The U.S. Department of Agriculture’s Microbiological Data Program will almost certainly be eliminated in fiscal year 2013 after the Senate Appropriations Committee decided to not include funding for the $5 million program in its budget bill.

The program, which was launched in 2001, currently tests about 15,000 samples of fruits and vegetables each year. Public health officials pull samples of alfalfa sprouts, cantaloupe, cilantro, hot peppers, bagged lettuce and spinach and tomatoes to gather data on E. coli (STEC), E. coli O157:H7 and other pathogens that can contaminate these products.

Samples are collected from produce distribution centers in 11 states and any isolated pathogens are then sent for pulsed field gel electrophoresis (PFGE) testing and the results are uploaded into the Centers for Disease Control PulseNet, which means they can be matched against illness or outbreaks.

Dubbed “A Tiny Food Program That Matters” by the New York Times editorial board, MDP does more for produce testing than any other state or federal entity, but the program has also been criticized for being slow and housed under the wrong agency, at the Agriculture Marketing Service.

In its budget request, the Obama administration called MDP a “lower-priority program because it has a low impact and is not central to the core mission of [USDA’s Agriculture Marketing Service], which is to facilitate the competitive and efficient marketing of agricultural products.”

The produce industry has long said that MDP is ineffective, overlaps with FDA, and is too slow to prevent outbreaks.

“We do see the MDP program as duplicative of similar efforts at FDA, so this would streamline efforts and reduce that duplication without reducing crucial food safety efforts done by government and industry,” said Kathy Means, vice president of government relations for the Produce Marketing Association. “FDA, as the primary regulator of produce safety, should be the single source for testing and data collection programs. The USDA program takes too long to bring results while products may still be in the marketplace – that is, the timing is too long for this testing program to impact safety in the event of an outbreak.”

The produce industry has also complained that MDP has overstepped its mission of data collection and turned into a regulatory program. 

The U.S. Food and Drug Administration, the agency with jurisdiction over produce safety, recently credited MDP with sparking an increase in produce reports to the Reportable Food Registry (RFR), a new program that helps keep contaminated food out of the marketplace. From September 2009 to 2010 there were 14 reports for produce and between 2010 and 2011 there were 27.

Last May shipments of Florida grape tomatoes carrying Salmonella were sent to retailers and processors in 10 states and Canada before the distributor, Six L’s Packing Co., learned the product was contaminated.

Through FDA’s RFR, the company was able to recall all of its shipments before any illnesses were reported, but it was USDA’s MPD New York lab that found the contamination.

State public health officials have also argued that MDP helps build state capacity to do routine pathogen testing and gives them funding to hire staff.

And, according to MDP, the program also provides close to 90 percent of all available bacterial pathogen data for fruit and vegetables and is a “significant contributor” to CDC’s PulseNet Database. 

At a hearing in February, Agriculture Secretary Tom Vilsack told an appropriations panel that he’d like to see FDA’s budget increased to absorb the program — saying, “we don’t think it’s consistent with the mission of [the Agricultural Marketing Service]” — but noted that the austere budget environment meant agencies had to make tough choices.