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Margaret and James Hamilton were a dog power couple, seemingly the perfect people for raising and selling purebreds.

Margaret was a breeder and a dog-show judge who owned prizewinning Chihuahuas. Some of her litters were registered with the American Kennel Club (AKC), a stamp of approval from an organization charged with maintaining breed standards and registering purebreds around the country. Her husband, James, was a leader in a local AKC Rottweiler club.

But when police entered a home in Burien, Wash., in October 2011, they wondered what standard the Hamiltons were being held to. The police said they found 38 dogs that were under James Hamilton’s care, mostly Chihuahuas, living in small crates filled with fur and feces, the cages stacked on top of one another in a dark basement, according to court documents.

A radio was blaring, drowning out the sound of barking, and many of the dogs were malnourished and had eye diseases and overgrown toenails, according to investigators. Thirteen dogs were euthanized the night of their rescue because of incurable health problems, including severe periodontal disease.

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The same day at the Hamiltons’ residence in Issaquah, 62 dogs were seized and one was euthanized. The Hamiltons were charged with animal cruelty in the second degree.

“It was a ‘Silence of the Lambs’ scene down there,” Kim Koon of Pasado’s Safe Haven, an animal shelter that was involved in the investigation, said of the basement. “Those animals were in horrible shape.”

The AKC said that although Margaret Hamilton “registered a total of four litters” with it, her operation had never been subject to inspection. The club stripped her of “all AKC privileges” including judging, and fined her $2,000 after the seizure of her dogs. James Hamilton died shortly after the raid in Burien.

“The dogs that were under her care and control were in good shape,” Brett Purtzer, a lawyer for Margaret Hamilton, said. “There were dogs that weren’t treated well, no question about that. But she had nothing to do with them.”

To most animal lovers, the AKC is best-known as the go-to place for registering purebred puppies and as the governing body for dog shows, including the regal Westminster Kennel Club Dog Show, which opens Monday in New York City. The AKC is “dedicated to upholding the integrity of its registry, promoting the sport of purebred dogs, and breeding for type and function,” according to its mission statement.

But the AKC is increasingly finding itself ostracized in the dog world, in the cross hairs of animal-protection services, law-enforcement agencies and lawmakers who say the club is lax in performing inspections and often lobbies against basic animal-rights bills because they could cut into dog-registration fees.

As recently as 2010, roughly 40 percent of the AKC’s $61 million in annual revenue came from fees related to registration. Critics say a significant part of that includes revenue from questionable breeders like the Hamiltons, or so-called puppy mills, which breed dogs en masse with little regard for basic living standards.

Ed Sayres, president and chief executive of the American Society for the Prevention of Cruelty to Animals (ASPCA), said a majority of the commercial breeders in the raids that his group participated in had ties to AKC-registered litters.

“The irony to the consumer is that they’re paying a lot for a fake Rolex,” Sayres said. “These dogs are often coming from a genetically traumatic environment and had cruel treatment in a crucial part of their development.”

The AKC disputes such accusations, calling the ASPCA’s claim baseless. The club says it is vigilant about protecting against substandard breeders. Lisa Peterson, AKC communications director, said the club was continually working to try to improve the care and conditions of dogs. “We are not a law-enforcement agency and not responsible for all breeders,” she said.

The AKC employs nine field agents, or inspectors, nationwide. It declined to say how many inspections were conducted each year or how many were reported to law enforcement.

Many people who raise AKC-registered litters are responsible breeders who care for their dogs and are concerned with their lifelong health. But some people argue that many high-volume breeders have an incentive to make quick sales to pet stores or individual buyers, but are less concerned about the consequences of where a dog ends up. And for some consumers, this part may be lost by what critics say can be a misleading stamp of approval from the AKC.

There is no consensus on what constitutes a puppy mill. In general, officials refer to puppy mills as operations geared more toward generating profits from the sale of dogs rather than animal welfare, and where dogs may live in substandard conditions.

Taxpayer dollars are spent in investigating claims of animal cruelty and may be spent sheltering the dogs. The ASPCA estimates the average raid results in costs of $25 to $34 a day in caring for a puppy, which may be for several months, depending on court proceedings.

On its website, the AKC said it had an “ongoing routine kennel-inspection program” and that since 2000, field inspectors had conducted more than 45,000 inspections nationwide.

That included inspections of Mike Chilinski’s kennel in Montana, which had AKC-registered litters. But when it was raided in 2011, officials found 161 severely malnourished malamutes living off their own feces in small cages, according to court documents.

Many of the dogs had diseases; one had advanced cancerous growths. Dead dogs were stacked outside small kennels, and empty, dirty water bowls were littered about, officials said. Five of the rescued dogs died within weeks. Authorities seized 18 pregnant females, and half of their litters died of lack of nutrition upon delivery. At least one malamute that should have weighed 85 pounds weighed 25 pounds.

In December, Chilinski received a sentence of five years on 91 counts of animal cruelty and neglect for running what law enforcement called a puppy mill. The malamute rescue cost more than $500,000 and employed more than 70 volunteers. The bulk of the cost was paid by the Humane Society of the United States, a national group that does not typically financially support the regular operations of local shelters.

In 2008 and 2009, AKC inspectors found Chilinski “in compliance,” Peterson said, with about 60 dogs at his kennel.

“Now that he has been convicted, the AKC will obtain the court records to conduct a review in accordance with the policy,” Peterson said.

Chilinski’s lawyer did not respond to requests for comment.

As for Margaret Hamilton in Burien, as part of a plea agreement with the court, she agreed to take care of only three dogs, surrendering ownership of the rest, and agreed to regular inspections and to pay restitution of $25,000.

“The dogs were her life,” Purtzer, Hamilton’s lawyer, said.

Critics say the AKC has opposed legislation that would improve conditions for animals and reduce the number of abusive high-volume breeders. The AKC and its members are active in federal and state politics, spending thousands of dollars in campaign donations and influencing efforts, including specific caps on the numbers of litters kennels could breed, and some codifications of minimal living standards and the use of tethers, including efforts in Oregon, North Carolina, Georgia, New York, New Hampshire and California.

Among the legislation the AKC opposed was a Rhode Island bill that would prevent dogs from being placed in cages or tethered for more than 14 hours a day.

“The AKC opposed the bill because it featured language that was far more burdensome than just regarding tethering and confinement,” Peterson said. “The bill was so broadly worded that it could impact the ability for individuals to keep animals confined in a fenced-in yard or in a suitable pen during the day while owners were at work and at night while owners are asleep.”

In Massachusetts, the AKC opposed a bill that further defined how law enforcement could go about seizing animals from people suspected of animal cruelty and charge those convicted with the costs of caring for the animals.

“AKC is critical of proposals that attempt to permanently take dogs away from their owner-defendants who have not been found guilty of any crime,” Peterson said, “from co-owners not party to the judicial procedure, and from individuals who because of the cost of litigation may not be able to afford expensive care bonds.”

Some breeders say there have been consequences for opposing the AKC.

In Oregon, lawmakers introduced a bill in 2009 that aimed to limit to 25 the number of sexually intact dogs a breeder could have. Ted Paul, a collie breeder and judge at dog shows for more than 40 years in South Salem, Ore., was asked by state lawmakers to support the bill. A longtime member and past president of the Collie Club of America, he agreed, saying he thought it could curb abuses.

Paul said he was branded a traitor on the Internet and that AKC-affiliated dog-show organizers stopped using him as a judge. “I was surprised by the backlash,” he said.

The Oregon bill passed, but Paul said he had been “completely ostracized” from judging competitions since he advocated breeding limits.

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