Quintez Adams, 28, was taken into custody by Philadelphia police on Wednesday. He was brought to an area hospital for evaluation due to injuries.
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According to the district attorney's office, the injuries are from "a physical assault involving one or more civilians."
Adams was wanted for a rape that occurred on April 24 on the Broad Street Line between SEPTA's Erie and Girard Avenue stations.
Authorities also said Adams was the suspect in an indecent exposure incident that happened on April 4 on the 700 block of Market Street. According to the district attorney's office, the incident took place at a Philadelphia probation office.
The D.A.'s office said Adams is also being charged with indecent exposure due to a March 8 incident at a hospital.
Adams is reportedly homeless and lives on the streets of Center City.
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City Councilman David Oh has criticized SEPTA for hiring dozens of unarmed security guards instead of more transit police officers -- calling it a failed experiment.
"Now that it's a failure. What are they gonna do? Are they gonna dig their heels in and continue to do this?" asked Oh.
The Transit Police Union has also been critical of the issue.
"Currently we're down approximately 60 officers; we'd like to see the department get the numbers up to somewhere around 300 just so we can regain control of our system," said Vice President Troy Parham of Transit Police Lodge 109.
SEE ALSO: Rape, 2 stabbings on SEPTA over the weekend under investigation
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Rape, 2 stabbings on SEPTA under investigation
In a statement, SEPTA said that its top priority is the safety and security of riders and employees, and that it is actively recruiting new police officers.
But Councilman Oh is threatening to push an amendment to withhold $10 million from SEPTA's budget until it promises to add more officers.
"I don't know if that amendment will pass or not, but I will introduce it and I think if nothing else, it is elevating the discussion," said Oh.
A City Council hearing on SEPTA's budget is scheduled for May 3.