Might your pathologist be speaking of cautery artefact? We get specimens 
every once in a while which have a cauterized margin- the tissue is literally 
burned- and there is nothing I know to do to reclaim this tissue.

We use the pneumocystis immuno in our lab but mostly as a confirmation (our 
GMS is reliable since it's been tweaked to death) and also if there are 
trophozoite forms of the organism suspected. It seems pretty reliable but does not 
highlight the capsule of the bug as well as the GMS does, so the pathologists 
need to realise the traditional look of the organisms will not be as obvious.

Questions? e-me JC (QIHC)
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