Special Issue "Fungal Pathogenesis in Humans: The Growing Threat"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 30 June 2018

Special Issue Editor

Guest Editor
Dr. Fernando Leal

Instituto de Biología Funcional y Genómica / Dpto. Microbiología y Genética Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
Interests: fungal pathogenesis; Aspergillus molecular genetics; virology; miRNAs

Special Issue Information

Dear Colleagues,

Cancer survival rates and successful organ transplantation in patients continues to increase due to improvements in early diagnosis and treatments. Since immuno-suppressive therapies are frequently used, the mortality rate due to secondary infections has become an ever-increasing problem. Opportunistic fungal infections are probably the deadliest threat to these patients due to their difficult early diagnosis, the limited effect of antifungal drugs and the appearance of resistances. In recent years, a considerable effort has been devoted to investigating the role of many virulence traits in the pathogenic outcome of fungal infections. New virulence factors (hypoxia adaptation, CO2 sensing, pH regulation, micronutrient acquisition, secondary metabolites, immunity regulators, etc.) have been reported and their molecular mechanisms of action are being thoroughly investigated. The recent application of gene-editing technologies such as CRISPr-Cas9, has opened a whole new window to the discovery of new fungal virulence factors. Accurate fungal genotyping, Next Generation Sequencing and RNAseq approaches will undoubtedly provide new clues to interpret the plethora of molecular interactions controlling these complex systems. Unraveling their intimate regulatory details will provide insights for a more target-focused search or a rational design of more specific antifungal agents.

This Special Issue is open to researchers in any related field willing to contribute significant discoveries, proofs of concept of new theories or relevant observations in fungal pathogenesis and its regulation.

Dr. Fernando Leal
Guest Editor

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 papers will be 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. Genes 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 1600 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.



  • Fungal virulence

  • Fungal genotyping

  • Biofilm formation

  • Immune evasion

  • CO2 sensing

  • pH regulation

  • Micronutrient acquisition

  • Trehalose biosynthesis

  • Secondary metabolites and toxins

  • Regulation of antifungals resistance

  • Criptococcus, Candida, Aspergillus, Scedosporium, Fusarium, Pneumocysits

Published Papers (2 papers)

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Open AccessFeature PaperArticle Portrait of Matrix Gene Expression in Candida glabrata Biofilms with Stress Induced by Different Drugs
Received: 6 March 2018 / Revised: 29 March 2018 / Accepted: 5 April 2018 / Published: 10 April 2018
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(1) Background: Candida glabrata is one of the most significant Candida species associated with severe cases of candidiasis. Biofilm formation is an important feature, closely associated with antifungal resistance, involving alterations of gene expression or mutations, which can result in the failure of
[...] Read more.
(1) Background: Candida glabrata is one of the most significant Candida species associated with severe cases of candidiasis. Biofilm formation is an important feature, closely associated with antifungal resistance, involving alterations of gene expression or mutations, which can result in the failure of antifungal treatments. Hence, the main goal of this work was to evaluate the role of a set of genes, associated with matrix production, in the resistance of C. glabrata biofilms to antifungal drugs. (2) Methods: the determination of the expression of BGL2, XOG1, FKS1, FKS2, GAS2, KNH1, UGP1, and MNN2 genes in 48-h biofilm’s cells of three C. glabrata strains was performed through quantitative real-time PCR (RT-qPCR), after contact with Fluconazole (Flu), Amphotericin B (AmB), Caspofungin (Csf), or Micafungin (Mcf). (3) Results: Mcf induced a general overexpression of the selected genes. It was verified that the genes related to the production of β-1,3-glucans (BGL2, XOG1, GAS2) had the highest expressions. (4) Conclusion: though β-1,6-glucans and mannans are an essential part of the cell and biofilm matrix, C. glabrata biofilm cells seem to contribute more to the replacement of β-1,3-glucans. Thus, these biopolymers seem to have a greater impact on the biofilm matrix composition and, consequently, a role in the biofilm resistance to antifungal drugs. Full article
(This article belongs to the Special Issue Fungal Pathogenesis in Humans: The Growing Threat)

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Open AccessArticle Genome-Wide Identification of circRNAs in Pathogenic Basidiomycetous Yeast Cryptococcus neoformans Suggests Conserved circRNA Host Genes over Kingdoms
Received: 9 January 2018 / Revised: 9 February 2018 / Accepted: 19 February 2018 / Published: 26 February 2018
PDF Full-text (2169 KB) | HTML Full-text | XML Full-text | Supplementary Files
Circular RNAs (circRNAs), a novel class of ubiquitous and intriguing noncoding RNA, have been found in a number of eukaryotes but not yet basidiomycetes. In this study, we identified 73 circRNAs from 39.28 million filtered RNA reads from the basidiomycete Cryptococcus neoformans JEC21
[...] Read more.
Circular RNAs (circRNAs), a novel class of ubiquitous and intriguing noncoding RNA, have been found in a number of eukaryotes but not yet basidiomycetes. In this study, we identified 73 circRNAs from 39.28 million filtered RNA reads from the basidiomycete Cryptococcus neoformans JEC21 using next-generation sequencing (NGS) and the bioinformatics tool circular RNA identification (CIRI). Furthermore, mapping of newly found circRNAs to the genome showed that 73.97% of the circRNAs originated from exonic regions, whereas 20.55% were from intergenic regions and 5.48% were from intronic regions. Enrichment analysis of circRNA host genes was conducted based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases. The results reveal that host genes are mainly responsible for primary metabolism and, interestingly, ribosomal protein production. Furthermore, we uncovered a high-level circRNA that was a transcript from the guanosine triphosphate (GTP)ase gene CNM01190 (gene ID: 3255052) in our yeast. Coincidentally, YPT5, CNM01190′s ortholog of the GTPase in Schizosaccharomyces pombe, protists, and humans, has already been proven to generate circRNAs. Additionally, overexpression of RNA debranching enzyme DBR1 had varied influence on the expression of circRNAs, indicating that multiple circRNA biosynthesis pathways exist in C. neoformans. Our study provides evidence for the existence of stable circRNAs in the opportunistic human pathogen C. neoformans and raises a question regarding their role related to pathogenesis in this yeast. Full article
(This article belongs to the Special Issue Fungal Pathogenesis in Humans: The Growing Threat)

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.


Tentative Title: Host-pathogen interactions mediated by MDR transporters in fungi: as pleiotropic as it gets!

Authors: Mafalda Cavalheiro1,2, Pedro Pais1,2, Mónica Galocha1,2, Miguel Cacho Teixeira1,2

Affiliations: 1Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; 2iBB – Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal

Tentative Abstract: Fungal infections caused by species of the Candida, Aspergillus and Cryptococcus genus are an increasing problem worldwide, associated to very high associated mortality rates. The successful prevalence of these human pathogens is due to their ability to thrive in stressful host niche colonization sites, to tolerate host immune system induced stress and to resist against antifungal drugs.

This review focuses on the key role played by multi-drug resistance (MDR) transporters, belonging to the ATP-binding cassette (ABC) superfamily and the major facilitator superfamily (MFS), in mediating fungal resistance to the referred pathogenesis-related stresses. This includes the traditional role attributed to fungal MDR transporters, the extrusion of antifungal drugs, with C. albicans CDR1 and MDR1 genes, and corresponding homologs in other fungal pathogens, playing a key role in this phenomenon. More recently, however, clues on the transcriptional regulation and physiological roles of MDR transporters, including the transport of lipids, ions and small metabolites, have emerged, linking these transporters to important pathogenesis features such as resistance to host niche environments, biofilm formation, immune system evasion and virulence.

The wider view of the activity of MDR transporters provided in this review highlights their relevance beyond drug resistance and the need to develop therapeutic strategies that successfully face the challenges posed by the pleiotropic nature of these transporters.


Tentative Title: Exploiting genomics approaches for unravelling Candida albicans biofilm and drug resistance

Authors: 1Priya Madhavan, 2Voon Kin Chin, 3Chung Yeng Looi, 4Won Fen Wong, 3Phelim Voon Chen Yong and 3Pei Pei Chong.

Affiliations: 1School of Medicine, Taylor's University, 47500 Selangor, Malaysia; 2 Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 Selangor, Malaysia; 3 School of Biosciences, Taylor's University, 47500 Selangor, Malaysia; 4 Department Of Medical Microbiology. Faculty Of Medicine. University of Malaya, Jalan Universiti, 50603 Kuala Lumpur, Malaysia;

Tentative Abstract: Candida albicans is an opportunistic fungal pathogen which causes a plethora of superficial as well as invasive infections in humans. The ability of this fungus in switching from commensalism to active infection is attributed to its many virulence traits. Biofilm formation is a key process which allows the fungus to adhere to and proliferate on medically implanted devices and cause serious life-threatening infections. Biofilms are complexed communities of fungal and yeast cells surrounded by extracellular matrix that confers a certain degree of resistance to antifungal drugs. Moreover, the recent discoveries of the extensive plasticity of the C. albicans genome have given this versatile fungus the added advantage of microevolution and adaptation to thrive within the unique environmental niches within the host. To combat these challenges in dealing with C. albicans infections, it is imperative that we target specifically the molecular pathways involved in biofilm formation as well as drug resistance. With the advent of the –omics era and whole genome sequencing platforms, novel pathways and genes involved in pathogenesis of the fungus had been unraveled. Researchers have used a myriad of strategies including transcriptome analysis for C. albicans cells grown in different environments, whole genome sequencing of different strains, functional genomics approaches to identify critical regulatory genes, as well as comparative genomics analysis between C. albicans and its closely related, much less virulent relative, Candida dubliniensis, in the quest to increase our understanding of the mechanisms underlying the success of C. albicans as a major fungal pathogen. This review attempts to summarize the most recent advancements in the field of biofilm and antifungal resistance research and offer suggestions for future directions in therapeutics development.


Tentative Title: Bioluminescent Mucor circinelloides – a promising new tool to study mucormycosis and antifungal drug efficacy

Authors: Ulrike Binder1, María Isabel Navarro-Mendoza2, Francisco E. Nicolás2, Cornelia Lass-Flörl1 and Victoriano Garre2

Affiliations: 1Division of Hygiene and Medical Microbiology, Medical University Innsbruck, Austria; 2Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain

Tentative Abstract:

Objectives: Invasive infections caused by members of the Mucorales (mucormycosis) have increased in the last years, making it the third most common invasive fungal infection after aspergillosis and candidiasis. Despite this increasing clinical relevance, little is known about the establishment of disease, its progression and successful therapy.

New tools to study this disease in more detail are needed, therefore the objective of this work was to construct a luciferase expressing Mucor circinelloides strain, as one representative of mucormycosis causing pathogens. Here, we describe the construction and functional analysis of the strains, which will further be used as a reporter system for in vivo and in vitro models of Mucorales infections.

Methods: A leucine auxotroph M. circinelloides strain, R7B, was used as recipient strain to allow selection of transformants on selective medium. Firefly luciferase gene without the peroxisomal target sequence was cloned in the pMAT1477 vector under the control of a constitutive promoter. Linear plasmid was used to transfect M. circinelloides protoplasts. The targeted integration of the whole construct in the carRP gene resulted in easy identification of transformants, appearing as white colonies.

Homokaryons were obtained by sequential plating on selective media and checked for light emission under various conditions in in vitro assays.

Results: Expression of firefly luciferase was successful in M. circinelloides at several conditions and light emission was detectable by imaging and with a luminometer. Data so far indicate the strain being suitable for further in vivo and in vitro studies. Phenotype, virulence potential and antifungal susceptibility are currently compared to wild-type strains.

Conclusion: The construction of this first bioluminescent Mucor strain will allow for the visualization of temporal and spatial progression of infection by a non-invasive method in insect and murine models, and the testing of antifungal efficacy by other means than survival only. This will give valuable new insights in the pathogenesis of Mucorales infections.


Tentative Title: Genome-Wide Comparative Analysis of Aspergillus fumigatus Strains: The Reference Genome as a Matter of Concern.

Authors: Garcia-Rubio R, Monzon S, Alcazar-Fuoli L, Cuesta I, and Mellado E

Affiliations: 1Mycology Reference Laboratory, National Centre for Microbiology. Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain. 2Bioinformatics Unit, Common Scientific Technical Units. Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain.

Tentative Abstract: Genomics and whole genome sequencing (WGS) have the potential to enhance the knowledge and understanding of infectious diseases such as fungal infections. Aspergillus fumigatus is a saprotrophic mold ubiquitously found in the environment. Despite having its primary niche in organic soil material, A. fumigatus has become a major pathogenic organism in those humans with compromised or suppressed immunity. The most relevant clinical manifestation caused by this species is invasive aspergillosis (IA). Triazole antifungal compounds are the first line treatment for IA patients. Over the last decade, a rapid and global emergence of azole resistance has been observed in this pathogenic fungus threatening the effectiveness of clinical and agricultural azole drugs. In this context, WGS has emerged as an invaluable tool for the analysis of genetic differences between A. fumigatus strains, their background lineage, and the study of resistance development. Although WGS analyses are very powerful and can provide a valuable amount of novel information based on genome-wide comparative data, there are some limitations that should be taken into consideration. The two major challenges associated with such studies are: i) obtaining high quality genomic sequences, and ii) determining relevant biological information from the genomic sequence. At present, most WGS analyses are based upon single nucleotide variants (SNVs) identified in a set of strains when compared against a strain reference genome. Consequently, analyses are dependent on the quality of sequencing and assembling, as well as the suitable selection of the reference genome, which means how genetically close the reference genome is to the other genomes included in the analysis. In the present work, 28 A. fumigatus strains have been sequenced and 73 A. fumigatus genomes available in public data bases have been added to the WGS analysis. This study highlights the importance of choosing the most suitable A. fumigatus reference genome to answer accurately to the proposed hypothesis. Also, based on the azole resistance acquisition routes, this analysis stresses the fact that some A. fumigatus strains seem to be genetically more closely related than others. The determination of the genome-wide basis of azole resistance in A. fumigatus would facilitate the search of new techniques for resistance surveillance and the discovery of new antifungal resistance mechanisms. 


Tentative Title: Strengthening the One Health agenda: The role of genomics in Aspergillus threat management.

Authors: Eta Ashu1,2, Ze-Chun Yuan2, and Jianping Xu1,

Affiliations: 1Department of Biology, McMaster University, Hamilton, Canada; 2London Research and Development Centre, Agriculture and Agri-Food Canada.

Tentative Abstract: There recently has been a tremendous amount of advocacy for global and local health bodies to use the One Health approach in attaining optimal health outcomes. Due to a variety of pathogen, host and pathogen-host environmental factors, Aspergillus species have recently emerged as a significant global health threat. In this review we explore the role of genomics in Aspergillus threat management and strengthening of the One Health scheme.  We suggest a framework that could be used in the management of Aspergillus threats, including those caused by resistant strains. Of the three major components of pathogen threat management, this review focuses on genomic components of preparedness and prevention. In regard to the genomic components of prevention, we highlight the role of molecular epidemiology in virulence characterization, transmission patterns identification and outbreak incidence investigation. We however note that little has been done in predicting drug resistance. Exploring molecular epidemiology and evolution methods, we suggest an experimental design that could be used in predicting resistance through drug exposure.  Regarding the genomic components of preparedness, we review currently available molecular diagnostic methods for the detection of Aspergillus species, including resistant genotypes. We highlight the need for molecular diagnostic training, especially in diagnosing cryptic and resistant species. In conclusion, we note that there is a need for standardization of loci and methods used for molecular diagnostics and surveillance. Given the growing threat caused by Aspergilli, national and global genotype databases could prove to be useful to current Aspergillus threat management efforts. In light of the One Health scheme, effectively managing the current Aspergillus threat will entail the significant incorporation of genomic components into Aspergillus threat preparedness and prevention.


Tentative Title: Pathogenesis of the Candida parapsilosis complex in the model host Caenorhabditis elegans

Authors: Ana Carolina Remondi Souza1,2, Beth Burgwyn Fuchs2, Viviane de Souza Alves3, Elamparithi Jayamani2, Arnaldo L. Colombo1, Eleftherios Mylonakis2*

Affiliations: 1Laboratório Especial de Micologia, Disciplina de Infectologia, Escola paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil; 2Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI, USA; 3Laboratório de Biologia Celular de Microrganismos, departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil


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