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Review
. 2018 Dec 3;9(1):5135.
doi: 10.1038/s41467-018-07556-5.

Molecular diagnostics in medical mycology

Brian L Wickes  1 , Nathan P Wiederhold  2
Affiliations
Review

Molecular diagnostics in medical mycology

Brian L Wickes et al. Nat Commun. .

Abstract

Diagnosing fungal infections poses a number of unique problems, including a decline in expertise needed for identifying fungi, and a reduced number of instruments and assays specific for fungal identification compared to that of bacteria and viruses.These problems are exacerbated by the fact that patients with fungal infections are often immunosuppressed, which predisposes to infections from both commonly and rarely seen fungi. In this review, we discuss current and future molecular technologies used for fungal identification, and some of the problems associated with development and implementation of these technologies in today's clinical microbiology laboratories.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
FDA approval pathways for medical devices. The approval process is based on risk to patients, with higher risk requiring more regulatory control. The FDA assists in the classification process through their database, which contains almost 2000 generic medical devices organized into 16 different panels. Classification is determined in part by location of the device on the patient, duration of device contact with the patient, and whether the device will be active or passive (active devices require power, usually electrical). Class I devices are the lowest risk and most are exempt from premarket notification. The device and company must be registered with the FDA but approval is not required. Class II devices need FDA clearance through the 510(k) premarket notification (PMN) process. Class III devices need premarket approval (PMA) and usually clinical trials. Examples of fungal devices (bold) are the PhenoTest BC (Accelerate Diagnostics, Inc.), which identifies Candida albicans and Candida glabrata, the Fungitell assay for fungal β-d-glucan (Associates of Cape Cod, Inc.), and the T2Candida assay (T2 Biosystems, Inc.), which identifies five species of Candida from blood cultures
Fig. 2
Fig. 2
DNA sequence encoding fungal ribosomal RNAs. The genes for fungal rRNAs are organized as a repeating unit. A single unit consists of the sequence encoding the 18S rRNA (for the small ribosomal subunit), internal transcribed spacer 1, sequence encoding the 5.8S rRNA, internal transcribed spacer 2, sequence encoding the 28S rRNA (for the large ribosomal subunit), intergenic sequence 1, sequence encoding the 5S rRNA, and intergenic sequence 2. The 18S, ITS1, 5.8S, ITS2, and 28S sequences are transcribed as a single RNA, which is then spliced to remove the ITS1 and ITS2 regions (blue cylinders) prior to assembly with the 5S rRNA into the complete ribosome consisting of the 18S, 5.8S, 28S, 5S (green cylinders) and assorted proteins. The ITS1 and ITS2 regions make up the ITS sequence, which is generally ~600bp in length although it can vary by more than 200bp. The D1/D2 region (blue shaded region on 28S) is similar in length. Both regions are informative with regard to sequence identification although the D1/D2 region is usually more conserved. Priming sites for PCR are shown as black arrowheads and can be used in various combinations. The 5S sequence is transcribed separately and is flanked by the two IGS regions (brown cylinders), which can be very informative, however, they vary tremendously in size, making amplification by PCR difficult
See this image and copyright information in PMC

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