After months of uncertainty over the future of the program, the Agricultural Marketing Service’s Microbiological Data Program, which tests produce for disease-causing pathogens like E. coli O157:H7, Salmonella, and Listeria, has officially gone into shutdown mode, a U.S. Department of Agriculture official confirmed Tuesday.

Department officials told states that participate in the $4.5 million program to stop pulling produce samples on Friday Nov. 9 to “ensure an orderly shutdown of the program by December 31.”

According to an analysis by Food Safety News, ending MDP will eliminate more than 80 percent of public produce testing for pathogens. The U.S. Food and Drug Administration, which has jurisdiction over the safety of produce, also has a produce testing program, but it is significantly smaller.

“This ‘tiny’ program was launched in 2001 simply to collect data about fresh produce contamination, but it now regularly sparks produce recalls when participating state labs find pathogens,” read the report, published in July. “Perhaps more importantly, the labs upload any positive test results to the Centers for Disease Control’s PulseNet, which helps public health officials link foodborne illness cases to food products. MDP is also the only federal program that tests for non-O157 E. coli strains like the one that caused the deadly, high profile sprout outbreak in Germany last year.”

It was MDP that in July discovered Listeria contamination in a North Carolina cantaloupe crop, prompting an immediate recall of hundreds of thousands of melons that eventually was expanded to the entire growing season, preventing any illnesses. A year earlier, it was Listeria contamination in cantaloupes that was responsible for the deadliest outbreak of foodborne illness in the last century.

According to updated MDP data from a state source, from 2009 to 2012, the testing program found Salmonella 111 times, E. coli O157:H7 twice, non-O157 STEC 82 times, and Listeria monocytogenes 12 times. During that time, the program sparked 38 recalls total, including 29 for Salmonella, 2 for E. coli O157:H7, and 7 for Listeria.

Of the pathogens the program identified in that time frame, 44 Salmonella isolates were matched to human illnesses — as were both E. coli O157:H7 isolates and 9 of the 12 Listeria isolates.

One AMS official said MDP was shutting down “due to budget cuts by Congress.” While it’s true Congress didn’t request funding for MDP, the Obama administration actually did not seek funding for the program in their last budget request, calling it a “lower-priority program because it is has a low impact and is not central to the core mission of AMS, which is to facilitate the competitive and efficient marketing of agricultural products.”

The produce industry has long complained that USDA’s produce testing program is just too slow to do any good for public health — by the time recalls are announced to the public and media the highly perishable produce products are often expired or have already been consumed.

The United Fresh Produce Association has lobbied for years to eliminate MDP. The group says they support moving produce testing to FDA, but there’s no word on whether FDA is willing, or able, to fill the void left by MDP. There’s also no evidence that FDA is faster at sampling, testing, and recalling than MDP was.

During a Food Safety News investigation last summer, it took FDA over a month to come up with testing numbers and the agency was unable to list the number of recalls sparked by the their testing program because the numbers weren’t easily captured in the agency’s data system.

State health officials argue that the surveillance MDP provided is important, even in cases where contamination is discovered after the products are off shelves, because the results shed light on an entire commodity’s food safety record.

“It’s not a preventative program,” said Kristi McCallum, the Microbiology Program Manager at the Colorado Department of Agriculture, last summer. “But this is the only program that does surveillance testing for produce.”

Though the states are no longer pulling new produce samples, they are still testing samples that were already collected and adding the results to their database, according to AMS.

When asked if USDA officials were coordinating with FDA on the program cut, an AMS official said discussions were ongoing, but declined to elaborate further.

“Many produce buyers and growers conduct microbiological testing as part of their internal food safety programs,” said FDA spokeswoman Carla Daniels, who confirmed that USDA and FDA are coordinating on the MDP shutdown.

“FDA will continue its existing efforts to collect and analyze fresh produce samples to provide some information regarding the level of contamination associated with fresh produce,” said Daniels. “FDA does not currently sample at the same level as the MDP program. FDA collects and analyzes produce samples primarily through its domestic and import produce sampling assignments and through some limited contract sampling.”

This story has been updated to include a comment from FDA, the latest MDP recall and isolate numbers, and a date clarification.

See below for an overview of MDP and FDA produce testing