If a disease gets past your biosecurity program it may be necessary to treat them with medications. There are a variety of medications available that are labeled for use with poultry. It is very important to read the label - medications can only be used as indicated on the label. If your species of poultry is not listed it is not cleared for use with those birds. Off-label use is only allowed under a veterinarian's supervision.
Compendium of poultry products (Fort Dodge)
Poultry diseases and medications for small flocks (University of Connecticut)
Preventive medicine for backyard poultry flocks (University of Nebraska)