Barns infested with flies, maggots and scurrying rodents, and overflowing manure pits were among the widespread food safety problems that federal inspectors found at a group of Iowa egg farms at the heart of a nationwide recall and salmonella outbreak.

Inspection reports released by the Food and Drug Administration on Monday described — often in nose-pinching detail — possible ways that salmonella could have been spread undetected through the vast complexes of two companies.

The inspections, conducted over the past three weeks, were the first to check compliance by large egg-producing companies with new federal egg safety rules that were written well before the current outbreak but went into effect only last month.

“Clearly the observations here reflect significant deviations from what’s expected,” said Michael Taylor, deputy commissioner for food for the FDA.

Taylor said that in response to the outbreak and recall, FDA inspectors would visit all 600 major U.S. egg-producing facilities over the next 15 months. Those farms, with 50,000 or more hens each, represent about 80 percent of nationwide egg production.

The recall, which began Aug. 13, involves more than half a billion eggs from the Iowa operations of two leading egg producers, Wright County Egg and Hillandale Farms. About 1,500 reported cases of Salmonella enteritidis have been linked to tainted eggs since the spring — the largest known outbreak associated with that strain of salmonella.

Poor sanitation

The FDA inspection reports portray areas of filth and poor sanitation at both operations, including many instances of rodents, wild birds or hens escaped from cages — all of which can carry salmonella — appearing to have had free run of the facilities.

It was difficult to gauge from the report how extensive the problems were. Both companies operate facilities housing 7 million hens. Wright County Egg says inspectors visited 73 barns on its five egg farms.

Both companies said that they had acted quickly to correct problems and were continuing to cooperate with regulators. The reports cited numerous instances in which both companies had failed to follow through on basic measures meant to keep chickens from becoming infected with salmonella, which can cause them to lay eggs containing the bacteria.

“That is not good management, bottom line,” said Kenneth Anderson, a professor of poultry science at North Carolina State University. “I am surprised that an operation was being operated in that manner in this day and age.”

Inspection visits to Wright County Egg found barns with abundant rodent holes and gaps in doors, siding and foundations where rodents could enter. Inspectors spotted mice scampering about 11 laying houses.

Inspectors said that many of the barns lacked separate entrances, so that workers had to walk through one barn to get into another — conditions that could allow workers to track bacteria between barns.

The report on Wright County Egg also described pits beneath laying houses where chicken manure was piled up to 8 feet high. It also described hens that had escaped from laying cages tracking through the manure.

Tracing the outbreak

Officials last week said that they were taking a close look at a feed mill operated by Wright County Egg, after tests found salmonella in bone meal, a feed ingredient, and in feed given to young birds, known as pullets. The young birds were raised to become laying hens at both Wright County Egg and Hillandale.

The inspection report helped fill in the picture of the feed mill as a potential source of contamination, saying that birds were seen roosting and flying about the facility.

(Officials said both wild birds and escaped hens were found at the mill.)

Officials said last week that they had found traces of salmonella similar to the strain associated with the outbreak in six test samples taken from Wright County Egg facilities. That included the two feed tests and four tests taken from walkways or other areas.

On Monday, officials said for the first time that they had also found salmonella at a Hillandale facility. The bacteria was found in water that had been used to wash eggs.

The inspection report on Hillandale showed many problems similar to those found at Wright County Egg, including hens tracking through manure piles and signs of rodent infestation.

FDA officials said that they were not permitted to discuss possible enforcement actions. But, according to Taylor, the law allows for civil actions like injunctions as well as criminal prosecution.