Cough?

How to treat really depends on what exactly is going on. Are there any other symptoms at all? Any runny noses or eyes? With respiratory diseases those things often go hand in hand. As far as what they have? No way to tell usually unless you have some tests done. There are blood tests and other tests an avian vet can do to try to get a diagnosis. Or have a necropsy done on a dead bird by a state poultry pathology lab. This is very, very helpful so that you know how to treat/manage it as well as what to expect in the future. Some of these things are very chronic, reappearing frequently so management and treatment become an ongoing problem. Others are not as severe. You can treat with antibiotic's and it's a good idea no matter what they have because, whether it's viral or bacterial, it easily and often morphs right into pneumonia and secondary bacterial infections. Those complications probably kill birds more often then the diseases themselves.

A fungal infection called aspergillosis is another possibility.

 

As Cafarmgirl said it could be a management problem. Dust, wet conditions, mold high ammonia levels from droppings, bad ventilation, and keeping the coop too warm to produce panting and open-mouth breathing can all lead to respiratory symptoms. Infectious bronchitis, mycoplasma gallisepticum (MG,) coryza, ILT, and aspergillosis are the most common respiratory diseases that can be viral, bacterial, or fungal in nature. Here is a good link to read and compare the symptoms you are seeing: http://edis.ifas.ufl.edu/ps044