The Colony collapse disorder has many theories and mysteries yet to be solved. One such theory as to why the honey bees are disappearing is Nosema apis, a microsporidian unicellular parasite. This protozoan pathogen is pretty resilient, and it the most common bee disease, for both west and eastern honey bees.
"The dormant stage of nosema is a long lived spore which is resistant to temperature extremes and dehydration. Nosema apis spores cannot be killed by freezing contaminated comb. Nosemosis is a listed disease with the Office International des Epizooties (OIE)." (Wikipedia)
The disease has nonspecific symptoms. However, dysentery is common, as well as crawler conditions (Inability to fly). It's hard to identity, but typically shows up in Spring after bad weather conditions.
The spread of the disease occurs through fecal matter. It then impairs the digestion of pollen and the honey bee has a shorter life span as a result. If the queen gets infected her ovaries stop functioning to full capacity and her eggs die off.
"Treatment with the antibiotic Fumidil B (prepared from Aspergillus fumigatus, the causative agent of Stone Brood) inhibits the spores reproducing in the ventriculus, but does not kill the spores... The spores are sensitive to chemicals: acetic acid, Formalin and physical radiation: ultrasonic and gamma radiation." (Wikipedia)
Florida in the United States has been hit pretty hard where 80-90% of the bee colonies has been disappearing. Although Nosema apis is just one contributing factor.