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We don't have any problems. We use high production breeds (commercial red sex-links). I buy them as ready-to-lay pullets at 18 weeks old. They are fully vaccinated against the common avian diseases and have titer tests done to ensure the integrity of the vaccines. They are fed a layer ration from the organic mill. We do not raise any of our own feed. I buy a ration from the mill or have bought organic grains from the neighbors to be banked at the mill for use in our rations. I have a couple acres in grass/alfalfa and have the neighbors make me about 100 small bales once a year for bedding/forage in the hen house. They have full access to pasture when there isn't snow on the ground and are kept inside when there is. The hen house is environmentally controlled and I keep them fairly warm in the winter, not necessarily because they aren't cold hardy, but because they would eat me out of house and home in cold weather. Providing supplemental heat by burning a little propane is cheaper than bird heat from expensive organic feed. They are kept in production for about 50 weeks. They are then sold to live markets where they become somebody's dinner. We could molt them to keep them in production longer, but molting has its own problems. There are questions about which methods are the most humane, and when they come back from molt the eggs are typically X-Large or Jumbo sized which our cooperative doesn't necessarily have a good market for. We avoid these issues by replacing the flock once a year. After the flock is gone, the hen house is cleaned of all manure, is sanitized, any repairs are done and all is made ready for a new flock about two weeks later. The two weeks down time helps to break any parasite or disease cycles. Manure is stacked and is spread on our hay fields, sold to gardeners, or sold to the neighbors for their organic crops.
Our mortality runs about 3%- 4% a year (75-100 hens out of 2500). Perhaps half of that is due to aggression in the flock and a small amount of predator losses. There generally isn't any treatment of ill birds. Either they are alive or dead. Once in a great while I find one that is down due to illness, but not dead, and I cull it, but that's fairly rare. It's more common to just find one dead in a nest box or laying there at first light in the morning.
Certification is not the big headache people make it out to be. Our agency provided questionnaire style forms to help us detail our organic plan. We filled out the forms and wrote in some notes to detail our plan. The inspector shows up, looks over the operation, asks a few questions, and the plan and inspector notes are then reviewed by committee at the certification agency. If all is well, a certificate is issued. Renewal is even easier. Annually, they just send forms for us to detail any changes/additions to our original plan. The inspector does a surprise inspection, asks a few questions, may audit some of the records and reports the results back to the agency. It is reviewed again, and if everything is good the certificate is renewed.
Our record keeping doesn't add up to much. I save all receipts for feed and any other inputs. Everything else is marked on a calendar in the hen house; daily mortalities, feed deliveries, when the hay is cut, when I've sold hay, etc.
It's not that big of a deal... Aside from a quality vaccination program and our "all in, all out" management of replacing our flock once a year, our operation isn't much different from the average backyard flock, just on a larger scale.