I hate to disagree with my respected BEE-L expert, Joel Govostes, but to
my way of thinking, the first thing you suspect when the brown dead pupa
pulls out to 1/2 inch is AFB, smell or no smell.  The other confirming
signs are 1) isolated small patches of dead brood rather than large
unified areas; 2) sunken cappings, often punctured; 3) dark scales on
the lower surface of the cells.
 
Ted Fischer
Dexter, Michigan USA