The CDC has a page explaining how to manage bird poop in a pool and what the particular organisms are of concern. Interestingly none are organisms that would seem likely to cause skin infections rather they are diarrhea inducing agents. So while OP's spouse had a "cut on his foot" and after being in a pool an infection was diagnosed, without specific bacteriologic identification it would not be correct to blame the pool water. It is also possible it became infected from the original injury, his own shoes, the flooring or any other exposure the foot may have had. (Not to suggest it could not have been duck related. It is just that too often I know that doctors make guesses to satisfy patients' need to know "why".)
CDC - Birds & Pools - Animals and Pools - Pools & Hot Tubs - Healthy Swimming & Recreational Water - Healthy Water
and
http://www.cdc.gov/healthywater/pdf/...mendations.pdf