A top official with the Centers for Disease Control and Prevention and a companion were indicted Friday on two counts of child molestation each.

Kimberly Quinlan Lindsey, deputy director for the Laboratory Science Policy and Practice Program Office at the CDC, was arrested in October 2011 along with her boyfriend, Thomas Joseph Westerman, after a medical professional alerted police about a child molestation allegation.

The arrest warrant cited two incidents — the first in January 2010 and the latest on Aug. 22, 2011 — involving a 6-year-old boy.

“These allegations outlined in this indictment are both disturbing and troubling,” DeKalb County District Attorney Robert James said Monday. “We will prosecute both of these individuals to the fullest extent of the law.”

Lindsey, 45, is alleged to have engaged in sexual activity with the boy in the presence of Westerman, a resource management specialist with the CDC at the time of his arrest. Westerman, 43, allegedly instructed the child to touch Lindsey while she was partially undressed, the indictment filed in DeKalb Superior Court states.

Westerman and Lindsey share a home in Decatur, according to public records.

Lindsey, an Emory University graduate, returned to work soon after her arrest. She’s been with the CDC since 1999 and at one point was responsible for overseeing a $1.5 billion fiscal allocation process for terrorism preparedness.

CDC spokesman Tom Skinner said Lindsey remains employed by the agency.

“Due process will play itself out,” he said, declining further comment.

Westerman no longer works for the CDC, Skinner said.

Lindsey’s attorney said he would withhold comment until Tuesday. Calls to Westerman’s counsel seeking comment were not returned.

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