In less than two weeks, Minnesota Department of Health investigators traced the source of a mysterious salmonella outbreak that had stumped federal health officials for two months and sickened more than 1,200 people in 43 states and Canada.

The culprit: jalapeno peppers.

Federal officials had focused on tomatoes as the source of the salmonella, causing restaurants and stores to pull tomatoes and severely hurting tomato farmers in suspect areas.

While tomatoes haven't been entirely cleared by federal authorities, attention has now turned to the peppers in what federal officials said was a major break in the case. A gee-whiz state lab, investigators dubbed "Team Diarrhea" and a unique approach to sleuthing illness contributed to the breakthrough.

The outbreak and the government's inability to find the source have exposed serious flaws in the U.S. food safety system, experts say.

Minnesota health officials first learned of a salmonella outbreak in the state on June 23. By July 9, they were on the phone with their federal counterparts making it "crystal clear" it was not tomatoes but jalapenos that were the likely source, said Kirk Smith, head of foodborne diseases at the Health Department.

Smith said that by mid-June, federal investigators already had begun to think tomatoes were not the sole culprit.

Food and Drug Administration (FDA) officials still have not completely ruled out tomatoes. Data indicate jalapeno peppers caused some illnesses but not all, said FDA spokesman Mike Herndon in an e-mail interview.

In Minnesota, the break came when 27 people who ate at the same Twin Cities restaurant fell ill from the exact rare salmonella strain in the national outbreak.

On Monday, federal officials said they found the same strain on a jalapeno pepper in a giant produce warehouse in McAllen, Texas -- the same warehouse identified by Minnesota investigators weeks ago.

"What happened in Minnesota should be the norm," said Mike Osterholm, University of Minnesota foodborne illness expert and an adviser to state and federal health agencies. "They did it quickly and they did it effectively and they were able to trace back what nobody else was able to trace back."

Suspicions about peppers

Until mid-June, Minnesota was largely untouched by the salmonella outbreak that appeared in April in New Mexico and Texas. Salmonella is a bacterial infection that can cause stomach cramps, fever and diarrhea.

Every week the cases mounted. Federal officials, suspecting tomatoes, warned against eating most kinds.

But Minnesota had only two cases, both people who had traveled in other states.

Then, suddenly, cases started rolling in. Clinics must report all salmonella cases to the Minnesota Health Department, which immediately identifies the strain from samples sent to its highly sophisticated laboratory in St. Paul. On June 23, technicians got two cases of the strain linked to the tomato outbreak -- ironically named salmonella saintpaul. Then seven more cases emerged. "It was pretty obvious there was an outbreak," Smith said.

He called in what is known at the Health Department as "Team Diarrhea" -- mostly University of Minnesota School of Public Health graduate students who extensively interview victims.

By Sunday, June 29, two victims named the same Twin Cities restaurant, which Smith declined to identify. On Monday, the manager told an investigator he had dumped all suspect tomatoes weeks before.

In short, it couldn't be coming from the tomatoes. Then, by comparing what both sick and healthy customers ate, investigators determined the source was a jalapeno garnish.

On June 30, Ben Miller, the state Agriculture Department's "traceback coordinator," began tracking the suspect peppers' roots. Using restaurant invoices to find the wholesale supplier, he followed the trail to California and Texas distributors. He found the farms that grew the peppers in Mexico.

On July 3, Smith gave the Centers for Disease Control and Prevention and the FDA information on Minnesota's cases and Miller's traceback. Smith called back on July 9 "so they could be crystal clear about the detail. The pepper [in Texas] was collected on the 11th." Federal officials were also looking at outbreaks in two Texas restaurants linked to salsa that used jalapenos.

Minnesota's edge

What made Minnesota's search quicker?

Smith said investigations are centralized at the state level. The CDC and the FDA rely on local health departments, usually at the county or city level, which can cause enormous logistical problems.

Minnesota also has a lab that can immediately identify pathogens down to their DNA, and investigators who interview everyone infected by salmonella, an average of 700 cases per year.

In other states, health officials often won't follow a trail beyond state borders. Miller follows it wherever it leads.

"There surely are going to be questions," Osterholm said, about whether the tomato warnings "were warranted by the data." In a recent interview he said, "this tomato-outbreak investigation has bordered on incompetence." Other experts have been equally critical.

Osterholm plans to testify before Congress next week that the national system should be modeled on Minnesota's. Once Minnesota's state epidemiologist, he was pivotal in building its system.

FDA defends probe

But Herndon, of the FDA, said the probe was "complex and difficult." Perishable produce is usually gone before investigators arrive, he said.

But a consumer advocate argues the FDA should have a better tracking system. "The FDA wasted a lot of time on tomatoes," said Jean Halloran, director of food policy at Consumers Union, publisher of Consumer Reports. "If there was better traceability, they would have more quickly figured out that they were barking up the wrong tree."

At the same time, she said, the FDA was right to raise alarms about the tomatoes, even without absolute proof. "This is kind of the danger of doing science in public," she said. "It's not always like 'CSI,' where in one hour you finally get the solution. Sometimes you go down the wrong path for a while before you figure out you took the wrong turn awhile back." • 612-673-7394 • 612-673-7384