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

Tony Gabaldón, the OPATHY Consortium, A Arastehfar, T Boekhout, G Butler, G Buda De Cesare, E Dolk, A Hafez, B Hube, F Hagen, et al.
(2019) FEMS MICROBIOLOGY REVIEWS. 43(5). p.517-547
Author
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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
yeast pathogens, diagnosis, Candida, candidemia, sequencing, proteomics, DESORPTION IONIZATION-TIME, FLIGHT MASS-SPECTROMETRY, IN-SITU HYBRIDIZATION, MALDI-TOF MS, CULTURE IDENTIFICATION PANEL, CLINICAL-PRACTICE GUIDELINE, ESCMID-ASTERISK GUIDELINE, BLOOD-STREAM INFECTIONS, LASER-DESORPTION/IONIZATION-TIME, INTERNAL TRANSCRIBED SPACER

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MLA
Gabaldón, Tony, et al. “Recent Trends in Molecular Diagnostics of Yeast Infections : From PCR to NGS.” FEMS MICROBIOLOGY REVIEWS, vol. 43, no. 5, 2019, pp. 517–47, doi:10.1093/femsre/fuz015.
APA
Gabaldón, T., OPATHY Consortium, the, Arastehfar, A., Boekhout, T., Butler, G., Buda De Cesare, G., … Vatanshenassan, M. (2019). Recent trends in molecular diagnostics of yeast infections : from PCR to NGS. FEMS MICROBIOLOGY REVIEWS, 43(5), 517–547. https://doi.org/10.1093/femsre/fuz015
Chicago author-date
Gabaldón, Tony, the OPATHY Consortium, A Arastehfar, T Boekhout, G Butler, G Buda De Cesare, E Dolk, et al. 2019. “Recent Trends in Molecular Diagnostics of Yeast Infections : From PCR to NGS.” FEMS MICROBIOLOGY REVIEWS 43 (5): 517–47. https://doi.org/10.1093/femsre/fuz015.
Chicago author-date (all authors)
Gabaldón, Tony, the OPATHY Consortium, A Arastehfar, T Boekhout, G Butler, G Buda De Cesare, E Dolk, A Hafez, B Hube, F Hagen, H Hovhannisyan, E Iracane, M Kostrzewa, M Lackner, C Lass-Flörl, C Llorens, V Mixão, C Munro, J Oliveira-Pacheco, M Pekmezovic, A Pérez-Hansen, Antonio Rodriguez Sánchez, FM Sauer, K Sparbier, AA Stavrou, Mario Vaneechoutte, and M Vatanshenassan. 2019. “Recent Trends in Molecular Diagnostics of Yeast Infections : From PCR to NGS.” FEMS MICROBIOLOGY REVIEWS 43 (5): 517–547. doi:10.1093/femsre/fuz015.
Vancouver
1.
Gabaldón T, OPATHY Consortium the, Arastehfar A, Boekhout T, Butler G, Buda De Cesare G, et al. Recent trends in molecular diagnostics of yeast infections : from PCR to NGS. FEMS MICROBIOLOGY REVIEWS. 2019;43(5):517–47.
IEEE
[1]
T. Gabaldón et al., “Recent trends in molecular diagnostics of yeast infections : from PCR to NGS,” FEMS MICROBIOLOGY REVIEWS, vol. 43, no. 5, pp. 517–547, 2019.
@article{8640794,
  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.}},
  author       = {{Gabaldón, Tony and OPATHY Consortium, the and Arastehfar, A and Boekhout, T and Butler, G and Buda De Cesare, G and Dolk, E and Hafez, A and Hube, B and Hagen, F and Hovhannisyan, H and Iracane, E and Kostrzewa, M and Lackner, M and Lass-Flörl, C and Llorens, C and Mixão, V and Munro, C and Oliveira-Pacheco, J and Pekmezovic, M and Pérez-Hansen, A and Rodriguez Sánchez, Antonio and Sauer, FM and Sparbier, K and Stavrou, AA and Vaneechoutte, Mario and Vatanshenassan, M}},
  issn         = {{0168-6445}},
  journal      = {{FEMS MICROBIOLOGY REVIEWS}},
  keywords     = {{yeast pathogens,diagnosis,Candida,candidemia,sequencing,proteomics,DESORPTION IONIZATION-TIME,FLIGHT MASS-SPECTROMETRY,IN-SITU HYBRIDIZATION,MALDI-TOF MS,CULTURE IDENTIFICATION PANEL,CLINICAL-PRACTICE GUIDELINE,ESCMID-ASTERISK GUIDELINE,BLOOD-STREAM INFECTIONS,LASER-DESORPTION/IONIZATION-TIME,INTERNAL TRANSCRIBED SPACER}},
  language     = {{eng}},
  number       = {{5}},
  pages        = {{517--547}},
  title        = {{Recent trends in molecular diagnostics of yeast infections : from PCR to NGS}},
  url          = {{http://doi.org/10.1093/femsre/fuz015}},
  volume       = {{43}},
  year         = {{2019}},
}
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