Introduction: Drug resistance to echinocandins, first-line drugs used to treat
Candida auris
infection, is rapidly emerging. However, the accumulation of mutations in genes other than
FKS
1 (before an isolate develops to resistance via
FKS
1 mutations), remains poorly understood.
Methods:
Four clinical cases and 29 isolates associated with the incremental process of echinocandin resistance were collected and analyzed using antifungal drug susceptibility testing and genome sequencing to assess the evolution of echinocandin resistance. Findings: Six echinocandin minimum inhibitory concentration (MIC)-elevated
C. auris
strains and seven resistant strains were isolated from the urinary system of patients receiving echinocandin treatment. Meanwhile, phylogenetic analyses illustrated that the echinocandin-resistant strains were closely related to other strains in the same patient. Genomic data revealed that the echinocandin-resistant strains had
FKS
1 mutations. Furthermore, three categories (ECN-S/E/R) of non-synonymous mutant SNP genes (such as
RBR
3,
IFF
6,
MKC
1,
MPH
1,
RAD
2, and
MYO
1) in
C. auris
appeared to be associated with the three-stage-evolutionary model of echinocandin resistance in
C. glabrata
: cell wall stress, drug adaptation, and genetic escape (
FKS
mutation). Interpretation: Echinocandin-resistant
C. auris
undergoes spatial and temporal phase changes closely related to echinocandin exposure, particularly in the urinary system. These findings suggest that
FKS1
mutations mediate an evolutionary accumulation of echinocandin resistance followed by modulation of chromosome remodelling and DNA repair processes that ultimately lead to
FKS
1 hot spot mutations and the development of drug resistance. This study provides an in-depth exploration of the molecular pathways involved in the evolution of
Candida auris
echinocandin resistance.