The first warning came before Memorial Day. An unusual strain of Salmonella bacteria was making people violently ill in homes scattered around the Southwest.

Seven weeks and 1,148 illnesses later, investigators are still searching for the source of what has become the largest foodborne disease outbreak in the last decade.

Erich Schlegel / Dallas Morning-News (ENLARGE)

Sam Aguilar, a U.S. Customs agent, inspects boxes of tomatoes coming in from Mexico. However the source of this latest Salmonella outbreak remains a mystery.

Related health articles: Study: Clozapine may have saved schizophrenics  Obesity a risk factor in swine flu?  Study: 1918 flu survivors seem immune to swine flu  Fall swine flu: Obama urges vigilance, not panic  Swine flu shots at school: Bracing for fall return  Topics: Atlanta hospitals | Weight loss | CDC | Cancer | Swine Flu Back to Health news DOCTOR IS IN Why worry? THINNER YOU Lose weight. Together.

The hunt has led from remote homes in the Navajo Nation to an upscale Mexican restaurant in North Carolina, from the drab concrete-block rooms of public health laboratories to samples taken from farms, warehouses and tractor trailers across the United States and Mexico. And still, no answer.

If investigators crack the case, the clue likely will come from work pieced together in a crisis management zone at the Centers for Disease Control and Prevention. That's no sure thing. Even with an arsenal of statisticians, databases, epidemiologists and some of the country's top food safety experts, investigators pinpoint the cause in just 60 percent of cases.

One morning last week, a team of epidemiologists and statisticians gathered at the CDC to share leads, a daily routine. First up is Mike Hoekstra, a statistician who's been investigating food-borne disease outbreaks for 10 years. He's giving a much-anticipated report on studies that could hold the key to solving the outbreak.

But his news is disappointing.

Hoekstra calls the case the most complicated he's worked on, because many of the victims ate the same three foods together — tomatoes, cilantro and jalapeño peppers — often in salsa. If they'd all shared exposure to just one ingredient, then finding the answer would be much easier. Hoekstra runs through an array of comparisons, differences in geography, gender and age groups that offer hints but nothing solid at this point.

The CDC would like to interview the initial victims again, but those people have gone through three rounds of questioning. Some politics are involved, a negotiating dance with state and local health departments who conduct most of an initial investigation, and the federal investigators who get called in for the complicated, multi-state disease outbreaks that have become more common as America's food supply system has centralized. The CDC has agreed to stick to talking to victims who got sick after June 1.

The first batch of studies, conducted by state health departments and the Indian Health Service in New Mexico and Texas, pointed to tomatoes as the most likely source of the salmonella. Some 86 percent of victims reported eating tomatoes, compared to 66 percent of a control group.

It looked like investigators had an answer.

That information sent U.S. Food and Drug Administration investigators to Florida, Mexico and other spots along the distribution chain, taking samples to culture for Salmonella bacteria.

Finding a match is considered the gold standard in a food-borne disease outbreak, proof that the strain of bacteria that sickened someone can be traced back to a farm or a processing plant or dirty machinery in a restaurant kitchen or factory. Investigators neatly wrapped up the cause of a 2006 Salmonella outbreak tied to peanut butter by finding the same strain of bacteria in jars of Peter Pan in victims' homes, and isolated E. coli 0157:H7 bacteria from bags of spinach still in victims' refrigerators.

But with 1,700 samples tested from tomato farms, packing sheds, restaurants and warehouses, the FDA has turned up no positive matches in this outbreak.

CDC investigators started looking back at the initial food studies, mostly conducted on people who'd gotten sick from food prepared in their homes. As reports of hundreds more cases came in from state, county and city health departments, clusters of people who had gotten sick at Mexican restaurants started appearing.

Some of those reports came in slowly, long after victims fell ill. Some health departments run DNA fingerprinting tests on Salmonella bacteria right away; others hold them until there's a batch, a practice that can mean federal investigators don't get confirmed reports of illness for as long as 10 days after state labs start checking into an infection.

Salmonella bacteria can cause diarrhea, nausea and fever, in an illness that lasts four to seven days. Most people recover without treatment, although the disease can be serious in the elderly, infants and those with weakened immune systems. Two deaths have been linked to the Salmonella Saintpaul outbreak, and more than 200 hospitalizations. Still, Salmonella is not as deadly as E. coli 0157:H7, a bacteria that labs usually test immediately because it is so dangerous.

Getting more case reports, with a few larger clusters, gave investigators more opportunities to track down a source. CDC epidemiologists drew up another questionnaire asking what foods people had eaten shortly before becoming ill. On the last weekend in June, CDC epidemiologists called 390 people with similar ages and residences to those who had become ill, to establish a control set of data. State and local health departments gave the same questionnaire to 170 Salmonella victims.

Then Hoekstra and his team got to work analyzing the answers, searching for patterns that would suggest whether investigators should look at foods other than tomatoes. In the meeting, Hoekstra runs through the results so far. Tomatoes are still showing up as a commonly eaten food. In the Southwest, where most cases are, victims were more likely to have eaten serrano peppers. Outside the Southwest, they were more likely to report jalapeños.

Still, investigators are working on an assumption that jalapeño peppers might be involved. At the same time, they haven't ruled out tomatoes, either.

A day after that meeting, the CDC warned individuals with compromised immune systems to avoid jalapeño and serrano peppers. Studies of three clusters of illnesses showed that victims in two of the clusters had eaten jalapeños, but not tomatoes. The FDA continues to advise consumers to avoid round red tomatoes, Roma and plum tomatoes from growing regions that haven't been cleared in the outbreak, but virtually all tomato producing areas have been cleared.

FDA investigators are now trying to trace back the source of those peppers, taking samples from farms and distributors to look for a bacteria match. And in other labs, including a University of Georgia lab in Griffin, microbiologists are studying samples of suspect foods.

Later on this day, as most days, there will be conference calls with state and local health departments, another with the FDA and another, referred to as a "wise person discussion." That's a brainstorming session with scientists outside the outbreak team, who may lend the fresh perspective that will send investigators in a direction that will crack the case.

A team of CDC investigators was on its way to Charlotte to investigate a cluster of illnesses at an upscale Mexican restaurant. More clues are coming in. But the answer remains elusive.

On Monday, a select group of the country's top food safety experts conferred with FDA Commissioner Andrew von Eschenbach. Mike Doyle, director of the University of Georgia's Center for Food Safety in Griffin, was among those invited to the brainstorming session. "It's not a typical outbreak," Doyle said. "There's a lot of out of the box thinking now."