changes. This setup allows supply chain participants to take action sooner in order to remedy potential problems or even pull contaminated goods out of the supply.

They can also help cut down on fraud or falsified records, which is a growing problem in the industry. Imagine an event where an employee says that a package was handled properly via forms or reporting tools, yet it was exposed to damaging elements. The implications of even simple fraud can be significant. Technology that automatically and consistently reports information—over manual entry—can help eliminate this possibility altogether.

Next-Generation Sequencing

NGS refers to a high-throughput DNA sequencing process that is now available to the food industry as a whole. It’s cheaper, more effective and takes a lot less time to complete, which means DNA and RNA sequencing is more accessible to food companies and suppliers now than it ever has been.

NGS can be used to assess and sequence hundreds of different samples at a time at rates of up to 25 million reads per experiment. What that means is that monitoring teams can accurately identify foodborne pathogens and contamination at the speed of the modern market. It is also a highly capable form of food safety measurement and is quickly replacing older, molecular-based methods like PCR.

Ultimately, NGS will lead to vastly improved testing and measurement processes, which can identify potential issues faster and in higher quantities than traditional methods. The food industry will be all the better and safer for it.

The Market Is Ever Evolving

While these technologies are certainly making a splash—and will shape the future of the food safety industry—they do not exist in a vacuum. There are dozens of other technologies and solutions being explored. It is important to understand that many new technologies could rise to the surface even within the next year.

The good news is that it’s all meant to improve the industry, particularly when it comes to the freshness, quality and health of the goods that consumers eat.

DNA sequencing

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

By Casey Schlenker, Jenna Brooks, Kent Oostra, Ryan McLaughlin
No Comments
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.

Continue to page 2 below.

Pages: 1 2
magnifying glass

Next-Generation DNA Sequencing Finds Unexpected Contaminants

By Food Safety Tech Staff
No Comments
magnifying glass

With more regulatory and consumer scrutiny being placed on the authenticity of food products, companies must use technologies that can verify products and ingredients, and detect contaminants. NSF International recently acquired AuthenTechnologies, a testing laboratory that provides DNA-species identification services to improve authenticity, safety and quality of natural products. Using shorter segments and validated reference materials, AuthenTechnologies employs a DNA sequencing method that can identify “almost any” species and detect contaminants that cannot be distinguished morphologically or chemically. The method also screens for allergens, GMOs, fillers and filth.

“As the food supply chain becomes more complex and regulations continue to evolve and become more rigorous, this technology is becoming essential to achieving regulatory compliance and brand protection while preventing issues associated with fraud, mislabeling and adulteration,” said Lori Bestervelt, Ph.D, international executive vice president and chief technology officer at NSF, in a company release. AuthenTechnologies’ co-founder Danica Harbaugh Reynauld, Ph.D., adds, “We’ve developed a more highly specific DNA methodology capable of identifying a single organism to a complex blend of unlimited ingredients.” Reynauld, who will join NSF as global director of scientific innovation, will lead the NSF AuthenTechnologies center of excellence with NSF’s global network of labs.

In comparison to DNA barcoding, next-generation DNA sequencing is highly specific and can identify species in highly processed materials and complex mixtures. DNA barcoding is unable to differentiate between closely related species and is less suitable in detecting extracts as well.