The Massachusetts specialty pharmacy linked to the deadly fungal meningitis outbreak knew it had extensive contamination by mold and bacteria throughout its operations but failed to take corrective action, a federal report says.

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The Massachusetts specialty pharmacy linked to the deadly fungal meningitis outbreak knew it had extensive contamination by mold and bacteria throughout its operations for making sterile drugs but failed to take corrective action, federal health officials said Friday.

In the first nine months of the year, New England Compounding Center’s (NECC) internal-monitoring program showed mold or bacterial contamination at more than 80 locations, including numerous places in its “clean rooms,” where sterile drugs are made.

In more than half the cases, the company’s own testing showed bacteria and mold above its “action” limits, but there is no evidence that it took action, according to a report issued by the Food and Drug Administration (FDA).

The report is based on FDA inspections at the Framingham company after the recall of tainted steroid shots implicated in the outbreak. The shots are mainly used to treat chronic back pain.

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FDA officials confirmed last week that the black fungus found in the company’s vials was the same fungus that has sickened 338 people in 18 states, causing 25 deaths.

In addition, up to 14,000 people are believed to have been exposed to the fungus from the injections. Though medical authorities say patients are most vulnerable to stroke and death within the first 42 days of injection, it can take up to three months for symptoms to appear.

The FDA report, known as a Form 483, is issued at the end of an inspection when investigators think that they have observed conditions or practices that may violate federal law.

The report documents significant failures to maintain a sterile environment, including proper low humidity, appropriate temperature and regular cleaning and disinfecting.

NECC said in a statement that it had received a copy of the report and would comment after reviewing it.

The FDA report provides new details about NECC’s conditions, first reported by state officials this week. The drug at the center of the investigation is made without preservative, so it’s very important that it be made under highly sterile conditions.

During an inspection Oct. 2, after the steroid was recalled, the FDA found that 83 vials from one lot of the tainted steroid, shipped between Aug. 17 and Sept. 25, contained “greenish black foreign matter.”

An additional 17 vials from that lot of methylprednisolone acetate had white material floating in them. Further testing found that an additional 50 out of 50 vials from the same lot had “viable microbial growth,” the report found.

During a second inspection two days later, inspectors found numerous places where critical sterilization equipment had “tarnished discoloration,” “greenish yellow discoloration,” and yellow and green residue. Three locations were in or near autoclaves, used in the final sterilization of products intended for injection such as the steroid linked to the outbreak, methylprednisolone acetate.

In a teleconference with reporters, FDA officials declined to characterize the findings. They also declined to answer questions about whether an FDA inspection in 2004-05 found similar conditions.

The extensive contamination and problems with sterile processing documented in the FDA report go beyond what Massachusetts officials had described in a report Tuesday.

“This reinforces the fact that this facility was just horrific,” said Eric Kastango, a consultant who works with compounding pharmacies on quality control and who read the reports. “The amount of the microorganisms in the clean room was out of control and were red flags that someone could have acted on to prevent these contamination events.”

Sarah Sellers, a former FDA official who is now a consultant on quality and sterility issues, also reviewed the report. “The entire pharmacy was an incubator for bacteria and fungus,” she said. “The pharmacy knew about the contamination and did nothing.”

The report said personnel told investigators the company shut off the air conditioning each night from 8 p.m. to 5:30 a.m., a practice that experts said would make it difficult for the pharmacy to maintain a steady temperature.

“How hot did that room get?” Kastango said. “That becomes like a giant incubator for things to thrive. You never shut down the air conditioning in the clean room.”

Material from The Associated Press, The New York Times and the Los Angeles Times is included in this report.

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