E. Coli Outbreaks & Factory Farms in the U.S. Are Largely Inextricable

Another day, another E. coli outbreak. In the last half of 2024 alone, E. coli has been found in ground beef, carrots, onions, walnuts and cheese, causing at least 186 illnesses, one death and several recalls. Why is E. coli popping up left and right — and what do these outbreaks have to do with factory farms?

The answers to these questions, respectively, are “we don’t know” and “a lot.” Harmful E. coli is produced primarily in the guts of ruminant animals, such as cows, sheep, goats and deer, and as a result, it’s often found in beef. It can easily infect other foods as well — but even when it does, beef production and cattle farms are often still the ultimate source of the contamination.

This can play out in several ways, but it’s important to note at the outset that there’s still a lot we don’t know about E. coli transmission. Often, researchers can’t identify with certainty the original source of contamination, and can only speculate on the path it took to reach whatever food it ultimately infected. The bacteria itself also changes and adapts over time, complicating these post-outbreak analyses even further.

“With many of the outbreaks, [investigators] cannot find the source of the infection,” Alfredo Torres, professor of microbiology and immunology at the University of Texas Medical Branch, tells Sentient. “There are all sorts of contaminations that we have no idea where they’re coming from.”

What Is E. Coli?

E. coli, or Escherichia coli, comes in many different varieties. The majority of them are harmless, and some serve important purposes in the human body, but there are six subvarieties of E. coli bacteria — often referred to as “The Big Six” — that can cause illness in humans.

In the United States, most E. coli outbreaks are caused by the strain O157:H7. This strain belongs to a group of E. coli subtypes called Shiga-toxin producing E. coli, or STEC. As the name implies, the STEC varieties of E. coli produce a toxin called Shiga, and when we talk of humans becoming sick with E. coli, it’s usually the Shiga toxin that’s responsible for causing the actual illness.

While there’s a lot that scientists still don’t understand about STEC, it’s believed that the bacteria’s initial development must take place in the intestinal tract of certain non-human animals, namely cows and other ruminants. From there, it can spread to humans in a number of ways, but to the best of scientists’ current understanding, it can’t develop in the first place without a ruminant’s gut.

Humans contract harmful E. coli strains by eating contaminated food and or water, interacting with infected animals or people, or coming into contact with feces with E. coli in it. It can be highly contagious; in 1993, a sixteen month-old boy died from E. coli after coming into contact with the stool of a classmate who had the disease.

Although this was an example of human-to-human transmission of the bacteria, it still began with a cow: The classmate’s mother worked at Jack In The Box, the source of the outbreak.

E. coli can produce a variety of symptoms. When it infects the large intestine, it can result in diarrhea, vomiting, nausea, stomach cramps and loss of appetite; when the bacteria is in the urinary tract, it causes pain during urination, cloudy urine and abdominal or pelvic pain.

Although most people who become sick from E. coli recover within a week or so, some patients develop serious and life-threatening conditions, such as haemolytic uraemic syndrome (HUS) and sepsis. Studies on the mortality rate of E. coli infections have come to a wide range of conclusions, from eight percent on the low end to 35 percent on the high end.

Where Does E. Coli Come From?

E. coli lives in many places, but the “Big Six” subtypes that sicken humans are all found primarily in the bodies of cattle, Torres tells Sentient.

“The bacteria can actually grow in the rectal anal junction of these animals without causing any disease, or any symptoms, or anything,” Torres says. “So when [the cows defecate], the fecal matter is contaminated with this organism, and anything that gets in contact with the manure, or water contaminated with the fecal matter, can get contaminated with the bacteria.”

Historically, E. coli outbreaks in the United States came from tainted beef, Torres says. The O157:H7 strain was first discovered in 1982, when 47 people contracted it after eating contaminated burgers from McDonald’s. The 1992 E. coli outbreak, which killed four people and sickened over 500, also originated from beef patties, this time from Jack In The Box.

The Jack In The Box outbreak received significant media attention and became something of a national scandal. In response, the USDA subsequently implemented a number of regulations to prevent beef from being contaminated with E. coli, and fast food restaurants implemented operational changes, such as separating beef patties with tongs instead of bare hands, in an attempt to accomplish the same.

These changes did reduce the frequency of beef-originated E. coli outbreaks, Torres says, but they didn’t put an end to the outbreaks entirely. The harmful strains of E. coli may originate in a cow’s gut, but they can survive in other environments as well. And thanks to this resilience, E. coli has the ability to infect plenty of foods other than meat.

How Factory Farms Cause E. Coli Outbreaks

Given E. coli’s affinity for cow intestines, it’s no surprise that cattle farms and slaughterhouses are often the source of E. coli outbreaks. Typically, this happens when E. coli in the cow’s gut cross-contaminates the rest of his or her body during the slaughtering process, and ends up in the resulting beef.

But because E. coli is found in manure as well as the body, anything that comes into contact with manure is also liable to be infected. This includes water — and unfortunately, it’s not uncommon for manure from cattle farms to make its way into nearby waterways. (The disease can also spread via human waste in waterways, but only if the human in question had already contracted E. coli).

There’s good reason to believe that this leakage, or runoff, contributes to the spread of E. coli. A 2023 study found that water samples taken from sources within a mile of factory farms had higher concentrations of E. coli than those located more than five miles away from said farms.

This year, an FDA study found that waterways contained a higher prevalence of STEC stains of E. coli in particular when they passed by factory farms. This occurred even when there was no apparent runoff from the farms to the water, leading researchers to speculate that the bacteria latched on to dust from the farms and traveled to the water via the air.

Complicating matters further is the fact that E. coli can also live in the leaves of certain vegetables. This was evident in 2006, when tainted spinach caused a massive nationwide E. coli outbreak that killed three people, sickened over 200, and depressed spinach sales for over a year.

The Spinach Outbreak: a Case Study in Uncertainty

The spinach incident is a good illustration of how E. coli outbreaks occur — and of why even vegetable-based outbreaks can often be traced back to meat production.

“That was the first time we learned that somehow, the bacteria is able to survive in leaves of spinach,” Torres tells Sentient. “If you use a microscope and you look inside of a leaf, there’s an area called the stroma, and you can actually find the bacteria attached to that area.”

The fact that E. coli can survive within the biological structure of spinach itself, as opposed to simply living in water on the surface of spinach, means that washing contaminated spinach isn’t sufficient to rid it of the bacteria.

Subsequent investigations of the 2006 outbreak found that the contaminated spinach originated from a single grower in California, and investigators were even able to trace it back to a specific ranch in San Benito County. That ranch was located next to a cattle farm, and manure and river water from the cattle farm was later found to have the same strain of E. coli that contaminated the spinach.

But incredibly, despite all of these findings, investigators weren’t able to determine precisely how the spinach became infected in the first place. They speculated that tainted river water could have made its way into the well that irrigated the spinach fields, or alternatively, that a wayward cow or pig might have inadvertently transferred the bacteria from the cattle farm to the spinach.

Nevertheless, a spokesperson for the California Department of Health said at the time that “we’ll never be able to make a definitive link” between the cattle farm and the spinach ranch.

The whole episode encapsulates an unfortunate truth about E. coli outbreaks: we often don’t get a full picture of how exactly they unfolded. We know that the disease originates in the stomachs of cows and a few other species, but the path it takes to infect humans is often impossible to fully understand.

Take the recent McDonald’s outbreak. Contaminated onions are believed to be the culprit here — but how did they get contaminated in the first place?

The short answer is that we don’t know. In an interview with Sentient earlier in the year, public health expert Sarah Sorscher said that the onions were “probably being processed in an environment with ground beef or some other high-risk food” that already had E. coli. Torres, meanwhile, suggests that they may have been contaminated via tainted water.

But these are merely guesses — educated guesses, to be sure, but guesses nonetheless. As of this writing, the precise manner in which the onions and carrots became contaminated with E. coli is unknown, and it’s entirely possible that it will never be known. Such is the nature of E. coli outbreaks.

But one thing is for sure: eventually, it always comes back to poop. And factory farms present the perfect opportunity for this poop to make its way into drinking water. Manure from these farms is typically stored in enormous outdoor lagoons, which can — and do — easily leak into nearby waterways.

How Can We Prevent E. Coli Outbreaks?

The federal government has taken a number of steps to lessen the risk of E. coli outbreaks. The Food Safety and Inspection Service (FSIS) of the USDA tests random samples of raw beef for E. coli before they’re sent to restaurants or retailers, and conducts regular inspections of produce farms.

But the government can’t test every piece of spinach or beef before it’s sent out into the world. The ambiguous and confusing nature of E. coli spread means that ultimately, it’s on individual farms to implement and follow best practices that can help stem the prevalence of outbreaks.

Some of these practices are mandated by the government, while others have been developed and voluntarily adopted by producers. Since 1996, the FDA has required meat and poultry producers to implement an inspection system called HACCP, or Hazard Analysis and Critical Control Points, to catch potential contaminations before sending their product to distributors.

But these kinds of rules are only effective if agricultural producers abide by them, and sometimes they don’t. The processor of the tainted spinach behind the 2006 outbreak, for instance, hadn’t been following its own water-inspection policies in the month that the tainted spinach was processed, a subsequent investigation found.

The FDA can warn, fine and even shutter facilities that ignore food safety practices. But much of the time, this only happens after there’s been an outbreak. In 2017, the FDA shut down Dixie Dew Products after discovering numerous food safety violations at its production facility — but only after the company’s soy nut butter gave E. coli to 29 people, nine of whom developed kidney failure as a result.

The Bottom Line

E. coli is something of a moving target. The ways in which it infects food still aren’t fully understood, and the government has at times been slow in implementing policies to reduce the frequency of outbreaks (the FDA only rolled out comprehensive safety rules for produce in 2016, for example). The fact that the bacteria keeps popping up in new foods creates yet another challenge.

One thing is clear, however: Industrial animal agriculture, and cattle farms in particular, are central to the spread of E. coli. While operational and regulatory steps can be taken to reduce the risk, E. coli’s prevalence on cattle farms is an unavoidable and intrinsic consequence of how the cow’s digestive system works. As long as we’re farming cattle for food, we’re going to be dealing with E. coli.