Development and characterization of complex DNA fingerprinting probes for the infectious yeast Candida dubliniensis

Using a strategy to clone large genomic sequences containing repetitive ele ments from the infectious yeast Candida dubliniensis, the three unrelated s equences Cd1, Cd24, and Cd25, with respective molecular sizes of 15,500, 10 ,000, and 16,000 bp, were cloned and analyzed for their efficacy as DNA fin gerprinting probes. Each generated a complex Southern blot hybridization pa ttern with endonuclease-digested genomic DNA. Cd1 generated an extremely va riable pattern that contained all of the bands of the pattern generated by the repeat element RPS of Candida albicans. We demonstrated that Cd1 does n ot contain RPS but does contain a repeat element associated with RPS throug hout the C. dubliniensis genome. The Cd1 pattern was the least stable over time both in vitro and in vivo and for that reason proved most effective in assessing microevelution. Cd24, which did not exhibit microevolution in vi tro, was highly variable in vivo, suggesting in vivo-dependent microevoluti on. Cd25 was deemed the best probe for broad epidemiological studies, since it was the most stable over time, was the only truly C. dubliniensis-speci fic probe of the three, generated the most complex pattern, was distributed throughout all C. dubliniensis chromosomes, and separated a worldwide coll ection of 57 C. dubliniensis isolates into two distinct groups. The presenc e of a species-specific repetitive element in Cd25 adds weight to the alrea dy substantial evidence that C. dubliniensis represents a bona fide species .