Diarrhea in 12 week olds

[sktlmt]

I have 16 chicks that are 12 weeks old. A couple of the roos have brown runny poop. When they were 3-4 weeks they had coccidiosis. Much to my dismay I treated them with antibiotics. It improved while they were medicated and came back as soon as the course was done. I did one more round and same thing. At this point they were 6-7 weeks old. I took them outside in a large pen. They seemed to improve and thrive. They sleep in a 4x4 cage at night but are free range during the day.
I am wondering what I should do with them.
I would prefer to not medicate them since they all drink from the same water. Cat Dog Alpaca Chicken and the neighbors goats.
Any natural way to kill off what ever bug they have?

 

[hicksfamily]

medicate all of the, even the ones without it. it could spread.