Probably chalkbrood is caused by a combination of several traits and bad luck. A colony that tries to raise too much brood too early and gets caught in a cold snap and is short on hygienic behavior (the instinct to remove the brood before it reaches the reproductive state of the fungus). If you use a queen from a colony without chalkbrood they were in the same environment so they must have the genetic traits to avoid chalkbrood and when they raise a new queen she is likely to have those same traits.
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