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Dog Boils.

My 3 week old lab puppies have marble size knots on their tails. Some of the knots are squishy and look like boils. They have puss and blood coming out of them and some are scabbed over. I took them too the vet and they said that my puppies had hook worms. Can worms cause this? What should I do? I have been putting peroxide and neosporen on it plus giving them the medicine that the vet gave. I have noticed long 1 inch worms in stool and some yellow dots in stool, but i thought hookworms were unable to be seen by the naked eye. I can send a pic if needed, when i get a camera.
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Yes, hookworms are unable to be seen by the naked eye. They are incredibly tiny. Some hookworm larvae can directly penetrate the dog's skin. Maybe that's what has happened here. They can be picked up from infested water (streams, rivers, etc) or from infested animal faeces, the soil, or from rodents.

Hookworms can also live in the intestines, they suck blood there and can cause severe anaemia. I think the heartworm meds also work for hookworm, but the treatment often has to be repeated, and faecal exams are necessary. I guess the vet knows what meds to use for this. I would keep using that, but take your dog for fairly regular reviews of the condition.

Be careful because hookworm larvae can penetrate the skin of people too!
I know all this sounds horrible, but if your dog is treated thoroughly for this, hopefully those hookworms will get eliminated!  
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