Abstract
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
Highlights
Laboratory diagnosis of fungal infections relies on isolation of the fungal pathogen and/or direct microscopic examination of the clinical specimens with the help of stains
We review the current use of next-generation sequencing (NGS) in laboratory diagnosis of fungal infections
This cell-free DNA test was developed based on blood samples from patients with invasive infections for pathogen detection, and it has been successfully applied for the diagnosis of fungal infection in several cases [36,47,69]
Summary
Laboratory diagnosis of fungal infections relies on isolation of the fungal pathogen and/or direct microscopic examination of the clinical specimens with the help of stains. The most sensitive, specific and widely available antigen or antibody detection test for fungal infection is the cryptococcal antigen assay [4]. In the recent few decades, DNA amplification and sequencing have been increasingly used for laboratory diagnosis of fungal infections [12]. In the last 10 years, pan-fungal PCR assays targeting DNA markers such as the internal transcribed spacer region (ITS) and 28S nrDNA (D1/D2 region) followed by Sanger sequencing have been widely used for both identification of fungi isolated as well as detection of fungal pathogens directly from clinical specimens [13]. The recent invention of Oxford Nanopore Techonologies’ MinION device has expedited the use of NGS in laboratory diagnosis, due to its low equipment cost, short turn-around-time and portable size. Details of the various NGS technologies, which have been reviewed in other articles [23,24,25], will not be covered
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