PCR fingerprinting of Trichophyton mentagrophytes var. interdigitale using polymorphic subrepeat loci in the rDNA nontranscribed spacer

• Published in: Journal of medical microbiology Vol. 55; no. 10; pp. 1349 - 1355
• Main Authors: Jackson, Colin J, Mochizuki, Takashi, Barton, Richard C
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.10.2006; Society for General Microbiology
• Subjects: Belgium; Biological and medical sciences; DNA Fingerprinting - methods; DNA, Fungal - genetics; DNA, Intergenic; DNA, Recombinant - genetics; Fundamental and applied biological sciences. Psychology; Humans; India; Infectious diseases; Japan; Medical sciences; Microbiology; Miscellaneous; Molecular Sequence Data; Mycological Typing Techniques - methods; Mycology; Polymerase Chain Reaction; Polymorphism, Genetic; Species Specificity; Tandem Repeat Sequences; Tinea - microbiology; Trichophyton - classification; Trichophyton - genetics; United Kingdom; Fungi; Polymerase chain reaction; Microbiology; Fingerprint method; Ribosomal DNA; Trichophyton mentagrophytes; Fungi Imperfecti; Thallophyta
• ISSN: 0022-2615; 1473-5644
• DOI: 10.1099/jmm.0.46691-0

1 Institute of Biological Sciences, University of Wales, Aberystwyth, Wales, UK 2 Department of Dermatology, Kanazawa Medical University, Uchinada, Japan 3 Mycology Reference Centre, Department of Microbiology, General Infirmary, and University of Leeds, Leeds, UK Correspondence Colin J. Jackson coj{at}aber.ac.uk Received 20 April 2006 Accepted 11 July 2006 The sequence of the nontranscribed spacer (NTS) region of the rDNA of Trichophyton mentagrophytes var. interdigitale strain 2111 was determined, and three individual subrepeat loci identified. The first repeat region contained eight tandem copies of a degenerate 33–43 bp sequence, whilst the second had two complete and two partial 300 bp repeats. The third locus contained six tandemly repetitive elements of between 67 and 89 bp, which showed sequence identity to the TrS2 repeats of Trichophyton rubrum . PCR amplification of the individual repetitive regions from 42 random isolates of T. mentagrophytes var. interdigitale identified fragment length polymorphisms at each locus. Sequence analysis of the PCR products revealed that the size variations resulted from differences in the copy number of each of the three sets of subrepeat elements, TmiS0, TmiS1 and TmiS2. In addition, some indels were present in the flanking regions of the TmiS1 repeats. Combining PCR fingerprints from each of the three polymorphic loci produced a total of 19 individual strain profiles. The method was rapid, reproducible and discriminatory, and the fragment patterns simple to interpret. PCR fingerprint analysis of variable tandem repeat loci in the T. mentagrophytes var. interdigitale NTS represents a valuable molecular typing method for future epidemiological investigations in this species. Abbreviations: LSU, large subunit; NTS, nontranscribed spacer; SRE, subrepeat element; SSU, small subunit; VIR, variable internal repeat. The GenBank/EMBL/DDBJ accession number for the NTS region of T. mentagrophytes var. interdigitale , containing the coordinates of the three subrepeat loci, is DQ486866. Supplementary data are available with the online version of this paper.