The Use of Whole Genome and Next-Generation Sequencing in the Diagnosis of Invasive Fungal Disease


Purpose of Review

This review examines how next-generation nucleic acid sequencing (NGS) is being used in the diagnosis of invasive fungal disease (IFD) and how well its implementation compares to PCR-based diagnosis. The comparison allows for the assessment of the advantages and potential limitations of NGS in the diagnosis of IFD.

Recent Findings

NGS is established as a method for sequencing of microbial genomes. It is increasingly being tested as a direct diagnostic method from various sample types including samples such as plasma, formalin fixed and paraffin embedded specimens, and bronchoalveolar lavage. In these cases, the methodology was generally able to identify the causative agents of IFD.


NGS-based methods will play an increasingly important role in diagnosis of IFD. The major limitation is currently cost, the need to standardise methods of nucleic acid isolation, and sequence analysis to enable broad uptake and application of the method.

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Correspondence to C. Oliver Morton.

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Sam El-Kamand, Alexie Papanicolaou and C. Oliver Morton declare no conflicts of interest relevant to this manuscript.

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El-Kamand, S., Papanicolaou, A. & Morton, C.O. The Use of Whole Genome and Next-Generation Sequencing in the Diagnosis of Invasive Fungal Disease. Curr Fungal Infect Rep 13, 284–291 (2019).

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  • Diagnosis
  • Invasive fungal disease
  • Invasive aspergillosis
  • Next-generation sequencing