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The signs may or may not be linked. I am assuming that because you got confirmation of an E. coli infection, that a urine culture was performed. Otherwise it is extremely difficult to put a name on a bacteria. E.Coli is a common rod shaped bacteria found in urine, and is more common in younger pets.
Any drug can cause a reaction in any pet or person. Therefore, yes it is POSSIBLE that the cipro is causing a side effect. A common side effect is nausea, vomiting, and listlessness. These signs often go away when the drug usage is stopped.
This drug belongs to the flouroquinolone family of drugs and this category of drug (but not all types of these drugs) are clinically documented to cause joint cartelage or defects later in life, when given to young growing puppies. This usually occurs in medium to large breed dogs and may not show up until they are older. I agree that your concerns are justified, and you may want to consider switching antibiotics.
The pain in the prepuce may be what is called a balanoposthitis (prepuce infection) and may be due to the bacterial contamination. I would suggest re-evaluating the pet by your regular veterinarian, or another one for a second opinion as he may need further medication or a change in medications.
The swelling, If it is on the penis itself, inside of the prepuce, is likely to be the glans of the penis, and is the canine equivalent of an erection. If it is outside of the penis, then you may have an ascending infection and I suggest seeking further medical care.
Your pet may also need anti-inflammatory/pain medications for the pain and swelling as well.
Please feel free to ask further questions if needed.
Wow, this is a much more complicated issue....It appears that your regular DVM is approaching this through the proper means, and that we do sometimes administer cipro (or other drugs of it's type) when the benefits may outweigh the risks (that i posted earlier). Without seeing the 'fits,' is hard for me to determine the cause, but it definately does not appear the same as an erection, based on what you describe. I am concerned that there may be some congenital defect, such as an ectopic ureter, because incontinence in such a young MALE is highly unusual. Knowing this further information, the cipro is likely not causing all of the signs, but may still be leading to lethargy and depression and possible nausea.
He may need evaluation by an internal medicine specialist. It does not appear to me to be an immediate emergency care situation, and will a day off of cipro cause a significant difference? PROBABLY not. So stopping it likley won't cause a problem.
He may need a contrast radiology series of his bladder performed to help determine the problem.
If he is not on pain medications, you may want to consider some for him. Although I usually discourage OTC medications, you may want to try aspirin based on his body weight. Usually 1 baby asprin for a 30 lb dog is sufficient. HOWEVER, if he is having any bleeding or any surgery is planned, DO NOT GIVE this medication.
Please let me know if I can be of further help.
A further search on VIN (a veterinary only access info network) listed a couple of other possible problems.
1. Fractured OS Penis (bone) - x rays needed for diagnosis
2. Hair wrapped around the penis inside of the prepuce
3. curling of the prepuce that traps the penis during an erection
4. brucella infection (unlikely because it has been cultured)
The specialists suggest videoing the events to be shown at the examination.
NSAIDS (Aspirin, Rimadyl, Deramaxx, Metacam) appear to be advised in all cases.
Message me if you need any further help!