"We will continue to co-operate with Phoenix Police and all other investigative agencies to uncover the facts in this deeply disturbing, but unprecedented situation", the company said in a statement. Awake but immobile, and apparently unaware, her universe consisted mostly of a room at a Phoenix Hacienda HealthCare facility where she received round-the-clock care.
According to the reports, the woman has been in a vegetative state since she was the victim of a near-drowning more than 10 years ago.
The birth has triggered a police investigation and reviews by state agencies.
The 29-year-old, who is a patient at the centre which cares for people with intellectual disabilities, unexpectedly gave birth on December 29.
Bill Timmons' resignation was accepted unanimously by the Hacienda Board of Directors.
It comes after a sex abuse probe was launched after a patient in a vegetative state gave birth.
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A Phoenix police spokesman told The Washington Post that the department is investigating but did not release details about the case.
Gary Orman, executive vice president of Hacienda HealthCare, said the company would "accept nothing less than a full accounting of this absolutely horrifying situation".
She added many people would have had access to the woman's room and cited a meeting with Mr Timmons in 1998 over concerns regarding the treatment of a separate patient. For example, an investigation in 2013 found that a staff member had made "inappropriate, sexual statements" about four clients.
Hacienda HealthCare said it welcomed the DNA testing of employees as detectives desperately try to solve the horrific case. The employee was sacked.
"Whether it's an employee or someone from the outside, the facility has an obligation to protect residents".
Sources also told ABC 15 in another report that investigators are looking into whether the patient suffered multiple sexual assaults, "including assaults on different parts of the body". "I myself have come in a back way many times with no one noticing me", the caregiver said. I can't believe someone would bathe her daily for nine months, never know she wasn't having her period, she wasn't growing in her mid-section. "We also don't have required training for providers", McFadden said.