Genomics and Proteomics as Compared to Conventional Phenotypic Approaches for the Identification of the Agents of Invasive Fungal Infections

Abstract

There is overwhelming evidence that prompt diagnosis coupled with timely instigation of appropriate antifungal therapy are critical determinants of clinical outcome in invasive fungal infections. However, since the clinical symptoms of infection are often nonspecific, the number and diversity of potential aetiological agents is vast, and many fungi exhibit species-specific differences in antifungal susceptibility, the accurate identification of the responsible pathogen is a cornerstone of the therapeutic decision pathway. Traditionally, identification was achieved by examination of the phenotypic characteristics of the fungus obtained in pure culture, ideally from a normally sterile site/sample. However, this standard culture-based approach lacks sensitivity and obtaining appropriate specimens for culture is often difficult. Moreover, numerous recent studies have demonstrated the existence of clinically relevant cryptic species within well-established morphospecies that can not be differentiated by phenotypic methods. Here we discuss recent advances in genomic and proteomic approaches for the rapid and accurate identification of the principal pathogenic fungi associated with invasive fungal infections.

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Acknowledgments

We are grateful to the other members of the UK MRL for their assistance with data collation and phenotypic and molecular analyses of isolates.

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Conflict of Interest

Elizabeth Johnson has consulted and received payment for development of educational presentations by Gilead, MSD, Pfizer and Astellas, and has had travel/accommodations expenses covered or reimbursed by Gilead, MSD and Astellas.

Andrew Borman has travel/accommodations expenses covered or reimbursed by Biotage (now Qiagen) and Whatman (now GE healthcare).

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.

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Correspondence to Elizabeth M. Johnson.

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Borman, A.M., Johnson, E.M. Genomics and Proteomics as Compared to Conventional Phenotypic Approaches for the Identification of the Agents of Invasive Fungal Infections. Curr Fungal Infect Rep 7, 235–243 (2013). https://doi.org/10.1007/s12281-013-0149-7

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Keywords

  • Diagnostic challenges
  • Invasive fungal infections
  • PCR assays
  • Microscopy
  • Culture
  • MALDI-TOF