Identifying Paracoccidioides phylogenetic species by PCR-RFLP of the alpha-tubulin gene.

Paracoccidioidomycosis is an important systemic fungal infection that occurs throughout Latin America. The etiological agents comprise a species complex that includes two major groups: P. brasiliensis (including subgroups S1, PS2, and PS3) and P. lutzii. A great number of phenotypes may overlap, especially among closely related groups, discouraging the use of morphology alone for species recognition. To overcome this problem, here we propose identifying cryptic Paracoccidioides spp. using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the alpha-tubulin (TUB1) gene. In silico analysis of 90 TUB1 sequences led to the identification of two restriction enzymes with the potential to identify Paracoccidioides: Bcl I and Msp I. A portion of the TUB1 gene was amplified and double digested in vitro with the Bcl I and Msp I endonucleases, which generated four different electrophoretic patterns corresponding to the four main genetic groups: S1, PS2, and PS3 of P. brasiliensis and P. lutzii. The major P. brasiliensis group recognized was S1 (n = 17; 42.5%), followed by PS2 (n = 9; 22.5%) and PS3 (n = 6; 15%). A total of eight (20%) P. lutzii isolates were identified, mainly from midwestern Brazil. Our data revealed that TUB1-RFLP is an efficient, fast, and inexpensive tool for identifying Paracoccidioides spp., which may be directly applied to the molecular epidemiological studies of paracoccidioidomycosis.