Advice on one rule-out: lung parasites.
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“Even when using the most sensitive, most appropriate fecal examination techniques, intermittent shedding means that infections may be missed from a single sample. Therefore, it is recommended that fresh feces be examined on at least three different occasions before ruling out lung parasites as a cause of respiratory disease.”
-Johnny D. Hoskins, DVM, PhD, DACVIM
From Understanding a cat's cough