Candida Auris: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I Isolation and Identification of Candida auris

1. Isolation of Candida auris in Clinical Specimens
Anamika Yadav, Ashutosh Singh, and Anuradha Chowdhary

2. Candida auris Identification and Profiling by MALDI-ToF Mass Spectrometry
Alireza Abdolrasouli and Mark A. Fraser

3. Molecular Tools for Candida auris Identification and Typing
Auke W. de Jong, Bert Gerrits van den Ende, and Ferry Hagen

4. qPCR Detection of Candida auris using the GPS(TM) CanAur MONODOSE dtec-qPCR Test
Antonio Martnez-Murcia, Patricia Ros-Trraga, Aaron Navarro, and Gema Bru

Part II Testing Susceptibility of Candida auris to Antifungal Drugs

5. Susceptibility Testing of Candida auris Isolates
Elizabeth M. Johnson and Andrew M. Borman

6. Deciphering Candida auris Paradoxical Growth Effect (Eagle Effect) in Response to Echinocandins
Milena Kordalewska and David S. Perlin

Part III Genetic Manipulation of Candida auris

7. An Optimized Electroporation Procedure for Genetic Transformation of Candida auris
Dalal Kasir, Marwan Osman, Monzer Hamze, Jean-Philippe Bouchara, Vincent Courdavault, and Nicolas Papon

8. Genetic Transformation of Candida auris via Homology-Directed Repair Using a Standard Lithium-Acetate Protocol
Gustavo Bravo Ruiz and Alexander Lorenz

9. Downregulation of Essential Genes in the Fungal Pathogen Candida auris
Kali R. Iyer, Sang Hu Kim, Nicole Robbins, and Leah E. Cowen

Part IV Phenotypic and Biochemical Characterization of Candida auris

10. Cell Viability Assays for Candida auris
Jason L. Brown, Bryn Short, Alicia Ware, Leighann Sherry, Ryan Kean, and Gordon Ramage

11. Measuring Gene Expression via mRNA Abundance in Candida auris
Mohd Wasi, Remya Nair, Nitesh Kumar Khandelwal, and Rajendra Prasad

12. Gas Chromatography-Mass Spectrometry (GC-MS) Analysis of Candida auris Metabolites
Bahgat Fayed, Ghalia Kohder, and Sameh S. M. Soliman

13. Isolation of Extracellular Vesicles from Candida auris
Daniel Zamith-Miranda, Lysangela R. Alves, Marcio L. Rodrigues, Leonardo Nimrichter, and Joshua D. Nosanchuk

14. Labelling of Candida auris Cell Walls to Examine Levels of PAMP Exposure by Flow Cytometry and Fluorescence Microscopy
Chloe Pelletier and Alexander Lorenz

15. High-Pressure Freezing and Transmission Electron Microscopy to Visualize the Ultrastructure of the C. auris Cell Wall
Gillian Milne and Louise A. Walker

Part V Bioinformatic Methods for Candida auris

16. Generating Complete Genome Assemblies of Candida auris
Terrance Shea and Christina A. Cuomo

17. MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris
Ujwal R. Bagal, John Phan, Rory M. Welsh, Elizabeth Misas, Darlene Wagner, Lalitha Gade, Anastasia P. Litvintseva, Christina A. Cuomo, and Nancy A. Chow

18. Bioinformatic Identification of ABC Transporters in Candida auris
Atanu Banerjee, Poonam Vishwakarma, Naveen Kumar Meena, Andrew M. Lynn, and Rajendra Prasad

Part VI Exploring Host-Pathogen Interactions of Candida auris

19. Examining Neutrophil-Candida auris Interactions with Human Neutrophils Ex Vivo
Chad J. Johnson and Jeniel E. Nett

20. Modeling Candida auris Colonization on Porcine Skin Ex Vivo
Chad J. Johnson, J. Z. Alex Cheong, Dhanansayan Shanmuganayagam, Lindsay R. Kalan, and Jeniel E. Nett

21. A Human Ex Vivo Skin Model to Study Candida auris Biofilms
Dora E. Corzo-Len, Catherine Mark, Donna M. MacCallum, and Carol A. Munro

22. In Vivo Skin Colonization/Decolonization Models for Candida auris
Janet Herrada, Ahmed Gamal, Lisa Long, and Mahmoud A. Ghannoum

23. Use of Galleria mellonella Larvae to Study the Pathogenicity and Clonal Lineage-Specific B