Bacterial Infections in Koi and Pond Fish

If you can't catch the fish and they have ulcers, consider   serial treatments with potassium permanganate. This is especially good in cooler water, has a spectrum against ciliates like Costia and Chilodonella and may even destroy Fluke infestations. Dosing is better described elsewhere. See notes. 

If you CAN catch the fish, consider injections of antibiotics for the valuable ones, iodine swabs on open wounds, and then water treatments (See remainder of this table) for uncatchable infected swimmers. 
This is the 7% iodine, which debrides and stains durably. It also stains the hands if you're not careful. No harm done, however. Avoid getting this topical under the gill cover. 

Scrubbing / debriding wounds in Koi depends on being able to "get through" slime and removing dead scales and NONWOVEN gauze is too slick. You need "Woven" gauze. Believe it or not, for HUMAN wounds it's undesirable. So it's CHEAPPPPPP.

Treatment with chloramine-T is potentially dangerous in the case of overdose. Dosing is beyond the scope of fish treatments website. If you're not sure about instructions in Dr Jill Spangenberg's notes, this might not be for you. 
At right, Chloramine-T powdered, pure. That's almost a hundred dollars worth of effective uncertainty. 

Antibiotic Baths
At left you see Tetra's new "Lifeguard" product which is essentially a safe, tablet form Chloramine. (It's actually a halamide extremely close-relative) with strong antibacterial properties and I could recommend pulling valuable Koi that you can't inject and putting them in a soft rubber tank and using the Lifeguard as a 6 hour bath. With this, a little is good, a LOT will burn fin tips. 

Soft rubber tanks
Aren't really rubber but they spare the noses of the Koi while they are bathed. They're actually made of UV resistant vinyl, (scrimmed with any luck) and they set up and take down easily. They're resistant to most chemicals used for Koi baths. Including Potassium. 
You should expect to pay about $300 but you HAVE to be able to cover it. 
This one ($100) has a zipper cover. HOWEVER if you fill this one all the way up it's more like a "ball" and can simply roll onto it's side. I'd recommend providing some lateral support so it doesn't just dump. 

Aeration in the holding / bath tank
These kind of air pumps are a little bit noisy but they last a long time, and they output more air than any plastic-bodied air pump can. And the price point is very low. I've used Active-Air, Vivosun and Eco-Plus brands. 

In holding, these sponge filters are soft on the Koi faces, (won't pick up eggs or fry) and they provide filtration AND aeration in one unit. They're cost-effective they BIOSEED very quickly. If you're using Lifeguard as a bath, forget bioseeding ha ha ha ha ain't no germ gonna live in the filter. Still, a soft, smushy 'airstone' is necessary. 

Medicated Food 
Well, there's no medicated food out there. The FDA put their foot down on that so you can't get fish food with antibiotics milled in, but the food at right from Blue Ridge is rich in ingredients that help fish fight infections. I would put some Oxolinic Acid or Naladixic Acid in a little oil and mix it into this food and then feed. 
There are like, ten different sizes of this food but the big bucket is surprisingly cheap. 

Oxolinic acid and Naladixic acid are antimicrobials related to the quinolone antibiotics. They're 'forgiving' on dosage when mixed with oil, or other binder to put on food. 

Confectioner's Glaze
Can be used to bind antimicrobials to food. It's pretty durable and you would simply mix a dose of Oxolinic acid in it, and then mix with the food. Spread the food out in a thin layer after mixing to allow the glaze to dry or you will end up with a big bucket full of a useless food block. 
Yes, this contains real shellac. Shellac itself, is not toxic to fish. What IS toxic in 'regular' furniture shellac is the toluene and other solvents. For confectioner's shellac they use safe solvents that evaporate, leaving an edible, durable safe cloating. 

There is no contest between all of the above and injections of antibiotics. If the fish are valuable and you want top-notch results, you need to be injecting the fish with legitimate antibiotics from a prescribing veterinarian.