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Nebraska was among the states affected by the recent E. coli outbreak traced to onions in McDonald's hamburgers. Federal officials said they are now certain about the source but broader questions about the overlap with beef production linger.

The outbreak caused at least one death and sickened dozens of people. This week, key federal agencies closed the investigation, which pinpointed onions from a Colorado farm, while also ruling out burger patties. Ahead of the conclusion, some food safety experts wondered more about bacteria in manure from factory farms, where livestock is raised, finding its way to produce operations.

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Prashant Singh, associate professor of health, nutrition and food science at Florida State University, explained the problem with having the different farming operations so close to each other.

"Manure, sometimes, if not properly processed in large operations, can spill over into a fresh produce area," Singh pointed out.

More specifically, contaminated dust particles from waste at concentrated animal feeding operations can land on fields of lettuce, for example, or get into irrigation canals. Separately, a California carrot company last month launched a voluntary recall because of an E. coli outbreak. Environmental groups noted many carrots in California are grown near factory farms.

Singh emphasized meat production has accelerated under evolving technology, with regulations enforced by the U.S. Department of Agriculture but produce is monitored by the Food and Drug Administration and he said the resources are vastly different.

"On the FDA side, they lack everything," Singh observed. "Their hands are very full. "

Even with the resource imbalance, other food safety experts note the meat lobby has focused heavily on avoiding strict regulations under the USDA, and existing laws have limits. Meanwhile, data from the Centers for Disease Control and Prevention show there have been nine multistate foodborne illness outbreaks in 2024.

This story is based on original reporting by Nina Elkadi for Sentient.