Restriction fragment length polymorphisms in the ribosomal gene spacers of Trypanosoma cruzi and Trypanosoma conorhini

Identification of Leishmania species by high-resolution DNA dissociation in cases of American cutaneous leishmaniasis

Background

American cutaneous leishmaniasis is an infectious dermatosis caused by protozoa of the genus Leishmania, which comprises a broad spectrum of clinical manifestations depending on the parasite species involved in the infections and the immunogenetic response of the host. The use of techniques for amplification of the parasites DNA based on polymerase chain reaction polymerase chain reaction and the recent application of combined techniques, such as high-resolution DNA dissociation, have been described as a viable alternative for the detection and identification of Leishmania spp. in biological samples.

Objectives

To identify the Leishmania species using the polymerase chain reaction high-resolution DNA dissociation technique in skin biopsies of hospital-treated patients, and compare with results obtained by other molecular identification techniques.

Methods

A retrospective study assessing patients with suspected American cutaneous leishmaniasis seen at a hospital in São Paulo/Brazil was conducted. The paraffin blocks of 22 patients were analyzed by polymerase chain reaction high-resolution DNA dissociation to confirm the diagnosis and identify the species.

Results

Of the 22 patients with suspected American cutaneous leishmaniasis, the parasite was identified in 14, comprising five cases (35.6%) of infection by L. amazonensis, four (28.5%) by L. braziliensis, two (14.4%) by L. amazonensis + L. infantum chagasi, two (14.4%) by L. guyanensis, and one (7.1%) by Leishmania infantum chagasi. In one of the samples, in which the presence of amastigotes was confirmed on histopathological examination, the polymerase chain reaction high-resolution DNA dissociation technique failed to detect the DNA of the parasite.

Study limitations

The retrospective nature of the study and small number of patients.

Conclusions

The method detected and identified Leishmania species in paraffin-embedded skin biopsies with a sensitivity of 96.4% and could be routinely used in the public health system.

The Trypanosoma cruzi genome; conserved core genes and extremely variable surface molecule families

The protozoan parasite Trypanosoma cruzi is an important but neglected pathogen that causes chagas disease, which affects millions of people, mainly in latin America. The population structure and epidemiology of the parasite are complex, with much variability among strains. The genome sequence of a reference strain, CL Brener, was published in 2005, and the availability of this sequence has both revealed the complexity of the parasite genome and greatly facilitated research into parasite biology and pathogenesis, by making the sequences of more than 8000 core genes available. The T. cruzi genome is highly repetitive, which has resulted in inaccuracies in the genome sequence, and attempts have been made to provide a deeper analysis of repeated genes as a complement to the genome sequence. The genome was found to be organized in stable core regions containing housekeeping and other genes, surrounded by highly repetitive, often sub-telomeric highly variable regions containing multiple members of large families of surface molecule genes. Comparative sequencing of T. cruzi strains has been initiated and the results show that the core gene content of the parasite is highly conserved, but that much sequence variability, 3-4% difference at the DNA level on average between strains in coding regions, is present. The additional genomes will improve the understanding of parasite biology and epidemiology.

Detection and genotyping of Giardia intestinalis isolates using intergenic spacers(IGS)-based PCR

Giardia intestinalis infections arise primarily from contaminated food or water. Zoonotic transmission is possible, and at least 7 major assemblages including 2 assemblages recovered from humans have been identified. The determination of the genotype of G. intestinalis is useful not only for assessing the correlation of clinical symptoms and genotypes, but also for finding the infection route and its causative agent in epidemiological studies. In this study, methods to identify the genotypes more specifically than the known 2 genotypes recovered from humans have been developed using the intergenic spacer (IGS) region of rDNA. The IGS region contains varying sequences and is thus suitable for comparing isolates once they are classified as the same strain. Genomic DNA was extracted from cysts isolated from the feces of 5 Chinese, 2 Laotians and 2 Koreans infected with G. intestinalis and the trophozoites of WB, K1, and GS strains cultured in the laboratory, respectively. The rDNA containing the IGS region was amplified by PCR and cloned. The nucleotide sequence of the 3' end of IGS region was determined and examined by multiple alignment and phylogenetic analysis. Based on the nucleotide sequence of the IGS region, 13 G. intestinalis isolates were classified to assemblages A and B, and assemblage A was subdivided into A1 and A2. Then, the primers specific to each assemblage were designed, and PCR was performed using those primers. It detected as little as 10 pg of DNA, and the PCR amplified products with the specific length to each assemblage (A1, 176 bp; A2, 261 bp; B, 319 bp) were found. The PCR specific to 3 assemblages of G. intestinalis did not react with other bacteria or protozoans, and it did not react with G. intestinalis isolates obtained from dogs and rats. It was thus confirmed that by applying this PCR method amplifying the IGS region, the detection of G. intestinalis and its genotyping can be determined simultaneously.

Comparative karyotyping as a tool for genome structure analysis of Trypanosoma cruzi

As a part of the Trypanosoma cruzi genome project, 239 genetic markers were hybridised to PFGE separated DNA from T. cruzi, in order to determine the number and size of chromosomes and to aid the assembly of the genome sequence. We used three strains, T. cruzi IIe CL Brener (the genome project reference strain) and two T. cruzi I strains, Sylvio X10/7 and CAI/72, to perform a comparative study of their karyotypes and to determine marker linkage. A densitometry analysis of the separations estimated the total chromosome numbers to be 55 in CL Brener and 57 in the two other strains. In all, 45 markers hybridised to single chromosomal bands and 103 markers to two bands in CL Brener, while the number of markers in Sylvio X10/7 and CAI/72 were 102/68 and 61/105, respectively. Size differences between homologous chromosomes were often large, up to 1900 kb (173%). The average difference was 36% for CL Brener and 23.5% for the T. cruzi I strains. Larger differences in CL Brener are consistent with a recent hybrid origin. Forty markers distributed into 15 linkage groups were found to identify specific chromosomes or chromosomes pairs. While the same markers are generally linked in all three strains, the sizes of the chromosomes vary extensively, indicating large chromosomal rearrangements. These data provide valuable information for the finishing of the CL Brener genome sequence.

Phytomonas and other trypanosomatid parasites of plants and fruit

Trypanosomatid parasites are fairly common in the latex, phloem, fruit sap, seed albumen, and even in the nectar, of many plant families. They are transmitted to the plants in the saliva of phytophagous hemipterous bugs (Insecta). Morphologically, plant trypanosomatids have no special characteristic, except perhaps a very twisted cell body. Most occur in plants as promastigotes and a few as choanomastigotes. It is still controversial whether or not they are pathogenic in lactiferous plants or fruit, but it is certain that the phloem parasites are pathogenic in coconut palms and coffee bushes. In these plants, they cause lethal diseases responsible for the destruction of many plantations in Central and South America, but fortunately nowhere else in the world. Probably more than one genus of Trypanosomatidae is represented among the plant parasites. The most important is certainly Phytomonas, but Leptomonas, Crithidia and Herpetomonas may also be present. The distinction between them is difficult and only recently have molecular markers become available to help in their identification. At present, Phytomonas can be identified by DNA hybridization with a specific probe (SL3') complementary to a sequence of the mini-exon or spliced leader gene. The development of a polymerase chain reaction coupled to SL3' hybridization has facilitated the detection of Phytomonas in plants. The phylogeny of Phytomonas is still being worked out. For the moment it can only be said that the genus is very close to Herpetomonas.

Trypanosoma evansi and T. equiperdum: distribution, biology, treatment and phylogenetic relationship (a review)

Trypanosoma evansi and T. equiperdum were compared regarding their ultrastructure, their mammalian hosts, way of transmission, pathogenicity, diagnosis and treatment, and biochemical and molecular characteristics. Electron microscopic investigation revealed no ultrastructural differences between the two species except that there were more coated vesicles in the flagellar pocket of T. equiperdum. Biological, biochemical and molecular studies were reviewed and exhibited many similarities between T. evansi and T. equiperdum. The most prominent differences between the two species are the presence of maxicircles in T. equiperdum, which are missing in T. evansi, and the route of transmission. While T. evansi is transmitted by biting flies, T. equiperdum is transmitted from one equine host to another during copulation when mucous membranes come into contact. Otherwise the two species are remarkably similar. The phylogenetic relationship between the two species and T. b. brucei is being discussed, and the hypothesis is proposed that T. evansi arose from a clone of T. equiperdum which lost its maxicircles.

Comparative sequence analysis of the intergenic spacer region of cyathostome species

The ribosomal DNA intergenic spacer was amplified by the polymerase chain reaction from 16 cyathostome species using primers derived from conserved regions within the flanking 18S and 26S rRNA genes. This generated a 1.5-2.5 kb fragment which was sequenced from five species. The areas covering the 26S and 18S rRNA genes were more than 99% similar among the five species. Furthermore, in all species there existed a highly conserved region of approximately 380 bp at the 3' end of the intergenic spacer. Subsequently, two cyathostome-specific primers were designed to amplify a smaller, more variable region of the intergenic spacer. Eleven further species were amplified using these primers and analysis showed that sequence similarities varied from 40 to 97% between species. The sequence information obtained in this study is being used to develop a PCR-based assay for the differentiation of preparasitic stages of cyathostomes.

Polymorphisms in Trypanosoma cruzi: evidence of genetic recombination

The ploidy of Trypanosoma cruzi is until now undetermined although analysis of isoenzymes, molecular karyotype and DNA content suggest diploidy in a very plastic genome. Also, there has been no convincing demonstration of genetic exchange and it has been proposed that reproduction is clonal. We have compared 18 T cruzi stocks and clones from the same area or host by means of isoenzyme analysis (12 loci) and restriction site polymorphisms in and around three glycolytic genes (glyceraldehyde-3-phosphate dehydrogenase, aldolase and glucosephosphate isomerase). The analysis demonstrated the presence of homozygotes and heterozygotes and is compatible with diploidy for these housekeeping genes. This strongly supports the hypothesis of genetic exchange in T cruzi and further elucidates the genetic diversity within natural T cruzi populations.

Intergenic region typing (IRT): a rapid molecular approach to the characterization and evolution of Leishmania

In the New World, Leishmania of the Viannia subgenus cause both cutaneous and mucocutaneous disease. These parasites show considerable intra-species genetic diversity and variation, which complicates taxonomic classification and epidemiology. We have used the variability of the transcribed noncoding regions between the small and large subunit rRNA genes to examine relationships in this group. In a method termed intergenic region typing (IRT), PCR amplification products were obtained for the rapidly evolving 1-1.2-kb internal transcribed spacers (ITS) between the SSU and LSU rRNAs, from 50 parasites isolated from different hosts and geographic areas. Amplified DNAs were digested with 10 different enzymes, and fragment patterns compared after acrylamide gel electrophoresis. High levels of intra- and inter-specific variation were observed, and quantitative similarity comparisons were used to associate different lineages. A complex evolutionary tree was obtained. Some species formed tight clusters (L. equatorensis, L. panamensis, L. guyanensis, L. shawi), while L. braziliensis was highly polymorphic and L. naiffi showed intraspecific distances comparable to the largest obtained within all Viannia. L. colombiensis, L. equatorensis and L. lainsoni clearly represent distinct lineages. Good agreement was obtained with molecular trees based upon isoenzyme or mini-exon repeat sequence comparisons. Overall, IRT appears to be a superb method for epidemiological and taxonomic studies of Leishmania, being sensitive, rapid and quantitative while simultaneously revealing considerable molecular diversity. IRT could also be applied to other nonconserved intergenic regions, including those separating protein-coding genes.

kDNA and rDNA sequences reveal a phylogenetic cluster of species originally placed in different genera of trypanosomatids

Hybridization using kDNA and rDNA sequences as probes was performed to study phylogenetic relatedness of different species of trypanosomatids. Using this approach, we identified five organisms which had been classified as Phytomonas and Herpetomonas that were more closely correlated to each other phylogenetically than to any other species or isolates from either genera. These findings raise doubts about the validity of the current classification of Trypanosomatidae. Finally, we demonstrated the usefulness of kDNA sequences as an alternative to genomic sequences in obtaining phylogenetic information on trypanosomatids.

Evidence for two single copy units in Theileria parva ribosomal RNA genes

Bacteriophage clones containing ribosomal RNA genes of Theileria parva were isolated from genomic DNA libraries. Physical mapping studies revealed 2 ribosomal DNA units, which were distinguishable by restriction enzyme site polymorphisms in flanking sequences. The cloned ribosomal DNA units were mapped to 2 separate T. parva chromosomes. Analysis of sequences contained in lambda EMBL3 recombinants, together with Southern blot analysis of genomic DNA and data on the copy number of the rRNA genes, suggested that the rDNA units were not tandemly repeated. This organisation of ribosomal transcription units is similar to that described for other genera of apicomplexan protozoa, but 2 rDNA units, each containing single copies of the rRNA coding genes, would be the lowest copy number described for any eukaryote in which amplification of rRNA genes is not known to occur. EcoRI restriction fragment length polymorphisms, which were revealed using rRNA gene probes, separated T. parva stocks into 2 categories. Nucleotide sequence analysis of polymerase chain reaction-amplified internal transcribed spacer DNA revealed 2 different ITS sequences derived from rDNA transcription units within the genome of a cloned T. parva parasite. Polymorphism was also observed between ITS sequences amplified from the DNA of different T. parva stocks. A synthetic oligonucleotide derived from T. parva Uganda ribosomal ITS DNA sequences hybridised to DNA from the T. parva Uganda stock, but not to the DNA of the T. parva Muguga stock. This oligonucleotide is potentially useful as a marker for the T. parva Uganda stock.

Detection of trypanosomatid Phytomonas parasitic in plants by polymerase chain reaction amplification of small subunit ribosomal DNA

To improve the diagnosis of Phytomonas infections in plants, we developed a polymerase chain reaction (PCR) assay using synthetic oligonucleotides complementary to conserved sequences of the 18S small subunit ribosomal (SSU) gene. From 10 ng upward of DNA of cultures of Phytomonas isolated from plants, fruits, and insects, PCR amplified an 800-bp DNA band that, after restriction analysis and probe hybridization, proved to be of 18S rDNA Phytomonas origin. PCR was also done with sap samples of tomatoes experimentally infected with Phytomonas, yielding amplified 800-bp ribosomal DNA bands before any flagellate could be detected by microscopic examination of the fruit sap.

Repetitive sequences in the ribosomal intergenic spacer of Trypanosoma cruzi

A fragment of Trypanosoma cruzi ribosomal intergenic spacer (IGS) located at 6.7 kb from the 3' end of the 24S rRNA gene was analyzed. This IGS fragment is characterized by the presence of three types of repetitive elements (designated Spacer Repetitive Elements, SRE), short direct repeats (5-6 bp) and chi-like recombinational sequences. SRE elements are composed of relatively short repeats (43-145 bp) which show variabilities consisting of nucleotide changes, insertions and deletions. SRE-1 element (145 bp) has a short oligo(dA) tail at the end of the repeat and can be found flanked by other SRE elements. SRE elements are species-specific, suggesting that probes based on them may be diagnostic for Trypanosoma cruzi.

Detection of polymorphisms among Theileria parva stocks using repetitive, telomeric and ribosomal DNA probes and anti-schizont monoclonal antibodies

A total of 21 Theileria parva stocks from 6 countries were characterized using T. parva repetitive and ribosomal DNA probes, a Plasmodium berghei telomeric oligonucleotide and a panel of anti-schizont monoclonal antibodies (MAbs). Hybridization of the repetitive DNA probe to Southern blots of EcoRI-digested T. parva DNA revealed 20 different restriction fragment patterns among DNA samples isolated from infections initiated using 16 parasite stocks. The panel of anti-schizont MAbs defined 8 different profiles among schizont-infected lymphoblastoid cell-cultures infected with the same 16 T. parva stocks. Many stocks, which were differentiated by the repetitive DNA probe, could not be distinguished using the anti-schizont MAbs. A cloned T. parva small subunit ribosomal RNA (SSUrRNA) gene probe separated 17 T. parva stocks into 2 groups, exhibiting either 1 or 2 restriction fragments, when hybridized to EcoRI-digested T. parva DNA. When hybridized to PvuII-digested DNA from 8 T. parva stocks, the ribosomal probe identified 4 groups with similar restriction fragment patterns. A synthetic oligonucleotide derived from a P. berghei telomeric sequence hybridized to 7 or 8 size-polymorphic restriction fragments in the EcoRI-digested DNA of most T. parva stocks. The telomeric and ribosomal probes defined the same 4 groups among 8 T. parva stocks as assessed by similarities in restriction fragment patterns. Based on the comparison of repetitive DNA sequences from the T. parva Uganda and Muguga stocks, a synthetic oligonucleotide was developed which distinguished the DNA of the T. parva Uganda stock from that of 4 other T. parva stocks on a positive/negative basis.

The Trypanosoma cruzi ribosomal RNA-encoding gene: analysis of promoter and upstream intergenic spacer sequences

The transcription start point (tsp) of the ribosomal RNA(rRNA)-encoding gene of Trypanosoma cruzi was mapped at 1550 bp upstream from the 18S rRNA coding sequence. The + 1 nucleotide (tsp) was determined to be a guanosine. As described for other eukaryotes, no consensus sequence was found when the putative promoter sequence (-200 to + 50) was compared with that described for Trypanosoma brucei and Crithidia fasciculata. However, a repeated element was found in the upstream intergenic spacer sequence (IGS) of T. cruzi. Motifs, present in this element, exhibit significant homology to the T. cruzi promoter sequence. Furthermore, the same motifs could be found, in a similar sequence organization, within the T. brucei promoter region. Therefore, the data described in this paper strongly indicate that the IGS rDNA (DNA coding for rRNA) organization in trypanosomatids appears similar to that found in higher eukaryotes.

Leishmania: genus identification based on a specific sequence of the 18S ribosomal RNA sequence

The analysis of PvuII restriction patterns of Leishmania spp. and Trypanosoma spp. genomic DNA showed genus distinctive profiles. A specific PvuII site was detected in the 5' domain of 18S ribosomal DNA of Leishmania. A 20-mer oligonucleotide encompassing this PvuII region was synthesized. This sequence, when utilized as probe, on short exposures of dot tests, detected 10(3) whole promastigotes of all Leishmania species analyzed but did not hybridize with T. cruzi or human nucleic acids. Two other oligonucleotides were synthesized to be used as primers for amplification through polymerase chain reaction of the 18S ribosomal DNA region containing the PvuII site. The probes described may be useful for the detection of Leishmania spp. under clinical and epidemiological trials.