Step one:
Relax. Panic won't do you any good and you risk doing more than you need and doing more harm than good.
This is what I would do if I had a mixed batch of chicks with and without vaccination for cocci all put together.
1
) Confirm cocci. If one is confirmed to have cocci though bloody poo and lethargic nature, or ideally a fecal float test from the vet, assume they all have some cocci and are at risk, regardless if they have enough to make them sick. They will always have some in their bodies if exposed, but it is only a problem IF numbers become higher than they can stand.
2) Assuming all have it and need to be treated, go ahead and give the sulmet as directed on the bottle. No more, no less. More will damage their internals as cocci is a protozoa, not a bacteria, and the general mode of action of these drugs is to inhibit the uptake of a particular nutrient essential for growth of the organism, or in this case, the oocysts of the cocci in the gut of the bird. Amprolium/corrid works as a thaimine blocker. Basically, too much of the drug will not only kill the target, but also affect the host. If you don't dose enough, or dose indiscriminately, you do have a chance of increasing the probability of resistant cocci strains that cannot be fought with the drugs. So Basically, follow bottle directions of the formulation you bought and are holding in your hand, as not all formulations are the same in dosage or concentration.
Treat fully and completely what is reccomended on the bottle YOU have.
3) Scrape out all the bedding in the coop and replace it with fresh stuff for them to play in. And just finish treatment of the drug. Extra vitamins in the water AFTER treatment is complete would be good, along with yoghurt and possibly smashed up egg yolk.
Clean brooder and give nutritious food AFTER treatment.
4) Done. If you do lose some it does happen. Don't sweat it. Often cocci will affect and kill individuals who have other problems going on which makes them more easily succumb to the parasite. Kind of like how a frost bit finger more easily get's frost bit again in the future.
Now... Take a DEEP breath.
On immunity.
You say they have no contact to the soil... well, somewhere they got contact to cocci so don't worry about the soil thing right now. They'll get it at some point in time. Don't worry about that...
So, if presented with a pathogen, they contain things called antigens which your body reacts to. Regardless if the pathogen is dead or alive, they still have these antigens that the body can recognize. Since this is the case, even if you are trying to kill the pathogen, you will still build an immunity since it is present. If I remember right, the cocci "vaccine" is in simple terms, a dead version of the most common form of cocci. Some say that the vaccine doesn't really work that well so it's not worth stressing the chicks over as it was developed for the "organic" market which doesn't allow medication in feed.
Meds for cocci often work by inhibiting the replication of the protozoa. In other words, it just keeps the cocci consumed by the bird from reproducing in the gut. If you stop the protoza (cocci) from reproducing, they can no longer do harm to the bird because of their small numbers. In this process, the birds themselves are still gaining an immunity.
In short, immunized, med feed, treatments and so on, they are always building an immunity.
I am now totally confused and concerned that I may not be doing the right thing for my new babies. I won't bore everyone with details, I have tried and gotten nowhere.
You start somewhere. Don't worry.
Essentially my problem is with the fact that baby chicks need to build an immunity to coccidiosis.
They will do that regardless of what you do unless you grow them in a sterile room.
Some of my chicks have it. One was vaccinated against it, so she has it too (right?).
All your chicks have it if they live together, it is the concentration of paracite that determines if there are any symptoms. If they have an immunity, load A won't affect them as badily as load A would affect a chick without immunity. If load A is small, no bird will be sick, if it is large, all birds will have it. It's like a sliding scale.
I am giving Sulmet because I can't stand for them to suffer, or to lose any, so the vaccinated one now presumably has no immunity (right?). I am treating them all so, presumably, none of them are building immunity....
Nope, they are building immunity regardless, just not as fast if there is not as much or as large of a variation of parasite present. Immunity relies on presented antigens, not what else is being pumped into the system.
At what stage do you decide to let them go through it on their own? I don't understand. The information is so conflicting.
Can anyone help and tell me what to do? One looks very sick, the others look fine. But what am I doing to the natural cycle here? Can they build an immunity to cocci if we treat the disease at the first signs? Why bother to vaccinate against it when it seems that most chicks are at risk of getting it, even when they have had no contact with the soil, as is the case with mine, and they need to get it in order to build immunity?
This no longer makes any sense to me.
Can anyone help? I am really having a hard time here.
I personally just don't worry that much. I don't get vaccines for the birds, and just feed them medicated feed from the get go. Medicated feed is not a vaccine and only inhibits the growth of the cocci so it doesn't overwhelm the system.
Buy chicks, feed them , give them a pan of clean dry dirt to play in, and don't worry so much. I have only treated chicks for cocci once in 10+ years. And I only treated after I saw the blood and the birds losing weight. If the chicks are under a week old, the "sick" chick might just have failure to thrive if you didn't see consistent bloody poo's or have a fecal float test done.
Good luck.