Application of polymerase chain reaction with specific and arbitrary primers to identification and differentiation of Leishmania parasites

Reverse Epidemiology: An Experimental Framework to Drive Leishmania Biomarker Discovery in situ by Functional Genetic Screening Using Relevant Animal Models

Leishmania biomarker discovery remains an important challenge that needs to be revisited in light of our increasing knowledge on parasite-specific biology, notably its genome instability. In the absence of classical transcriptional regulation in these early-branching eukaryotes, fluctuations in transcript abundance can be generated by gene and chromosome amplifications, which have been linked to parasite phenotypic variability with respect to virulence, tissue tropism, and drug resistance. Conducting in vitro evolutionary experiments to study mechanisms of Leishmania environmental adaptation, we recently validated the link between parasite genetic amplification and fitness gain, thus defining gene and chromosome copy number variations (CNVs) as important Leishmania biomarkers. These experiments also demonstrated that long-term Leishmania culture adaptation can strongly interfere with epidemiologically relevant, genetic signals, which challenges current protocols for biomarker discovery, all of which rely on in vitro expansion of clinical isolates. Here we propose an experimental framework independent of long-term culture termed “reverse” epidemiology, which applies established protocols for functional genetic screening of cosmid-transfected parasites in animal models for the identification of clinically relevant genetic loci that then inform targeted field studies for their validation as Leishmania biomarkers.

Molecular identification of an old clinical isolate of Indian Kala-azar

Molecular characterization is an important task for species identification of the isolates belonging to different Leishmania species. Clinical symptoms, tissue tropism, vector preference, reservoir and geographical distribution may act as distinguishing parameters but not always decisive. On the other hand, modern taxonomic tools employed to divulge characteristics of the genome or protein molecules of the parasite would be convincing and for Leishmania sp., they include nuclear and kDNA buoyant density, multi locus enzyme electrophoresis (MLEE), RAPD, RFLP or use of monoclonal antibodies etc. In the present study, we intend to establish the identification of an old clinical isolate of Indian Kala-azar, familiarly known as 'UR6' by MLEE, RAPD, RFLP and species specific monoclonal antibodies. UR6 has been isolated from a confirmed Kala-azar patient admitted in Calcutta School of Tropical Medicine, Kolkata in 1978. From then it is being regularly used for various scientific studies by the Leishmania Research Group of India and abroad. The isozyme profile of UR6 showed similar electrophoretic mobility that of WHO reference strain for Leishmania tropica, K27. Similar findings were obtained in the RAPD and RFLP assays. Screening with species specific monoclonal antibodies showed its strong reactivity towards L. tropica. The Jaccard's Similarity Indices were calculated.

Species typing in dermal leishmaniasis

Leishmania is an infectious protozoan parasite related to African and American trypanosomes. All Leishmania species that are pathogenic to humans can cause dermal disease. When one is confronted with cutaneous leishmaniasis, identification of the causative species is relevant in both clinical and epidemiological studies, case management, and control. This review gives an overview of the currently existing and most used assays for species discrimination, with a critical appraisal of the limitations of each technique. The consensus taxonomy for the genus is outlined, including debatable species designations. Finally, a numerical literature analysis is presented that describes which methods are most used in various countries and regions in the world, and for which purposes.

Molecular characterization of Leishmania infection in sand flies from Al-madinah Al-munawarah province, western Saudi Arabia

Cutaneous leishmaniasis (CL) is caused by various species of the genus Leishmania. The disease is considered a major health problem in different areas of Saudi Arabia including Al-madinah Al-munawarah province. We aimed to identify Leishmania species isolated from sand fly vectors by molecular analysis. Sand fly sampling was carried out from May 2010 to October 2010 in province of Al-madinah Al-munawarah from four different localities. Female sand flies collected were subjected to DNA extraction followed by molecular analysis using the semi-nested PCR and conventional PCR protocols, respectively, against minicircle kDNA and ribosomal internal transcribed spacer 1 (ITS1-rDNA). The PCR positive specimens against ITS1-rDNA locus were digested for further confirmation of species identification. A total of 2910 sand flies were collected. Phlebotomus papatasi accounted for 93.8% (1673 males and 1057 females), however, the number of Phlebotomus sergenti was only 180 (109 males and 71 females). Sixty-two out of 250 (23.7%) female P. papatasi tested for Leishmania parasite were positive for Leishmania major using the semi-nested PCR method against kDNA. All of the 62 positive specimens produced a band size 650 bp. A 31% of female P. sergenti were positive against kDNA of Leishmania tropica and produced a 720 bp band. These positive P. sergenti for L. tropica DNA produced ITS1-PCR-RFLP profile showed two bands of ∼200 bp and 57 bp which are specific for L. tropica, confirming the presence of L. tropica in P. sergenti. However, the ITS1-PCR-RFLP profile showed two bands of ∼203 bp and 132 bp which are specific for L. major in P. papatasi. We concluded that, the semi-nested PCR method against kDNA and the ITS1-PCR-RFLP analysis are useful tools for molecular identification of both L. major and L. tropica. A multicenter study is necessary in order to evaluate the extent of the disease and functional analysis of new Leishmania genes.

RFLPs of ITS, ITS1 and hsp70 amplicons and sequencing of ITS1 of recent clinical isolates of Kala-azar from India and Bangladesh confirms the association of L. tropica with the disease

Visceral Leishmaniasis or Kala-azar (KA) is a serious health concern in India. In the present study, Restriction Fragment Length Polymorphism (RFLP) of three genetic markers viz., Internal Transcribed Spacer (ITS), ITS1 and heat shock protein 70 (hsp70) have been employed for typing the clinical isolates [n=15] of KA and post Kala-azar Dermal Leishmaniosis (PKDL) collected from India and Bangladesh in the period of 2006-2010. Experimentally, ITS, ITS1 and hsp70 regions of genomes of all the clinical isolates were separately amplified by PCR and then digested with restriction enzymes: ITS with Alu1, EcoR1 and Msp1, ITS1 with Hae III and Rsa1 and hsp70 with Hae III. The resultant fragments were analyzed by agarose gel electrophoresis and the RFLP profiles of the clinical isolates were compared with that of the WHO reference strains for Leishmania donovani (DD8) and Leishmania tropica (K27), respectively. Also, the ITS1 regions of all the clinical isolates along with the two WHO reference strains were sequenced and a phylogram was constructed to ascertain the extent of similarity or dissimilarity. Interestingly, the RFLP profiles of one of the isolates showed a significant homology with K27 and the phylogram revealed its closeness with the same putting credence to our earlier typing of isolates by RAPD method. This observation also supported an earlier report claiming that both the species are responsible for KA in India and thus, emphasizes urgent need for thorough systematic characterization of the clinical isolates of Indian KA as appropriate treatment regime relies primarily on proper diagnosis.

Characterization of the recent clinical isolates of Indian Kala-azar patients by RAPD-PCR method

Leishmaniasis is one of the most important vector borne diseases caused by kinetoplastid protozoa Leishmania sp. Among all forms of Leishmaniasis, Visceral leishmaniasis (VL) or Kala-azar is the severest form of the illness. VL is characterized by fever, hepatosplenomegaly, anaemia, edema, weight loss and invariably fatal if left untreated. Characterization of Leishmania sp. is extremely necessary to understand the epidemiology, taxonomy and population genetics of the parasites which ultimately helps in designing appropriate drug regimen to combat the disease. In this study, we aimed to type the clinical isolates of Leishmania species collected in the period 2006-2010 from patients (n = 9) diagnosed with Kala-azar and post Kala-azar dermal leishmaniasis (PKDL) by RAPD-PCR method using eight selected primers. Genome of the clinical isolates were amplified and electrophoresed in agarose gel. These were compared with the RAPD PCR profiles of WHO reference strains for L. donovani (DD8) and L. tropica (K27) respectively. We calculated the Jaccard's Similarity Coefficient and found one (study code T5) out of nine isolates as L. tropica while the rest were L. donovani. This pilot study supports the earlier single report claiming that both the species are responsible for Kala-azar in India and it also emphasizes the need for more systematic typing of clinical isolates of Indian Kala-azar.

Genotypic characterization of cutaneous leishmaniasis at Al Baha and Al Qasim Provinces (Saudi Arabia)

Fifty samples of skin ulcers were collected from the western region of Saudi Arabia Kingdom (Al Baha and Al Qasim) to study genotypic characterization of Cutaneous Leishmaniasis in this area. Thirty-six samples were recorded as Leishmania isolates. The same isolates were subsequently tested with fingerprinting with single arbitrary primers. The primers used derived from the core sequence of the phage M13, and the repeat sequences (GTG)5 and (GACA)4. The 36 isolates were all identified as Leishmania major (n = 25 isolates) or Leishmania tropica (n = 11 isolates). All produced polymorphic patterns, which were grouped depending on the species they belonged to, next to the relevant well-characterized strains of the same species. Within the L. major and L. tropica group the subgroupings formed were mainly related to the geographical origin of the strains. A nested polymerase chain reaction-based schizodeme method for identifying Leishmania kinetoplast minicircle classes was used as a diagnostic tool for L. major and L. tropica.

Identification of Old World Leishmania spp. by specific polymerase chain reaction amplification of cysteine proteinase B genes and rapid dipstick detection

We used the cysteine proteinase B (cpb) gene family of the trypanosomatid genus Leishmania as a target to develop rapid, specific, and easy-to-use polymerase chain reaction (PCR) tests to discriminate Leishmania infantum, Leishmania donovani, Leishmania tropica, Leishmania aethiopica, and Leishmania major. Identification of all 5 Old World species and validation of intraspecies variability are features lacking in other species-specific PCRs. Amplicon analysis was done on agarose gels and was further simplified by using an oligochromatography dipstick to detect L. infantum and L. donovani products. Because the analytical sensitivity is lower than that of certain other species- and genus-specific PCRs, our assays are especially valuable for use on cultured isolates or directly on cryostabilates. As such, they can be implemented by research and health centers having access to culturing, DNA isolation, and PCR.

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.

Genetic variation in populations of Leishmania species in Brazil

The population structure of strains of Leishmania (Viannia) braziliensis sensu lato from Pará State and Paraná State in Brazil, of L. (V.) shawi and L. (Leishmania) amazonensis from Pará State, and the relationships of type strains of the subgenera L. (Viannia) and L. (Leishmania) were examined by the random-amplified polymorphic deoxyribonucleic acid (RAPD) technique. Four different primers (M13-40, QG1, L15996 and delta gt11R) were used. The bands were analysed using the neighbor-joining (NJ) and unweighted pair-group method with arithmetic averages (UPGMA) algorithms of the MEGA package. The topology of the NJ and UPGMA trees was very similar but they were not always identical. Both trees differentiated the standard strains of the different species. Strains from the same location were grouped together only in the UPGMA phenogram of the M13-40 primer. L. (V.) braziliensis isolates from Paraná State were genetically closer to those from Paragominas, Pará State than to those from the Amazonian regions of Carajás in Pará State and Peru. The relationship was not dependent on geographical distance. It is postulated that the groups arose from different origins, in which the Amazonian stocks were related to Psychodopygus sand flies while the Paraná strains originated from a gene pool transmitted by Lutzomyia sand flies such as Lutzomyia (Nyssomyia) whitmani. Transmission by Ps. complexus in Paragominas is considered to be a secondary adaptation from the Lutzomyia leishmanial gene pool. Although the vectors of L. (V.) braziliensis are poorly known in the Amazon region, there is strong evidence that the major vectors are all Psychodopygus spp. There was a high degree of genetic variability amongst the L. (V.) shawi strains and there was no clear grouping according to the strains' origins. The genetic variability amongst L. (L.) amazonensis strains from the same locations was much lower but they formed 2 groups which coincided with their origin. Our results support the clonal population structure of Leishmania isolates and suggest that their distribution is related to the origin of the gene pool as well as to present vector and reservoir movements.

Visceral leishmaniasis in India: promises and pitfalls of a PCR-based blood test

Traditional methods of diagnosing visceral leishmaniasis (kala-azar) in India suffer from a number of disadvantages. Amplification of multicopy nuclear genes and messenger ribonucleic acid of Leishmania by the polymerase chain reaction (PCR) was evaluated as an alternative assay under various clinical conditions. PCR of peripheral blood has the highest absolute sensitivity among all the available procedures, and is particularly useful for detecting parasites in early infections, post kala-azar dermal leishmaniasis, concurrent infections and immunocompromised cases, but is not so reliable for late infections. PCR of immunopurified blood mononuclear cells indicated the association of parasites with monocytes as well as non-monocyte cell types.

Usefulness of sampling with cotton swab for PCR-diagnosis of cutaneous leishmaniasis in the New World

In this study, we tested the polymerase chain reaction (PCR)-method to diagnose cutaneous leishmaniasis (CL) by taking exudate materials from lesions with cotton swabs, using our previously tested (PCR) panel comprised of Leishmania (Viannia) panamensis, L. (V.) braziliensis, L. (V.) guyanensis, L. (Leishmania) mexicana and L. (L.) amazonensis. The objectives of the present study were to improve the sampling method convenient for the patients and to test the usefulness of samples taken with cotton swabs. Sixteen patients were clinically diagnosed to have CL including one case of diffuse cutaneous leishmaniasis (DCL) in Ecuador and the causative Leishmania parasites were identified by PCR. All the 12 samples from CL patients of La Mana, positive for Leishmania DNA, were identified as L. (V.) panamensis, while two from CL of Huigra and one from DCL of San Ignacio were L. (L.) mexicana. In the field condition, taking biopsy material is not only painful but sometimes causes iatrogenic bacterial infections. Considering the sensitivity of the test, and convenient sampling procedure, it may be suggested that collection of exudates using cotton swabs may be a better alternative to biopsy sample for PCR-diagnosis of CL.

Optimization of random-amplified polymorphic DNA producing amplicons up to 8500 bp and revealing intraspecies polymorphism in Leishmania infantum isolates

In the case of investigation of polymorphism in closely related strains, the highest possible complexity of the patterns obtained by random-amplified polymorphic DNA PCR (RAPD-PCR) is required to assure revealing of limited polymorphism. In the present work, most parameters (reaction components concentration, additives, different polymerases, and thermal profiles) affecting RAPD-PCR were examined, in an effort to increase pattern complexity. A long PCR thermal profile, betaine as cosolvent, and Dynazyme EXT polymerase produced longer amplicons and higher pattern complexity, revealing polymorphism among Leishmania infantum isolates from infected dogs originating from Northern Greece (Macedonia).

PCR-ELISA for diagnosis of mucocutaneous leishmaniasis

In this work we demonstrate that the PCR-ELISA technique is sufficiently sensitive and specific for use as a diagnostic test in cases of mucocutaneous leishmaniasis. DNA was extracted from cultures of Leishmania braziliensis, Leishmania infantum, Leishmania tropica, Leishmania mexicana, Trypanosoma cruzi, and blood samples from individuals who presented a clinical diagnosis of leishmaniasis as well as from healthy individuals. The DNA was PCR amplified and the product obtained was hybridised with a biotin-labelled probe, the sequence of which was designed in our laboratory. The result of the hybridisation was visualised by means of an ELISA technique using antifluorescein antibody labelled with alkaline phosphatase and p-nitrophenylphosphate (pNFF) as chromogen. The optical density of the products of the pNFF hydrolysis was quantified in a spectrophotometer at a wavelength of 405 nm. Using this technique the percentage of detection was 83.3% in blood samples from patients clinically diagnosed as having mucocutaneous leishmaniasis. No false positive results were obtained.

Leishmania (Viannia) braziliensis is the predominant species infecting patients with American cutaneous leishmaniasis in the State of Minas Gerais, Southeast Brazil

Skin biopsies from 53 patients with American cutaneous leishmaniasis (ACL) from the State of Minas Gerais, Brazil, were used for a characterization of the Leishmania parasites. A pair of primers flanking the conserved region of the Leishmania minicircle kDNA was used to obtain amplified DNA via the polymerase chain reaction. The amplified products were subsequently hybridized with Leishmania subgenus-specific radiolabeled probes. Parasites from 49 out of 53 samples (92.5%) were characterized as belonging to the subgenus Viannia and four (7.5%) as belonging to the subgenus Leishmania. Clinical, epidemiological and molecular evidence allow us to conclude that Leishmania (V.) braziliensis and Leishmania (L.) amazonensis are the species present in the patients studied and that L. (V.) braziliensis is the predominant species in the State of Minas Gerais, Brazil.

Leishmania: identification of Old World species using a permissively primed intergenic polymorphic-polymerase chain reaction

We have developed a permissively primed intergenic polymorphic-polymerase chain reaction (PPIP-PCR) which distinguishes between the Old World Leishmania complexes L. major, L. tropica, L. donovani, and L. aethiopica. This technique pairs one parasite-specific and one nonspecific oligonucleotide primer for the PCR. The specific primer was chosen from a unique leishmanial DNA sequence, clone pDOG 2, isolated from a L. donovani chagasi genomic DNA expression library. This sequence has a high DNA homology to the intergenic region of the L. major B/C genes which belong to the polymorphic LmcDNA16 gene family. The specific intergenic primer contains a high GC content, a stem-loop, and a 3'-CG residue. The nonspecific primer was selected from within the pBluescript (SK) plasmid. Using PPIP-PCR, parasites belonging to the L. major, L. tropica, L. donovani, and L. aethiopica complexes could be easily identified directly following agarose gel electrophoresis by the simple profiles of their PCR products. In addition, it was possible to discriminate between strains of L. major or L. donovani from distant geographical regions. Amplification of genomic DNA isolated from several nonleishmanial kinetoplastids yielded either no PCR products or unique bands which were distinct from the leishmanial profiles. Genomic DNA from nonkinetoplastid parasites, plants, or mammals was not amplified by PPIP-PCR. This technique is a rapid and reproducible method for the characterization of Old World Leishmania.

Rapid identification of Leishmania species from formalin-fixed biopsy samples by polymorphism-specific polymerase chain reaction

The precise identification and classification of Leishmania species is important for public health surveillance since different species cause different clinical features of the disease. A highly specific polymerase chain reaction (PCR) panel was developed to enable the identification of the five major Leishmania species that cause New World cutaneous leishmaniases. The primers used for this panel were designed to distinguish the polymorphism in sequences of commonly amplified DNA bands of the parasites produced by arbitrarily primed PCR. These polymorphism-specific PCR diagnoses were performed with formalin-fixed biopsy specimens of the leishmanial lesions from four patients in Ecuador and one hamster skin lesion, and these lesions were determined to be caused by Leishmania (Viannia) panamensis, L. (Leishmania) mexicana, and L. (L.) amazonensis. The PCR panel may offer an important and practical approach to the standardized identification of Leishmania species in field examinations.

Development of a genus specific primer set for detection of Leishmania parasites by polymerase chain reaction

We have compared the sequences of a major class of kinetoplast DNA (kDNA) minicircle (pLURkE3) of Leishmania strain UR6 with other minicircle sequences from different Leishmania species. Alignment of these sequences allowed the selection of a pair of oligonucleotides suitable as primers in polymerase chain reaction (PCR) which is specific for Leishmania parasites. PCR with this genus-specific primer set is capable of detecting 1 femtogram of kDNA. These primers have been tested with kDNAs from both old world and new world Leishmania species. The results indicate that the primers may be suitable for detection of any kind of leishmaniasis.

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.