Genomic Epidemiology of Fungal Diseases

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Pathogenesis and Disease Control".

Deadline for manuscript submissions: 1 August 2024 | Viewed by 3218

Special Issue Editors

Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
Interests: fungal infections diagnosis; Aspergillus; fungi; infectious diseases; fungal epidemiology and public health; antifungal resistance; molecular biology
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Guest Editor
Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
Interests: microbial genomics; evolutionary biology; microbiology; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Special Issue entitled "Genomic Epidemiology for Fungal Diseases 2023" aims to present the most recent research on genomic approaches to study fungal diseases.

Opportunistic fungal infections are characterized by the interaction between the host, its microbiome, the invading fungal species, and the environment. New molecular tools have emerged aiming to reveal a deeper knowledge of these intricate interactions and show how fungal genomics may answer to biological questions about fungal growth, development, pathogenesis, and development of disease. With this Special Issue, we aim to highlight genomic traits of a variety of possible pathogenic fungi, to deepen epidemiological studies in healthcare settings worldwide, to explore human mycobiome, to better understand fungal evolution and pathogenesis or to characterize outbreaks caused by fungal infections.

Reviews, original research, short communications and clinical cases where fungal genomics is applied will be welcome.

Dr. Raquel Sabino
Dr. Joao Paulo Gomes
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungal diseases
  • genomics
  • whole genome sequencing
  • mycobiome
  • fungal exposome

Published Papers (2 papers)

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Research

10 pages, 1594 KiB  
Communication
An Autochthonous Susceptible Candida auris Clade I Otomycosis Case in Iran
by Bahram Ahmadi, Behrouz Naeimi, Mohammad Javad Ahmadipour, Hamid Morovati, Theun de Groot, Bram Spruijtenburg, Hamid Badali and Jacques F. Meis
J. Fungi 2023, 9(11), 1101; https://doi.org/10.3390/jof9111101 - 11 Nov 2023
Cited by 3 | Viewed by 1377
Abstract
Candida auris is a newly emerging multidrug-resistant fungal pathogen considered to be a serious global health threat. Due to diagnostic challenges, there is no precise estimate for the prevalence rate of this pathogen in Iran. Since 2019, only six culture-proven C. auris cases [...] Read more.
Candida auris is a newly emerging multidrug-resistant fungal pathogen considered to be a serious global health threat. Due to diagnostic challenges, there is no precise estimate for the prevalence rate of this pathogen in Iran. Since 2019, only six culture-proven C. auris cases have been reported from Iran, of which, five belonged to clade V and one to clade I. Herein, we report a case of otomycosis due to C. auris from 2017 in a 78-year-old man with diabetes mellitus type II without an epidemiological link to other cases or travel history. Short tandem repeat genotyping and whole genome sequencing (WGS) analysis revealed that this isolate belonged to clade I of C. auris (South Asian Clade). The WGS single nucleotide polymorphism calling demonstrated that the C. auris isolate from 2017 is not related to a previously reported clade I isolate from Iran. The presence of this retrospectively recognized clade I isolate also suggests an early introduction from other regions or an autochthonous presence. Although the majority of reported C. auris isolates worldwide are resistant to fluconazole and, to a lesser extent, to echinocandins and amphotericin B, the reported clade I isolate from Iran was susceptible to all antifungal drugs. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Fungal Diseases)
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8 pages, 648 KiB  
Communication
Candida auris in Intensive Care Setting: The First Case Reported in Portugal
by João Henriques, Verónica Mixão, Joana Cabrita, Tiago Isidoro Duarte, Tânia Sequeira, Sofia Cardoso, Nuno Germano, Liliana Dias, Luís Bento, Sílvia Duarte, Cristina Veríssimo, João Paulo Gomes and Raquel Sabino
J. Fungi 2023, 9(8), 837; https://doi.org/10.3390/jof9080837 - 9 Aug 2023
Cited by 2 | Viewed by 1511
Abstract
Candida auris is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of C. auris in Portugal, which was associated with a [...] Read more.
Candida auris is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of C. auris in Portugal, which was associated with a patient transferred from Angola to an ICU in Portugal for liver transplantation after a SARS-CoV-2 infection. C. auris was isolated during the course of bronchoalveolar lavage, and it was subjected to antifungal susceptibility testing and whole-genome sequence analysis. This isolate presents low susceptibility to azoles and belongs to the genetic clade III with a phylogenetic placement close to African isolates. Although clade III has already been reported in Europe, taking into account the patient’s clinical history, we cannot discard the possibility that the patient’s colonization/infection occurred in Angola, prior to admission in the Portuguese hospital. Considering that C. auris is a fungal pathogen referenced by WHO as a critical priority, this case reinforces the need for continuous surveillance in a hospital setting. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Fungal Diseases)
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