A former nurse accused of raping and impregnating an incapacitated woman under his care last year at a Phoenix nursing home pleaded not guilty on Tuesday to charges of sexual assault and child abuse.

In a brief arraignment hearing, the former nurse, Nathan D. Sutherland, who appeared in an orange jumpsuit, spoke only to provide his name and date of birth. The judge announced that a not guilty plea had been entered by Mr. Sutherland, 36, who was swiftly taken back to the Maricopa County Jail, where he has been held since his arrest on Jan. 23.

The roughly minute-long proceeding was the latest development in a sexual assault case that has shocked the authorities in Arizona, raised questions about the treatment of patients in long-term disability care there and brought intense scrutiny to the nursing home’s operator, Hacienda HealthCare.

The criminal case started to unfold in late December, when a woman at Hacienda who cannot talk or walk unexpectedly gave birth to a boy. Over the following weeks, the investigation became the main focus of the Phoenix Police Department, its chief said, and led to questions about the company’s operations and conduct.

The police said that a DNA sample taken from Mr. Sutherland, a Hacienda nurse assigned to treat the woman, matched that of the newborn.

On Tuesday, Gov. Douglas A. Ducey of Arizona, a Republican, raised the possibility of deploying the state attorney general’s office in a wide-ranging investigation into the company. The governor requested an inquiry into how Hacienda employees did not know that the 29-year-old patient, who has been at the nursing center since 1992, had been raped or notice that she was pregnant, according to a copy of the letter he sent the attorney general, Mark Brnovich.