The discovery of Salmonella in bagged organic baby spinach that led to a nationwide recall Tuesday has been attributed to a small government testing program that, ironically, is set to be eliminated in the 2013 federal budget plan.

The Microbiological Data Program, a network of 11 labs that screen fresh produce for pathogens, discovered the contamination during routine testing, according to a program employee. The program, also known as MDP, has been fighting to survive for years as the produce industry has lobbied to have it eliminated.

Now, after its $5 million in funding was cut out of the coming year’s budget, MDP, housed within the USDA’s Agricultural Marketing Service, is scheduled to be shut down in July.

In its budget request for FY 2013, the Obama administration justified cutting MDP, calling it a “lower-priority program because it 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.”

But this latest recall, along with an MDP-prompted recall of nearly 800 cases of bagged lettuce mixes in April, has raised questions about whether this surveillance system really is dispensable.

Industry members have claimed that the program — originally only a monitoring system but now relied on by FDA for recall tip-offs — has overstepped its bounds and caused unnecessary harm to fruit and vegetable producers.

“Does a single sample positive make any sense to cause a recall without reported illnesses? We do not believe this program is adding to public safety. There must be other alternatives,” read the minutes of a United Fresh Food Safety & Technology Council meeting in January 2011.

But those involved in the small program argue that its impact is huge.

“Product has been removed based on MDP results that may well have prevented an outbreak,” said Dan Rice, director of New York State’s Food Laboratory, a designated MDP lab, in an interview with Food Safety News.

MDP labs tests produce, both imported and domestic, using samples collected at distribution centers. This means that by the time results come back (in around a week), produce is likely still in commerce and a recall of the product could still prevent illnesses.

With a loss of funding from MDP, state labs will not only stop monitoring produce, but they will also lose staff members funded by MDP money.

“We’re going to be losing staff that are trained in the most recent molecular methods for screening,” he explained. “These are ag sector food testing labs so we use those people to respond to outbreaks.”

MDP does a lot with the little money it has, says Rice.

“It’s a very efficient program. It’s less than $5 million a year and 22,000 samples a year get tested.”

In addition to prompting at least 19 produce recalls in the past two years, MDP testing can also help pinpoint the source of an outbreak linked to fruits or vegetables.

In 2009, routine testing by the program discovered Salmonella Javiana in green onions. The bacteria were found to be indistinguishable from the strain that was causing an ongoing outbreak linked to green onions, thus the specific source of the outbreak was located.

Over the 3 year interval between 2008 and 2011, MDP isolated 33 pathogens associated with human illness – 28 strains of Salmonella, 2 of E. coli O157:H7 and 3 of Listeria monocytogenes, according to a presentation given Wednesday by Rice at the Association of Public Health Laboratories Annual Meeting in Seattle.

Although the demise of MDP as a USDA program looks certain, there has been talk among government officials of migrating the program over to FDA to be funded by that agency, which is in charge of all other aspects of produce safety.

In a document that outlined United Fresh’s government relations priorities for 2012, the group said that now that the program has been zeroed out, “it will be necessary to ensure that USDA sunsets the program and that protocols shift to FDA. Then, regulatory agencies at the state and federal level must agree on the appropriate steps to protect public health, without massive penalties to growers, when a positive sample unrelated to any illness, is found.”

But it’s not clear whether FDA will be ramping up fresh produce testing to replace MDP’s surveillance in the near future. The proposed produce safety rule, which was mandated under the Food Safety Modenrization Act, has been languishing in the White House Office of Management and Budget and when the proposal is released, it will mark only the beginning of the rulemaking process for creating national produce safety standards.

Helena Bottemiller contributed reporting to this article.