The determination was made after months of work and DNA examination by epidemiologists at the University of Wisconsin-Madison School of Veterinary Medicine, the Milwaukee Journal Sentinel reported Tuesday.
Tissue from Mahal, who died Dec. 29, showed traces of what was eventually identified as tapeworm DNA, Bruce Beehler, the zoo's deputy director of animal management and health said.
"It was an astonishing performance in diagnosis -- unimaginable a few years ago," he said.
The death of Mahal at age 5 shocked zookeepers and zoo visitors alike, as orangutans normally have a life expectancy of 30 years or more.
The tapeworm was the cause of "an overwhelming infection" that had spread throughout the orangutan's body to major organs, including his liver and lungs, Beehler said.
Mahal was born at the Cheyenne Mountain Zoo in Colorado Springs, Colo., in 2007 but after being rejected by his mother he was flown to the Milwaukee zoo in 2008 to live with a surrogate mother, becoming one of the zoo's star attractions.
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