Police arrested Dr. Kimberly Quinlan Lindsey, 44, in DeKalb County, Georgia, on Sunday.
Authorities also charged Lindsey's live-in boyfriend, Thomas Joseph Westerman, 42, with two counts of child molestation.
The two are accused of "immoral and indecent" sexual acts involving a 6-year-old, according to information from DeKalb County Magistrate Court and an arrest warrant.
The bestiality charge says Lindsey "did unlawfully perform or submit to any sexual act with an animal."
The alleged incidents took place between January 1, 2010, and August 22, 2011.
Westerman is out of jail on bail; Lindsey remains in jail with bail set at $20,000, said Lt. Pam Kunz of the DeKalb County Police Department.
Neither has made a public statement. Westerman did not immediately return a call from CNN.
Both went to court on Sunday for an initial appearance and have a preliminary hearing scheduled for December 1, said Reggie Silverman, deputy clerk with DeKalb Magistrate Court.
Lindsey is the deputy director for the Laboratory Science Policy and Practice Program Office at the CDC, according to her biography on the agency's website.
Prior to her current role, Lindsey was the senior health scientist in the Office of Public Health Preparedness and Response. That office oversees the allocation process for $1.5 billion in terrorism preparedness.
In her 12 years at the CDC, Lindsey has received 12 awards for outstanding performance on projects and programs, according to her bio on Emory University's Biological and Biomedical Sciences website. Lindsey earned her doctorate in immunology and molecular pathogenesis from the university in 1998, a year before she began work at the CDC.
A LinkedIn Web page for a Thomas Westerman lists him as having been a watch officer at the CDC from November 2009 to November 2010 and a resource management specialist since August 2011.
CDC spokesman Tom Skinner said the agency is aware of the case but cannot comment on personnel issues.
Dr Lindsey has worked at the CDC for a decade and earned a doctorate from Emory Universityhttp://edition.cnn.com/2011/10/11/justi ... index.html
http://www.huffingtonpost.com/2011/10/1 ... 04881.html