A retrotransposon-derived probe for discriminating strains of Cryptococcus neoformans

Hybridization of digested DNA to probes derived from repeated sequences has proven to be an extremely powerful epidemiologic tool for studying the relatedness of fungi. The dispersed nature of these sequences throughout the genome provides the discriminatory power for distinguishing two independent isolates from each other based on banding pattern. The genome of Cryptococcus neoformans contains a number of classes of transposable elements, which are often present in multiple copies. We characterized a probe related to the Ty3/gypsy class of transposable elements called TCN1 and used it to screen multiple isolates from all four serotypes of C. neoformans. DNA with TCN1 homology could be amplified from each isolate of serotypes A and D and all isolates hybridized to a probe derived from TCN1. Isolates from serotype B and C were also tested for the presence of a TCN1 homolog, however, only some of these isolates yielded both a TCN1-specific PCR product or hybridization signal. Comparison of the TCN1 hybridization patterns of serotypes A and D to multiple RAPD patterns of the same isolates suggested that TCN1 was more discriminating and therefore, a useful epidemiological tool.