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Review
. 2021 Oct;186(5):589-608.
doi: 10.1007/s11046-021-00573-x. Epub 2021 Sep 7.

Fungal Genomics in Respiratory Medicine: What, How and When?

Amelie P Brackin  1 , Sam J Hemmings  2 , Matthew C Fisher  2 , Johanna Rhodes  3
Affiliations
Review

Fungal Genomics in Respiratory Medicine: What, How and When?

Amelie P Brackin et al. Mycopathologia. 2021 Oct.

Abstract

Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.

Keywords: Aspergillus fumigatus; Genomics; Mycoses; Respiratory diseases.

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Conflict of interest statement

MCF receives speaker fees from Gilead.

Figures

Fig. 1
Fig. 1
Illustration of common azole-resistance mutations that occur within the cyp51A gene within the promoter and coding regions (adapted from Zhang et al., 2017)
Fig. 2
Fig. 2
Schematic highlighting notable techniques for the diagnosis of respiratory mycoses
See this image and copyright information in PMC

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