SAN FRANCISCO — President Barack Obama’s proposed budget would eliminate the nation’s only program that regularly tests fruits and vegetables for deadly pathogens, leaving public health officials without a crucial tool used to investigate deadly foodborne illness outbreaks.

The budget plan the president sent to Congress Monday would ax the Agriculture Department’s tiny Microbiological Data Program, which extensively screens high-risk fresh produce throughout the year for bacteria including salmonella, E. coli and listeria. If samples are positive, they can trigger nationwide recalls, and keep tainted produce from reaching consumers or grocery store shelves.

Food safety advocates and a top-ranking U.S. Centers for Disease Control and Prevention official said the information also can help pinpoint foods tied to illness outbreaks, and would not easily be replaced by companies’ internal tests or more modest federal sampling programs.

“It’s the radar gun that keeps the industry honest and if that’s eliminated, we don’t have a program that will keep the industry in check,” said Mike Doyle, director of the University of Georgia’s Center for Food Safety, which works with the produce industry to improve safety measures on farms and in packinghouses.

White House Office of Management and Budget spokeswoman Meg Reilly said the decision to cut the $5 million program was made after USDA decided it had limited impact. She said it also USDA determined it did not fit within its Agricultural Marketing Service division, which is partially funded by fees from produce growers.