Food week on SciAm blogs would not be complete without scary stories. This year marks the 20th anniversary of the Jack in the Box E. coli O157:H7 hamburger outbreak that sickened 623 people and killed 4 children. There still are major outbreaks, including Listeria from cantaloupe (2011) and, most recently, the parasite Cyclospora from pre-packaged salad.

I’ve long been fascinated by mysteries and wondered how outbreaks of foodborne infections have been solved. How did the sleuths find that raspberries from Guatemala were the source of a previous Cyclospora outbreak, affecting 1465 people? Or how did an Orthodox Jewish family come down with an infection from pork tapeworm? These were two of my favorite foodborne outbreak detective stories. We’ll look behind the scenes at how the epidemiologists at health departments and the Center for Disease Control (CDC) solve these puzzles.

Each year, food poisoning affects about 1 in 6, or 48 million people in the US. 128,000 are hospitalized, and 3000 die. Can you name the top pathogens? They include a virus, parasite, and bacteria. They are norovirus, Salmonella, Clostridium perfringens, and Campylobacter. But Toxoplasma, E. coli O157, and Listeria are among the top for serious infections and death, in addition to Salmonella.

The most recent outbreak, still ongoing, involves a parasite called Cyclospora cayetanensis [named for Cayetano Heredia University in Lima, Peru, where I had the pleasure of studying briefly]. It was first detected in two people ill with diarrhea in Iowa on June 28, 2013. Since then, cases have been identified in 636 people and in 23 states. Patient ages ranges from less than 1 year to 92 years. One of the puzzles is that the cases in Texas appear unrelated to those in Iowa, Nebraska, and elsewhere—the question is, once again, why is Texas different?

First step: Recognizing a problem

Recognizing an infection due to food isn’t always so easy, especially if cases just come trickling in, rather than dozens of people abruptly becoming violently ill. Doctors often don’t order stool cultures initially, hoping an illness will be mild and self-limited. If some specific diarrheal pathogens are isolated by the microbiology lab, e.g. Salmonella, Shigella, E. coli O157, the labs are required to report these to the health department for investigation. Others are not reportable. Public health case workers will then interview the patient and look for other cases and try to determine the source of the illness or risk for spread to others. For example, if the ill person is a food worker, they will be prohibited from working until their infection has cleared.

The state public health lab will do further testing on the bacterial isolate by serotyping, to identify a specific strain. Another technique is pulse-field gel electrophoresis (PFGE) for DNA fingerprinting, which identifies the specific genetic pattern of a given bacteria, and thus can be used to detect identical isolates involved in a cluster of cases, even if they are widespread geographically or temporally. Conversely, fingerprinting can show that some cases are not related to an outbreak. Results are submitted to a large database, PulseNet, and state health departments can compare their isolate to others.

Next Steps

Next, epidemiologists have to carefully define what a case is, characterizing symptoms, time-course, geographic range, and infectious cause, if known. They look for other cases, often alerted by the microbiology lab or by PulseNet. Affected people are then interviewed in detail, looking for specific foods that those who became ill had in common. Sometimes it is not one food, like cheese, but rather an ingredient. Even spices are regularly implicated. Epidemiologists then employ statistics to analyze this data and compare cases to controls (people who did not become ill). They also may test suspect food for infectious pathogens. Increasingly, “Big Brother” is useful, as grocery shopper’s rewards cards track all purchases, and can be used to identify possible foods. Unfortunately, “investigators [still only] identify a specific food as the source of illness in about half of the foodborne outbreaks reported to CDC.”

Tracking down the source of the contamination is quite complicated. This is because the investigation may involve not only a restaurant, but tracebacks of products require inspection of processors and suppliers, and often need to be tracked overseas.


Globalization contributes to the marked increase in foodborne outbreaks, especially from fresh fruit. The risk of infection is the price we pay to satisfy our cravings, as food is increasingly imported from Latin and South America. So, we see problems with mangoes from Brazil, and green onions from Mexico. This week’s news is of contaminated spices from India, with 9% bringing you Salmonella as well as sumptuous flavors. Similarly, 15% of spices from Mexico were contaminated, but far more spices are imported from India.

Because outbreaks are no longer “point source,” like a summer picnic in origin, they are harder to detect. As we saw with Listeria and now with Cyclospora, outbreaks can involve multiple states or other countries, making detection and tracing more difficult. This is why a rapid, standardized techniques like PFGE and PulseNet are vital.

Lab Diagnosis

Traditionally, diagnosis of a bacterial gastroenteritis is done by stool culture, and can take several days in the microbiology lab for final identification and susceptibility testing. That’s why treatment is often done empirically, based on “educated judgement,” if one is being charitable, or “by guess and by gosh,” if one is feeling more cynical. Besides not always guessing correctly, this has the problem of promoting overuse of certain antibiotics, especially Cipro and Bactrim, with resultant high rates of resistance. Another problem is that infections with E. coli O157:H7 can become worse if the victim receives antibiotics, resulting in increased complications such as hemolytic uremic syndrome. This complication is, unfortunately, especially more likely in kids. Similarly, Salmonella carriage can become more prolonged in patients who receive antibiotics.

Another problem is that the lab often does not test for many pathogens unless the physician specifically knows to request the test. Additionally, many labs don’t have the capability to test for specific pathogens, like Vibrio or Yersinia, which require special media which would rarely be used. Diagnosis of parasitic infections is even worse, with many labs lacking the diagnostic capabilities and increasingly relying on “send-outs.” It can take days to get results back. Norovirus is simply not tested for routinely, as community hospitals generally don’t have any capability for viral cultures. We had a nerve racking outbreak some years ago. When I had several patients seriously ill in the ICU with hypotension and diarrhea, some with bleeding, I asked for the health department’s help in finding the etiology. It turned out to be from norovirus.

As noted above, a major advance has now occurred with development of PulseNet, which allows DNA fingerprinting by PFGE in 24 hours. (Further information about this technique can be found here. As of 2001, PulseNet is available to all states. Unfortunately it, too, is in jeopardy because of budget cuts. Its parent program, the Epidemiology and Laboratory Capacity for Infectious Diseases program, has had steep funding cuts, as have many other public health programs.

While PFGE is handy from a public health perspective, rapid diagnostics have problems for clinicians and those tracking antibiotic resistance, since these new techniques don’t involve culturing organisms for antibiotic susceptibility testing. This is a serious problem both for the clinician caring for the patient and for those who are concerned about and who track antibiotic resistance. A combination of techniques would be more useful clinically, but may not be done because of cost constraints, as short-sighted as that is.

Food Safety

So how do plants and produce become contaminated with pathogens? We long assumed that they were contaminated during handling, or by water or soil contaminated by stool from farm workers laboring under difficult conditions. More recently, other routes of contamination have been found. For example, strawberries in Washington were found to be contaminated with E. coli O157:H7 left by deer droppings. Baby spinach were similarly contaminated by wild animals or livestock. This is the source for the admonition to always wash fresh fruits and vegetables carefully before eating. However, it is difficult to adequately wash fruit with creviced surfaces, like strawberries and raspberries, or the nooks in leafy vegetables.

Now we are learning that even thorough washing is not always good enough. It turns out that some plants can take up pathogens and “internalize” them, either by root uptake or through pores in their leaves. For example, mangoes have been shown to draw in pathogens when washed in cold water. While such uptake doesn’t appear common, it does warrant further exploration to help understand if this is species or pathogen specific, inoculum related, or dependent on environmental growing conditions.

Internalization is thought more likely to occur when cut or damaged produce takes up pathogens from contaminated soil or water. This is thought to be the likely route of the recent cantaloupe outbreak.

Food Safety Advice

So many things we thought we knew about food safety are being challenged. For one, washing fruits and vegetables might not be as protective as we thought. It is still a good idea, however, to wash fruits like cantaloupes thoroughly before cutting them, especially if the fruit will be kept for some time before serving, so as not to transmit bacteria from the surface into the flesh of the fruit, where it might multiply.

On the other hand, some authorities advise against washing pre-washed bagged salad greens, believing it actually increases risk. “The panel also advised that additional washing of ready-to-eat green salads is not likely to enhance safety. The risk of cross contamination from food handlers and food contact surfaces used during washing may outweigh any safety benefit that further washing may confer.”

Finally, the long-standing practice of rinsing poultry prior to cooking has now fallen in disrepute. Apparently, the rinsing spreads bacteria all over you and your kitchen—up to 3 feet away. So much for tradition…

So, as Carl Winter advises, don’t be a gambler with food safety:

You gotta know when to heat 'em

Know when to eat 'em

Know when to wash your hands

And decontaminate

There's no need to gamble

When you're eatin' at the table

Or you'll be sick in the bathroom

When the evening's late

Every expert knows

That the secret to survive is

Knowin' what to throw away,

And knowin' what to keep

Cause if you're a gambler

You might just be a loser

And the best that you can hope for

Is to die in your sleep


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Tracing Food Contamination - CDC

Laos market images - Judy Stone

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