I had an email from a Labrador that had "boil like" bumps between the toes. The bumps would rupture and there was a small crater in the center. I suspected that these were interdigital cysts.
These cysts are caused by pododermatitis and interdigital pyoderma. These have been extremely frustrating to treat successfully with any one approach. So the following is a list of things that have worked, with some notes about how they may be useful:
Mupirocin ointment (Bactoderm Rx)--can be put on the cysts and sometimes works well.
Metronidazole (Flagyl Rx)--strangely enough it can help with these cysts.
Doxycyline, like metronidazole, has worked well for a couple of dogs.
Fluoroquinolones (Baytril Rx, Dicural Rx, Orbax Rx, others) are the most commonly recommended antibiotics in the dermatology literature. These are broad spectrum antibiotics that generally penetrate tissue well.
Clindamycin (Antirobe Rx) is an antibiotic that has good activity against anerobic bacteria which seem to be involved in some cases of interdigital cysts. It is often used in combination with fluoroquinolones but can also be effective alone in some dogs.
Cephalexin ( Keflex Rx) is our general favorite antibiotic for skin disease. It can be used long-term to control skin infections. It seems to be among the safer of antibiotics, although no antibiotic is totally risk free. If there seems to be any response to cephalexin early in treatment we usually try it for at least three weeks.
So you may want to talk to your vet about starting with cephalexin and then move on to the other medications on the list, except that we often use cephalexin and metronidazole together rather than withdrawing the cephalexin. You can use fluoroquinolones last, mostly based on expense.
These cysts can come back so you may have to start the treatment again. You may want to consider keeping your dog indoors, if you have a kennel, while the antibiotics work. Sometimes there are things such as pollen that can cause allergies. Also, you may want to switch to a different food,especially one that is natural and does not have corn. I suggest one of the Wellness or Nutro foods.