Stanton was arrested Feb. 9 and was charged with burglary, theft, criminal trespass, and receiving stolen property, the District Attorney's Office said. He remained in custody Friday.
Melissa Weiler Gerber, the council's executive director, said Friday night that Stanton served as a peer counselor in the council's HIV program.
"We had good reason to hire him," she said. "Obviously we regret that decision." She declined to discuss what background-checking procedures the council uses.
The council said earlier in the day that there was no indication that the missing patient data had been inappropriately used.
The data included patients' names, addresses, phone numbers, Social Security numbers, dates of birth, and insurance and medical information.
Weiler Gerber said in a statement, "While no abuse of the stolen data has come to light, we regret deeply even the appearance of a breach, and as executive director of the council, I offer my personal and professional apology to all patients whose confidentiality may have been violated."
She said the council was taking steps to ensure that such a breach did not occur again.
Public notification is required under federal law.
The data were contained on a flash drive kept in another employee's desk. Other items also were stolen from the office between Dec. 23 and 27.
The health-care providers affected by the data breach include Children's Hospital of Philadelphia, Planned Parenthood Southeastern Pennsylvania, Planned Parenthood Association of Bucks County, Spectrum Health Services Inc., and Public Health Management Corp.
The providers are notifying all affected patients, the council said. Free credit-protection and monitoring services for those patients will be offered by the council, located at 1700 Market St.
Contact staff writer Robert Moran at 215-854-5983 or bmoran@phillynews.com.
