The entire CYP51B locus in azole-resistant isolates of the dermatophyte Trichophyton indotineae revealed by optical genome mapping.

The resistance of Trichophyton indotineae to azoles is mainly due to the overexpression of TinCYP51B, resulting from additional copies of this gene in two types of strains (type I and type II). Due to its large size and the significant number of duplicated blocks, whole-genome sequencing has been unable to cover the entire TinCYP51B locus. Through optical genome mapping (OGM), we have successfully determined the copy number of the TinCYP51B gene in the genomes of resistant strains. The TinCYP51B copy number was lower in the type I strains than in the type II strains, while the TinCYP51B expression level was higher in the type I strains. To explain this paradox, we have revealed that polycistronic transcription of multiple TinCYP51B open reading frames (ORFs) alongside monocistronic transcription occurs in type I azole-resistant strains. In contrast, type II strains generated only the transcripts encoding one CYP51B polypeptide. OGM has also revealed that a 970 kb region on chromosome 3 is inverted in type I strains and the azole-susceptible strain TIMM20115, as compared to type II strains and the azole-susceptible strain TIMM20114. This has led to the hypothesis that under azole stress, type I resistant strains originate from susceptible strains such as TIMM20115, which possesses a single TinCYP51B gene. Conversely, it is believed that type II azole-resistant strains evolve from susceptible strains such as TIMM20114, which also has only one TinCYP51B gene. In conclusion, strains of Trichophyton indotineae can be divided into two groups in which a distinct type of resistance has developed.