Table 1.

Summary of rapid assays for fungi identification and invasive fungal infections (IFIS) diagnosis.

Invasive fungal infections and non-culture based assays in laboratory mycology
Suspected fungi and patients samples		Conventional microscopic examination	Immuno assays	Molecular assays
Candida spp. or other fungal insolates	Positive blood culture or isolates from primarly sterile regions			PNA FISH – QuickFISH (20 min) MALDI-TOF MS (20–60 min)
Candida spp. infection	Serum	Positive blood culture/Bactec + Gram staining (24–48 h)	Screening – Ag detection by ICT (20 min) Candida MN Ag/anti Candida MN Ab-biomarkers by ELISA (3–4 h) 1,3 β-D-glucan – chromogenic, quantitative enzyme immunoassay (EIA) (40 min)	Standard, nested, real-time or multiplex PCR (1 h directly from positive blood cultures – 3 h for sera samples)
Cryptococcus spp.infection	Cerebrospinal fluid/ Sputum	Indian ink preparation of CSF wet mounts (1 h) Standard CSF, sputum or skin culture (48–72 h)	Screening – Ag detection by ICT (≤ 10 min) Latex agglutination tests	Multiplex PCR analysis of CSF (1 h) Quantitative PCR (q-PCR) (within 3 h)
Aspergillus spp. infection	BAL fluid/ Sputum/ Blood Tissues	Standard BAL fluid or sputum culture (4–7 days)	Screening – Ag detectionby ICT (20 min)	Standard, nested, real-time, quantitative or multiplex PCR (4–8 h)
Pneumocystis jirovecii infection	BAL fluid/ Induced sputum/ Serum/ Oropharyngeal wash fluid	Standard Wright-Giemsa and modified Giemsa stain methods of BAL fluid or induced sputum (up to 60 min)	Direct immunofluorescence assay 1,3 β-D-glucan – chromogenic, quantitative enzyme immunoassay (EIA) (40 min)	Standard, nested, real-time, quantitative or multiplex PCR (2.5–4 h)

ICT: immunochromatographic test; Ag: antigen; MALDI-TOF MS: Matrix-assisted laser desorption ionization-time of flight mass spectrometry; PNA FISH: peptide nucleic acid fluorescent in situ hybridization.