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Yesterday, Caltrain’s board unanimously approved a contract with Herzog subsidiary TransitAmerica Services Inc. to operate the commuter-rail system.

The new five-year contract, which will go into effect next year, will represent the first time in 20 years that Caltrain will not be operated by Amtrak.

Caltrain sought competitive proposals last year “to obtain the best value and most innovative approaches,” Caltrain officials said in a prepared statement.

“The result is an opportunity for a partnership between TransitAmerica and Caltrain that can meet the high expectations we have for a safe, reliable, viable Peninsula commuter-rail service now and in the future,” said Caltrain Executive Director Michael Scanlon.

The first full year of the contract (in fiscal-year 2013) will cost $59.5 million, within projected Caltrain operating and capital budgets. Subsequent contract amounts will be subject to annual negotiations. Under federal regulations, Caltrain’s current employees will have their jobs protected, according to Caltrain.

The agreement, which includes five one-year options, includes the daily staffing and operations of trains, as well as inspection and maintenance of tracks, the passenger-rail fleet, right of way, structures, signaling and communication network, stations and other facilities.

The contract calls for a five-month transition period to enable TransitAmerica to mobilize its new management team.

“During that time, Caltrain and Amtrak will remain in a partnership, and Amtrak will continue to operate the railroad as it participates in the transition,” Caltrain officials said.

Caltrain officials expect the contract to produce “savings and efficiencies” during the next five years, they said. In addition, the contract includes an “innovative clause” that will require TransitAmerica to achieve “certain performance standards around management, safety, on-time performance, and other critical tasks that are imperative to the operation of the railroad prior to receiving its full management fee,” they said.