Abstract：
Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.
摘要：
念珠菌是一种紧迫的公共卫生威胁，其特点是高耐药率和在全球医疗机构中迅速传播。作为C.auris反应的一部分，分子监测帮助公共卫生官员追踪全球传播并调查当地疫情。这里,我们描述了在美国用于常规C.auris分子监测的全基因组测序分析方法；方法包括参考选择，参考准备，测序读数的质量评估和控制，读取对齐,以及单核苷酸多态性调用和过滤。我们还描述了新开发的管道MycoSNP，一种便携式工作流程，用于对真菌生物（包括C.auris）进行全基因组测序分析。
