A company that bred beagles for medical research agreed Monday to pay a record $35 million as part of a criminal plea admitting it neglected thousands of dogs at its breeding facility in rural Virginia.

Prosecutors said the penalties amount to the largest ever levied in an animal-welfare case.

The plea deal also bars the company that operated the facility, Envigo RMS, as well as parent company Inotiv, from breeding or selling dogs in the future.

The federal investigation of Envigo drew national attention in May 2022 when federal authorities conducted a search of the breeding facility in Cumberland County, Virginia, and found nearly 450 animals in acute distress.

The company later agreed to relinquish all 4,000 beagles at the facility, which were sent around the country for adoption.

U.S. Attorney for the Western District of Virginia Christopher Kavanaugh, whose office prosecuted the case, said Monday after a plea hearing at federal court in Charlottesville that Envigo and Inotiv “prioritized profits and convenience over following the law.”

He said the company generated $16 million in revenue between 2019 and May 2022, when the search occurred, through the sale of 15,000 beagles over that time.

But he said the company refused to make the investments necessary to provide for the animals’ basic care. Cages were cleaned twice a month rather than every day as required. Animals were euthanized, including by direct injections to their heart, without sedation, he said. Dogs were routinely injured by getting their paws caught in flooring composed of metal grates that left space for paws to easily fall through. Food and water were lacking and unclean

Court records show that 300 puppies died over a seven-month stretch around 2021 for what was described as “unknown causes.”

He said the company continued to employ a veterinarian who had botched surgeries and oversaw numerous violations because executives believed it would be too difficult to find a replacement.

Todd Kim, assistant attorney general for the environment and natural resources division of the Justice Department, said Envigo “unlawfully enriched itself by failing to spend the necessary money for upgrades and by failing to hire enough trained and competent staff.”

The Cumberland facility, which employed nearly 40 people, has been shuttered. Kavanaugh said it was woefully understaffed to care for thousands of dogs.

The plea deal calls for an $11 million fine for violating the Animal Welfare Act and an $11 million fine for violating the Clean Water Act. The deal also requires Inotiv to spend $7 million over the next three years to improve its facilities and meet standards in excess of the Animal Welfare Act requirements.

The plea deal includes an admission that Envigo violated the Clean Water Act by discharging hundreds of thousands of gallons of improperly treated wastewater.

It also includes $3.5 million for environmental repairs in Cumberland County and requires the company to pay the cost of a compliance monitor while it’s on probation, which will run for a period of three to five years.

The plea agreement also requires the companies to pay roughly $1.9 million to the Humane Society of the United States for assistance it provided to the investigation.

Prosecutors also said their investigation is ongoing and that criminal cases against individual employees remain possible.

West Lafayette, Indiana-based Inotiv issued what it called a “statement of contrition” Monday after the plea hearing.

“In committing the crimes identified in the charging document, and by not making the necessary infrastructure upgrades and hiring the requisite staff, we fell short of our standards for animal and environmental welfare and apologize to the public for the harm caused by our conduct, the company said. “In resolving this matter, we renew our commitment to maintaining the highest standards of animal care.”