The entire <i>CYP51B</i> locus in azole-resistant isolates of the dermatophyte <i>Trichophyton indotineae</i> revealed by optical genome mapping

The resistance of <i>Trichophyton indotineae</i> to azoles is mainly due to the overexpression of <i>TinCYP51B,</i> 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 <i>TinCYP51B</i> locus. Through optical genome mapping (OGM), we have successfully determined the copy number of the <i>TinCYP51B</i> gene in the genomes of resistant strains. The <i>TinCYP51B</i> copy number was lower in the type I strains than in the type II strains, while the <i>TinCYP51B</i> expression level was higher in the type I strains. To explain this paradox, we have revealed that polycistronic transcription of multiple <i>TinCYP51B</i> 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 <i>TinCYP51B</i> gene. Conversely, it is believed that type II azole-resistant strains evolve from susceptible strains such as TIMM20114, which also has only one <i>TinCYP51B</i> gene. In conclusion, strains of <i>Trichophyton indotineae</i> can be divided into two groups in which a distinct type of resistance has developed.