Whole Genome Sequencing - FungiNet Training Toolkit


Candida auris is a pathogenic, drug-resistant fungus that has emerged in healthcare facilities across the world in the span of a decade. In the United States, C. auris typically affects individuals in healthcare settings. Patients who have been in a healthcare facility a long time, have a central venous catheter, or other lines or tubes entering their body, or have previously received antibiotics or antifungal medications, appear to be at highest risk of infection.

Since C. auris was first identified as a public health threat, whole genome sequencing (WGS) has helped guide public health response to control its spread. FungiNet, a network for molecular surveillance and genomic epidemiology of fungal disease, supports the generation and analysis of C. auris WGS data to support public health investigations.


This goal of this course is to describe the basic epidemiology of C. auris and how WGS has helped public health officials learn more about its molecular epidemiology. Additionally, it provides an overview of the laboratory and analytic methods for C. auris WGS when using the data for epidemiologic purposes.


This self-guided e-learning course consists of two interactive modules designed for learners to complete at their own pace. Each module consists of sub-modules, which include guides, videos, and/or knowledge checks to support learning. Each module concludes with a quiz. Results from knowledge-checks and quizzes are not recorded. The modules do not need to be completed sequentially. Additionally, there is no registration or certification for this course.


This virtual training is intended to be a primer for laboratorians, bioinformaticians, and epidemiologists interested in learning how to generate, analyze, and interpret C. auris WGS for epidemiologic purposes.

Time required

Approximately 2 hours to complete both modules. Modules do not have to be completed in one sitting. Learners can start and stop as needed but must note where to resume the course, as the place will not be saved between sessions. 



Online Modules

Module 1: Introduction to C.auris Molecular Surveillance
Module 2: Implementation of C. auris WGS

Downloadable Version

The FungiNet Training Toolkit is also accessible offline. For the offline version, please download the below zip file.

In order to open the zip file and run the course:

  • Step One: Download the zip file
  • Step Two: Once it is downloaded, right-click the zip file to extract all
  • Step Three: Open the extracted folder
  • Step Four: Start each module by clicking the files named "Launch Module" for each


This eLearning course was supported by Cooperative Agreement number NU2GGH001873, funded by the Centers for Disease Control and Prevention through TEPHINET, a program of The Task Force for Global Health. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention, the Department of Health and Human Services, The Task Force for Global Health, Inc. or TEPHINET.