Are you sure it is pythium rot? Is the base of the stem turning yellow? The reason i ask is that pythium rot is usually in soil. lIf it is just your roots turning brown it is likely it could be plain old root rot. The usual cause of general root rot is a lack of oxygen to the roots. Either way you would need to make sure your grow stays clean, make sure your nitrogen isnt too high, make sure you have enough calcium, and if its hydro the ph should stay below 6.