Generation of species-specific DNA probes for Leishmania aethiopica

A Leishmania minicircle DNA footprint assay for sensitive detection and rapid speciation of clinical isolates

BACKGROUND

Diversity in clinical outcome, due to different species of Leishmania, and its presence in asymptomatic blood donors in endemic areas warrant development of methods that are sensitive and can rapidly identify infecting species.

STUDY DESIGN AND METHODS

The kinetoplast minicircle DNA is known to have heterogeneity in sequence and is present in many thousands of copies in Leishmania. Fluorescence-based polymerase chain reaction (PCR) was used to amplify minicircle DNA from six Leishmania species from different geographic locations. The sequences were then used to construct a phylogenetic tree. Speciation of 46 blinded parasite clinical isolates from various geographic regions was validated using the assay.

RESULTS

Analysis displayed a distinct cluster for each species or strain. Forty-three of 46 isolates were correctly assigned to the same species identified by isoenzyme electrophoresis. The three untyped isolates were all either new species or samples from a unique geographic region. The minicircles of the three isolates formed new clusters in the tree analysis. Using minicircle DNA as PCR target, the sensitivity of the parasite detection in the spiked blood samples was five parasites per mL.

CONCLUSION

Increased sensitivity and speciation without the need for parasite culture will be useful for diagnosis and treatment in clinical settings.

Molecular biological applications in the diagnosis and control of leishmaniasis and parasite identification

Molecular biology is increasingly relevant to the diagnosis and control of infectious diseases. Information on DNA sequences has been extensively exploited for the development of polymerase chain reaction-based assays for the diagnosis of leishmaniasis and the identification of parasite species. It has also led to the use of cloned antigen for serodiagnosis. It is expected that the sequencing of the Leishmania major genome and the genomes of other Leishmania species will enable important progress in further improving diagnosis and control. The ability to use genome data to clone and sequence genes, which, when expressed, provide antigens for vaccine development, will increase the possibilities for rational vaccine development. Moreover, DNA on its own will provide the basis for the development of DNA vaccines that may overcome some of the problems encountered with protein-based vaccines. One of the greatest threats to parasite control is the development of drug resistance in parasites. Knowing the molecular basis of drug resistance and the ability to monitor its development with sensitive and specific DNA-based assays for 'resistance alleles' may aid maintaining the effectiveness of available anti-Leishmania drugs. Finally, techniques such as microarrays and nucleic acid sequence-based amplification will eventually allow rapid screening for specific parasite genotypes and assist in diagnostic and epidemiological studies.

Chromosome structure and sequence organization between pathogenic and non-pathogenic Leishmania spp

We have used a chromosome fragmentation strategy based on systematic genomic insertions of the rare cutting yeast I-SceI endonuclease to assess structure and sequence organization of homologous chromosomes between evolutionary divergent pathogenic and non-pathogenic Leishmania species. This method was combined to physical mapping and hybridization studies using a number of specific chromosomal markers as probes. Our studies have concentrated on two different chromosomes of Leishmania major (L. major), L. donovani and L. infantum and of the non-pathogenic species L. tarentolae. Specific chromosome fragmentation events at the level of multiple I-SccI genomic integrations indicated that very similar distances separated internal genomic sequences between homologous chromosomes and that distances from chromosome ends were more variable. The order and orientation of genes along the homologous chromosomes were also conserved between species. With only few exceptions, genome organization between pathogenic and non-pathogenic Leishmania species was found to be highly conserved. Genomic comparison of pathogenic and non-pathogenic species may be useful for depicting regions involved in species-specific related pathologies.

Leishmania donovani: development and characterisation of a kinetoplast DNA probe and its use in the detection of parasites

The polymerase chain reaction is used increasingly widely for the diagnosis of both cutaneous and visceral leishmaniasis and for the identification of asymptomatic carriers in the population in endemic disease areas. The use of complex-specific hybridisation probes in conjunction with the polymerase chain reaction increases the specificity as well as the sensitivity of the diagnostic procedure as it discriminates between different infecting Leishmania species. A minicircle kinetoplast DNA probe, B4 Rsa, which hybridizes to all members of the Leishmania (L.) donovani complex has been identified and characterised. It is a segment of a minicircle highly conserved in Bangladeshi and Indian L. (L.) donovani isolates.

An oligonucleotide probe derived from kDNA minirepeats is specific for Leishmania (Viannia)

Sequence analysis of Leishmania (Viannia) kDNA minicircles and analysis of multiple sequence alignments of the conserved region (minirepeats) of five distinct minicircles from L. (V.) braziliensis species with corresponding sequences derived from other dermotropic leishmanias indicated the presence of a sub-genus specific sequence. An oligonucleotide bearing this sequence was designed and used as a molecular probe, being able to recognize solely the sub-genus Viannia species in hybridization experiments. A dendrogram reflecting the homologies among the minirepeat sequences was constructed. Sequence clustering was obtained corresponding to the traditional classification based on similarity of biochemical, biological and parasitological characteristics of these Leishmania species, distinguishing the Old World dermotropic leishmanias, the New World dermotropic leishmanias of the sub-genus Leishmania and of the sub-genus Viannia.

Early parasite containment is decisive for resistance to Leishmania major infection

We investigated the early spread of Leishmania major in various mouse strains. In BALB/c mice, which are extremely vulnerable to L. major infection, the parasites disseminated within 10-24 h from the site of subcutaneous footpad infection in to the popliteal lymph node, spleen, lung, liver and bone marrow. Application of recombinant (r)IL-12 prior to infection prevented the early dissemination of parasites into visceral organs and the animals healed the infection. In three mouse strains tested, C57BL/6, CBA/J and C3H/HeJ, which are all resistant to L. major infection, the parasites remained localized in the footpad and in the draining LN for 3 days without evidence of dissemination. In C57BL/6 mice, depletion of NK1.1+ cells or neutralization of interferon (IFN)-gamma prior to infection led to rapid parasite spreading with kinetics similar to those seen in susceptible animals. Depletion of either CD4+ or CD8+ T cells in vivo prior to infection did not alter the kinetics of dissemination in any mouse strain tested. Experiments with severe-combined immunodeficient mice provided further evidence that parasite containment depends on natural killer cells and IFN-gamma, but is independent of T cells. The finding that all resistant mouse strains restrict the spread of the parasites within the first 24 h after infection strongly suggests that early parasite containment is closely associated with a resistant phenotype. The data show that local restriction of parasites in the pre-T cell phase of the infection is mediated by the innate immune system and suggest that this function plays an important role in the development of a protective T cell response.

Mini-exon gene variation in human pathogenic Leishmania species

We have used polymerase chain reaction to amplify the mini-exon gene repeat from 18 Leishmania strains. DNA sequence analysis of the cloned products reveals high conservation of both the exon and intron (i.e. transcribed region). In contrast, variation is evident in both the length and primary sequence of the non-transcribed spacers. Dermotropic species of the New World subgenus Leishmania possess a 0.3-kb gene that differs from the 0.25-kb gene of New World dermotropic species of the subgenus Viannia. The Old/New World viscerotropic species and Old World dermotropic species possess a 0.4-kb mini-exon gene. However, the genes from the viscerotropic and dermotropic groups may be distinguished on the basis of sequence differences in the non-transcribed spacer. Comparative analysis of the -86 to -1 region from all species has been used to measure relatedness within the genus. In general, all the observed differences correlate with the four major groups of Leishmania (New World dermotropic Leishmania, New World dermotropic Viannia, Old World dermotropic Leishmania and viscerotropic Leishmania). Two of the three repeats cloned from L. donovani show short deletions. The missing sequence is flanked by direct, 7-bp repeats suggesting that the sequences may have been deleted by homologous recombination. Such rearrangements could account for the diversity detected in the non-transcribed spacers of the mini-exon genes.

DNA-based methods for the identification of insect vectors

Many insect vectors are members of complexes composed of morphologically identical sibling species. The identification of individual species, a requirement of epidemiological studies and control programmes, has traditionally relied upon techniques such as chromosomal analysis or isoenzyme typing. Owing to the limitations of these techniques, the last few years have seen many developments in DNA-based technologies for identification. DNA-based protocols have advantages over the other techniques utilized, in that they may identify all insect stages of both sexes using alcohol-preserved, dried, fresh or frozen specimens. The methods ultimately rely upon either DNA probe hybridization or the polymerase chain reaction (PCR). This review describes a number of approaches taken towards the development of these techniques. The aim of these approaches, whether directed or random, is to produce a methodology that is cheap, accurate and easy to use. In this review, the DNA-based techniques developed for the identification of Anopheles gambiae complex mosquitoes are used to illustrate the power of these methods, although, as the review demonstrates, the technology is directly applicable to many other mosquito or insect vectors. In addition, the methods discussed may be utilized for generating additional epidemiological data, such as identification of parasites within the vector or origin of the bloodmeal. A comprehensive survey of the probe systems available for the identification of insect vectors and the disease-causing organisms they transmit to the human population is therefore included. Given further advances in this technology, it may be anticipated that DNA-based approaches to identification may eventually supersede more traditional methodologies in the fields of tropical medicine and parasitology.

Characterization of a tandemly repetitive DNA sequence from Haemonchus contortus

Genomic DNA from the sheep parasitic nematode Haemonchus contortus was shotgun cloned in the plasmid vector pUC18. Recombinants which gave the strongest hybridization signals to 32P-radiolabelled genomic DNA were selected as representatives of the repetitive component of the parasite DNA. One repetitive sequence which hybridized only with DNA from H. contortus and not with DNA from two other sheep nematodes (Trichostrongylus colubriformis and Ostertagia circumcincta) was further characterized by sequencing and dot blot analysis. A related repeat was found in the closely related species Haemonchus placei. Experiments to determine the genomic organization of the repeat showed that it existed in a multi-copy number tandem array. This is the first report on the characterization of repetitive DNA in sheep parasite nematodes.

Intra- and interspecific polymorphisms of Leishmania donovani and L. tropica minicircle DNA

A pair of degenerate polymerase chain reaction (PCR) primers (LEI-1, TCG GAT CC[C,T] [G,C]TG GGT AGG GGC GT; LEI-2, ACG GAT CC[G,C] [G,C][A,C]C TAT [A,T]TT ACA CC) defining a 0.15-kb segment of Leishmania minicircle DNA was constructed. These primers amplified not only inter- but also intraspecifically polymorphic sequences. Individual sequences revealed a higher intraspecific than interspecific divergence. It is concluded that individual sequences are of limited relevance for species determination. In contrast, when a data base of 19 different sequences was analyzed in a dendrographic plot, an accurate species differentiation was feasible.

[Molecular biological techniques in the diagnosis of tropical parasitic diseases]

Recent advances in the development of molecular biological techniques have resulted in their supplementary application for improved diagnosis of tropical parasitic diseases. The main areas of interest are the production of recombinant antigens for immunodiagnosis, and the detection of parasites by hybridization of nucleic acids and by DNA amplification (PCR) in vitro.

Comparison of parasitological and immunological methods in the diagnosis of leishmaniasis in Ethiopia

The sensitivity and specificity of parasite demonstration methods (smear, culture and histology) and serological assays (enzyme-linked immunosorbent assay [ELISA], direct agglutination test and immunoblot) were compared in the diagnosis of leishmaniasis in Ethiopia. Culture was found to be the most sensitive diagnostic method, followed by ELISA, for the diagnosis of cutaneous leishmaniasis (CL). When the clinical type of CL was taken into consideration, serological and parasitological methods were equally good for the diagnosis of diffuse cutaneous leishmaniasis. Overall, the serological assays were not sensitive enough to diagnose all the parasitologically confirmed cases of localized cutaneous leishmaniasis. Both groups of diagnostic methods performed equally well in the diagnosis of visceral leishmaniasis patients. In cases of CL where clinical diagnosis was a problem and histology could not give a definitive diagnosis due to the absence of demonstrable parasites, one of the serological assays, preferably ELISA, was very useful in establishing the final diagnosis.

The use of DNA hybridization for the detection of Leishmania aethiopica in naturally infected sandfly vectors

Hybridization with kinetoplast deoxyribonucleic acid (kDNA) probes was used to detect Leishmania aethiopica in naturally infected sandflies in south-west Ethiopia, an endemic area for cutaneous leishmaniasis. 396 sandflies were dissected; microscopy revealed flagellates in the midgut of 5 Phlebotomus pedifer. The infecting flagellates were confirmed as L. aethiopica by isoenzyme typing. Gut specimens for all dissected sandflies were hybridized with total L. aethiopica kDNA as well as with a cloned kDNA probe specific for L. aethiopica. Samples from sandflies which were found to be infected microscopically also hybridized with the L. aethiopica kDNA probes. One additional sandfly hybridized but was not shown to be infected by microscopical examination. Hybridization experiments with 65 whole squash-blotted sandflies gave results that correlated very well with results obtained using microscopy. Our results indicate that DNA probing is a useful method to detect Leishmania infection in sandfly midguts as well as in whole squash-blotted sandflies, and can be used to follow changes of infection rate. DNA probing is therefore an alternative to microscopy in large-scale epidemiological studies as well as monitoring control programmes aimed at human leishmaniasis.