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Thank you, this is the best information I’ve found.Depending on the disease, they are always contagious. They will never not be contagious, no matter what antibiotic you give them.
Chicken respiratory diseases are not like the ones mammals get. With just a couple of exceptions, these diseases never go away. They carry them and spread them for life, and will also have symptom flare-ups whenever they are stressed out and their immune systems are a bit down.
The exception would be infectious bronchitis, which the birds do eventually stop shedding, usually within a year of infection. This one also affects their reproductive tract, so if this were the one they had, you'd probably also be seeing some weird eggs from them. Also, it's a virus, so antibiotics wouldn't do anything for it.
I would recommend getting testing done, to see which disease they have. Zoologix will do a full respiratory panel for $98, and you need only send them three throat swabs from a sick bird.
However, most likely they do have a disease that they will never be rid of. The only way to make them not contagious in that case is to cull them and then immediately burn or bury the bodies.
The other alternative is to completely close your flock - no birds, hatching eggs, or even newly hatched chicks from an incubator out, and no new birds in. You wait for the sick birds to die off, and then start over. You also would have to keep antibiotics on hand to treat the flareups that they are going to have.
Also, if they were already in with your flock before showing symptoms, chances are good your entire flock already has whatever this is. I'd work under that assumption to be safe.