IntroductionCandida aurisis a newly emerging pathogenic fungus of global concern and has been defined by the World Health Organization (WHO) as a member of the critical group of the most health-threatening fungi.MethodsThis study reveals and reports for the first time that a rough morphotypeC. aurisstrain causes urinary tract infections in non-intensive care unit (ICU) inpatients. Furthermore, the morphology, the scanning electronmicroscopy (SEM), Whole-genome resequencing and RNA sequencing ofC. aurispossessing rough morphotype colonies compared to their smooth morphotype counterparts.ResultsThe newly identified phenotypic variation ofC. aurisappears round, convex, dry, and burr-like with a rough texture. SEM shows that rough typeC. aurishas a rough and uneven colony surface with radial wrinkles and irregular spore arrangement. Cells of the rough morphotypeC. aurisnaturally aggregate into clusters with tight connections in the liquid, and it seems that the cell division is incomplete. A genome-wide analysis of the rough typeC. aurisconfirmed its genetic association with the smooth type ofC. aurisprevalent in China (Shenyang) two years ago; however, single nucleotide polymorphism (SNP) mutations of five genes (ACE2,IFF6,RER2,UTP20, andCaO19.5847) were identified more recently. RNA-seq revealedIFF2/HYR3,DAL5,PSA31, andSIT1were notably up-regulated, while multiple cell wall-associated genes (ALS1,MNN1,PUL1,DSE1,SCW11,PGA38,RBE1,FGR41,BGLI,GIT3,CEP3, andSAP2) were consistently down-regulated in rough morphotypeC. auris.DiscussionThe rough phenotypic variation ofC. aurisis likely to be related to the structural and functional changes in cell wall proteins. This novel rough morphotypeC. auriswill provide a basis for further studies concerning the evolutionary characteristics ofC. auris.