The Crescent Duck Farm in Aquebogue, which lost its entire flock of 99,000 to an outbreak of bird flu, has begun the long, methodical process of sanitizing its facilities.

The avian flu outbreak that has led to the slaughter of millions of birds at U.S. poultry farms and driven up the price of eggs struck the Crescent Duck Farm this week, leading federal officials to order the destruction of the operation’s entire flock.

The highly infectious H5N1 strain has caused outbreaks across the country. Now, Long Island’s last duck farm must kill its entire flock and may go out of business, its owner said.