There are several different strains of MG affecting poultry (you can see some here:
http://www.nwhc.usgs.gov/publications/field_manual/chapter_11.pdf
(table 11.2)
which causes conjunctivitis in poultry...
...I am wondering if if an MG is involved?
From the article EYE DISORDERS OF POULTRY:
"...Bacterial Infections
A number of bacterial infections can lead to damage of the eye. Salmonella bacteria, particularly Salmonella typhimurium and Salmonella arizona , are known to cause severe purulent conjunctivitis and ophthalmitis (inflammation of the eyeball and conjunctiva with pus) and blindness. Often young birds acquire the infections from the hen or through navel or yolk sac infections.
Fungal Infections
Molds readily grow on a number of different materials, including poultry feed and litter. A common mold is Aspergillus . Birds can be exposed to Aspergillus or other fungi in the hatchery, or more commonly in poorly dried litter. While Aspergillus is usually considered a respiratory tract pathogen, it can also invade the brain and eye. Yellow plaques develop and can be found under the eyelid. The eye becomes inflamed and severe damage can occur.
Nutrional Deficiencies
Certain vitamin deficiencies, such as vitamin A and vitamin E, can result in damage to the eye. Vitamin A is necessary for the production of visual pigment of the retina and for maintenance of the lining of the tear ducts. Vitamin E is necessary for maintenance of the lens protein in the developing embryo. Vitamin E is passed from the breeder hen to the egg. If the breeder is receiving inadequate vitamin E in the diet, the embryo will suffer from a vitamin E deficiency and possible blindness. Vitamin deficiencies are rare when commercial poultry feeds are used. ..."