Alison Young

USA TODAY

A laboratory operated by the Centers for Disease Control and Prevention is among the handful of facilities that have secretly had their permits suspended in recent years for serious safety violations while working with bioterror pathogens, according to documents obtained by USA TODAY after winning a Freedom of Information Act appeal.

The CDC's own labs also have been referred for additional secret federal enforcement actions six times because of serious or repeated violations in how they've handled certain viruses, bacteria and toxins that are heavily regulated because of their potential use as bioweapons, the CDC admitted for the first time on Tuesday. Before USA TODAY won access to records of the lab suspension, the CDC had repeatedly refused to answer questions about its own labs' enforcement histories.

The revelations show the CDC's facilities are among a small group of biolab operators that have the worst regulatory histories in the country, receiving repeated sanctions under federal regulations.

Citing security reasons and a federal bioterrorism law, the names of labs that have been suspended or faced other enforcement actions have been a closely guarded secret by the CDC and the U.S. Department of Agriculture. The two agencies not only operate high-security biolabs, but they also co-run the Federal Select Agent Program that regulates government, university, military and private labs that work with bioterror pathogens such as anthrax, plague and Ebola. The government calls these kinds of pathogens "select agents."

Only five labs have been suspended from the Federal Select Agent Program since 2003, and another five labs have faced repeated referrals for enforcement actions, according to information the CDC provided last year to USA TODAY and later to congressional investigators. The revelation that CDC's own labs are among these small groups that have faced serious and repeated sanctions raised questions among some lab safety watchdogs about the agency’s secrecy motives.

“There is no security rationale for withholding the identities of the suspended labs,” said Richard Ebright, a biosafety expert at Rutgers University in New Jersey who has testified before Congress. “The sole rationale is a CYA rationale, in which the CDC seeks to cover its derriere by covering up violations and shielding staff and management responsible from accountability for violations.”

A heavily redacted USDA letter obtained by USA TODAY shows a CDC-operated lab was suspended from doing select agent research around 2007 and reinstated in 2010 because of federal violations in the handling and transfer of a virus. The USDA blacked out the name of the virus.

The CDC said Tuesday the suspension involved an individual lead scientist and the labs associated with that scientist's research, which was located at the agency's lab complex in Fort Collins, Colo. The violations involved research with Japanese encephalitis virus, which can cause a deadly inflammation of the brain and is often transmitted by mosquitoes. As a result of the USDA inspection and findings that the research was not in compliance, the remaining samples of the virus were destroyed or transferred to another facility that was registered to possess them. The CDC noted in its statement that as of 2012, Japanese encephalitis virus was no longer considered by the federal government to be a select agent.

In response to USA TODAY's questions about how many CDC labs have faced select agent sanctions, the CDC said its own labs have been referred six times since 2003 to the Office of Inspector General at the U.S. Department of Health and Human Services, which handles enforcement actions for select agent violations.

"None of these violations resulted in a risk to the public or illness in laboratory workers," the CDC said. The agency provided few details about each of the cases:

Three referrals involved sending improperly killed select agent pathogens to entities not approved to receive them.

Two referrals involved the discovery of select agent pathogens in un-registered spaces in CDC facilities.

One involved inventory and oversight concerns.

Five of the cases were closed after the CDC "demonstrated enhanced procedures to prevent future occurrence," the agency's statement said. One enforcement action case remains open, but the CDC would not say what it involves. The agency would not answer questions about the dates of the cases or pathogens involved. "CDC has nothing more to offer beyond the statement," the agency said in an email.

CDC’s lab operations have been under scrutiny since 2014 because of a series of high-profile safety incidents at the agency’s headquarters in Atlanta that involved anthrax, Ebola and a deadly strain of influenza that revealed a lax safety culture inside the world-renowned agency.

The agency noted it has taken numerous actions in the past year to improve safety at its labs and said it is "committed to doing all we can to protect laboratory workers and the communities around them, while supporting scientific advancement to combat evolving threats."

Inside America's secretive biolabs

USDA officials this week would not answer USA TODAY's questions about its suspension of the CDC lab in Fort Collins or about any other enforcement actions the USDA has taken against the CDC's labs.

The January 2010 select agent reinstatement letter from the USDA cited only a select agent lab facility at the CDC’s National Center for Infectious Diseases but withheld the name of the scientist in charge and did not release that it was in Fort Collins. The USDA had initially refused to release the letter and other enforcement action documents in its responses to Freedom of Information Act (FOIA) requests filed by USA TODAY in September and December 2014. The letter was among 41 pages of records recently released by USDA as a result of an appeal filed by a lawyer for the news organization.

But the USDA still wouldn't answer questions this week. "After reviewing the latest additional questions posed by USA Today, it is clear that the Bioterrorism Act prevents us from releasing additional specifics beyond what was already provided as part of the FOIA request," the USDA said in a statement.

The USDA did not explain how the law prohibits it from answering general questions about the incidents in light of a White House directive last fall calling for greater transparency by federal agencies about select agent labs and incidents. White House homeland security experts said that in most cases withholding information about select agent labs “has negligible security value” since the labs routinely publicize their research. And they said any restrictions on the release of information under the Freedom of Information Act (FOIA) "do not preclude research institutions or government laboratories from voluntarily disclosing such information."

Sanctioned biolabs' names still kept secret despite White House memo

Although details about the CDC lab's suspension were limited, Melissa Morland, president of the American Biological Safety Association, said in an email that the suspension of a CDC lab shows that the current oversight system is working, because it involved an incident being reported and actions taken to ensure corrections were made.

Yet, Sean Kaufman, a biosafety consultant who previously worked for CDC, expressed frustration that the public is only learning about sanctions of CDC labs because of USA TODAY.

“What continues to disappoint me is the blatant disregard for accountability and this dodging of questions and transparency that is just damaging the trust factor of a wonderful organization,” said Kaufman, CEO of Behavioral-Based Improvement Solutions in Georgia.

A USA TODAY NETWORK investigation last year revealed that more than 100 U.S. labs have faced a variety of enforcement actions from the Federal Select Agent Program since 2003 – including suspensions, revocations and being put on performance improvement plans. At least 79 labs have been referred for enforcement actions – five of them repeatedly. But, with a few exceptions, the CDC and USDA have refused to publicly name the labs that have the nation’s worst regulatory histories working with dangerous viruses, bacteria and toxins that have the potential to be used as bioweapons.

The CDC privately provided many of the sanctioned labs’ names last summer to the bi-partisan leadership of the House Energy and Commerce Committee, which has been investigating lab safety issues and cited USA TODAY’s reporting in its request. The committee has not made the labs' names public and has said it is evaluating security concerns expressed by CDC. In response to a FOIA request from USA TODAY last year, the CDC released what it sent to the committee — with lab names removed.

Last year, amid intense media scrutiny about a lab incident that had the potential to allow a deadly bioterror bacteria to colonize soil outside the Tulane National Primate Research Center near New Orleans, the CDC publicly acknowledged it had suspended the facility’s select agent research. The lab has since been reinstated. The USDA, confronted with USA TODAY’s reporting, acknowledged it had suspended a portion of the select agent research program at Louisiana State University’s AgCenter because of a serious biosafety lapse in 2008.

In December, the CDC released the names of two labs that had had their select agent registrations’ revoked years earlier. The CDC provided the names, which it had previously kept secret, only after USA TODAY cited the recent White House memo calling for greater transparency about select agent labs and their incidents.

Despite the secrecy by CDC and USDA, the USA TODAY NETWORK's investigation has identified several other major labs that have faced enforcement actions, including those operated by Kansas State University, the University of Hawaii at Manoa and Brigham Young University.

After serious lab mishaps, CDC says it needs 3 years to release records

Beth Willis, former chair of a citizen lab advisory panel in Frederick, Md., where several federal biodefense labs are located, said the continued secrecy about lab incidents and enforcement actions makes it impossible for the public and policy makers to adequately assess potential risks.

“Secrecy just creates problems,” Willis said. “It creates alarm in the public and it makes it very difficult for labs across the country to understand what’s going on and to learn from it.”

Read USA TODAY's ongoing investigation of safety and security issues in labs nationwide at biolabs.usatoday.com.

Follow investigative reporter Alison Young on Twitter: @alisonannyoung.