In December 2012, federal prosecutors charged 14 former NECC employees, including president Barry Cadden and pharmacist Glenn Chin, with a host of criminal offenses.

The FDA Commissioner also stated, "In light of growing evidence of threats to the public health, the administration urges Congress to strengthen standards for non-traditional compounding."

The U.S. Centers for Disease Control and Prevention traced the outbreak to fungal contamination in three lots of a medication called methylprednisolone used for epidural steroid injections.

[9] On November 14, 2012, members of a congressional committee investigating the outbreak accused the Food and Drug Administration (FDA) of failing to prevent the crisis by moving too slowly against the Massachusetts pharmacy.

[12] On September 4, 2014, pharmacist Glenn Adam Chin was arrested at Boston's Logan International Airport before boarding a plane headed to Hong Kong, and was charged with one count of mail fraud.

The FDA affidavit stated that Chin had used improper sterilization and testing techniques, unsafe practices, falsified cleaning logs, and ordered pharmacy technicians to fraudulently mislabel vials.

[16][17] On December 17, 2014, 14 former NECC executives and technicians, including co-founder and president Barry Cadden, were indicted on a host of federal charges related to the outbreak.

[25] Next, on October 4, the Massachusetts Department of Public Health issued a recall of all NECC medications, advising hospitals and clinics to remove and segregate all lots from their stock inventory.

[26] NECC also announced on that day they were suspending all of their operations and voluntarily surrendered their licenses to the Massachusetts Department of Health and Human Services, while continuing to cooperate with the ongoing investigations by the CDC and the FDA.

NPR interviewed patients who had recovered but still experience debilitating aftereffects such as pain, extreme fatigue, mental confusion and inability to concentrate.

On October 23, 2012, the CDC issued an "Official Health Advisory Issuance of Guidance on Management of Asymptomatic Patients Who Received Epidural or Paraspinal Injections with Contaminated Steroid Products".

According to The New England Journal of Medicine, "... it's important to note that many patients received these sterile injections for back and joint pain, a procedure that lacks high-quality evidence of efficacy.

[24][48] An editorial in The New England Journal of Medicine suggested that while NECC appeared to be in clear violation of existing FDA policy[43] the 2002 Supreme Court decision may have weakened federal-state cooperation.

[50] From November 2011 to April 2012, 33 eye-surgery patients in seven states suffered a rare fungal eye infection tied to injectable drug products made by a compounding pharmacy in Ocala, Florida.

Inspectors went to the Waltham, Massachusetts, location of the Rhode Island–based Infusion Resource company and found, "significant issues with the environment in which drugs were being mixed".

That included "incidents when women given Ameridose's oxytocin, a drug used to bring on labor, reported fetal distress, severe post birth bleeding and shortness of breath.

Pallimed Solutions, based in Woburn, was told to halt production of sildenafil citrate, which is sold as Viagra, after inspectors found it had been prepared with improper components.

[56] Investigations also found that medical staff were using fake names such as "Harry Potter," "Baby Jesus," and "Chester Cheeto" to create fraudulent prescriptions for drugs.

In 2004, state health officials charged the pharmacy with failure to comply with accepted standards when mixing methylprednisolone acetate, the same steroid that was the source of the 2012 meningitis outbreak.

[59][60] On November 12, the Oversight and Investigations Subcommittee of the House Energy and Commerce Committee released a detailed report of NECC's regulatory history.

In 2002, the FDA investigated reports that five patients had become dizzy and short of breath after receiving a steroid used to treat joint pain and arthritis different from the one linked to the current meningitis outbreak.

When officials from the FDA and Massachusetts Board of Pharmacy questioned Cadden, he said vials of the steroid returned by the hospital had tested negative for bacterial contamination.

[61][62] Speaking to the committee in a statement, the interim commissioner of the Massachusetts Department of Public Health said, "It is clear that NECC knowingly disregarded sterility tests, prepared medicine in unsanitary conditions, and violated their pharmacy license.

Hamburg replied that the agency was obligated to defer to Massachusetts authorities, who have more direct oversight over pharmacies and stated, "In light of growing evidence of threats to the public health, the administration urges Congress to strengthen standards for non-traditional compounding."

Although the FDA had repeatedly found reports of adverse events, faulty products, and medication errors in the last decade, no warning letter had ever been issued.

In December 2012, the company filed for bankruptcy and U.S. District Judge Dennis Saylor ruled that meningitis lawsuits pending in Massachusetts federal court would be consolidated and allowed to move forward.

[12] In May 2015, federal bankruptcy judge Henry Boroff approved a $200 million settlement plan that would set aside funds for victims of the outbreak and their families.

It alleged that from 2006 to 2012, NECC knowingly sent out drugs that were mislabeled, unsanitary, or contaminated—forming the basis for a massive RICO indictment against six individuals, including Cadden and Chin.

[70][71] On December 20, 2016, director of sales, Robert A. Ronzio, pled guilty to unrelated conspiracy charges of defrauding the FDA, actions that were discovered during the compounding investigation.

[75] Michelle Caetano Thomas, an assistant pharmacy professor at the University of Rhode Island, and Kathy Chin were convicted on two felony counts for their role in the scheme for filling obviously phony prescriptions for patients such as Coco Puff, LL Bean, and Mary Lamb.