I just would not use an aminoglycoside if Baytril or Azactam or Chloramphenicol were available.

Amikacin / Aminoglycosides Dosing
Aminoglycosides - by Doc Johnson
Amikacin/Amiglyde
Gentamicin/Garamycin - NOT recommended due to toxicity
Hardly new to fish medicine, the injectable drugs Gentamycin and Amikacin are used worldwide in the treatment of fish diseases. It is generally agreed by folks who do, or have injected alot of these particular drugs that after the third or fourth injection, a significant percentage of the treated fish will die; exhibiting severe neurological signs that include tetanic spasms, inversion, curling of the body, and extremely sudden death, usually associated with handling or any stress. [Lembke/Mixon personal communication 1997] In 1991 I killed a significant number of fish with Gentamicin before expanding into safer drugs like Chloramphenicol and Baytril.

The Aminoglycosides show a ferocious ability to kill the newer Japanese Aeromonas strains, however, and in the instance of several of my patients where I was unable to effect a cure any other way, two injections well spaced of Amikacin resolved them completely. It is speculated that Amikacin is less toxic than Gentamicin and I believe it. Amikacin is also ten times more expensive!
The route for injection of these drugs is Intra-Peritoneal although I am sure the IM route is also acceptable. When I injected these, I mixed the drugs with another small volume of sterile saline to aid the dispersion of the drug through the peritoneal space.
I recommend injection of the Aminoglycosides, particularly avoiding the use of Gentamicin, EVERY OTHER DAY - and for no more than THREE injections. Please understand you use these drugs at your own risk and at the first symptom of spasticity, you are warned to abort injections and avoid stressing the fish as much as possible!!!
Fish length in inches Volume of Amikacin
40-50 mg/ml Volume of Sterile saline (optional) Total volume of injection, IP

Try not to over-use the Amikacin. It should be used twice to three times for best results, and stopped as soon as the fish return to the school or resume eating. Never use Gentamicin. It's toxic in a dose or two. Fish can die or be destroyed by Gentamicin up to three weeks after dosing.
~ Doc Johnson

Amikacin Dosing - Injectable
Amikacin Dosing - Revisited - by Dr. Erik Johnson
Question: Amikacin Dosing
Hi Doc,
I am injecting some sick koi, supported by my vet who is new to koi. I've had mixed results with Baytril so I'd like to try Amikacin. The basic dosage in your book is given at 5 mg/kg, but the dosage by length in your chart appears to give 20 - 25 mg/kg. Isn't this a major difference? What is your reference for the dosage by weight. please?
Answer:
Major difference - sort of. (Maybe this is why Gentamycin was so poor in my hands)
First, the 5mg/kg dose is from mammallian work. There was no fish dose when I started. The dosing chart is from what I was actually doing with fish at the time.
Because there were unproven mammallian doses, juxtaposed with "what I was getting away with" at the time, I presented both in the book, so if a person thought better of dosing using cat and dog dosing, they could do that on a "weigh the fish" basis, which is fine, but no one had actually proven that fish could get by on 5mg/kg
Or, they could use the dosing chart which I used successfully for a couple years before publishing that chart. I had very few problems.
Still, I *would* add that if you dose Amikacin (any Aminoglycoside) more than three times, you could kill or cripple the fish. I really, really dislike Amikacin compared to Azactam and the rest.
I think I am going to re-do the Amikacin dosing chart, using ACTUAL weights (what a pain), and basing it on 10mg/kg - for what it's worth.