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.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance
Lass-Flörl C. The changing face of epidemiology of invasive fungal disease in Europe. Mycoses. 2009;52:197–205.
Richardson M, Lass-Flörl C. Changing epidemiology of systemic fungal infections. Clin Microbiol Infect. 2008;14:5–24.
Neofytos D, Fishman JA, et al. Epidemiology and outcome of invasive fungal infections in solid organ transplant recipients. Transpl Infect Dis. 2010;12:220–9.
Lewis RE. Overview of the changing epidemiology of candidemia. Curr Med Res Opin. 2009;25:1732–40.
Barnes PD, Marr KA. Risks, diagnosis and outcomes of invasive fungal infections in haematopoietic stem cell transplant recipients. Br J Haematol. 2007;139:519–31.
Balajee SA, Gribskov JL, et al. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot Cell. 2005;4:625–32.
Zbinden A, Imhof A, et al. Fatal outcome after heart transplantation caused by Aspergillus lentulus. Transpl Infect Dis. 2012;14:E60–3.
Perkhofer S, Lass-Flörl C, et al. The Nationwide Austrian Aspergillus Registry: a prospective data collection on epidemiology, therapy and outcome of invasive mould infections in immunocompromised and/or immunosuppressed patients. Int J Antimicrob Agents. 2010;36:531–6.
Michallet M, Ito JI. Approaches to the management of invasive fungal infections in hematologic malignancy and hematopoietic cell transplantation. J Clin Oncol. 2009;27:3398–409.
Hahn-Ast C, Glasmacher A, et al. Overall survival and fungal infection-related mortality in patients with invasive fungal infection and neutropenia after myelosuppressive chemotherapy in a tertiary care centre from 1995 to 2006. J Antimicrob Chemother. 2010;65:761–8.
Bassetti M, Trecarichi EM, et al. Incidence, risk factors and predictors of outcome of candidemia : survey of 2 Italian university hospitals. Diagn Microbiol Infect Dis. 2007;58:325–31.
Caillot D, Casasnovas O, et al. Improved manangement of invasive pulmonary aspergillosis in neutropenic patients using early thoracic computed tomographic scan and surgery. J Clin Oncol. 1997;15:139–47.
Morrell M, Fraser VJ, et al. Delaying the empiric treatment of Candida bloodstream infection until positive blood culture results are obtained: a potential risk factor for hospital mortality. Antimicrob Agents Chemother. 2005;49:3640–5.
Garey KW, Rege M, et al. Time to initiation of fluconazole therapy impacts mortality in patients with candidemia: a multi-institutional study. Clin Infect Dis. 2006;43:25–31.
Golan Y, Wolf MP, et al. Empirical anti-Candida therapy among selected patients in the intensive care unit: a cost-effectiveness analysis. Ann Intern Med. 2005;143:857–69.
Von Eiff M, Roos N, et al. Pulmonary aspergillosis: early diagnosis improves survival. Respiration. 1995;62:341–7.
Barnes RA. Early diagnosis of fungal infection in immunocompromised patients. J Antimicrob Chemother. 2008;61:i3–6.
Simoneau E, Kelly M, et al. What is the clinical significance of positive blood cultures with Aspergillus sp in hematopoietic stem cell transplant recipients? A 23 year experience. Bone Marrow Transplant. 2005;35:303–6.
Barnes PD, Marr KA. Aspergillosis: spectrum of disease, diagnosis and treatment. Infect Dis Clin North Am. 2006;20:545–61.
Berenguer J, Buck M, et al. Lysis-centrifugation blood cultures in the detection of tissue-proven invasive candidiasis: disseminated versus single-organ infection. Diagn Microbiol Infect Dis. 1993;17:103–9.
Pemán J, Zaragoza R, et al. Clinical factors associated with a germ tube antibody positive test in intensive care unit patients. BMC Infect Dis. 2011;11:60.
Clancy CJ, Nguyen MH. Finding the "missing 50%" of invasive candidiasis: How non-culture diagnostics will improve understanding of disease spectrum and transform patient care. Clin Infect Dis. 2013 . [Epub ahead of print].
Sheppard DC, Locas M-C, et al. Utility of the germ tube test for the direct identification of Candida albicans from positive blood culture bottles. J Clin Microbiol. 2008;46:3508–9.
Fraser M, Borman AM, et al. Evaluation of the commercial rapid trehalose test (GLABRATA RTT) for the point of isolation identification of Candida glabrata isolates in primary cultures. Mycopathologia. 2012;173:259–64.
Johnson EM. Rare and Emerging Candida Species. Current Fungal Infection Reports. 2009;3:152–9.
Hata DJ, Hall L, Fothergill AW, et al. Multicenter evaluation of the new VITEK 2 Advanced Colorimetric Yeast Identification Card. J Clin Micro. 2007;45(4):1087–92.
Vyzantiadis T-AA, Johnson EM, Kibbler CC. From the patient to the clinical mycology laboratory: how can we optimise microscopy and culture methods for mould identification. J Clin Pathol. 2012;65:475–83.
Varga J, Houbraken J, et al. Aspergillus calidoustus sp. nov., causative agent of human infections previously assigned to Aspergillus ustus. Eukaryot. Cell. 2008;7:630–8.
Balajee SA, Gribskov J, et al. Mistaken identity: Neosartorya pseudofischeri and its anamorph masquerading as Aspergillus fumigatus. J Clin Microbiol. 2005;43:5996–9.
Balajee SA, Lindsley MD, et al. Nonsporulating clinical isolate identified as Petromyces alliaceus (Anamorph Aspergillus alliaceus) by morphological and sequence-Based Methods. J Clin Microbiol. 2007;45:2701–3.
Hong SB, Go SJ, et al. Polyphasic taxonomy of Aspergillus fumigatus and related species. Mycologia. 2005;97:1316–29.
Tavanti A, Davidson AD, et al. Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol. 2005;43:284–92.
Balajee SA, Gribskov JL, et al. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot Cell. 2005;4:625–32.
Borman AM, Petch R, et al. Candida nivariensis, an emerging pathogenic yeast with multi-drug resistance to antifungal agents J. Clin Microbiol. 2008;46:933–8.
Barton RC, Borman AM, et al. Isolation of the fungus Geosmithia argillacea in sputum of people with cystic fibrosis. J Clin Microbiol. 2010;48:2615–7.
• Balajee SA, Borman AM, et al. Sequence-based identification of Aspergillus, Fusarium and Mucorales species in the clinical mycology laboratory: where are we and where should we go from here? J Clin Microbiol. 2009;47:877–84. Good overview of the current thinking on the most appropriate loci for molecular identification of Aspergillus, Fusarium and the mucorales.
Borman AM, Linton CJ, et al. Molecular identification of pathogenic fungi. J Antimicrob Chemother. 2008;61 Suppl 1:i7–12.
Linton CJ, Borman AM, et al. Molecular identification of unusual pathogenic yeast isolates by large ribosomal subunit gene sequencing: 2 years of experience at the United kingdom mycology reference laboratory. J Clin Microbiol. 2007;45:1152–8.
• Borman AM, Linton CJ, et al. Rapid molecular identification of pathogenic yeasts by pyrosequencing analysis of 35 nucleotides of internal transcribed spacer 2. J Clin Microbiol. 2010;48:3648–53. Demonstration that pyrosequencing technology robustly identifies most commonly encountered pathogenic yeasts.
Montero CI, Shea YR, et al. Evaluation of Pyrosequencing ® technology for the identification of clinically relevant non-dematiaceous yeasts and related species. Eur J Clin Microbiol Infect Dis. 2008;27:821–30.
Borman AM, Linton CJ, et al. Pyrosequencing analysis of 20 nucleotides of internal transcribed spacer 2 discriminates Candida parapsilosis, Candida metapsilosis and Candida orthopsilosis. J Clin Microbiol. 2010;48:3648–53.
•• Quiles-Melero I, Garcia-Rodriguez J, et al. Rapid identification of yeasts from positive blood culture bottles by pyrosequencing. Eur J Clin Microbiol Infect Dis. 2011;30:21–4. Proof of concept that pyrosequencing can be applied directly to blood samples.
Johnson EM, Borman AM. Identification of Aspergillus at the species level: the importance of conventional methods; microscopy and culture. pp 55–74. In Aspergillus and Aspergillosis, 2009. Ed. Alessandro Pasqualotto. Springer Press.
O’Donnell K, Sutton DA, et al. Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex. J Clin Microbiol. 2008;46:2477–90.
O’Donnell K, Sarver BA, et al. Phylogenetic diversity and microspehere array-based genotyping of human pathogenic fusaria, including isloates from the 2005–2006 multistate contact lens-associated US keratitis outbreaks. J Clin Microbiol. 2007;45:2235–48.
Lackner M, de Hoog GS, et al. Species-specific antifungal susceptibility patterns of Scedosporium and Pseudallescheria species. Antimicrob Agents Chemother. 2012;56:2635–42.
Kaltseis J, Rainer J, et al. Ecology of Pseudallescheria and Scedosporium species in human-dominated and natural environments and their distribution in clinical samples. Med Mycol. 2009;47:398–405.
Gilgado F, Cano J, et al. Different virulence of the species of the Pseudallescheria boydii complex. Med Mycol. 2009;47:371–4.
Lackner M, Najafzadeh, et al. Rapid identification of Pseudallescheria and Scedosporium strains by using rolling circle amplification. J Clin Microbiol. 2012;78:126–33.
Buitrago MJ, Aguado JM, et al. Efficacy of DNA amplification in tissue biopsy samples to improve the detection of invasive fungal disease. Clin Microbiol Infect. 2012. doi:10.1111/1469-0691.12110.
Rickerts V, Khot PD, et al. Comparison of quantitative real time PCR with sequencing and ribosomal RNA-FISH for the identification of fungi in formalin fixed, paraffin-embedded tissue specimens. BMC Infect Dis. 2011;11:202.
von Lilienfeld-Toal M, Lehmann LE, et al. Utility of a commercially available multiplex real-time PCR assay to detect bacterial and fungal pathogens in febrile neutropenia. J Clin Microbiol. 2009;47:2405–10.
Lucignano B, Ranno S, et al. Multiplex PCR allows rapid and accurate diagnosis of bloodstream infections in newborns and children with suspected sepsis. J Clin Microbiol. 2011;49:2252–8.
Balada-Llasat J-M, LaRue H, et al. Detection of yeasts in blood cultures by the Luminex xTAG fungal assay. J Clin Microbiol. 2012;50:492–4.
Babady NE, Miranda E, et al. Evaluation of Luminex xTAG fungal analyte-specific reagents for rapid identification of clinically relevant fungi. J Clin Microbiol. 2011;49:3777–82.
Trnovsky J, Merz W, et al. Rapid and accurate identification of Candida albicans isolates by use of PNA FISH flow. J Clin Microbiol. 2008;46:1537–40.
Hall L, Le Febre KM, et al. Evaluation of the yeast traffic light PNA FISH probes for identification of Candida species from positive blood cultures. J Clin Microbiol. 2012;50:1446–8.
Goyer M, Lucchi G, et al. Optimization of the pre-analytical steps of Matrix-Assisted Laser adesorption Ionization-Time of Flight Mass Spectrometry identification provides a flexible and efficient tool for identification of clinical yeast isolates in medical laboratories. J Clin Microbiol. 2012;50:3066–8.
Murray PR, Masur H. Current approaches to the diagnosis of bacterial and fungal bloodstream infections in the intensive care unit. Crit Care Medicine. 2012;40:1–6.
Santos C, Paterson RRM, et al. Filamentous fungal characterizations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Applied Microbiol. 2010;108:375–85.
Steensels D, Verhaegen J, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of bacteria and yeasts in a clinical microbiological laboratory: A review. Acta Clin Belg. 2011;66(4):267–73.
Seng P, Drancourt M, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption inonization time-of-flight mass spectrometry. Clin Infect Dis. 2009;49:543–51.
Seyfarth F, Wiegand C, et al. Identification of yeast isolated from dermatological patients by MALDI-TOF mass spectrometry. Mycoses. 2012;5:276–80.
Qian J, Cutler JE, et al. MALDI-TOF mass signatures for differentiation of yeast species, strain grouping and monitoring of morphogenesis markers. Anal Bioanal Chem. 2008;392:439–49.
Marklein G, Josten M, et al. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for fast and reliable identification of clinical yeast isolates. J Clin Microbiol. 2009;47:2912–7.
• Bader O, Weig M, et al. Improved clinical laboratory identification of human pathogenic yeasts by martix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Microbiol Infect. 2011;17:1359–65. Large study of protoemic methods for the identification of yeast and yeast-like fungi.
Firacative C, Trilles L, et al. MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex. PLoS One. 2012;7(5):e37566.
Stevenson LG, Drake SK, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J Clin Microbiol. 2010;48:3482–6.
Pinto A, Halliday C et al. Matrix-assisted laser desorpton ionization-time of flight mass spectrometry identification of yeasts is contingent on robust reference spectra. PloS ONE 6(10): e25712. doi:10.1371/journal.pone.0025712
Borman AM, Szekely A, et al. Epidemiology, antifungal susceptibility and pathogenicity of Candida africana isolates from the United Kingdom. J Clin Microbiol. 2013;51:967–72.
Schrodl W, Heydel T, et al. Direct analysis and identification of pathogenic Lichtheimia species bu matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry. J Clin Microbiol. 2012;50:419–27.
Marchetti-Deschmann M, Winkler W, et al. Using spores for Fusarium spp. classification by MALDI-based intact cell/spore mass spectrometry. Food Technol Biotechnol. 2012;50:334–42.
Alanio A, Beretti J-L, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species. Clin Microbiol Infect. 2011;17:750–5.
Alshawa K, Beretti J-L, et al. Successful identification of clinical dermatophyte and Neoscytalidium species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2012;50:2277–81.
Coulibaly O, Marinach-Patrice C, et al. Pseudallescheria / Scedosporium complex species identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Medical Mycology. 2011;49:621–6.
Marinach-Patrice C, Lethuillier A, et al. Use of mass spectrometry to identify clinical Fusarium isolates. Clin Microbiol Infect. 2009;15:634–42.
•• Lau AF, Drake SK, et al. Development of a clinically comprehensive database and a simple procedure for identification of molds from solid media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2013;51:828–34. This paper describes a simplified technique for the proteomic analysis of filamentous fungi that considerably enhances rapid identification of clinical isolates.
Fothergill A, Kasinathan V, et al. Rapid identification of bacteria and yeasts from positive-blood-culture bottles by using a lysis-filtration method and matrix-assisted laser desorption ionization-time of flight mass spectrum analysis with the SARAMIS database. J Clin Microbiol. 2013;51:805–9.
• Spanu T, Posteraro B, et al. Direct MALDI-TOF Mass Spectrometry Assay of Blood Culture Broths for Rapid Identification of Candida Species Causing Bloodstream Infections: an Observational Study in Two Large Microbiology Laboratories. J Clin Microbiol. 2012;50:176–9. Large two centre study confirming utility of proteomic analysis for rapid identification of yeast directly from blood culture.
•• Yan Y, He Y, et al. Improved identification of yeast species directly from positive blood culture media by combining Sepsityper specimen processing and Microflex analysis with the matrix-assisted laser desorption ionisation Biotyper system. J Clin Microbiol. 2011;49:2528–32. Proof of concept that proteomic identification of yeast can be routinely applied directly to positive blood cultures.
Ferroni A, Suarez S, et al. Real –time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2010;48:1542–8.
Marinach-Patrice C, Fekkar A et al. Rapid species diagnosis for invasive candidiasis using mass spectrometry. 2010; PloS One:e8862.
Dhiman N, Hall L, et al. Performance and cost analysis of matix-assisted laser desporption ionization-time of flight mass spectrometry for routine identification of yeast. J Clin Microbiol. 2011;49:1614–6.
We are grateful to the other members of the UK MRL for their assistance with data collation and phenotypic and molecular analyses of isolates.
Compliance with Ethics Guidelines
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.
About this article
Cite this article
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
- Diagnostic challenges
- Invasive fungal infections
- PCR assays