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Remove dirty litter an manures. Provide proper ventilation and make sure all bedding materials are kept dry.
As to the OP. I mention fungus as a possiblity because of symptoms. Read this,
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.
Ammonia Toxicity
The most common eye irritant in intensive animal production systems is ammonia gas (NH 3 ). Ammonia gas is extremely irritating to the membranes that line the eyelids, eyes, sinuses and trachea. Conjunctivitis is inflammation of the conjunctiva (membranes that line the eyelids) and the exposed sclera (white part of the eye). Affected birds have reddened, swollen eyelids, and are sensitive to and avoid light. If high ammonia levels persist, the cornea, the outermost part of the front of the eyeball, becomes ulcerated and blindness may occur.
Ammonia gas is a bacterial breakdown product produced when uric acid from poultry manure combines with water forming a suitable environment for bacterial growth. Bacterial growth, and the resulting NH 3 production, is also dependent upon litter or manure pH and temperature.
In intensive production systems, high levels of ammonia gas buildup are associated with inadequate ventilation. Ammonia is not typically a problem for birds raised in extensive or semi-extensive systems
The OP mentioned that they had not removed or replaced all the bedding materials and that the birds where in a small cage. They also mentioned the yellow plaques under the eyelids, they having to remove a large chunk from the eye before treating with neosporin. Added the fact that Aspergillus is also a respiratory pathogen which could account for the breathing problems the birds exhibited.
Notice with Ammonia toxity, the eyes will become swollen and sensitive to light, there is no mention of the yellowish plaque buildup under the eyelid. Causes and treatments for the fungal as well as amonia toxicity are very similar. While one is fungal and the other bacterial, both can be caused by dirty and damp litter, manure buildup and improper ventilation. A cleaning and disinfecting of the cages will help prevent either problems from reoccuring and spreading.
Disclaimer, I am not an expert in diagnoseing or treating any diseases and all postings are just my opinions and should not be construded to be accurate as they pertain to this thread. My posting this does not mean I am right or someone else is wrong. If in doubt, always seek the advice of a professional.
