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 The 22-year-old woman, known only as Beatriz for privacy reasons, underwent the operation in the afternoon after 27 weeks of pregnancy, the ministry said. Her baby girl was born without a brain.
"No one can say how long she will live," Morena Herrera of the Feminist Collective for Local Development told The Associated Press. "It was painful to see the little creature. That's what the grandmother told us, and the doctors confirmed it."
The country's Supreme Court last week prohibited an abortion for Beatriz, who suffers from lupus and kidney failure and whose lawyers said the pregnancy was threatening her life. Her plight drew international attention and a ruling from the Inter-American Court on Human Rights that El Salvador should protect her life and help her end the pregnancy.
The Health Ministry stepped in late last week after the ruling and said it would allow the C-section because the pregnancy was already at 26 weeks and the country's strict abortion laws were no longer at play. Ultrasound images had indicated her fetus was developing with only a brain stem.
The Health Ministry can determine what is most medically sound for a mother versus the unborn baby and was lauded internationally for working to save the woman's life.
Doctors at the Maternity Hospital had been preparing to perform the C-section at the slightest danger signs to save Beatriz's life, said Maria Isabel Rodriguez of the health ministry.
The woman was recovering under the close watch of doctors late Monday.
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 El Salvador's laws prohibit all abortions, even when a woman's health is at risk. Beatriz and any doctor who terminated her pregnancy would have faced arrest and criminal charges.
A majority of judges on the high court rejected the appeal by Beatriz's lawyers, saying physical and psychological exams by the government-run Institute of Legal Medicine found that her diseases were under control and that she could continue the pregnancy.
Just as the Health Ministry was resolving the case, the Inter-American Court issued its ruling, but it no longer applied in the case.
Abortion opponents said the case was being used to press for legalized abortion in El Salvador, which has some of the toughest abortion laws in Latin America, along with Chile, Dominican Republic, Haiti, Honduras, Nicaragua and Suriname.
[Associated
Press; By MARCOS ALEMAN]
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