A pair of federal fish hatcheries in Wisconsin will help Minnesota with trout stocking for the next three years while the Department of Natural Resources re-establishes a hatchery near Altura, Minn., that was devastated by a persistent outbreak of disease.

The Crystal Springs hatchery in southeastern Minnesota was shut down last week with the removal and incineration of all 18,465 pounds of brook trout and lake trout in its tanks. The fish were exposed to a pathogen that causes furunculosis, a disease that forms boils and lesions on fish and eventually kills them.

It was first detected in 2014 and spread throughout the hatchery despite numerous attempts to root it out. Paula Phelps, the DNR’s coldwater fish production supervisor, said the pathogen seemed to be under control for some time but then became widespread.

The pathogen is a bacteria found in surface water in concentrations that don’t usually cause disease outbreaks. It is believed to have found its way into the hatchery via floodwaters in 2007.

Once the facility is thoroughly sanitized and upgraded for maintenance reasons, it will resume the rearing of brook trout using the eggs of native fish. If the facility remains disease-free for three years, stocking will resume, Phelps said. In the meantime, the DNR will pick up the slack in stocking with brook trout raised at national fish hatcheries in Iron River and Genoa, Wis.

“We tried to treat [the disease] and it was under control for some time … but it continued to spread,” Phelps said.

The Crystal Springs hatchery, operated by the DNR since 1932, was the only place where the state raised brook trout and lake trout. For years, the lake trout were released into Lake Superior, while the brook trout were released primarily in northeastern and southeastern Minnesota. Phelps said the hatchery won’t resume the rearing of lake trout unless the Lake Superior fish management plan — now under review — calls for it.

She also said brown trout and rainbow trout raised in the DNR hatchery in Lanesboro, Minn., will be stocked in certain waters over the next three years to help make up for the shortfall at Crystal Springs.