Pilkington initially pleaded not guilty to aggravated murder charges. Prosecutors had sought genetic testing for Pilkington to rule out genetic disorders as a cause of death for the three boys.
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Judge Mark Connor ordered that Pilkington's sentences run back to back because of the seriousness of the crimes, a move advocated by prosecutors.
Pilkington, 27, suffered lead poisoning as a child followed by years of physical and sexual abuse with no intervention by authorities, said Kort Gatterdam, one of her attorneys. Her parents, social service agencies and schools all failed to protect her, he said. A scan identified brain damage.
"Sadly, she's safer living a better life in jail than on the outside," Gatterdam said, calling his client "irreparably damaged."
Attorney Tina McFall, reading a statement on behalf of Pilkington, said she "loves and misses all of her children and grieves for them every day."
Pilkington's husband, Joseph Pilkington, pleaded guilty to a misdemeanour charge of sexual imposition for having sex with his wife before they were married, when she was underage. He originally was charged with sexual battery for beginning a sexual relationship with Pilkington, who was two decades younger, and impregnating her in 2009, when she was 17.
He'd had a romantic relationship with Pilkington's mother prior to that, and his indictment indicated he had been living with Pilkington as a sort of stepfather for years.
He wasn't a suspect in the boys' deaths.
-Additional reporting, AP