In two separate tests, Ms. Franklin identified characteristics of the MRSA bacteria growing in the seat. The first test confirmed the presence of staphylococcus aureus, the skin-borne bacteria. A second confirmed that the bacteria, like MRSA, was resistant to the antibiotics methicillin and penicillin. But a third test intended to isolate the MRSA bacteria was negative.

MRSA is known as the “superbug” because it is resistant to antibiotics. It infects people through open wounds, attacking the immune system; 19,000 deaths each year are related to MRSA infections, according to the Centers for Disease Control and Prevention.

“There’s a probability that it is MRSA, but more tests would need to be done,” Ms. Franklin said. “Somebody probably was wearing shorts and had an infection, and there you go. It is concerning.”

Ms. Franklin identified two other bacteria strains that she said resulted from fecal contamination of the BART seat. Those strains were also resistant to antibiotics. The other bacteria did not appear to be harmful and are found throughout the environment, Ms. Franklin said.

The soft seat is a BART trademark, going back to Sept. 11, 1972, the day the first train rolled down the track. The seat covers are made of 90 percent wool and 10 percent nylon and are filled with foam padding, which was made fire-resistant after a fire in the Transbay Tube in 1979.

A BART brochure proclaimed that the new trains were designed to “lure the commuter out of the comfort of his automobile.” The trains were “almost as wide as a Boeing 707, and every bit as comfortable,” according to the brochure, which was printed in the shape of a BART car.

“BART was an all-new system, and they wanted everything to be different,” said Mike Healey, who was a BART spokesman at the time. “They wanted cushioned seats and rugs on the floors. Comfort was certainly a key selling point for the system.”