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

  • Sam El-Kamand
  • Alexie Papanicolaou
  • C. Oliver MortonEmail author
Advances in Diagnosis of Invasive Fungal Infections (O Morrissey, Section Editor)
Part of the following topical collections:
  1. Topical Collection on Advances in Diagnosis of Invasive Fungal Infections

Abstract

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.

Summary

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.

Keywords

Diagnosis Invasive fungal disease Invasive aspergillosis Next-generation sequencing 

Notes

Compliance with Ethical Standards

Conflict of Interest

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

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.

References

Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Sam El-Kamand
    • 1
  • Alexie Papanicolaou
    • 2
  • C. Oliver Morton
    • 1
    Email author
  1. 1.School of Science and HealthWestern Sydney UniversityPenrithAustralia
  2. 2.Hawkesbury Institute for the EnvironmentWestern Sydney University, Hawkesbury CampusRichmondAustralia

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