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Fungal Infections in Immunocompromised Hosts Fungal Infections in Immunocompromised Hosts Edited by Dimitrios P. Kontoyiannis and Monica Slavin Printed Edition of the Special Issue Published in Journal of Fungi www.mdpi.com/journal/jof Fungal Infections in Immunocompromised Hosts Fungal Infections in Immunocompromised Hosts Special Issue Editors Dimitrios P. Kontoyiannis Monica Slavin MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Dimitrios P. Kontoyiannis The University of Texas MD Anderson Cancer Center USA Monica Slavin Department of Infectious Diseases and Infection Prevention, Peter MacCallum Cancer Centre Australia Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Journal of Fungi (ISSN 2309-608X) from 2018 to 2019 (available at: https://www.mdpi.com/journal/ jof/special issues/ICHS2018) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-716-2 (Pbk) ISBN 978-3-03897-717-9 (PDF) Cover image courtesy of Dimitrios P. Kontoyiannis and Monica Slavin. c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editors ..................................... vii Preface to ”Fungal Infections in Immunocompromised Hosts” ................... ix Nathan P. Wiederhold and Connie F. C. Gibas From the Clinical Mycology Laboratory: New Species and Changes in Fungal Taxonomy and Nomenclature Reprinted from: J. Fungi 2018, 4, 138, doi:10.3390/jof4040138 ..................... 1 Thomas F. Patterson and J. Peter Donnelly New Concepts in Diagnostics for Invasive Mycoses: Non-Culture-Based Methodologies Reprinted from: J. Fungi 2019, 5, 9, doi:10.3390/jof5010009 ...................... 16 Robin Patel A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification Reprinted from: J. Fungi 2019, 5, 4, doi:10.3390/jof5010004 ...................... 26 Sevtap Arikan-Akdagli, Mahmoud Ghannoum and Jacques F. Meis Antifungal Resistance: Specific Focus on Multidrug Resistance in Candida auris and Secondary Azole Resistance in Aspergillus fumigatus Reprinted from: J. Fungi 2018, 4, 129, doi:10.3390/jof4040129 ..................... 42 Marta Stanzani and Russell E. Lewis Development and Applications of Prognostic Risk Models in the Management of Invasive Mold Disease Reprinted from: J. Fungi 2018, 4, 141, doi:10.3390/jof4040141 ..................... 55 Thomas J. Walsh, Aspasia Katragkou, Tempe Chen, Christine M. Salvatore and Emmanuel Roilides Invasive Candidiasis in Infants and Children: Recent Advances in Epidemiology, Diagnosis, and Treatment Reprinted from: J. Fungi 2019, 5, 11, doi:10.3390/jof5010011 ...................... 74 Savvas Papachristou, Elias Iosifidis and Emmanuel Roilides Invasive Aspergillosis in Pediatric Leukemia Patients: Prevention and Treatment Reprinted from: J. Fungi 2019, 5, 14, doi:10.3390/jof5010014 ...................... 83 Chris D. Lauruschkat, Hermann Einsele and Juergen Loeffler Immunomodulation as a Therapy for Aspergillus Infection: Current Status and Future Perspectives Reprinted from: J. Fungi 2018, 4, 137, doi:10.3390/jof4040137 .....................104 Flavio Queiroz-Telles, Renata Buccheri and Gil Benard Sporotrichosis In Immunocompromised Hosts Reprinted from: J. Fungi 2019, 5, 8, doi:10.3390/jof5010008 ......................121 Jo˜aoN. de Almeida Jr., Paula M. Pe¸canhaand Arnaldo L. Colombo Paracoccidioidomycosis in Immunocompromised Patients: A Literature Review Reprinted from: J. Fungi 2019, 5, 2, doi:10.3390/jof5010002 ......................144 v Sarah Delli`ere, Romain Guery, Sophie Candon, Blandine Rammaert, Claire Aguilar, Fanny Lanternier, Lucienne Chatenoud and Olivier Lortholary Understanding Pathogenesis and Care Challenges of Immune Reconstitution Inflammatory Syndrome in Fungal Infections Reprinted from: J. Fungi 2018, 4, 139, doi:10.3390/jof4040139 .....................156 Nikolaos Spernovasilis and Diamantis P. Kofteridis Pre-Existing Liver Disease and Toxicity of Antifungals Reprinted from: J. Fungi 2018, 4, 133, doi:10.3390/jof4040133 .....................178 vi About the Special Issue Editors Dimitrios P. Kontoyiannis is the Texas 4000 Distinguished Endowed Professor and Deputy Head in the Division of Internal Medicine at MD Anderson Cancer Center in Houston, TX. Dr. Kontoyiannis has authored over 550 peer-reviewed manuscripts and has given over 330 lectures in international conferences and institutions in US and abroad. He is considered a leading mycology expert worldwide with an H index of 98 and over 42,000 citations. His research group is credited for many and sustained contributions to clinical, translational and experimental mycology. He has been the recipient of many national and international awards and was the president elect of Immunocompromised Host Society (2016–2018). Monica Slavin is Director of the Department of Infectious Diseases at Peter MacCallum Cancer Centre and a National Health and Medical Research Council funded Centre of Research Excellence in Infections in cancer. She is Professor, in the Department of Medicine, the University of Melbourne. Her research focuses on identifying risk factors, improving early diagnosis, prevention, and treatment of infection, particularly fungal infection in hematology and transplant patients. She was a founding member of the Australasian Society for Infectious Diseases Mycoses Interest Group and is the current president of the International Immunocompromised Host Society. vii Preface to ”Fungal Infections in Immunocompromised Hosts” First convened in 1980, the International Immunocompromised Host Society (ICHS) symposium is the premier, international, multi-disciplinary forum for scientific and clinical exchange to improve understanding and management of infections in an immunocompromised host. Since its inception, mycology has been a key theme throughout the bi-annual meetings. The recent meeting in June 2018 in Athens, Greece similarly had a cutting edge mycology program delivered by leading international experts addressing current and future innovations in mycology. Worldwide deaths from Candida, Aspergillus, Pneumocystis, and Cryptococcus infections are estimated to exceed 1.4 million annually with individual patient mortality rates in excess of 30%. Invasive fungal diseases (IFDs) are occurring in expanding populations at risk such as those with liver disease and receiving novel treatments such as biologics and small molecule protein kinase inhibitors, providing insight into fungal pathogenesis. Outbreaks occurring in healthcare or after natural disasters are increasingly identified and require specialized investigation. The emerging global problem of antifungal resistance has prompted an increasing focus on antifungal drug discovery as well as optimizing PK/PD of antifungals, and on fungal biofilms that may select resistance. Approaches such as harnessing the mycobiome and immunotherapy may offer new options for managing IFD. The development and integration of improved diagnostic tests for IFD including MALDI-TOF, nucleic acid and biomarker detection, and immunogenetic assays offers promise for implementing more precise individual risk profiles and early intervention to prevent or treat IFD. At a population level, these tests offer important antifungal stewardship tools to support the judicious use of antifungals. In this unique supplement, we have compiled several state-of-the-art topics that are based on lectures delivered by eminent mycology experts during the 37th ICHS meeting. We hope that the esteemed audience of the Journal of Fungi will enjoy and appreciate the ever-evolving and complex field of fungal infections in vulnerable hosts. Dimitrios P. Kontoyiannis, Monica Slavin Special Issue Editors ix Journal of Fungi Review From the Clinical Mycology Laboratory: New Species and Changes in Fungal Taxonomy and Nomenclature Nathan P. Wiederhold * and Connie F. C. Gibas Fungus Testing Laboratory, Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; [email protected] * Correspondence: [email protected] Received: 29 October 2018; Accepted: 13 December 2018; Published: 16 December 2018 Abstract: Fungal taxonomy is the branch of mycology by which we classify and group fungi based on similarities or differences. Historically, this was done by morphologic characteristics and other phenotypic traits. However, with the advent of the molecular age in mycology, phylogenetic analysis based on DNA sequences has replaced these classic means for grouping related species. This, along with the abandonment of the dual nomenclature system, has led to a marked increase in the number of new species and reclassification of known species. Although these evaluations and changes are necessary to move the field forward, there is concern among medical mycologists that the rapidity by which fungal nomenclature is changing could cause confusion in the clinical
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