The most common reason koi experience a bacterial infection is when their slime coat or epidermal layer is broken and the bacteria is allowed to infect the Koi. These sores can grow very quickly if they are not treated.
 

Injecting A Fish
By far the most effective way to treat a bacterial infection is to inject the Koi with antibiotics. This gets the proper amount of medication directly into the Koi. The easiest way to inject a Koi is to guide it into a clear plastic bread bag, drain out the excess water, roll the Koi over on its back, pull the excess bag back until the bag is tight around the it and then inject through the bag in the area between the anus and the ventral fins at a slight angle toward the head. The Koi should be given an injection once a day for three days in a row and then every other day for two more injections. If the water is below 55 degrees spread out the injections to one every other day for a total of 5 injections. This is necessary because the Koi’s metabolism is very slow below 55 degrees. To inject, use a 1cc diabetic syringe with a 25 gauge, ¾ inch needle. You will need to get the antibiotics through your local veterinarian.