It's most likely Vent disease / VD / rabbit Syphilis (not to be confused with human syphilis).
*Important Note: rabbit syphilis is NOT zoonotic, and cannot be passed from rabbits to humans*
The Vet started a culture, and is waiting on that for confirmation, but he's certain it's VD.
This both sucks and is great news - it's a pain in the ass to treat, treatment is really hard on the rabbits and may cause stomach upset and diarrhea, it takes 3 weeks, BUT it's treatable, and in fact, CURABLE.
http://www.merckmanuals.com/vet/exotic_and_laboratory_animals/rabbits/bacterial_and_mycotic_diseases_of_rabbits.html#v3306565?qt=&sc=&alt=
TREPONEMATOSIS
(Vent disease, Syphilis, Spirochetosis)
Treponematosis, a specific venereal disease of domestic rabbits, is caused by the spirocheteTreponema paraluis cuniculi. It occurs in both sexes and is transmitted by coitus and from the doe to offspring. Although closely related to the organism (T pallidum) that causes human syphilis, T cuniculiis not transmissible to other domestic animals or humans. The incubation period is 3–6 wk. Small vesicles or ulcers are formed, which ultimately become covered with a heavy scab. These lesions usually are confined to the genital region, but the lips and eyelids may be involved. Infected rabbits should not be mated. Diagnosis is based on the lesions and observation of the spirochete's corkscrew motility under darkfield microscopy. Serologic tests used to diagnose T pallidum, such as the VDRL slide test and the rapid-plasma regain card test are widely available and can be used to diagnose T cuniculi. Hutch burn is a differential diagnosis.
Benzathine penicillin G, 42,000 IU/kg, SC, at weekly intervals for 3 wk, is necessary to eradicate treponematosis from a herd. All rabbits must be treated even if no lesions are present. Lesions usually heal within 10–14 days, and recovered rabbits can be bred without danger of transmitting the infection. A potential side effect of penicillin treatment is diarrhea and the possibility of an enteritis outbreak due to proliferation of gram-negative bacteria in the gut. Rabbits treated with penicillin should be switched to hay and treated with antidiarrheals immediately if needed (see Rabbits: Enterotoxemia).
With this information, I have decided on a solid course of action.
1. My rabbitry will be temporarily closed during the 3 week treatment period - I will not attend any shows, no rabbits or visitors in or out, for any reason.
2. Infected and exposed rabbits will be treated with Pen G Procaine Benzathine.
3. The primary carrier will be quarantined, treated, and sent to a pet home, and the meat rabbits will be culled.
4. During treatment, there will be a regular schedule of using a bleach solution to sanitize the rabbitry: hutches, feed dishes and J feeders, water bottles, carriers, and all other equipment.
After the 3 week treatment, my rabbitry will be clear of VD, and all of my remaining rabbits will be safe to show and use in breeding programs again.
Ah, the joys of raising rabbits ;)