[Ecology and the genetic structure of sympatric leishmania species circulating in the intra-continental deserts of the south Palaearctic region]

A PCR fingerprinting approach with single non-specific primers--(GTG)5 and T3B--was apply to investigate variations in the genotyping of three species of Leishmania species within the Rhombomys opimus area. Forty-three strains of Leishmania major, L. turanica, and L. gerbilli circulating among great gerbils in Turkmenistan, Uzbekistan, Kazakhstan, and Mongolia were examined. PCR fingerprint revealed a high genetic intraspecific heterogeneity among L. turanica strains. Three groups of strains were clearly identified. The strains from Mongolia greatly differed from other L. turanica ones. The second group was formed by strains from Kazakhstan, they also demonstrated rather different patterns. L. turanica strains from Turkmenistan and Uzbekistan showed only minor differences, but greatly different from those from Kazakhstan and Mongolia. The groups identified by the PCR fingerprint correlate with the conditions of circulation: the duration of a transmission season and as the result of different periods of retention of Leishmania in the skin of great gerbils, as well as the presence or absence of L. major as coexisting species. There were no differences between L. turanica strains isolated from different hosts in the same geographical region, as well as between L. turanica strains isolated in the hyper- or meso and hypoendemic foci. There was no correlation between the genotypic and phenotypic characteristics of L. turanica. No intraspecific polymorphism was found among L. major and L. gerbilli strains from different geographical regions within the great gerbil area.

Molecular epidemiology and population genetics in Leishmania

Polymorphic DNA sequences have been amplified using different PCR-based techniques and used for species identification, strain discrimination and population genetic studies in Leishmania. A PCR fingerprinting method that uses single non-specific primers generates species-specific banding patterns with some intraspecies variation. This approach can be used to identify Leishmania species and also to discriminate strains of different Leishmania species. Cultivation of the parasites is, however, mandatory. PCR-restriction fragment length polymorphism of the internal transcribed spacer (ITS) in the ribosomal operon differentiates all Leishmania species, except members of the L. donovani and L. brasiliensis complexes. ITS-single-strand conformation polymorphism or ITS sequencing can detect strain specific-variation (except in L. infantum); culturing is not required. Species of Leishmania exhibit different degrees of genetic variation (L. tropica > L. aethiopica > L. major > L. donovani). Population analysis using co-dominant DNA markers developed by sequence-confirmed amplified region analysis revealed a primarily clonal structure in a L. donovani population from Sudan and suggested that occasional recombination events may occur in this population.

Leishmania donovani: intraspecific polymorphisms of Sudanese isolates revealed by PCR-based analyses and DNA sequencing

Four polymerase chain reaction (PCR)-based approaches were used to analyze diversity within 23 Sudanese isolates of Leishmania donovani. Methods compared were fingerprinting with single nonspecific primers, restriction analysis of the amplified ribosomal internal transcribed spacer (ITS) locus, single-stranded conformation polymorphism (SSCP), and sequencing of the ITS region. When PCR fingerprinting and restriction analysis of ITS were applied, highly similar fragment patterns were observed for all strains of L. donovani studied. The ITS1 locus gave five different SSCP profiles among the 23 Sudanese isolates, whereas the ITS2 locus was highly conserved with the exception of 1 isolate. Strains of L. donovani derived from other geographical areas were found to have different ITS2 patterns. SSCP analysis correlated well with results of DNA sequencing and confirmed that SSCP was able to detect genetic diversity at the level of a single nucleotide. SSCP had advantages over the other methods employed for investigation of sequence variation within the species L. donovani. There was no correlation between the form of clinical manifestation of the disease and the PCR fingerprinting, ITS-RFLP, or ITS-SSCP characteristics.

Molecular and conventional taxonomy of the Microsporum canis complex

The validity of taxa around Microsporum canis was evaluated by a combination of phenetic and molecular methods. Morphological and physiological features were compared with results of sequencing of the internal transcribed spacer (ITS) region of the ribosomal operon, polymerase chain reaction (PCR) fingerprinting and amplified fragment length polymorphism (AFLP) analysis. The seven species investigated seem to be infraspecific taxa and were reclassified or synonymized as M. canis (teleomorph: Arthroderma otae), M. ferrugineum, and M. audouinii.

Development of an oligonucleotide probe specific for Trichophyton rubrum

A species-specific DNA probe was developed to detect the dermatophyte species Trichophyton rubrum. The selected oligonucleotide sequence is derived from the highly variable internal transcribed spacer 2 region of the ribosomal DNA operon. The specificity of the non-radioactive labelled oligonucleotide probe was tested against related dermatophytes, other eukaryotic microorganisms and against human DNA. No cross-hybridization was found, and hybridization signals were invariably detected in all T. rubrum strains investigated. In addition, no homologous sequences were found searching the EMBL database. Experiments to establish a method for isolating DNA directly from clinical specimens gave successful amplification and hybridization products in about 30% of the samples.

Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region

The internal transcribed spacer (ITS) region, covering the ITS1, ITS2 and 5.8S ribosomal DNA was used to evaluate phylogenetic relationships within the fungal family Arthrodermataceae. Sequences of variable length, ranging between 522 and 684 base pairs were aligned. An unrooted consensus tree based on parsimony analysis showed Trichophyton to be polyphyletic, and Microsporum to be paraphyletic. Non-monophyly of these two genera is in conflict with traditional classification. But this relation is not strongly supported by bootstrap analysis. Phylogenetic analysis showed that the two known members of the genus Epidermophyton grouped widely apart from each other. Within Trichophyton, our results suggest a separation of human pathogenic species and primarily geophilic species. Bootstrap support for these two groups is fairly high and both groups are recognized by current taxonomy. Three lineages were revealed within the T. mentagrophytes species complex. Microsporum canis, M. audouinii and M. equinum were found to be closely related. The topology of the tree was robust to various methods of analysis (parsimony and distance) and a different weighting scheme. Weighting of transversions over transitions did not improve the status of poorly supported branches of the tree.

Molecular phylogeny and taxonomy of medically important fungi

Some recent advances in study of molecular evolution and taxonomy of human pathogens are discussed. In systemic Onygenales as well as in Chaetothyriales, pathogenic species are phylogenetically intermingled with non-pathogenic taxa. When a teleomorph of Coccidioides immitis is eventually found, it is predicted to resemble Uncinocarpus, a genus otherwise comprising environmental species. In the dermatophytes, Trichophyton and Microsporum are paraphyletic, whereas Epidermophyton is polyphyletic. On the basis of 18S and ITS rDNA sequencing data, Exophiala anamorphs (black yeasts) are confirmed to be closely related to the ascomycete genus Capronia. The related neurotropic species Cladophialophora bantiana is remarkable in consistently having introns in its 18S rDNA gene.