Strain identification of Trichophyton rubrum by specific amplification of subrepeat elements in the ribosomal DNA nontranscribed spacer

Trichophyton rubrum is the commonest cause of dermatophytosis of skin and n ail tissue. Molecular characterization of the T, rubrum ribosomal DNA nontr anscribed-spacer region revealed two novel tandemly repetitive subelements (TRSs): TRS-1, containing a 27-bp palindromic sequence, and TRS-21. Specifi c amplification of TRS-1 produced strain-characteristic banding patterns (P CR types), with 21 TRS-1 PCR types recognized from 101 clinical isolates. F our simple patterns representing 1 to 4 copies of TRS-1 accounted for 75 (7 5%) of all 101 strains, whereas more complex patterns were observed for 21 (20%) of the 101 isolates. The copy number of TRS-2 was 0 to 3 repeats per cistron, with a majority of isolates having two copies of this element. Ele ven isolates were polymorphic for TRS-2, and in combination, 23 separate PC R types were recognized by amplification of both TRS-1 and TRS-2. The PCR p atterns from both elements were stable and reproducible. Elements with homo logy to TRS-1 were present in three phylogenetically related species, Trich ophyton violaceum, Trichophyton gourvilli, and Trichophyton soudanense, but these elements were not identified in other dermatophyte taxa, There was n o clear correlation of PCR type with specimen (skin or nail tissue), but ce rtain PCR types appeared to show a bias in geographic distribution. This ne w method of typing T, rubrum will enable important questions about pathogen esis and epidemiology of this fungus to be addressed.