Study on genetic polymorphism of Leishmania infantum through the analysis of restriction enzyme digestion patterns of kinetoplast DNA

Trans-Atlantic Spill Over: Deconstructing the Ecological Adaptation of Leishmania infantum in the Americas

Pathogen fitness landscapes change when transmission cycles establish in non-native environments or spill over into new vectors and hosts. The introduction of Leishmania infantum in the Americas into the Neotropics during European colonization represents a unique case study to investigate the mechanisms of ecological adaptation of this important parasite. Defining the evolutionary trajectories that drive L. infantum fitness in this new environment are of great public health importance as they will allow unique insight into pathways of host/pathogen co-evolution and their consequences for region-specific changes in disease manifestation. This review summarizes current knowledge on L. infantum genetic and phenotypic diversity in the Americas and its possible role in the unique epidemiology of visceral leishmaniasis (VL) in the New World. We highlight the importance of appreciating adaptive molecular mechanisms in L. infantum to understand the parasites' successful establishment on the continent.

High-throughput sequencing of kDNA amplicons for the analysis of Leishmania minicircles and identification of Neotropical species

Leishmania kinetoplast DNA contains thousands of small circular molecules referred to as kinetoplast DNA (kDNA) minicercles. kDNA minicircles are the preferred targets for sensitive Leishmania detection, because they are present in high copy number and contain conserved sequence blocks in which polymerase chain reaction (PCR) primers can be designed. On the other hand, the heterogenic nature of minicircle networks has hampered the use of this peculiar genomic region for strain typing. The characterization of Leishmania minicirculomes used to require isolation and cloning steps prior to sequencing. Here, we show that high-throughput sequencing of single minicircle PCR products allows bypassing these laborious laboratory tasks. The 120 bp long minicircle conserved region was amplified by PCR from 18 Leishmania strains representative of the major species complexes found in the Neotropics. High-throughput sequencing of PCR products enabled recovering significant numbers of distinct minicircle sequences from each strain, reflecting minicircle class diversity. Minicircle sequence analysis revealed patterns that are congruent with current hypothesis of Leishmania relationships. Then, we show that a barcoding-like approach based on minicircle sequence comparisons may allow reliable identifications of Leishmania spp. This work opens up promising perspectives for the study of kDNA minicercles and a variety of applications in Leishmania research.

Discovery and study of cutaneous leishmaniasis in Karamay of Xinjiang, West China

Cutaneous leishmaniasis (CL) was discovered in the farms of the Karamay suburb, Xinjiang Uygur Autonomous Region in the 1990s. Between 1992 and 1994, a house-to-house survey revealed a prevalence of 1.0-1.6% in the residents. The clinical types of skin lesions included papule, plaque, ulcer and nodular prurigo. Observations verified that, in some cases, the skin lesions healed spontaneously in 10-14 months, whilst in other cases, they persisted for several years. Sporadic cases of CL have continued to appear at the dermatology clinic of the local hospital since 2000. Phlebotomus wui (Ph. wui), subgenus Larroussius was confirmed as the transmitting vector. The causative agent is Leishmania infantum sensu lato.

Genetic diversity of human zoonotic leishmaniasis in Iberian Peninsula

Leishmaniasis caused by Leishmania (Leishmania) infantum is a zoonotic disease endemic in South Europe, from Portugal to the Middle East. The aim of the present study was to investigate the genetic diversity of L. infantum parasites in Iberian Peninsula. Twenty-four L. infantum strains isolated from immunocompetent patients with leishmaniasis from several localities of Portugal and Spain were studied. The use of kinetoplast DNA-PCR-restriction fragment length polymorphism as a molecular marker revealed intra-specific variation. No association was found between genotype and clinical form of the disease or patients age group. Two main clusters were identified with this marker: (i) zymodeme MON-1 strains and (ii) non-MON-1 strains. However, no association was found between strains variability and geographical distribution suggesting that parasite populations of different regions in the Iberian Peninsula are homogenous.

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.

Application of kDNA as a molecular marker to analyse Leishmania infantum diversity in Portugal

Around the Mediterranean basin Leishmania infantum is an important parasite causing canine leishmaniasis and visceral and cutaneous clinical forms in both immunocompetent and immunocompromised humans. Efficient monitoring and evaluation of epidemiology with discriminatory molecular markers are required. We investigated the genetic diversity of L. infantum in Portugal by polymerase chain amplification and restriction fragment length polymorphism analysis of kinetoplastid DNA, as molecular marker. We analysed 120 Portuguese isolates of L. infantum plus 16 other non-Portuguese isolates (as a reference group) from humans, dogs and sand flies. The Portuguese population showed a high degree of polymorphism with a total of 13 profiles identified. The predominant profile was A, which was only detected in the Portuguese samples. The kinetoplastid DNA PCR-RFLP assay described here was suitable for use directly with biological samples and the profiles obtained were stable during long-term growth in vitro and in laboratory animals.

Characterization of Leishmania infantum strains in blood samples from infected dogs and humans by PCR-RFLP

Characterization of Leishmania infantum is based on zymodeme analysis, which requires parasite isolation and therefore is not routinely employed. Moreover, the majority of strains in the Mediterranean Basin belong to zymodeme MON-1, and this is a major limitation for this technique in epidemiological studies in this region. We developed a PCR-RFLP method based on kDNA amplification, which was able to discriminate L. infantum strains directly from peripheral blood. Twenty-eight samples were tested with this technique: four obtained from promastigote cultures, and 24 collected from dogs (18) and human donors (six) from traditionally endemic and newly endemic areas of northwestern Italy. Extracted DNAs were amplified using RV1-RV2 primers and PCR products were digested using two restriction enzymes separately: BsiY I and Mlun NI. Some patterns were specific to certain areas. In particular, the identity of PCR-RFLP patterns from a human patient from a newly endemic area and three dogs allow the confirmation of the autochthonous origin of this case. This approach could be applied to epidemiological studies in order to trace the diffusion of L. infantum within dog populations, as well as its transmission to humans.

Leishmania chagasi/infantum: further investigations on Leishmania tropisms in atypical cutaneous and visceral leishmaniasis foci in Central America

In Central America, apparently genetically identical Leishmania chagasi/infantum parasites cause cutaneous (CL) and visceral leishmaniasis (VL), the latter being more frequent in young children. The present study investigated if there were pathology-related differences in virulence between Honduran CL and VL strains using Mediterranean L. infantum strains as a reference. Macrophage infectivity and serum sensitivity, properties thought to be associated with virulence, were similar between CL and VL strains from both regions. Attention focused on the genome organisation of genes for two candidate virulence factors: Leishmania mitogen activated protein kinase (LMPK) and cysteine proteinase b (Cpb). Interestingly, the Mediterranean strains exhibited restriction enzyme polymorphisms associated with tropism for both LMPK and Cpb genes whereas no differences were observed for the Honduran strains. We also report relative genetic homogeneity of the Honduran strains as compared to the Mediterranean strains and discuss it in terms of the probable origin for the Central American L. chagasi/infantum.

Molecular epidemiology of Leishmania infantum on the island of Majorca: a comparison of phenotypic and genotypic tools

In the Mediterranean basin, Leishmania infantum is the causative agent of both visceral and cutaneous leishmaniasis, and is an important opportunistic parasite in patients infected with human immunodeficiency virus (HIV). The commonest method used to study the variability of Leishmania spp. is isoenzyme analysis. In addition to this, we employed 3 assays based on the polymerase chain reaction (PCR): random amplified polymorphic deoxyribonucleic acid (RAPD), intergenic region typing (IRT), based on the amplification of ribosomal ribonucleic acid internal transcribed spacers and restriction fragment length polymorphism (PCR-RFLP). We used 54 L. infantum stocks isolated from HIV co-infected patients, 38 isolated from dogs, 3 isolated from immunocompetent patients and 3 isolated from 1826 sand files in the island of Majorca (Spain), a closed ecological niche. Zymodemes MON-1 (70%), MON-24 (11%) and MON-34 (18%) were found among the human isolates, and MON-1 (95%) and MON-108 (5%) among those from dogs. RAPD and IRT could not discriminate among the strains as they all gave the same pattern, even when different zymodemes were examined. In contrast, PCR-RFLP was able to distinguish the strains and, furthermore, a dendrogram (unweighted pair group method with arithmetic average [UPGMA]) was constructed from the genetic distances derived from RFLP data. The Leishmania isolates from HIV-infected subjects formed a single cluster, supporting the existence of an artificial anthroponotic cycle previously proposed by our group, in which syringes have been substituted for sand flies, and in which certain clones have been spread among intravenous drug users. This contrasts with the clusters representing a zoonotic cycle, involving dogs, sand flies and both immunocompetent and immunocompromised humans.

Correlation between in vitro and in vivo infectivity of Leishmania infantum clones

Eleven clones of a single strain of Leishmania infantum (MCAN/ES/88/ISS441, Doba) were analyzed for biological behavior in vivo and in vitro. Different clones showed differences in growth dependent upon the two culture media employed. All clones displayed only slight differences in H2O2 and NaNO2 sensitivity compared to the original strain, whereas in vitro infectivity for mouse peritoneal macrophages differed significantly among the clones. In vivo infections in hamsters correlated strongly with in vitro infectivity. The phenotypic differences found suggest a polyclonal structure for the Leishmania infantum strain studied.

Molecular tracking of infections by Leishmania infantum

Leishmania infantum is a major opportunistic parasite in patients with acquired immune deficiency syndrome and is very variable in these subjects. Isoenzyme characterization is not able to explain this variability, since half of the stocks isolated from patients co-infected with human immunodeficiency virus and Leishmania belong to zymodeme MON-1. Amplification of L. infantum minicircles by the polymerase chain reaction (PCR) and digestion of the amplified product to reveal restriction fragment length polymorphisms (RFLP) has proved very useful in distinguishing between relapses and reinfections in co-infected, treated patients. We have confirmed the existence of a leishmaniasis outbreak among intravenous drug users in north-east Spain, previously detected by isoenzymatic analysis. We have documented persistence of the same strain of Leishmania in 2 treated co-infected patients throughout several years, regardless of the theoretical rapid evolution ascribed to kinetoplast deoxyribonucleic acid minicircle sequences. We suggest using this PCR-RFLP technique to detect reinfections in treated co-infected subjects.

Leishmania mexicana mexicana: genetic heterogeneity of mexican isolates revealed by restriction length polymorphism analysis of kinetoplast DNA

Leishmania mexicana mexicana isolates from 23 patients with localized, diffuse, and an atypical "pseudodiffuse" form of cutaneous leishmaniasis were obtained in various endemic regions of Mexico. Restriction fragment length polymorphism analysis of kinetoplast DNA was done with nine different endonucleases in addition to an in vitro growth pattern analysis. We found that the 23 L. mexicana mexicana isolates could be consistently classified into six groups, according to the endonuclease digestion patterns obtained with HaeIII, HpaII, and MseI. Whereas localized cutaneous leishmaniasis isolates could have any of five patterns, diffuse cutaneous leishmaniasis showed only two patterns and pseudodiffuse cutaneous leishmaniasis consistently showed only one pattern. Thus, a clear correlation among digestion pattern, clinical disease, and geographical localization was obtained for the pseudodiffuse cutaneous leishmaniasis group. Additionally, the L. mexicana mexicana isolates could be differentiated into fast- and slow-growing groups. Diffuse cutaneous leishmaniasis isolates were found to be fast growing, whereas localized cutaneous leishmaniasis isolates fell into both categories. In contrast, all pseudo diffuse cutaneous leishmaniasis isolates were slow growing. Here we report the first study in which distinct and persistent genotypic characteristics of kinetoplast DNA heterogeneity within the L. mexicana mexicana species could be directly correlated with clinical disease and its growth behavior, suggesting that a distinctive restriction pattern could have important biological implications. Additionally, this study sheds new light on the biological significance of parasite kinetoplast DNA, since the heterogeneity seems not to be random but to form a distinct pattern.

Detection of Leishmania infantum in dogs by PCR with lymph node aspirates and blood

The PCR technique was applied to the diagnosis of leishmaniasis in dogs, both serologically negative and positive. DNA was taken from lymph node aspirates and blood. The primers 13a and 13b, derived from Leishmania amazonies and Leishmania braziliensis kinetoplast DNA (kDNA), also amplified Leishmania infantum IPT1 constant region of minicircle kDNA. The amplified fragment is 116 bp long. It was cloned and the sequence was determined. A 70-bp inner fragment was designed and used as a probe in dot blot hybridization. A group of 124 dogs was examined, 37 of which showed typical symptoms of disease. PCR was performed on 124 blood samples and 52 lymph node aspirates. Using microscopic examination as the "gold standard," we calculated sensitivity, specificity, and positive and negative predictive values of 100% using lymph node aspirates and values of 85, 80, 95, and 57%, respectively, using blood samples. We found that 40% of the animals without lesions and 38% of the animals with clinical signs gave false-negative results by indirect immunofluorescence antibody testing. These animals could contribute to the spreading of infection among dogs, and represent a potential risk for human health as well.

A nested-PCR-based schizodeme method for identifying Leishmania kinetoplast minicircle classes directly from clinical samples and its application to the study of the epidemiology of Leishmania tropica in Pakistan

A nested PCR was developed to amplify the variable region of the kinetoplast minicircles of all Leishmania species which infect mammals. Each Leishmania parasite contains approximately 10,000 kinetoplast DNA minicircles, which are unequally distributed among approximately 10 minicircle classes. The PCR primers were designed to bind within the 120-bp conserved region which is common to all minicircle classes; the remaining approximately 600 bp of each minicircle is highly conserved within each minicircle class but highly divergent between classes. The nested PCR generated a strong signal from a minimum of 0.1 fg of Leishmania DNA. Restriction digests of the amplicons from the highest dilutions suggested that minicircles from only a limited number of minicircle classes had acted as template in the reaction. One PCR product was directly sequenced and found to be derived from only one minicircle class. Since the primers amplify all minicircle classes, this indicated that as little as 1/10 of one Leishmania parasite was present in the PCR template. This demonstrated that the nested PCR achieved very nearly the maximum theoretically possible sensitivity and is therefore a potentially useful method for diagnosis. The nested PCR was tested for sensitivity on 20 samples from patients from the Timargara refugee camp, Pakistan. Samples were collected by scraping out a small amount of tissue with a scalpel from an incision at the edge of the lesion; the tissue was smeared on one microscope slide and placed in a tube of 4 M guanidine thiocyanate, in which the sample was stable for at least 1 month. DNA for PCR was prepared by being bound to silica in the presence of 6 M guanidine thiocyanate; washed in guanidine thiocyanate, ethanol, and acetone; and eluted with 10 mM Tris-HCl. PCR products of the size expected for Leishmania tropica were obtained from 15 of the 20 samples in at least one of three replicate reactions. The negative samples were from lesions that had been treated with glucantime or were over 6 months old, in which parasites are frequently scanty. This test is now in routine use for the detection and identification of Leishmania parasites in our clinical laboratory. Fingerprints produced by restriction digests of the PCR products were defined as complex or simple. There were no reproducible differences between the complex restriction patterns of the kinetoplast DNA of any of the parasites from Timargara camp with HaeIII and HpaII. The simple fingerprints were very variable and were interpreted as being the product of PCR on a limited subset of minicircle classes, and consequently, it was thought that the variation was determined by the particular minicircle classes that had been represented in the template. The homogeneity of the complex fingerprints suggests that the present epidemic of cutaneous leishmaniasis in Timargara camp may be due to the spread of a single clone of L. tropica.

Leishmania chagasi: genotypically similar parasites from Honduras cause both visceral and cutaneous leishmaniasis in humans

In the Mediterranean region Leishmania infantum causes both visceral and cutaneous leishmaniasis. These two pathologies tend to be caused by distinct parasite zymodemes. We have studied 33 isolates of Leishmania, 2 from sandflies, 5 from visceral cases, and 26 from cutaneous cases in Honduras, to determine if there is a correlation between pathology and parasite type in the New World similar to that in the Mediterranean region. Nine of the 26 cutaneous cases were caused by L. mexicana parasites, which have not been previously reported from Honduras; the remaining 17 cutaneous cases were due to L. chagasi. Only minor differences were found between the Honduran L. chagasi parasites by random amplified polymorphic DNA, differential display, pulsed-field gel electrophoresis, and schizodemes. This suggests that in Honduras the parasite type may not be the only factor determining the clinical outcome of L. chagasi infections.

Induction of interleukin 1 alpha in murine macrophages infected in vitro with different species and strains of Leishmania

It is now generally agreed that several cytokines released by immunocompetent cells such as macrophages play a crucial role in the outcome of infections caused by protozoa belonging to the genus Leishmania. In particular, tumor necrosis factor (TNF) induction during the course of cutaneous leishmaniasis has been related to resistance to L. major infection in mice. However, the role played by interleukin 1 (IL-1) in the host response to leishmaniasis has yet to be completely elucidated. The aim of this work was to study whether different species and strains of Leishmania could induce IL-1 alpha in murine macrophages in vitro. Resident peritoneal macrophages of BALB/c and C3H/HeN mice were infected with L. donovani, L. major, or different strains of L. infantum. It was found that L. donovani did not induce IL-1 alpha in macrophages from either mice strain. Infection with L. major or with three out of six strains of L. infantum induced consistent amounts of IL-1 alpha, but only in macrophages from genetically resistant C3H/HeN mice. No relationship was found between the rate of infection of macrophages and the amount of IL-1 alpha detected in the supernatants of infected macrophages. Data obtained confirm that the release of IL-1 alpha by murine macrophages infected in vitro with Leishmania is influenced by the genetic background of the cells as well as by the parasite species.

A DNA fingerprinting method for individual characterization of Toxoplasma gondii strains: combination with isoenzymatic characters for determination of linkage groups

The genetic polymorphism of Toxoplasma gondii was evaluated for 14 strains by isoenzyme and DNA analysis. The 14 strains belonged to 5 different zymodemes defined by the variable patterns of 6 enzyme systems. A restriction-fragment-length polymorphism analysis was carried out with two endonucleases (Sal I and Pst I) and two repetitive probes (TGR1E and TGR6). This kind of repetitive probe allowed an individual identification of strain, with 13 schizodemes being observed among 14 strains. Only two strains were found to be totally identical when DNA and isoenzyme characters were considered. The numerical taxonomy methods applied to the results obtained for both types of characters allowed determination of linkage groups. Strain clustering obtained by numerical analysis of DNA characters alone is similar to the clustering obtained by analysis of isoenzyme and DNA characters together. A relationship was observed between the defined groups and virulence in Swiss mice.

Leishmania infantum Tropism: Strain genotype or host immune status?

In apparently immunocompetent patients, Leishmania infantum provokes a spectrum of disease, ranging from simple skin lesion to severe visceral leishmaniasis, that is determined mainly by the protozoan genotype. In HIV-positive individuals, leishmanial infection results almost exclusively in visceral disease. In this review, Luigi Grodoni and Marina Gromiccia discuss the role o f the intrinsic virulence of L. infantum strains and the immune condition of the host, and focus on recently described mechanisms of immunological control of leishmanial infection.

A kinetoplast DNA probe diagnostic for Leishmania infantum

A 196 bp fragment of cloned kinetoplast (k) DNA of Leishmania infantum has been sequenced and shown to be diagnostic for this species. The DNA from 10(4)-10(5) promastigotes was routinely and specifically detected in crude dot blots of whole cells lysed in situ, and there was no cross-hybridization with 10(6) cells of L. major, L. tropica, L. killicki, L. aethiopica, L. braziliensis and L. mexicana. A low degree of hybridization was found with L. donovani and L. chagasi. This probe will be of particular use in Mediterranean countries, such as Italy, in which dermotropic zymodemes of L. infantum can be difficult to isolate and grow in numbers sufficient for isoenzyme typing.