WASHINGTON (MCT) — Salmonella poisoning has sickened more than 1,000 people in 41 states, the District of Columbia and Canada, and federal health officials have now linked jalapeno and serrano peppers to the outbreak.

Illinois has reported 100 salmonella-related illnesses, the second highest total among affected states, according to the Centers for Disease Control and Prevention, and 26 state residents have been hospitalized. Texas and New Mexico, where the outbreak was first detected, have 384 and 98 cases respectively.

As of Wednesday, 1,017 cases in all had been confirmed, with 203 hospitalizations.

Officials from the CDC and the Food and Drug Administration said the outbreak is one of the largest in recent memory, and also one of the most complex.

"It's just been a spectacularly complicated and prolonged outbreak," David Acheson, associate FDA commissioner for foods, said Wednesday. "I don't have any explanation for it." Acheson said that federal investigators are working with state scientists to trace the origins of tomatoes — originally suspected as the source of the outbreak — and peppers to determine where salmonella may have entered the food chain. The bacteria, which can cause stomach aches, vomiting, diarrhea and high fevers, can be introduced to food through a variety of methods, including contact with animals, dirty water or contaminants in food processing and packing equipment.

Interviews with patients revealed that many of them had consumed raw tomatoes or salsa in restaurants. But more recent tests have linked illnesses to the peppers and possibly other salsa ingredients like cilantro, according to Robert Tauxe, deputy director of the CDC's division of foodborne, bacterial and mycotic diseases.

"We are learning that jalapeno peppers caused some of the illnesses in the outbreak," Tauxe said. "It is not clear that they explain all illnesses."

Acheson said Wednesday that the FDA is not warning consumers against eating jalapeno and serrano peppers, but that a warning could come as the investigation continues. Tauxe said that the concern about peppers does not include salsa in jars that consumers purchase in stores.

The Illinois cases form clusters of illnesses related to eight restaurants where peppers and cilantro were consumed in foods such as salsa.

Connie Austin, an epidemiologist with the division of infectious diseases at the Illinois Department of Public Health, said that those who have fallen ill in Illinois ate salsa or guacamole.

As in several other states, however, the salmonella cases seem to be tapering off in Illinois. The last confirmed case, Austin said, was reported on June 23. Federal and state public health officials attribute the drop-off to the perishable nature of the produce that is believed to be at fault.

But that condition has also made it difficult to determine the sources of the salmonella. More than 1,700 tests on tomatoes and tests conducted so far on peppers have failed to detect the St. Paul strain of salmonella, which has been found in those who have fallen ill.

The illnesses, which federal and state health officials have struggled to control, began to emerge in April and have grown in numbers. The decision to name tomatoes as a culprit came in late May, after a series of conference calls with state health officials in New Mexico and Texas.

That early epidemiological work showed that people who fell ill had eaten tomatoes, state officials said in interviews. Control studies done since of those who had eaten at the same restaurants or shopped at the same stores as those who fell ill continue to implicate tomatoes, the officials said.

"The control studies still point to tomatoes," said Linda Gaul, an epidemiologist and head of the food-borne illness division of the Texas Department of State Health Services.

The FDA warned consumers not to eat red plum, red roma and round red tomatoes from certain states, but noted last month that tomatoes grown in 43 states and some Florida counties were not affected and OK to buy and eat. The warning remains in effect.

Gaul, like her federal counterparts, admitted that the salmonella outbreak has proved confusing, especially since some people fell ill after eating in restaurants, while others became ill after eating at home.

The FDA-CDC announcement that other foods like peppers might be to blame has opened the agencies to widespread criticism from produce farmers and distributors, restaurants and other groups that have had to scramble to remove and destroy certain types of tomatoes, and now must worry about the sale and consumption of jalapeno and other types of peppers, onions and other produce.

"The produce industry is not happy with how this has gone," said Julia Stewart, spokeswoman for the Produce Marketing Association.