Primarily, the antimycotic amphotericin B (a polyene) is used for treating protothecosis caused by P. wickerhamii.
Interestingly and worryingly, there are very few antimycotics and there aren't enough new ones in the pharma pipeline. C. auris is on the verge of being untreatable because of resistances to all 3 classes: triazoles, polyenes, and echinocandins.
Something I wonder about is whether anti-malarials would work against Prototheca as well, given that some have herbicidal properties. My cursory search for whether they've been tried turns up nothing, which is unsurprising given the rarity of the disease.
Interestingly and worryingly, there are very few antimycotics and there aren't enough new ones in the pharma pipeline. C. auris is on the verge of being untreatable because of resistances to all 3 classes: triazoles, polyenes, and echinocandins.
PS: IANA[LD]