Evolutionary accumulation of <i>FKS</i>1 mutations from clinical echinocandin-resistant <i>Candida auris</i>

Introduction: Drug resistance to echinocandins, first-line drugs used to treat <i>Candida auris</i> infection, is rapidly emerging. However, the accumulation of mutations in genes other than <i>FKS</i>1 (before an isolate develops to resistance via <i>FKS</i>1 mutations), remains poorly understood. <i>Methods:</i> 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 <i>C. auris</i> 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 <i>FKS</i>1 mutations. Furthermore, three categories (ECN-S/E/R) of non-synonymous mutant SNP genes (such as <i>RBR</i>3, <i>IFF</i>6, <i>MKC</i>1, <i>MPH</i>1, <i>RAD</i>2, and <i>MYO</i>1) in <i>C. auris</i> appeared to be associated with the three-stage-evolutionary model of echinocandin resistance in <i>C. glabrata</i>: cell wall stress, drug adaptation, and genetic escape (<i>FKS</i> mutation). Interpretation: Echinocandin-resistant <i>C. auris</i> undergoes spatial and temporal phase changes closely related to echinocandin exposure, particularly in the urinary system. These findings suggest that <i>FKS1</i> mutations mediate an evolutionary accumulation of echinocandin resistance followed by modulation of chromosome remodelling and DNA repair processes that ultimately lead to <i>FKS</i>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 <i>Candida auris</i> echinocandin resistance.

引言：作为治疗耳念珠菌（Candida auris）感染的一线用药，棘白菌素类药物（echinocandins）的耐药性正快速出现。然而，在分离株通过FKS1基因（FKS1）突变产生耐药性之前，FKS1以外基因的突变积累机制仍有待阐明。
方法：本研究收集了4例与棘白菌素类药物耐药性逐步演化过程相关的临床病例及29株分离株，通过抗真菌药物敏感性试验与基因组测序，分析棘白菌素类药物耐药性的演化历程。
结果：从接受棘白菌素类药物治疗的患者泌尿系统中，分离得到6株最低抑菌浓度（Minimum Inhibitory Concentration，MIC）升高的耳念珠菌（Candida auris）菌株与7株耐药菌株。系统发育分析显示，耐药菌株与同患者体内的其他菌株亲缘关系紧密。基因组数据表明，耐药菌株携带FKS1基因（FKS1）突变。此外，耳念珠菌（Candida auris）中三类（ECN-S/E/R）非同义突变单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因（如RBR3、IFF6、MKC1、MPH1、RAD2及MYO1），似乎与光滑念珠菌（Candida glabrata）中棘白菌素类药物耐药性的三阶段演化模型相关：细胞壁应激、药物适应与遗传逃逸（FKS突变）。
讨论：耐药性耳念珠菌（Candida auris）会发生时空相位变化，且与棘白菌素类药物暴露密切相关，这一现象在泌尿系统中尤为显著。本研究结果提示，FKS1基因（FKS1）突变介导了棘白菌素类药物耐药性的演化积累，随后伴随染色体重塑与DNA修复过程的调控，最终导致FKS1基因热点突变与耐药性产生。本研究深入解析了耳念珠菌（Candida auris）棘白菌素类药物耐药性演化所涉及的分子通路。