The two most common bacteria that cause problems on koi fish are Aeromonas and Pseudomonas. Both of these bacteria are naturally occurring and are found in all pond and lake water.
These bacteria are non existent in tap water because chlorine is added to kill any bacteria. Never the less, you can start up a brand new pond with tap water and within 3 weeks after the chlorine has evaporated, you will find at least a low level of these bacteria in your water.
Normally, in a clean healthy pond, the levels of bacteria are so low that they will not cause a problem on their own. The outer slime coat or epidermis normally protects the fish from these harmful bacteria. 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.