"We continue to thoroughly test and treat fish in all sections of the hatchery and are taking all precautions necessary to contain this disease," said Division of Fish and Wildlife Director David Chanda.
Pennsylvania has treated trout for furunculosis but never euthanized any, said Brian Wisner, director of the Bureau of Hatcheries of the state's Fish and Boat Commission.
The infection, which is apparently carried by birds, was found in one of eight long raceways at the Pequest hatchery, state officials said.
Birds of prey, such as the osprey, "eat infected fish in the wild, and we suspect they brought the disease" to the hatchery, said Larry Ragonese, a spokesman for the New Jersey Department of Environmental Protection. "There is no solid roof over it.
"You can put up netting, but the birds attack it," he said. "We don't definitely know what happened, but [the disease] could have come from bird droppings or from a bird biting into a fish, then dropping it."
The affected trout were humanely euthanized Wednesday and Thursday through the veterinarian-approved introduction of carbon dioxide into the water, Ragonese said. The raceway will be drained, dried, steam-cleaned, and disinfected before the next round of fish is brought in.
"Weighing all the factors with this most recent outbreak, it is in the best interest of the hatchery now and to safeguard the 2015 stocking program that the 114,000 brook trout that tested positive for furunculosis are euthanized," Chanda said.
The dead fish were being disposed of at a landfill, officials said.
Other hatchery trout that may have been exposed to the disease were treated, and fish that will be added to their numbers have tested negative.
As part of a modified stocking program, the treated trout will be released only in locations that don't have wild trout, state officials said. The change was necessary to produce existing populations from fish that might carry the pathogen.
Furunculosis is fairly common, officials said. In addition to New Jersey and Pennsylvania, it's been reported in Delaware, Maryland, New York, Connecticut, and others bordering the Great Lakes.
"We have kept the [Pequest] hatchery clean and pristine," Ragonese said. "We take as many precautions as we can."
To access the hatchery's fish, birds have to evade various defenses, which include air cannons, and wires strung across the raceways, officials said.
The disease problems last fall and this year at Pequest were the first at any state hatchery in about 40 years, Ragonese said. The last outbreak had been at the state's other facility at Hackettstown, Warren County, which now raises other kinds of fish.
About 300,000 pounds of trout are produced each year at Pequest, which utilizes Artesian wells to provide a constant flow of cold water necessary for the rearing of trout.
To avoid reoccurrences of the disease, New Jersey Fish and Wildlife officials are working with their New York counterparts to breed brook and brown trout that are resistant to the disease.
The trout also will be vaccinated and production of disease-resistant rainbow trout will be increased, officials said.
Physical changes to the hatchery are being considered, too, including the construction of "fabric domes or barnlike structures" to enclose the raceways, and the installation of extra wells to allow each raceway to have its own water supply for each group of fish.
"We hated to euthanize the trout," Ragonese said, "but it was for the future protection of the species.
"We had to take that step. There was no choice."
For More Information: On spring trout stocking program, go to: http://www.nj.gov/dep/fgw/pdf/
On the Pequest Trout Hatchery, go to: http://www.state.nj.us/