Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

FEMS Microbiol Rev. 2019 Sep 1;43(5):517-547. doi: 10.1093/femsre/fuz015.

Abstract

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Keywords: Candida; candidemia; diagnosis; proteomics; sequencing; yeast pathogens.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Antifungal Agents / pharmacology
  • Antifungal Agents / therapeutic use
  • Drug Resistance, Multiple, Fungal
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / trends*
  • Humans
  • Mycoses / diagnosis*
  • Mycoses / drug therapy
  • Mycoses / microbiology
  • Pathology, Molecular / methods*
  • Pathology, Molecular / trends*
  • Point-of-Care Systems / trends
  • Polymerase Chain Reaction / trends
  • Proteomics
  • Whole Genome Sequencing / trends
  • Yeasts / drug effects
  • Yeasts / genetics*
  • Yeasts / pathogenicity

Substances

  • Antifungal Agents