Candida auris

ISBN-13: 9781071624197 / Angielski / Miękka / 2023

Opis

This volume covers the latest experimental protocols used by researchers to study the recently emerged fungal pathogen of humans, Candida auris, and also explores the pathogen’s antifungal resistance, virulence, and pathogenicity. The chapters in this book cover topics such as the identification of C. auris in clinic samples by PCR and mass spectrometry; molecular typing to identify clade affiliation; genetic manipulation; genome analysis by bioinformatics; and phenotypic characterization using various biochemical, mass spectrometry, microscopy, and flow cytometry approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and practical, Candida auris: Methods and Protocols is a valuable resource for researchers interested in learning more about this developing field.

Spis treści

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™ CanAur MONODOSE dtec-qPCR Test
Antonio Martínez-Murcia, Patricia Ros-Tárraga, 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-León, 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 Behaviors of the Emerging Fungal Pathogen Candida auris
Andrew M. Borman

24. Drosophila melanogaster as a Rapid and Reliable In Vivo Infection Model to Study the Emerging Yeast Pathogen Candida auris
Sebastian Wurster, Nathaniel D. Albert, and Dimitrios P. Kontoyiannis

25. An Immunocompromised Mouse Model of Candida auris Systemic Infection
Janet Herrada, Kyle Roberts, Ahmed Gamal, Lisa Long, and Mahmoud A. Ghannoum

26. Mouse Gastrointestinal Colonization Model for Candida auris
Stylianos C. Simantirakis and Donna M. MacCallum

Subject Index List…