The Food and Drug Administration (FDA) raised concerns about sterility and cleanliness at the NECC.
So far 16 people have died from a rare fungal form of meningitis, apparently after using contaminated drugs.
More than 200 people in 15 US states have been affected.
Steroids and heart drugs produced by the Boston-based NECC are under investigation and the FDA has warned doctors not to prescribe any of the company’s products.
Meningitis is an inflammation of the membranes covering the brain and spinal cord. Symptoms include severe headache, nausea and fever as well as slurred speech and difficulty walking.
Fungal meningitis is not contagious, according to US health officials.
Criminal investigators from the FDA searched the NECC premises on Tuesday as part of a broad state and federal investigation into the deadly outbreak.
Paul Cirel, a lawyer for the pharmaceutical company, told Associated Press that it was “difficult to understand the purpose” of the FDA search. He said the company has made clear it would provide, and has provided, anything requested by investigators.
They have been several calls by US congressmen for a full-scale criminal investigation into the NECC’s practices.
The outbreak has raised questions about the practice of drug compounding, where pharmacies prepare specialized doses of medication. Compounding is not regulated by the FDA, which generally oversees drug makers.
NECC has suspended operations and recalled the steroid injection initially linked with the outbreak, methylprednisolone.
The FDA says it is looking into reports of a patient with possible meningitis who received an injection of triamcinolone, a different steroid, from NECC.
Two transplant patients also developed a fungal infection after receiving an unnamed heart drug made by the firm.
The FDA has not confirmed that these three infections were caused by NECC products, and has said that it is very possible that the heart patients were infected by another source.
On Monday, the drug regulator expanded its recommendation for doctors to warn anyone who received any injection made by the company, including drugs used in eye surgery.
Last week, health officials said 12,000 of the roughly 14,000 people in 23 states who received the steroid shots had been contacted.
The CDC has published a list of clinics that received shipments of the drug, which was recalled on 26 September.
Drug compounding:
• Drug compounding is used to make unique drugs for individual patients when there are no existing licensed treatments
• It is common practice around the world to make medicines for rarer conditions and children, for example
• Individual pharmacists or specialist drug companies combine, mix, or alter ingredients to create medications to meet these specific needs
• In the US, compounded drugs are not approved by the regulator the FDA, which means their safety and efficacy are unverified
• Poor practices on the part of drug compounders can result in contamination or in products that don’t possess the strength, quality and purity required
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