So the troubling brown stains on Hive B are confirmed to be a result of dysentry (the runs). But apparently dysentry does not always indicate the presence of nosema. While that still seems the most likely diagnosis, I can't be sure until I perform a nosema field test, which involves a rather crude disection to remove the digestive tract.
This weekend I will dose with the antibiotic Fumagilin again, and try to perform some field tests to confirm the diagnosis.
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