In addition to what Dr. Upton suggested, consider the possibility of
intestinal reflux. Does the patient have a nasogastric tube in place?
Ruminant animals occasionally have gastric reflux and aspiration during
agonal respiration, which results in rumen protozoa showing up in the
lungs at necropsy (usually found on histopath sections). The gastric
environment of monogastric species, including people, does not harbor
protozoans, but if it's possible that upper/mid small intestinal
secretions could have been aspirated, this could explain your findings.
Bob Garrison, DVM, MS