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Pathogens
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Epidemiology and Molecular Detection of Emerging Fungal Pathogens
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Epidemiology and Molecular Detection of Emerging Fungal Pathogens

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Fungal Pathogens".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 1033

Special Issue Editor

Dr. Claudio Farina

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Guest Editor
Department of Infectious/Tropical Diseases and Microbiology, IRCCS Sacro-Cuore Don Calabria, Negrar di Valpolicella, Verona, Italy
Interests: medical mycology; clinical microbiology; antibiotic resistance; epidemiology of hospital infections; diagnosis of sepsis

Special Issue Information

Dear Colleagues,

Fungi are an increasing threat and a growing challenge both for clinical management and public health.

The field of mycology and mycoses aligns closely with the One Health approach proposed by the WHO. This highlights how changes in human activities, environmental factors, and climate have significant epidemiological repercussions. These innovations impact both human, veterinary, and agricultural health, and contribute to the rise in resistance to antifungal drugs, particularly concerning emerging fungal pathogens with limited treatment options. The WHO has included fungi in its list of priority pathogens, but new epidemiological data suggest that this is not exhaustive. There are growing efforts to enhance diagnostics and strengthen resistance surveillance through biomolecular technologies.

In response to these challenges, we propose a Special Issue on “Epidemiology and Molecular Detection of Emerging Fungal Pathogens”. It will address key topics relating to the new etiology, epidemiology, geographic medicine, and clinical aspects of mycoses caused by yeasts, hyaline and dematiaceous fungi, dermatophytes, and lignicolous  and dimorphic mycetes in various clinical settings, including pediatric and elderly patients in LTFCs, travelers, workers, immunocompromised and immunocompetent individuals, and people affected in conflicts or natural disasters. Additionally, we aim at addressing the role of the human mycobiome in fungal infections. Through this Special Issue, we hope to foster a deeper understanding of the risks and challenges posed by fungal pathogens today.

Dr. Claudio Farina
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. Pathogens 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 2200 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

  • epidemiology
  • molecular detection
  • emerging fungi
  • uncommon presentation

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Published Papers (2 papers)

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Research

17 pages, 2415 KiB  
Article
Dancing with the Dust Devil: Examining the Lung Mycobiome of Sonoran Desert Wild Mammals and the Effect of Coccidioides Presence
by Ana Fabio-Braga, Jaida Salois, Mitchell L. Bryant, Daniel R. Kollath and Bridget Barker
Pathogens 2025, 14(8), 807; https://doi.org/10.3390/pathogens14080807 - 14 Aug 2025
Abstract
Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, Coccidioides can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of Coccidioides-positive and -negative samples obtained from wildlife. If [...] Read more.
Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, Coccidioides can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of Coccidioides-positive and -negative samples obtained from wildlife. If Coccidioides is not causing infection, we predict there will be no differences in the mycobiome between positive and negative samples. Lung samples were obtained from mammals previously trapped in Tucson, Arizona, USA (n = 26), and Mesa, Arizona, USA (n = 14). Samples were screened for Coccidioides with CocciDx, and mycobiome was characterized through Illumina-based amplicon sequencing of the internal transcribed spacer 2 (ITS2). We compared alpha and beta diversity of the mycobiome to assess the effects of Coccidioides’ presence and host taxonomy. A greater number of reads were captured from Tucson samples (114,706.4 ± 57,945.8) than from Mesa (384.9 ± 953.5); however, Mesa (16.8 ± 8.8) and Tucson (12 ± 7.8) had a similar number of fungal genera per sample. CocciDx detected Coccidioides in more samples than the ITS2 amplicon sequencing. All samples from Mesa and five from Tucson tested positive for Coccidioides. Therefore, Mesa samples were excluded from statistical analysis. No difference in alpha and beta diversity was associated with Coccidioides presence, which is consistent with the endozoan hypothesis. Host taxonomy had a significant effect on beta diversity. This effect is likely driven by host behavioral and physiological differences. Full article
(This article belongs to the Special Issue Epidemiology and Molecular Detection of Emerging Fungal Pathogens)
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13 pages, 1789 KiB  
Article
Genetic Epidemiology and Resistance Investigations of Clinical Yeasts in Alexandria, Egypt
by Bram Spruijtenburg, Carolina Melchior do Prado, Mats van Kempen, Sherine M. Shawky, Jacques F. Meis, Vânia Aparecida Vicente, Flavio Queiroz-Telles, Theun de Groot, Mohammed A. El-Kholy and Eelco F. J. Meijer
Pathogens 2025, 14(5), 486; https://doi.org/10.3390/pathogens14050486 - 15 May 2025
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Abstract
Yeast bloodstream infections lead to high mortality and morbidity and are mostly observed in immunocompromised patients. In Africa, only a few studies have characterized clinical yeasts. To increase insight into yeast resistance and transmission in Africa, we identified various yeasts from Alexandria, Egypt [...] Read more.
Yeast bloodstream infections lead to high mortality and morbidity and are mostly observed in immunocompromised patients. In Africa, only a few studies have characterized clinical yeasts. To increase insight into yeast resistance and transmission in Africa, we identified various yeasts from Alexandria, Egypt and performed antifungal susceptibility testing (AFST) and genotyping. A total of 1307 single isolates from unique patients, recovered from different anatomical sites including the bloodstream, retrieved from a reference laboratory in Alexandria, Egypt were studied. All isolates were identified with MALDI-TOF MS, while some were initially identified with a Vitek 2 Compact system. Short tandem repeat (STR) genotyping was performed for the most common species, and AFST was performed with microbroth dilution. Among bloodstream isolates (n = 71), C. albicans was the most common etiological agent, followed by C. tropicalis and C. parapsilosis. Comparison of yeast identification methods demonstrated that 22% of isolates were incorrectly identified with the Vitek 2 Compact system compared to MALDI-TOF MS. Multiple rare yeasts showed reduced antifungal susceptibility. STR genotyping demonstrated potential events of nosocomial transmission with N. glabratus and C. parapsilosis. Moreover, an azole-resistant C. tropicalis clade identified earlier in Alexandria was still present. To conclude, clinical yeasts in Alexandria, Egypt, are overall susceptible common species. Full article
(This article belongs to the Special Issue Epidemiology and Molecular Detection of Emerging Fungal Pathogens)
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