The latest tools, like whole genome sequencing, are allowing food outbreaks to be identified and stopped more quickly.
With the pandemic at the forefront of everyone's minds, many people have wondered if food could be a source of coronavirus transmission. Luckily, that "seems unlikely," according to the CDC, but foodborne illnesses do still sicken a whopping 48 million people per year.
Whole genome sequencing is like "going from an eight-bit image—maybe like what you would see in Minecraft—to a high definition image."
In normal times, when there isn't a historic global health crisis infecting millions and affecting the lives of billions, foodborne outbreaks are real and frightening, potentially deadly, and can cause widespread fear of particular foods. Think of Romaine lettuce spreading E. coli last year— an outbreak that infected more than 500 people and killed eight—or peanut butter spreading salmonella in 2008, which infected 167 people.
The technologies available to detect and prevent the next foodborne disease outbreak have improved greatly over the past 30-plus years, particularly during the past decade, and better, more nimble technologies are being developed, according to experts in government, academia, and private industry. The key to advancing detection of harmful foodborne pathogens, they say, is increasing speed and portability of detection, and the precision of that detection.
Getting to Rapid Results
Researchers at Purdue University have recently developed a lateral flow assay that, with the help of a laser, can detect toxins and pathogenic E. coli. Lateral flow assays are cheap and easy to use; a good example is a home pregnancy test. You place a liquid or liquefied sample on a piece of paper designed to detect a single substance and soon after you get the results in the form of a colored line: yes or no.
"They're a great portable tool for us for food contaminant detection," says Carmen Gondhalekar, a fifth-year biomedical engineering graduate student at Purdue. "But one of the areas where paper-based lateral flow assays could use improvement is in multiplexing capability and their sensitivity."
J. Paul Robinson, a professor in Purdue's Colleges of Veterinary Medicine and Engineering, and Gondhalekar's advisor, agrees. "One of the fundamental problems that we have in detection is that it is hard to identify pathogens in complex samples," he says.
When it comes to foodborne disease outbreaks, you don't always know what substance you're looking for, so an assay made to detect only a single substance isn't always effective. The goal of the project at Purdue is to make assays that can detect multiple substances at once.
These assays would be more complex than a pregnancy test. As detailed in Gondhalekar's recent paper, a laser pulse helps create a spectral signal from the sample on the assay paper, and the spectral signal is then used to determine if any unique wavelengths associated with one of several toxins or pathogens are present in the sample. Though the handheld technology has yet to be built, the idea is that the results would be given on the spot. So someone in the field trying to track the source of a Salmonella infection could, for instance, put a suspected lettuce sample on the assay and see if it has the pathogen on it.
"What our technology is designed to do is to give you a rapid assessment of the sample," says Robinson. "The goal here is speed."
Seeing the Pathogen in "High-Def"
"One in six Americans will get a foodborne illness every year," according to Dr. Heather Carleton, a microbiologist at the Centers for Disease Control and Prevention's Enteric Diseases Laboratory Branch. But not every foodborne outbreak makes the news. In 2017 alone, the CDC monitored between 18 and 37 foodborne poison clusters per week and investigated 200 multi-state clusters. Hardboiled eggs, ground beef, chopped salad kits, raw oysters, frozen tuna, and pre-cut melon are just a taste of the foods that were investigated last year for different strains of listeria, salmonella, and E. coli.
At the heart of the CDC investigations is PulseNet, a national network of laboratories that uses DNA fingerprinting to detect outbreaks at local and regional levels. This is how it works: When a patient gets sick—with symptoms like vomiting and fever, for instance—they will go to a hospital or clinic for treatment. Since we're talking about foodborne illnesses, a clinician will likely take a stool sample from the patient and send it off to a laboratory to see if there is a foodborne pathogen, like salmonella, E. Coli, or another one. If it does contain a potentially harmful pathogen, then a bacterial isolate of that identified sample is sent to a regional public health lab so that whole genome sequencing can be performed.
Whole genome sequencing can differentiate "virtually all" strains of foodborne pathogens, no matter the species, according to the FDA.
Whole genome sequencing is a method for reading the entire genome of a bacterial isolate (or from any organism, for that matter). Instead of working with a couple dozen data points, now you're working with millions of base pairs. Carleton likes to describe it as "going from an eight-bit image—maybe like what you would see in Minecraft—to a high definition image," she says. "It's really an evolution of how we detect foodborne illnesses and identify outbreaks."
If the bacterial isolate matches another in the CDC's database, this means there could be a potential outbreak and an investigation may be started, with the goal of tracking the pathogen to its source.
Whole genome sequencing has been a relatively recent shift in foodborne disease detection. For more than 20 years, the standard technique for analyzing pathogens in foodborne disease outbreaks was pulsed-field gel electrophoresis. This method creates a DNA fingerprint for each sample in the form of a pattern of about 15-30 "bands," with each band representing a piece of DNA. Researchers like Carleton can use this fingerprint to see if two samples are from the same bacteria. The problem is that 15-30 bands are not enough to differentiate all isolates. Some isolates whose bands look very similar may actually come from different sources and some whose bands look different may be from the same source. But if you can see the entire DNA fingerprint, then you don't have that issue. That's where whole genome sequencing comes in.
Although the PulseNet team had piloted whole genome sequencing as early as 2013, it wasn't until July of last year that the transition to using whole genome sequencing for all pathogens was complete. Though whole genome sequencing requires far more computing power to generate, analyze, and compare those millions of data points, the payoff is huge.
Stopping Outbreaks Sooner
The U.S. Food and Drug Administration (FDA) acquired their first whole genome sequencers in 2008, according to Dr. Eric Brown, the Director of the Division of Microbiology in the FDA's Office of Regulatory Science. Since then, through their GenomeTrakr program, a network of more than 60 domestic and international labs, the FDA has sequenced and publicly shared more than 400,000 isolates. "The impact of what whole genome sequencing could do to resolve a foodborne outbreak event was no less impactful than when NASA turned on the Hubble Telescope for the first time," says Brown.
Whole genome sequencing has helped identify strains of Salmonella that prior methods were unable to differentiate. In fact, whole genome sequencing can differentiate "virtually all" strains of foodborne pathogens, no matter the species, according to the FDA. This means it takes fewer clinical cases—fewer sick people—to detect and end an outbreak.
And perhaps the largest benefit of whole genome sequencing is that these detailed sequences—the millions of base pairs—can imply geographic location. The genomic information of bacterial strains can be different depending on the area of the country, helping these public health agencies eventually track the source of outbreaks—a restaurant, a farm, a food-processing center.
Coming Soon: "Lab in a Backpack"
Now that whole genome sequencing has become the go-to technology of choice for analyzing foodborne pathogens, the next step is making the process nimbler and more portable. Putting "the lab in a backpack," as Brown says.
The CDC's Carleton agrees. "Right now, the sequencer we use is a fairly big box that weighs about 60 pounds," she says. "We can't take it into the field."
A company called Oxford Nanopore Technologies is developing handheld sequencers. Their devices are meant to "enable the sequencing of anything by anyone anywhere," according to Dan Turner, the VP of Applications at Oxford Nanopore.
"The sooner that we can see linkages…the sooner the FDA gets in action to mitigate the problem and put in some kind of preventative control."
"Right now, sequencing is very much something that is done by people in white coats in laboratories that are set up for that purpose," says Turner. Oxford Nanopore would like to create a new, democratized paradigm.
The FDA is currently testing these types of portable sequencers. "We're very excited about it. We've done some pilots, to be able to do that sequencing in the field. To actually do it at a pond, at a river, at a canal. To do it on site right there," says Brown. "This, of course, is huge because it means we can have real-time sequencing capability to stay in step with an actual laboratory investigation in the field."
"The timeliness of this information is critical," says Marc Allard, a senior biomedical research officer and Brown's colleague at the FDA. "The sooner that we can see linkages…the sooner the FDA gets in action to mitigate the problem and put in some kind of preventative control."
At the moment, the world is rightly focused on COVID-19. But as the danger of one virus subsides, it's only a matter of time before another pathogen strikes. Hopefully, with new and advancing technology like whole genome sequencing, we can stop the next deadly outbreak before it really gets going.
Edible Silverware Is the Next Big Thing in Sustainable Eating
A new edible spoon is durable enough for mass market assembly and is already alleviating consumer waste.
Sure, you may bring a reusable straw when you go out to eat. But what about digesting your silverware at the restaurant? The future is already here.
Edible cutlery feels like a natural progression post-reusable straw.
Air New Zealand just added the new edible coffee cup Twiice into their in-flight service. Made from vanilla, wheat flower, sugar, egg and vanilla essence, the Twiice cups will be standard issue for the international airline.
On the ground, the new, award-winning startup IncrEDIBLESpoon has shipped more than a quarter million edible scoopers. The spoons are all-natural, vegan, and made from wheat, oat, corn, chickpea and barley.
The technological breakthrough is in creating tasty, mass-market material durable enough for delivery in an assembly line environment like airplane service, as well as stable enough to hold a hot cup of coffee or a freezing scoop of ice cream. Twiice cups can last several hours after hot coffee is added, while IncrEDIBLESpoon cutlery holds up to 45 minutes.
"We already caught the interest of a couple major ice cream chains," says Dinesh Tadepalli, co-founder of the IncrEDIBLESpoon parent company Planeteer. "If all goes well, one of them will test out our spoons at their scoop shop early this year."
Next Up
Edible cutlery feels like a natural progression post-reusable straw. And more is already on the menu.
The coffee cup company Twiice is already planning on expanding. Co-founder Jamie Cashmore says other serving items are coming later this year.
IncrEDIBLESpoon is also getting into more utensils. "We plan to mass produce the complete set by year's end: Edible straws, edible forks and edible coffee stirrers," Tadepalli says.
Most notably, Twiice's partner Air New Zealand sees the coffee cup as just a start to other sustainable solutions. The airline estimates it currently serves eight million cups of coffee annually. It's even suggesting customers bring their own reusable cup to the plane – though that isn't as ergonomic nor as attractive as eating everything you are served.
Open Questions
Making everything edible has a few challenges. First is cultural acceptance: With respect to current success, changing eating habits will require going beyond eco-focused and curious eaters.
Second, it's unclear if the short-term economics will add up in favor of airline carriers and other companies. Like alternative fuel, organizations will be more likely to adopt new science when it doesn't require a retrofitting or expensive change to their current business model – even if it does create long-term benefits.
The changes will likely be lopsided, influencing cultures at different times. Airplanes are a great start, as passengers are a captive audience interested in removing waste as soon as possible.
"Imagine eating a black pepper spoon after your soup or a chocolate spoon after your ice cream?"
We can expect edible cutlery to make an easier impact with certain cultures or foods. For instance, injera, the spongy Ethiopian bread, has served as an African plate of sorts for years. It makes sense that IncrEDIBLESpoon's four flavors, Salt, Masala, Spinach and Root, all fit in another bread-as-plate friendly culture: Indian.
Coffee and desserts sound like a good bet for now, though, especially for foodies. "People are curious to try edible spoons as they never heard or experienced them before," Tadepalli says. "Imagine eating a black pepper spoon after your soup or a chocolate spoon after your ice cream?"
Some people can eat red meat without negative health consequences, which may be due to variability between people's gut microbes.
In different countries' national dietary guidelines, red meats (beef, pork, and lamb) are often confined to a very small corner. Swedish officials, for example, advise the population to "eat less red and processed meat". Experts in Greece recommend consuming no more than four servings of red meat — not per week, but per month.
"Humans 100% rely on the microbes to digest this food."
Yet somehow, the matter is far from settled. Quibbles over the scientific evidence emerge on a regular basis — as in a recent BMJ article titled, "No need to cut red meat, say new guidelines." News headlines lately have declared that limiting red meat may be "bad advice," while carnivore diet enthusiasts boast about the weight loss and good health they've achieved on an all-meat diet. The wildly successful plant-based burgers? To them, a gimmick. The burger wars are on.
Nutrition science would seem the best place to look for answers on the health effects of specific foods. And on one hand, the science is rather clear: in large populations, people who eat more red meat tend to have more health problems, including cardiovascular disease, colorectal cancer, and other conditions. But this sort of correlational evidence fails to settle the matter once and for all; many who look closely at these studies cite methodological shortcomings and a low certainty of evidence.
Some scientists, meanwhile, are trying to cut through the noise by increasing their focus on the mechanisms: exactly how red meat is digested and the step-by-step of how this affects human health. And curiously, as these lines of evidence emerge, several of them center around gut microbes as active participants in red meat's ultimate effects on human health.
Dr. Stanley Hazen, researcher and medical director of preventive cardiology at Cleveland Clinic, was one of the first to zero in on gut microorganisms as possible contributors to the health effects of red meat. In looking for chemical compounds in the blood that could predict the future development of cardiovascular disease, his lab identified a molecule called trimethylamine-N-oxide (TMAO). Little by little, he and his colleagues began to gather both human and animal evidence that TMAO played a role in causing heart disease.
Naturally, they tried to figure out where the TMAO came from. Hazen says, "We found that animal products, and especially red meat, were a dietary source that, [along with] gut microbes, would generate this product that leads to heart disease development." They observed that the gut microbes were essential for making TMAO out of dietary compounds (like red meat) that contained its precursor, trimethylamine (TMA).
So in linking red meat to cardiovascular disease through TMAO, the surprising conclusion, says Hazen, was that, "Without a doubt, [the microbes] are the most important aspect of the whole pathway."
"I think it's just a matter of time [before] we will have therapeutic interventions that actually target our gut microbes, just like the way we take drugs that lower cholesterol levels."
Other researchers have taken an interest in different red-meat-associated health problems, like colorectal cancer and the inflammation that accompanies it. This was the mechanistic link tackled by the lab of professor Karsten Zengler of the UC San Diego Departments of Pediatrics and Bioengineering—and it also led straight back to the gut microbes.
Zengler and colleagues recently published a paper in Nature Microbiology that focused on the effects of a red meat carbohydrate (or sugar) called Neu5Gc.
He explains, "If you eat animal proteins in your diet… the bound sugars in your diet are cleaved off in your gut and they get recycled. Your own cells will not recognize between the foreign sugars and your own sugars, because they look almost identical." The unsuspecting human cells then take up these foreign sugars — spurring antibody production and creating inflammation.
Zengler showed, however, that gut bacteria use enzymes to cleave off the sugar during digestion, stopping the inflammation and rendering the sugar harmless. "There's no enzyme in the human body that can cleave this [sugar] off. Humans 100% rely on the microbes to digest this food," he says.
Both researchers are quick to caution that the health effects of diet are complex. Other work indicates, for example, that while intake of red meat can affect TMAO levels, so can intake of fish and seafood. But these new lines of evidence could help explain why some people, ironically, seem to be in perfect health despite eating a lot of red meat: their ideal frequency of meat consumption may depend on their existing community of gut microbes.
"It helps explain what accounts for inter-person variability," Hazen says.
These emerging mechanisms reinforce overall why it's prudent to limit red meat, just as the nutritional guidelines advised in the first place. But both Hazen and Zengler predict that interventions to buffer the effects of too many ribeyes may be just around the corner.
Zengler says, "Our idea is that you basically can help your own digestive system detoxify these inflammatory compounds in meat, if you continue eating red meat or you want to eat a high amount of red meat." A possibly strategy, he says, is to use specific pre- or probiotics to cultivate an inflammation-reducing gut microbial community.
Hazen foresees the emergence of drugs that act not on the human, but on the human's gut microorganisms. "I think it's just a matter of time [before] we will have therapeutic interventions that actually target our gut microbes, just like the way we take drugs that lower cholesterol levels."
He adds, "It's a matter of 'stay tuned', I think."