Last week two brothers plead guilty to federal criminal charges related to the United States’s worst foodborne illness outbreak in the past 25 years. The unusual charges indicate that the U.S. Food and Drug Administration (FDA) is gearing up for an era of tighter food safety regulations and more serious consequences.

The Colorado farmers, Eric and Ryan Jensen, were charged with counts of introducing adulterated food to interstate commerce. They face penalties that could include up to six years in jail and $1.5 million in fines. A sentencing hearing is scheduled for late January 2014. The brothers are the former owners of Jensen Farms, which sold cantaloupes contaminated with the bacteria Listeria monocytogenes in 2011. The melons killed 33 people and sickened 147 in 28 states. The outbreak began when seven cases of listeriosis—food poisoning caused by L. monocytogenes—hit Colorado hospitals in late August 2011. Typically, the state would have seen one or two cases in the entire month. Listeriosis is rare but dangerous, and can kill victims by infecting the central nervous system and blood. Individuals most at risk include the elderly, babies and people who have compromised immune systems. The illness can cause miscarriage and premature labor in pregnant women.

Fortunately, health officials reacted quickly, says Jeff McCollum, who was an Epidemic Intelligence Service officer with the Colorado Department of Public Health and Environment and the U.S. Centers for Disease Control and Prevention (CDC) at the time. The CDC matched the DNA signatures of bacteria samples with cases in multiple states. By interviewing patients, agencies tentatively linked the illness to cantaloupes grown in Colorado. Pulsed-field gel electrophoresis, a method to analyze bacterial DNA, revealed that five different strains were involved in the outbreak. Given that food was a likely source, the FDA started working the case as well.

Of the four cantaloupe growers in the state, only two still had fruit in production, says McCollum, who is now an officer with the U.S. Public Health Service working at the Armed Forces Health Surveillance Center. At Jensen Farms in Holly, Colo., federal and state officials collected 39 swabs from equipment and food processing surfaces. Of those swabs, 12 matched patient samples. A further five out of 10 swabs from cantaloupes in the producers’ cooler also matched. Unlike many other food-borne pathogens, Listeria thrives in cool, moist environments that match those found at food processing facilities. The full case report was published in September in The New England Journal of Medicine.

A further investigation (pdf) by the FDA pointed to two pieces of refurbished cleaning equipment and a truck used to haul rejected fruit to a nearby cattle facility as possible sources of the Listeria contamination.

Investigators are good at tracking Listeria through the food processing environment, explains Benjamin Silk, a CDC Listeria specialist. But “much less is known about how the bacteria spreads” from facility to facility, he says. The CDC is currently conducting a pilot project to sequence the genomes of Listeria samples from patients around the country. Gathering this data will help researchers connect the dots between isolated cases and clusters of illness to identify how the pathogen spreads throughout the food supply system. Molecular tools like whole genome sequencing make this kind of investigation possible. “We are probably right at the beginning of a revolution in understanding the molecular epidemiology of Listeria and other food-borne pathogens,” Silk says.

While researchers hunt down Listeria, regulating agencies are cracking down on producers who put contaminated food on the market. The FDA is using the Jensen Farms case to send a message, says Michael Roberts, a professor and director of the Resnick Program for Food Law and Policy at the University of California, Los Angeles. The FDA Food Safety and Modernization Act (FSMA), signed into law in January 2011, gives the agency stronger enforcement authorities such as mandatory recall power. Although the FDA did not have to use those powers during the outbreak, the criminal charges also “reflect a different tenor and attitude,” Roberts says.

The act includes a proposed produce rule, which sets standards for producing, harvesting, packaging and storing fruits and vegetables as it minimizes the risk of microbial contamination. The draft has been released to the public and is open for comment until November 15.

The draft does not change a problematic inspection practice that may have contributed to the 2011 outbreak, however. Just days before the first illness, a food safety auditor contracted by a California-based safety consultant, PrimusLabs, inspected Jensen Farms’s facilities and gave the producers a high score of 96 percent. These audits are typically required by produce retailers and follow guidelines they established. Under FSMA, reliance on such third-party auditors continues. The proposed rule includes an FDA certification process for foreign entities but does not require a similar process for domestic auditors. Furthermore, the rule does not address the conflict of interest inherent in requiring farms to pay for their own audits, Roberts says. “I’m not questioning the auditors integrity,” he adds. “But the auditor wants business and there is a natural inclination for the auditor not to be as confrontational.”

Despite lack of FDA certification, third-party auditors may take initiatives to tighten their standards, given another development in the melon saga: The Jensen brothers are suing PrimusLabs. “The third-party auditors are unquestionably more vulnerable to legal action,” says David Acheson, the founder and CEO of the Acheson Group, a consulting firm for the food industry. He predicts that the parties will settle.

Acheson also predicts that after comments are submitted, the final produce rule will include an accreditation process for domestic auditors as well as foreign importers. The FDA is more aggressive under FSMA and will take producers and processors to court, he says, adding, “The consequences today for not getting [food safety] right are more significant than they ever were before.”