WASHINGTON — Government inspectors finally have a big clue in the nationwide salmonella outbreak: They found the same bacteria strain on a single Mexican-grown jalapeno pepper handled in Texas — and issued a stronger warning for consumers to avoid fresh jalapenos.

But yesterday’s discovery, the equivalent of a fingerprint, doesn’t solve the mystery: Authorities still don’t know where the pepper became tainted — on the farm, or in the McAllen, Texas, plant, or at some stop in between, such as a packing house.

Nor are they saying the tainted pepper exonerates tomatoes sold earlier in the spring that consumers until last week had been told were the prime suspect.

Still, “this genetic match is a very important break in the case,” the Food and Drug Administration’s food safety chief, Dr. David Acheson, said.

For now, the government is strengthening its earlier precaution against hot peppers to a full-blown warning that no one should eat fresh jalapenos — or products such as fresh salsa made from them — until it can better pinpoint where tainted ones may have sold.

Tomatoes currently on the market, in contrast, now are considered safe to eat.

The Texas plant, Agricola Zaragoza, has suspended sales of fresh jalapenos and recalled those shipped since June 30 — shipments it said were made to Georgia and Texas.

FDA said no other produce currently in the plant has tested positive for salmonella, and was continuing to probe where the produce came from and went.

But a sign over Agricola Zaragoza’s spot inside a huge produce warehouse yesterday displayed pictures of tomatoes, onions, and tomatillos alongside jalapenos — suggesting the small vendor might have handled both major suspects in the outbreak that has sickened 1,251 people.

McAllen, Texas, near the Mexican border, is in a region deemed a major hub for both Texas-grown and imported produce. Although Agricola Zaragoza is a small operation, it’s unclear whether inspectors have yet visited the company’s neighboring vendors inside the huge warehouse filled with tractor-trailers loading and unloading fruits and vegetables.

“I recognize there is a need to narrow this as soon as possible,” Mr. Acheson added — as parts of the country are entering prime hot pepper season.

A person who answered the phone at Agricola Zaragoza declined comment.

The pepper industry was bracing for an economic hit and urged FDA to quickly clear jalapenos grown in certain areas, like it earlier did with tomatoes.

“That is a very broad brush to tar the industry with,” the president of the Texas Produce Association, John McClung, said.

Tomato producers have insisted their summertime staple couldn’t be to blame, and are estimating that industry losses may reach $250 million.