From my understanding, Cocci is a parasite that is very commonly found nearly everywhere. Virtually every chicken is exposed to it to some extent or another. Think of it as being similar to Staphylococcus (Staph Infections). It is a bacteria that is found on virtually everyone's skin and never poses a problem. Occasionally, it will get out of hand and become an "infection." Cocci appears to be the same way. It is transmitted by wild birds, other flocks, clothing, shoes, equipment and contaminated food or water. There are nine known forms of the cocci bacteria. Obviously, with the wild birds being involved in the spread of this disease, there is no perfect method of preventing it. Likewise, there is no reason to destroy the flock, start over or even prevent ever introducing knew birds at that location.
There are several things that can be done to prevent this. First, you can either vaccinate day-old chicks or provide medicated chick starter. Allegedly, providing both the vaccination and the medicated feed negate each other, rendering the chicks susceptible to the disease, but that just doesn't seem logically possible. Of course, as with any disease or parasite, providing clean and dry living areas is vital. Moist and warm conditions are breeding grounds for bad bacteria. Always ensure adequate ventilation to ensure these clean, dry conditions exist.
That being said, the single best method for controlling cocci is by prevention. Maintain an extremely healthy flock, give a properly nutritious diet and clean coops or runs. Ironically, the deep litter method appears to attract large amounts of beneficial bacteria that force out the bad bacteria like cocci. It maintaining the deep litter method, however, you must ensure adequate dry compost material (leaves, grass, pine shavings, etc.) that will properly complement the fecal matter from your chickens. It is not simply a huge pile of poop.
As Bee mentioned, the higher acidity of the fermented feed should aid in the prevention of cocci. If you have exposed your flock to fermented feed and they have the appropriate levels of gastrointestinal flora, this particular disease should not pose a problem. Fermented feed has a pH of approximately 4.5, which is considered "extremely acidic" by most standards. Distilled white vinegar has an average pH of 3.0 and it's considered a common disinfectant. It's even been scientifically proven to kill the flu virus. Common sense leads us to the conclusion that fermented feed would prevent a host of numerous bacteria as well, although not quite as well as vinegar. Personally, I get a bit of a burning sensation on my skin when I splash some on my hands. I may be a bit more sensitive to this than others, so your results may vary. But it's a dietary philosophy that dates back countless years in human culture, most notably in the Chinese and German cultures. Think sauerkraut and soy sauce.
Personally, I think cocci is overblown from a commercial standpoint. I think that a combination of poor flock husbandry and commercialism have led to this overly common concern where every death (or a high percentage) is attributed to cocci, regardless of the actual cause of death. But that's a discussion for another time.
