Tag Archives: genetics

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
David Chambliss, IBM Research
In the Food Lab

Scientific Breakthrough May Change Food Safety Forever

By David Chambliss
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David Chambliss, IBM Research

How safe is a raw diet? Could sterilizing our food actually make us more prone to sickness? Are vegans healthier than carnivores? In the last few decades, global food poisoning scares from beef to peanut butter have kept food scientists and researchers around the world asking these questions and searching for improved methods of handling and testing what we eat.

It’s been more than 150 years since Louis Pasteur introduced the idea of germ theory—that bacteria cause sickness—fundamentally changing the way we think about what makes our food safe to eat. While we’ve advanced in so many other industrial practices, we’re still using pasteurization as the standard for the global food industry today.

Although pasteurization effectively controls most organisms and keeps the food supply largely safe, we continue to have foodborne outbreaks despite additional testing and more sophisticated techniques. The potential health promise of genomics, and the gut microbiome genetics and bacterial ecosystems, could be the key to the next frontier in food safety.

The scientific community is once again at the cusp of a new era with the advent of metagenomics and its application to food safety.

What is metagenomics? Metagenomics is the study of the bacterial community using genetics by examining the entire DNA content at once. Whole genome sequencing of a single bacterium tells us about the DNA of a specific organism, whereas metagenomic testing tells us about the interaction of all the DNA of all the organisms within a sample or an environment. Think of the vast quantity of genetic material in the soil of a rice patty, a lettuce leaf, your hand, a chicken ready for cooking, or milk directly from a cow. All of them have thousands of bacteria that live together in a complex community called the microbiome that may contain bacteria that are sometimes harmful to humans—and possibly also other bacteria that help to keep the potentially harmful bacteria in check.

Metagenomics uses laboratory methods to break up cells and extract many millions of DNA molecular fragment, and sequencing instruments to measure the sequences of A’s, C’s, G’s, and T’s that represent the genetic information in each of those fragments. Then scientists use computer programs to take the information from millions or billions of fragments to determine from what bacteria they came. The process is a little like mixing up many jigsaws, grabbing some pieces from the mix, and figuring out what was in the original pictures. The “pictures” are the genomes of bacteria, which in some cases carry enough unique information to associate a given bacterium with a previously seen colony of the same species.

Genomics of single bacterial cultures, each from a single species, is well established as a way to connect samples of contaminated foods with reported cases of foodborne illnesses. With metagenomics, which essentially looks for all known species simultaneously, one hopes to do a better job of early detection and prevention. For example, if a machine malfunction causes pasteurization or cleaning to be incomplete, the metagenomics measurement will likely show compositional shifts in which bacterial phyla are abundant. This can make it possible to take remedial action even before there are signs of pathogens or spoilage that would have led to a costly recall.

Up until now, keeping food safe has meant limiting the amount of harmful bacteria in the community. That means using standard methods such as pasteurization, irradiation, sterilization, salt and cooking. To determine whether food is actually safe to eat, we test for the presence of a handful of specific dangerous organisms, including Listeria, E. coli, and Salmonella, to name a few. But what about all the “good” bacteria that is killed along with the “bad” bacteria in the process of making our food safe?

Nutritionists, doctors and food scientists understand that the human gut is well equipped to thrive unless threatened by particularly dangerous contaminants. The ability to determine the entire genetic makeup within a food could mean being able to know with certainty whether it contains any unwanted or unknown microbial hazards. Metagenomic testing of the food supply would usher in an entirely new approach to food safety—one in which we could detect the presence of all microbes in food, including previously unknown dangers. It could even mean less food processing that leaves more of the healthful bacteria intact.

More than 150 years ago, Pasteur pointed us in the right direction. Now the world’s brightest scientific minds are primed to take the food industry the next leap toward a safer food supply.