Heterogeneity of Leishmania infantum chagasi kinetoplast DNA in Teresina (Brazil)

Genetic variability of Leishmania (Leishmania) infantum causing human visceral leishmaniasis in the Southeastern Brazil

Leishmania infantum is a protozoan that causes visceral leishmaniasis (VL) in the Americas and some regions of Europe. The disease is mainly characterized by hepatosplenomegaly and fever, and can be fatal. Factors related to the host and parasite can contribute to the transmission of Leishmania and the clinical outcome. The intraspecific genetic variability of L. infantum strains may be one of these factors. In this study, we evaluated the genetic variability of L. infantum obtained from bone marrow smear slides from patients in the Sao Paulo State, Brazil. For this, the minicircle of the kDNA hypervariable region was used as target by Sanger sequencing. By analyzing the similarity of the nucleotides and the maximum likelihood tree (Fasttree), we observed a high similarity (98%) among samples. Moreover, we identified four different profiles of L. infantum. In conclusion, L. infantum strains from Sao Paulo State, Brazil, showed low diversity measured by minicircle of the kDNA hypervariable region.

Development of Quantitative Rapid Isothermal Amplification Assay for Leishmania donovani

Quantification of pathogen load, although challenging, is of paramount importance for accurate diagnosis and clinical management of a range of infectious diseases in a point-of-need testing (PONT) scenario such as in resource-limited settings. We formulated a quantification approach to test the standard-curve based absolute quantification ability of isothermal recombinase polymerase amplification (RPA) assay. As a test of principle, a 10-fold dilution series of Leishmania donovani (LD) genomic DNA prepared in nuclease-free-water (NFW), and from culture-spiked-blood (CSB) were tested, and a 15 min assay was performed. A modified algorithm was formulated to derive the detection outcome. The threshold-record times (Tr) in seconds thus obtained were plotted against the initial load of parasite genomes for log-linear regression analysis. The quantitative RPA (Q-RPA) assay was further evaluated against a LD quantitative (q)-PCR assay with DNA extracted from visceral and post-Kala-azar dermal leishmaniasis case specimens and stratified into different ranges of threshold cycle (Ct). The best-fitted regression models were found linear with mean r²/root mean square error (RMSE) values of residual points (in seconds) estimated as 0.996/8.063 and 0.992/7.46 for replicated series of NFW and CSB, respectively. In both series, the lower limit of detection reached less than 0.1 parasite genome equivalent DNA. Absolute agreement between Q-RPA and LD-qPCR was found for test positivity, and strong positive correlations were observed between the Tr and Ct values (r = 0.89; p < 0.0001) as well as between the absolute parasite loads (r = 0.87; p < 0.0001) quantified by respective assays. The findings in this very first Q-RPA assay for leishmaniasis are suggestive of its potential in monitoring LD load in clinical specimens, and the development of rapid Q-RPA assays for other infectious diseases.

Evaluation of molecular assays to detect Leishmania donovani in Phlebotomus argentipes fed on post-kala-azar dermal leishmaniasis patients

BACKGROUND

Post-kala-azar dermal leishmaniasis (PKDL) caused by Leishmania donovani (LD) is a skin disorder that often appears after treatment of visceral leishmaniasis (VL) patients. PKDL patients are potential reservoirs of LD parasites, which can initiate a new epidemic of anthroponotic VL. Therefore, host infectiousness to its sand fly vector is a critical factor for transmission, and its accurate estimation can facilitate control strategies. At present, conventional microscopy serves as the reference method to detect parasites in its vector. However, low sensitivity of microscopy can be a limiting factor.

METHODS

In this study, real-time quantitative PCR (LD-qPCR) and recombinase polymerase amplification (LD-RPA) assays were evaluated against microscopy for the detection of LD DNA extracted from live sand flies five days after controlled feeding on PKDL cases.

RESULTS

The sensitivity of LD-qPCR and LD-RPA assays were found to be 96.43 and 100%, respectively, against microscopy for the selected fed sand flies (n = 28), and an absolute specificity of both molecular tools for apparently unfed sand flies (n = 30). While the proportion of infectious cases among 47 PKDL patients was estimated as 46.81% as defined by microscopic detection of LD in at least one fed sand fly per case, LD-RPA assay evaluation of only the microscopy negative sand flies fed to those 47 PKDL cases estimated an even greater proportion of infectious cases (51.06%). In overall estimation of the infectious cases in retrospective manner, discordance in positivity rate was observed (p < 0.05) between LD-RPA (59.57%) assay and microscopy (46.81%), while LD-RPA had slightly better positivity rate than LD-qPCR (55.32%) as well.

CONCLUSIONS

Considering the sensitivity, cost, detection time, and field applicability, RPA assay can be considered as a promising single molecular detection tool for investigations pertaining to LD infections in sand flies and/or host infectiousness in PKDL, while it can also be useful in confirmation of microscopy negative sand fly samples.

A critical review of the applicability of serological screening for Leishmaniasis in blood banks in Brazil

Leishmaniasis is a group of diseases caused by several species of protozoa. It is a major public health concern in its visceral form, accounting annually for 59,000 deaths, and an estimated 12 million infected patients per year. The importance of VL resides not only in its high incidence and wide distribution but also in the possibility of the disease progressing to the severe and lethal forms, especially in children and immunosuppressed individuals, when associated with malnutrition and concomitant infections. This study is a bibliographical review, aiming to understand the sensitivity and specificity parameters of the tests used to detect Leishmaniasis, as well as to understand if there is any relevance in proposing a serological screening for Leishmaniasis in blood banks. In general, we observed that there are currently several types of tests for detecting Leishmaniasis: parasitological, serological and molecular. In such tests, many serological methods and kits are available for the detection of asymptomatic visceral leishmaniasis, but there is variability in sensitivity and specificity among the methods. The gold standard for the diagnosis of visceral leishmaniasis is the parasitological method, through the aspiration of bone marrow, with higher sensitivity by splenic puncture. Due to the relevance of the disease and the available data from research centers, there is evidence to propose a transfusion serological screening for visceral Leishmaniasis, pointing to the need for further studies.

Phylogenetic position of Leishmania tropica isolates from an old endemic focus in south-eastern Iran; relying on atypical cutaneous leishmaniasis

Cutaneous leishmaniasis (CL) is a major health problem in Iran, with a heavy burden on human health and society. There is little knowledge about the molecular epidemiology of the disease, as well as phylogenetic relationship of causative agents in south-eastern Iran. The aim of the present study was to investigate the molecular aspects of CL, especially atypical CL in the Bam district, Kerman province, south-eastern Iran, as an endemic region of CL in Iran. The smears were collected from lesion samples of 353 patients clinically suspected to CL, who attended local health centres in the Bam district during 2016-2017. Direct smears were examined for Leishmania parasites using the Giemsa staining technique. Amplification of kinetoplast DNA (kDNA) and the ribosomal internal transcribed spacer 1(ITS-1) gene were carried out using polymerase chain reaction (PCR). Then, the ITS1-PCR products were sequenced for phylogenetic analysis. Overall, 278 cases were confirmed as CL by microscopic examination of Giemsa-stained slides. Clinical presentation of the lesions was basically of two types: (a) typical lesions and (b) atypical including lupoid ulcers, sporotrichoid, nodular and exudative lesions. The PCR assay on all specimens of skin lesions proved L. tropica as the main pathogenic agent. Phylogenic analysis revealed high similarity among isolates from the Bam district in the south-east with isolates from Birjand in eastern Iran, as well as with isolates from Herat province in western Afghanistan. The study provided valuable information concerning the genetic diversity of the parasite as one of the factors influencing the clinical manifestations in CL in south-eastern Iran, which could be the basis for planning future control strategies.

First molecular characterization of Leishmania infantum species in patients infected with visceral leishmaniasis in Misiones province, Argentina

Introduction: Cutaneous leishmaniasis caused by L. braziliensis has been historically endemic in Argentina and several cases of visceral leishmaniasis following initial cutaneous leishmaniasis have been reported. Visceral leishmaniasis started to appear in Argentina in 2006 in the city of Posadas, Misiones province, affecting both humans and dogs. Objective: To identify the etiologic agent to species level in patients with visceral leishmaniasis diagnosis in Misiones province and describe its clinical and epidemiological characteristics. Materials and methods: A cohort of 24 patients from Misiones province was studied from 2009 to 2016, all with a confirmed diagnosis of visceral leishmaniasis. To identify the Leishmania species involved, patient samples were analyzed by microscopy, serologic studies, DNA detection, and sequencing. Variables such as age, sex, place of residence, clinical signs and symptoms consistent with visceral leishmaniasis were also recorded. Results: 75% (18/24) of the patients studied were males and 25% (6/24) were younger than 4 years. The most frequent symptom was a prolonged fever in 87.5% of the patients (21/24), followed by splenomegaly in 70.8% (17/24). Leishmania infantum was the only parasite species identified in all patients. Conclusion: This finding constitutes the first molecular identification of the Leishmania infantum species in autochthonous patients of Misiones province, Argentina. This study highlights the importance of PCR for species identification in epidemiological studies of visceral leishmaniosis in Argentina.

Analysis of genetic polymorphisms and tropism in East African Leishmania donovani by Amplified Fragment Length Polymorphism and kDNA minicircle sequencing

Visceral leishmaniasis (VL), the most severe form of leishmaniasis, is caused by Leishmania donovani. In addition to fatal VL, these parasites also cause skin diseases in immune-competent and -suppressed people, post-kala azar dermal leishmaniasis (PKDL) and HIV/VL co-infections, respectively. Genetic polymorphism in 36 Ethiopian and Sudanese L. donovani strains from VL, PKDL and HIV/VL patients was examined using Amplified Fragment Length Polymorphism (AFLP), kDNA minicircle sequencing and Southern blotting. Strains were isolated from different patient tissues: in VL from lymph node, spleen or bone marrow; and in HIV/VL from skin, spleen or bone marrow. When VL and PKDL strains from the same region in Sudan were examined by Southern blotting using a DNA probe to the L. donovani 28S rRNA gene only minor differences were observed. kDNA sequence analysis distributed the strains in no particular order among four clusters (A - D), while AFLP analysis grouped the strains according to geographical origin into two major clades, Southern Ethiopia (SE) and Sudan/Northern Ethiopia (SD/NE). Strains in the latter clade were further divided into subpopulations by zymodeme, geography and year of isolation, but not by clinical symptoms. However, skin isolates showed significantly (p < 0.0001) fewer polymorphic AFLP fragments (average 10 strains = 348.6 ± 8.1) than VL strains (average 26 strains = 383.5 ± 3.8).

Population Structure of Leishmania tropica Causing Anthroponotic Cutaneous Leishmaniasis in Southern Iran by PCR-RFLP of Kinetoplastid DNA

Iran is one of the six countries with the most cutaneous leishmaniasis (CL) patients. Understanding better the genotypes of the parasite population in relation to geography and climate is critical to achieving better CL control. We aimed to characterise the population structure of Leishmania tropica, the cause of anthroponotic cutaneous leishmaniasis (ACL), from important foci in southeast (Bam and Kerman) and southwest (Shiraz) Iran. A total of 39 L. tropica isolates from ACL patients from southeast (Bam 14, Kerman 12) and southwest (Shiraz 13) Iran were analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of the kinetoplast DNA (kDNA) using restriction enzymes MspI (HpaII) and ClaI. 37 genotypes were identified among south Iran L. tropica isolates. The unweighted pair group method with arithmetic mean (UPGMA) tree obtained from the banding patterns of ClaI digested kDNA RFLP distinguished southeast from and southwest L. tropica isolates with some subclustering but the MspI derived tree showed greater discrimination with greater subclustering and divergence of the two foci of southeast region but with some overlapping. Although a monophyletic structure has been defined for southeast L. tropica, isolates from two foci of southeast Iran were partly discriminated in the current study.

Molecular-Based Detection of Leishmania infantum in Human Blood Samples in a New Focus of Visceral Leishmaniasis in Lorestan Province, Iran

BACKGROUND

The fatal form of leishmaniasis is visceral form (VL), found in some of the countries in the world. Visceral leishmaniasis has been reported sporadically from all provinces in Iran, including Lorestan. This study aimed to characterize parasite species in DAT positive and some of the DAT negative human blood samples of Delfan district, Lorestan Province, central Iran.

METHODS

Blood samples were collected from different geographical areas of Delfan. Serum was used for DAT test and remained part of molecular study. DNA was extracted by using DNG-plus extracted kit (Cinagen, Iran). Polymerase chain reaction amplification of Leishmania kDNA and PCR-RFLP of ITS1 was done to identify Leishmania species. Some amplicons were sequenced, submitted to GenBank and analyzed by BLASTn.

RESULTS

Expected band of kDNA for L. infantum (720bp) was amplified in 16 out of 186 (8.6%) samples which showed previously anti-Leishmania antibody at different titers or were negative serologically. Using BLASTn, 93% similarity with L. infantum has been shown. The rDNA-ITS1 was amplified only in 9 samples (4.7%). RFLP pattern was similar to what expected for L. infantum.

CONCLUSION

A new emerging hypo-endemic focus, caused by L. infantum, is going to be established in Delphan District, Lorestan Province. Further studies on vector and reservoirs are necessary for the region and other parts of Lorestan Province.

Genetic diversity of Leishmania donovani that causes cutaneous leishmaniasis in Sri Lanka: a cross sectional study with regional comparisons

BACKGROUND

Leishmania donovani is the etiological agent of visceral leishmaniasis (VL) in the Indian subcontinent. However, it is also known to cause cutaneous leishmaniasis (CL) in Sri Lanka. Sri Lankan L. donovani differs from other L. donovani strains, both at the molecular and biochemical level. To investigate the different species or strain-specific differences of L. donovani in Sri Lanka we evaluated sequence variation of the kinetoplastid DNA (kDNA).

METHODS

Parasites isolated from skin lesions of 34 CL patients and bone marrow aspirates from 4 VL patients were genotyped using the kDNA minicircle PCR analysis. A total of 301 minicircle sequences that included sequences from Sri Lanka, India, Nepal and six reference species of Leishmania were analyzed.

RESULTS

Haplotype diversity of Sri Lankan isolates were high (H d  = 0.757) with strong inter-geographical genetic differentiation (F ST  > 0.25). In this study, L. donovani isolates clustered according to their geographic origin, while Sri Lankan isolates formed a separate cluster and were clearly distinct from other Leishmania species. Within the Sri Lankan group, there were three distinct sub-clusters formed, from CL patients who responded to standard antimony therapy, CL patients who responded poorly to antimony therapy and from VL patients. There was no specific clustering of sequences based on geographical origin within Sri Lanka.

CONCLUSION

This study reveals high levels of haplotype diversity of L. donovani in Sri Lanka with a distinct genetic association with clinically relevant phenotypic characteristics. The use of genetic tools to identify clinically relevant features of Leishmania parasites has important therapeutic implications for leishmaniasis.

Genetic variability of Leishmania infantum in naturally infected dogs in the state of Bahia, Brazil

In Brazil, Leishmania infantum mainly affects humans and dogs. The state of Bahia presents many dogs that are positive for this parasite. Despite the importance of epidemiology in this region, there are still very few studies that have assessed the genetic characteristics of L. infantum. The aim of this study is to investigate the genetic variability of L. infantum isolated identified in naturally infected dogs, in order to verify occurrence of subpopulation of this parasite in the different biomes existing in the state of Bahia. Thirty-two samples of L. infantum were analyzed, which were obtained isolated in dogs from the Mata Atlântica (rainforest), Caatinga (semi-arid scrub forest), and Cerrado (a vast tropical savannah eco-region) Bahia municipalities' biomes. All animals presented with clinical changes suggestive of Leishmania spp. and they exhibited positive reactions to serological tests. kDNA analysis with RFLP markers revealed the presence of genetic variability and gene flow in subpopulations of L. infantum; samples from the Mata Atlântica areas were genetically more similar to those from the areas of Caatinga and they were less likely to resemble those of the Cerrado. This data may be used to investigate the dissemination of parasite in the canine population of state of Bahia.

Mobile suitcase laboratory for rapid detection of Leishmania donovani using recombinase polymerase amplification assay

BACKGROUND

Leishmania donovani (LD) is a protozoan parasite transmitted to humans from sand flies, which causes Visceral Leishmaniasis (VL). Currently, the diagnosis is based on presence of the anti-LD antibodies and clinical symptoms. Molecular diagnosis would require real-time PCR, which is not easy to implement at field settings. In this study, we report on the development and testing of a recombinase polymerase amplification (RPA) assay for the detection of LD.

METHODS

A genomic DNA sample was applied to determine the assay analytical sensitivity. The cross-reactivity of the assay was tested by DNA of Leishmania spp. and of pathogens considered for differential diagnosis. The clinical performance of the assay was evaluated on LD positive and negative samples. All results were compared with real-time PCR. To allow the use of the assay at field settings, a mobile suitcase laboratory (56 × 45.5 × 26.5 cm) was developed and operated at the local hospital in Mymensingh, Bangladesh.

RESULTS

The LD RPA assay detected equivalent to one LD genomic DNA. The assay was performed at constant temperature (42 °C) in 15 min. The RPA assay also detected other Leishmania species (L. major, L. aethiopica and L. infantum), but did not identify nucleic acid of other pathogens. Forty-eight samples from VL, asymptomatic and post-kala-azar dermal leishmaniasis subjects were detected positive and 48 LD-negative samples were negative by both LD RPA and real-time PCR assays, which indicates 100 % agreement. The suitcase laboratory was successfully operated at the local hospital by using a solar-powered battery. DNA extraction was performed by a novel magnetic bead based method (SpeedXtract), in which a simple fast lysis protocol was applied. Moreover, All reagents were cold-chain independent.

CONCLUSIONS

The mobile suitcase laboratory using RPA is ideal for rapid sensitive and specific detection of LD especially at low resource settings and could contribute to VL control and elimination programmes.

Leishmania infantum Genetic Diversity and Lutzomyia longipalpis Mitochondrial Haplotypes in Brazil

Leishmania infantum is the etiological agent of visceral leishmaniasis (VL) in the Americas with domestic dogs being its major reservoir hosts. The main VL vector is the sandfly Lutzomyia longipalpis, while other Lutzomyia species may play a role in disease transmission. Although the genetic structure of L. infantum populations has been widely evaluated, only a few studies have addressed this subject coupled to the genetic structure of the respective sandfly vectors. In this study, we analyzed the population structure of L. infantum in three major VL endemic areas in Brazil and associated it with Lutzomyia longipalpis geographic structure.

Genetic homogeneity among Leishmania (Leishmania) infantum isolates from dog and human samples in Belo Horizonte Metropolitan Area (BHMA), Minas Gerais, Brazil

BACKGROUND

Certain municipalities in the Belo Horizonte Metropolitan Area (BHMA), Minas Gerais, Brazil, have the highest human visceral leishmaniasis (VL) mortality rates in the country and also demonstrate high canine seropositivity. In Brazil, the etiologic agent of VL is Leishmania (Leishmania) infantum. The aim of this study was to evaluate the intraspecific genetic variability of parasites from humans and from dogs with different clinical forms of VL in five municipalities of BHMA using PCR-RFLP and two target genes: kinetoplast DNA (kDNA) and gp63.

METHODS

In total, 45 samples of DNA extracted from clinical samples (n = 35) or L. infantum culture (n = 10) were evaluated. These samples originated from three groups: adults (with or without Leishmania/HIV co-infection; n = 14), children (n = 18) and dogs (n = 13). The samples were amplified for the kDNA target using the MC1 and MC2 primers (447 bp), while the Sg1 and Sg2 (1330 bp) primers were used for the gp63 glycoprotein target gene.

RESULTS

The restriction enzyme patterns of all the samples tested were monomorphic.

CONCLUSIONS

These findings reveal a high degree of genetic homogeneity for the evaluated gene targets among L. infantum samples isolated from different hosts and representing different clinical forms of VL in the municipalities of BHMA studied.

Genetic diversity of Leishmania infantum field populations from Brazil

Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

An assessment of the genetic diversity of Leishmania infantum isolates from infected dogs in Brazil

Correlations between the genetic diversity of Leishmania infantum (syn. L. chagasi) isolates and their respective geographic origins support the theoretic assumption that visceral leishmaniasis probably originated in the Old World. Because dogs are widely considered to be the main reservoir of this disease, the present study aimed to investigate the degree of genetic divergence among 44 leishmanial canine isolates from two Brazilian cities, Jequié and Campo Grande, located approximately 2,028 km from each other. We hypothesized that a low degree of genetic divergence would be observed among these isolates. In fact, statistical analyses found no significant differences between the isolates using both random amplified polymorphic DNA and multilocus microsatellite typing genotyping techniques with three and seven markers, respectively. These findings provide support for the recent introduction of L. infantum into the New World.