A Peekskill-based health care network will take over this fall as the operator of two Suffolk County-subsidized clinics in Shirley and Patchogue, officials said Tuesday.

The clinics, currently managed by Brookhaven Memorial Hospital Medical Center in East Patchogue, will be transferred to Hudson River HealthCare Inc., also known as HRHCare, by about Nov. 1.

The change is expected to save the county $31 million over the next five years, Deputy County Executive Jon Schneider said.

The clinics, which primarily serve low-income residents and provide services such as primary care, family planning, diabetes education and prenatal care, will add services such as dental and mental health care as part of the change, Schneider said.

Brookhaven hospital officials said in a news release that most clinic employees are expected to transfer to Hudson River HealthCare. The state Labor Department said 48 employees may be affected by the move.

"The current staff will have the opportunity to transition to the Hudson River HealthCare as well as appropriate job possibilities" at Brookhaven hospital, the hospital said in a statement, adding that "patients will have a seamless transition."

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Hudson River HealthCare officials could not be reached for comment.

Schneider said the move was prompted in part by a steep reduction in state subsidies for the county's health clinics. Subsidies have been cut from $28 million in 2010 to $15 million last year, he said.

The county in recent years had turned over management of clinics in Coram, Southampton and Amityville to Hudson River HealthCare, for an anticipated savings of $19 million over five years, Schneider said. The firm, which operates 22 facilities on Long Island and in the Hudson River valley, is able to hold down costs in part because its malpractice costs are covered by the federal government, he said.

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"Just about everyone who has seen the job they've done has been very impressed," Schneider said.

Legis. John M. Kennedy Jr. (R-Nesconset) said he supported the change because of the projected savings, but expressed concern that "a handful" of county employees working at the clinics may lose their jobs.