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Morphological characterization and multi-locus DNA sequence analysis of fungal isolates obtained from 32 clinical cases of equine fungal keratitis (FK) was performed to identify species and determine associations with antifungal susceptibility, response to therapy and clinical outcome. Two species of  Aspergillus  ( A .  flavus  and  A .  fumigatus ) and three species of  Fusarium  ( F .  falciforme ,  F .  keratoplasticum , and  F .  proliferatum ) were the most common fungi isolated and identified from FK horses. Most (91%) equine FK  Fusarium  nested within the  Fusarium solani  species complex (FSSC) with nine genetically diverse strains/lineages, while 83% of equine FK  Aspergillus  nested within the  A .  flavus  clade with three genetically diverse lineages. Fungal species and evolutionary lineage were not associated with clinical outcome. However, species of equine FK  Fusarium  were more likely ( p  = 0.045) to be associated with stromal keratitis. Species of  Aspergillus  were more susceptible to voriconazole and terbinafine than species of  Fusarium , while species of  Fusarium  were more susceptible to thiabendazole than species of  Aspergillus . At the species level,  A .  fumigatus  and  A .  flavus  were more susceptible to voriconazole and terbinafine than  F .  falciforme . Natamycin susceptibility was higher for  F .  falciforme  and  A .  fumigatus  compared to  A .  flavus . Furthermore,  F .  falciforme  was more susceptible to thiabendazole than  A .  flavus  and  A .  fumigatus . These observed associations of antifungal sensitivity to natamycin, terbinafine, and thiabendazole demonstrate the importance of fungal identification to the species rather than genus level. The results of this study suggest that treatment of equine FK with antifungal agents requires accurate fungal species identification.

Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States