Molecular typing for fungi -: a critical review of the possibilities and limitations of currently and future methods

Invasive fungal infections represent an increasing problem in patients with inherited and acquired immunodeficiencies. Molecular biotyping techniques, such as DNA fingerprinting, are useful tools to increase our knowledge of the pathogenic organisms that cause them, and thus to improve their treatment and develop prevention strategies. In the present review, we evaluate and discuss the possibilities and limitations of the methods currently used for biotyping strains of fungal species. These include techniques based on restriction fragment length polymorphism (RFLP) with or without hybridization to probes (Southern), PCR-based techniques, electrophoretic karyotyping (EK), and multilocus enzyme electrophoresis (MLEE). Additionally, we discuss newer techniques that are being developed for the fingerprinting of fungal strains. Among them, we review conformation-based polymorphism scanning methods, such as single-strand conformation polymorphism analysis (SSCP) and heteroduplex mobility assays, sequencing strategies such as multilocus sequence typing (MLST) and DNA microarrays.