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Next-Generation Sequencing and Whole-Genome Sequencing in Medical Mycology
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Next-Generation Sequencing and Whole-Genome Sequencing in Medical Mycology

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 10264

Special Issue Editor

Prof. Dr. Jean-Pierre Gangneux

E-Mail Website
Guest Editor
UMR_S 1085—Inserm, Institut de Recherche en Santé, Environnement et Travail, CHU de Rennes, Université de Rennes, 35000 Rennes, France
Interests: fungal diagnosis; treatment; prevention and assessment of environmental risk
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human body hosts billions of commensal, symbiotic, and pathogenic microorganisms, mainly bacteria, known as the human microbiota. In recent years, substantial efforts have been made to investigate the composition of the microbiota in different body sites. Although the contribution of fungi is limited to approximately 0.1% of the total microbiome, it is thought that fungi play a pivotal role in maintaining microbial communities and physiological processes in the body. It becomes clearer that microbiota, including fungi, are in balance with each other as well as with the host and that disturbance of this balance can be involved in numerous diseases.

As the human microbiome has emerged as an important but complex trait influencing health and diseases, we propose to dedicate a Special Issue of the Journal of Fungi to next-generation sequencing (NGS) and whole genome sequencing (WGS) techniques that have clearly renewed methodology to characterize host-associated microbiota in a more comprehensive way. Manuscripts on technical and pathophysiological issues will be welcome, in the field of human, veterinary, and environmental health.

Prof. Dr. Jean-Pierre Gangneux
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 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.

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Published Papers (3 papers)

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Research

13 pages, 1057 KiB  
Article
Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization
by Zackary Salem-Bango, Travis K Price, June L Chan, Sukantha Chandrasekaran, Omai B Garner and Shangxin Yang
J. Fungi 2023, 9(2), 183; https://doi.org/10.3390/jof9020183 - 29 Jan 2023
Cited by 16 | Viewed by 4510
Abstract
Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and [...] Read more.
Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population. Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Medical Mycology)
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14 pages, 1482 KiB  
Article
A Whole Genome Sequencing-Based Approach to Track down Genomic Variants in Itraconazole-Resistant Species of Aspergillus from Iran
by Sanaz Nargesi, Reza Valadan, Mahdi Abastabar, Saeed Kaboli, Jose Thekkiniath and Mohammad Taghi Hedayati
J. Fungi 2022, 8(10), 1091; https://doi.org/10.3390/jof8101091 - 17 Oct 2022
Cited by 3 | Viewed by 2476
Abstract
The antifungal resistance in non-fumigatus Aspergillus spp., as well as Aspergillus fumigatus, poses a major therapeutic challenge which affects the entire healthcare community. Mutation occurrence of cyp51 gene paralogs is the major cause of azole resistance in Aspergillus spp. To obtain [...] Read more.
The antifungal resistance in non-fumigatus Aspergillus spp., as well as Aspergillus fumigatus, poses a major therapeutic challenge which affects the entire healthcare community. Mutation occurrence of cyp51 gene paralogs is the major cause of azole resistance in Aspergillus spp. To obtain a full map of genomic changes, an accurate scan of the entire length of the Aspergillus genome is necessary. In this study, using whole genome sequencing (WGS) technique, we evaluated the mutation in cyp51A, cyp51B, Cdr1B, AtrR, Hmg1, HapE and FfmA genes in different clinical isolates of Aspergillus fumigatus, Aspergillus niger, Aspergillus tubingensis, Aspergillus welwitschiae and Aspergillus terreus which responded to minimum inhibitory concentrations of itraconazole above 16 µg mL−1. We found different nonsynonymous mutations in the cyp51A, cyp51B, Cdr1B, AtrR, Hmg1, HapE and FfmA gene loci. According to our findings, Aspergillus species isolated from different parts of the world may represent different pattern of resistance mechanisms which may be revealed by WGS. Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Medical Mycology)
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8 pages, 596 KiB  
Article
Identification of Fungi Involved in Onychomycosis in Patients of a Spanish Rural Area
by Felix Marcos-Tejedor, Marta Mota, María José Iglesias-Sánchez, Raquel Mayordomo and Teresa Gonçalves
J. Fungi 2021, 7(8), 623; https://doi.org/10.3390/jof7080623 - 31 Jul 2021
Cited by 8 | Viewed by 2484
Abstract
Onychomycosis is one of the most frequent reasons for visiting podiatrist clinics. Complementary tests and the accurate identification of the infectious agents are key issues for a successful treatment of onychomycosis. This is particularly important when lifestyle, age and immunodepressed patients increase the [...] Read more.
Onychomycosis is one of the most frequent reasons for visiting podiatrist clinics. Complementary tests and the accurate identification of the infectious agents are key issues for a successful treatment of onychomycosis. This is particularly important when lifestyle, age and immunodepressed patients increase the prevalence of non-dermatophyte fungal infection. In this paper, we describe issues related to onychomycosis prevalence in a population of patients, mostly with rural lifestyles, visiting a podiatry clinic in a rural area of Spain. A total of 51 cases were studied with an average age of 65.96 ± 21.28 years (the youngest being 16 years and the oldest being 95 years). Fungal agents were isolated using conventional sampling and microbiological culture techniques. The results obtained with these techniques were compared with the results obtained with a direct methodology using molecular biology, by PCR and nucleotide sequencing of the ITS-5.8S rDNA fragment. The classical culture methodology confirmed the infection in 76.5% of the samples (n = 39), while the PCR confirmed the infection in 84.3% (n = 51) of the nails, although the difference between these results did not show statistical significance (p = 0.388). We found a high variability in agents, with more yeasts than dermatophytes as etiological agents of onychomycosis. However, only among individuals older than 65 years, was the difference between yeasts (82%) and dermatophytes (18%) was statistically significant (p = 0.004). Among the agents of non-dermatophyte onychomycosis, we found predominantly fungi (yeasts) of the Candida genus, interestingly with no isolates of Candida albicans, and moulds of the Aspergillus genus. Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Medical Mycology)
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