Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review

In vitro growth of Leishmania parasites from biopsy samples of suspected cutaneous and visceral leishmaniasis cases in Sri Lanka: An observational study

Sri Lanka reports a large focus of Leishmania donovani caused cutaneous leishmaniasis (CL). Subsequent emergence of visceral leishmaniasis (VL) was also reported recently. Expansion of the on-going disease outbreak and many complexities indicate urgent need to enhance early case detection methods. In vitro cultivation (IVC) of parasites causing visceral leishmaniasis (VL) is important for disease confirmation and to obtain sufficient quantities of parasites required in many scientific studies. IVC is carried out as a useful second line investigation for direct microscopy negative patients with CL in this setting. Along with the emergence of VL, current study was carried out to evaluate in vitro growth of local VL parasites and to identify their differences associated with in vitro growth characteristics. Routine parasitological diagnostic methods, i.e., light microscopy (LM), polymerase chain reaction (PCR) were used for confirmation of suspected cases. Lesion samples from 125 suspected CL cases and bone marrow or splenic aspirations from 125 suspected VL patients were used to inoculate IVCs. Media M199 (about 70 μl) supplemented with 15-20% of heat inactivated fetal bovine serum was used for initial culturing procedures in capillaries. Capillary cultures were monitored daily. Total of 44 different compositions/conditions were used for evaluating in vitro growth of VL causing parasite. Daily records on parasite counts, morphological appearance (size, shape, and wriggly movements) were maintained. In vitro transformation of Leishmania promastigotes to amastigotes and outcome of the attempts on recovery of live Leishmania from culture stabilates was also compared between CL and VL parasites. Proportion of cultures showing a transformation of promastigotes were 40/45 (88.9%) and 4/10 (40.0%) for CL and VL respectively. In the transformed cultures, parasites showing typical shape, size and movement patterns were less in VL (1/4, 25.0%) compared to CL (28/40, 70.0%). CL cultures showed a growth up to mass culturing level with mean duration of two weeks while it was about five weeks for VL cultures. Proportion of cultures that reached a parasite density of 1 × 106 cells/ml (proceeded to mass cultures) was significantly low in VL (4/10, 40%) as compared to CL (28/40, 70.0%). None of media compositions/conditions were successful for mass culturing of VL parasites while all of them were shown to be useful for growing CL strains. Also in vitro transformation to amastigote form and recovering of culture stabilates were not successful compared to CL. There were clear differences between in vitro growth of Leishmania parasites causing local CL and VL. Further studies are recommended for optimization of in vitro culturing of VL parasite which will be invaluable to enhance case detection in future.

The Association of Human Leucocyte Antigen (HLA) Class I and II Genes with Cutaneous and Visceral Leishmaniasis in Iranian Patients: A Preliminary Case-Control Study

Background

Leishmaniasis is currently considered a re-emerging or emerging infection based on the geographic region. The outcome of leishmaniasis vastly depends on Leishmania-host interaction. This preliminary study aimed to show the association of human leukocyte antigen (HLA) class I and II genes with healed and non-healed cutaneous leishmaniasis (CL), and symptomatic and asymptomatic visceral leishmaniasis (VL) compared with control groups in Iran.

Methods

Ninety-five people, including 31 patients versus 64 individuals in the control group, were enrolled. Among them, 20 patients had confirmed CL based on amastigote observation, 10 had improved CL and 10 non-healed CL. Eleven patients were suffering from confirmed VL based on direct agglutination test (Five asymptomatic and six symptomatic VL cases). Besides, they were residents in an endemic area of VL in the northwest of Iran. To select a control group, it was ensured that they had no history of leishmaniasis. Peripheral blood samples were collected from each patient. After DNA extraction, HLA typing was conducted using polymerase chain reaction - sequence-specific priming (PCR-SSP). Subsequently, data were statistically analyzed by SPSS.

Results

There was a statistical relationship between the presence of HLA-A26 and CL, healed CL and the existence of the B38 allele, C1 allele and symptomatic VL, as well as B1.4 allele and asymptomatic VL (P<0.05).

Conclusion

This primary finding indicates that several HLA genes have a potential role in the susceptibility of Iranian people to CL and VL.

Serological studies on rK39 negative Visceral Leishmaniasis in an endemic focus of Leishmania donovani induced Cutaneous Leishmaniasis

Sri Lanka reports a focus of L. donovani induced cutaneous leishmaniasis (CL). Our more recent parasite and clinical studies and historical evidence point towards long term existence of Leishmania in the country, indicating a possible evolution leading to antigenic heterogenicity as well. In-house enzyme-linked immunosorbent assay (ELISA) that was developed during phase 1 study indicated >80% sero-positivity in local CL, while visceral leishmaniasis (VL) remained very rare with majority being negative when tested with rK39 assay. A novel serological tool was developed and sero-positivity of VL was assessed for the first time. The assay showed 100.0% sensitivity and 98.3% specificity for detection of VL. Samples were showed less positivity with established direct agglutination test (DAT) and rK39 strip test. The assay was less expensive than that of established rapid diagnostic tests (RDTs), culture and PCR assays. This assay may be useful in diagnosing clinical VL infections, detection of light microscopy (LM) negative patients, tracking post treatment stages, field screening of asymptomatic cases and in further serological studies.

Spatial and Temporal Variability of Visceral Leishmaniasis in Colombia, 2007 to 2018

Visceral leishmaniasis (VL) is a neglected tropical disease associated with poverty and is endemic in 56 countries worldwide. Brazil, Venezuela, and Colombia are the most affected countries in South America. In Colombia, the National Public Health Surveillance System (SIVIGILA) consolidates epidemiological information and monitors all VL cases nationwide. However, to date, no studies have investigated the occurrence of VL in Colombia using metadata analysis. We studied the demographic data, the spatial and temporal distribution of VL cases, and the association with vector distribution of Leishmania species in Colombia from 2007 to 2018. We found 306 VL cases reported to SIVIGILA for this period, with a coverage of 25.5 cases/year, and a mortality of 2.28% (seven deaths). The highest number of confirmed cases (N = 52) occurred in 2007; the lowest (N = 9) occurred in 2012. The cases were reported mainly in children (< 7 years) affiliated with the subsidized health regimen. Regarding the geographic distribution, the cases were reported by 42 municipalities distributed in 10 departments. The occurrence of VL cases toward the northeast of Colombia, and the distribution of vectors, such as Lutzomyia longipalpis and Lu. evansi, may be changing the panorama of VL in the country. We conclude that VL, mainly in recent years, shows a temporal and spatial variability associated with the occurrence of cases in new settings. Our findings increase our understanding and knowledge of this disease, and suggest the need to monitor and prioritize areas with changes in geographic expansion to improve prevention and control actions in the country.

HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

Prevalidation of an ELISA for Detection of a New Clinical Entity: Leishmania donovani-Induced Cutaneous Leishmaniasis

Human leishmaniasis which is considered a neglected tropical parasitic disease presents in three main clinical forms (i.e., cutaneous leishmaniasis (CL), mucocutaneous leishmaniasis (MCL), and visceral leishmaniasis (VL)) that are mainly determined by its causative species. Leishmania donovani, the most virulent and visceralizing parasite, is increasingly reported to cause CL in many countries in the world. Although CL is generally not considered to evoke a humoral immune response except for a nonrobust and a variable response in minority of cases, VL is associated with a clear strong humoral response. However, humoral response in L. donovani-induced CL has not been well evaluated before. A suitable serology-based assay is an essential primary step in such a study. An indirect enzyme-linked immunosorbent assay (ELISA) based on Leishmania promastigote crude antigen (Ag) was designed and optimized in order to utilize in further serological studies on this new clinical entity. Optimization included quantification of crude Ag, checkerboard titration method for determination of optimal concentrations for coating Ag, human sera and secondary antibody (Ab) with suitable coating buffer, blocking buffer, and incubating temperatures. The selected coating buffer was 0.02 M phosphate buffer, pH 6.8, and the blocking buffer was 2% fetal bovine serum with 0.01 M phosphate-buffered saline. At least 1 μg of crude Ag was required for coating the ELISA plate, while 1 : 1000 serum was used as primary Ab. The optimized concentration of secondary Ab was 1 : 64000 which might be altered according to manufacturer recommendations. The assay specificity was pre-evaluated using sera (n = 20 from each category) from confirmed CL patients and controls (other skin diseases which mimic CL, other systemic diseases that mimic VL, nonendemic healthy controls, and endemic healthy controls). This procedure described an optimization procedure of an ELISA technique for detection of anti-Leishmania antibodies in patients with L. donovani caused CL.

A Comprehensive Review of Cutaneous Leishmaniasis in Sri Lanka and Identification of Existing Knowledge Gaps

Purpose

Sri Lanka is endemic to cutaneous leishmaniasis and reported as the latest focus of leishmaniasis in the Asian subcontinent. Annually, the number of leishmaniasis cases is increasing; therefore, more efficient diagnostic tools, treatment methods and effective prevention measures are indispensable. For this reason, many studies were conducted regarding leishmaniasis infections in Sri Lanka; however, some areas need more attention. Thus, in this review, we comprehensively discussed the studies on leishmaniasis carried out in Sri Lanka.

Methods

Published articles on leishmaniasis in Sri Lanka were searched on PubMed, Google Scholar and ResearchGate databases. Inclusion criteria for the articles were based on keyword searches including ‘Leishmaniasis in Sri Lanka’, ‘Leishmaniasis vector in Sri Lanka’, ‘Sandfly species in Sri Lanka’, ‘Leishmaniasis epidemiology in Sri Lanka’ which are publicly accessible as of 15th July 2019.

Results

In this study, we evaluated and summarized the leishmaniasis reports in Sri Lanka and mainly focused on clinical presentation of leishmaniasis infection, genetic characteristics of Leishmania donovani Sri Lankan strain, geographical distribution and associated environmental factors, immunological aspects of the infection, vector, reservoir host, risk factors, diagnosis and treatment, and prevention and control. Furthermore, we identified the areas where further research is needed to fill the essential knowledge gaps.

Conclusions

Leishmaniasis has become a critically important parasitic infection in Sri Lanka, whereas the significant clinical form is cutaneous leishmaniasis. Prevalence of the leishmaniasis infections is reported from all the districts of the country. Therefore, more studies are essential to be carried out to fill the existing knowledge gaps emphasized in this review.

Designing of precise vaccine construct against visceral leishmaniasis through predicted epitope ensemble: A contemporary approach

Visceral leishmaniasis (VL) caused by Leishmania donovani is a fatal parasitic disease affecting primarily the poor population in endemic countries. Increasing number of deaths as well as resistant to existing drugs necessitates the development of an effective vaccine for successful treatment of VL. The present study employed a combinatorial approach for designing monomer vaccine construct against L. donovani by applying forecasted B- and T- cell epitopes from 4 genome derived antigenic proteins having secretory signal peptides and glycophosphatidylinositol (GPI) anchors with ≤ 1 transmembrane helix. The forecasted population coverage of chosen T cell epitope ensemble (combined HLA class I and II) cover 99.14 % of world-wide human population. The predicted 3D structure of vaccine constructs (VC1/VC2) were modeled using homology modeling approach and docked to innate immune receptors TLR-2 and TLR-4 with respective docking energies -1231.4/-910.3 and -1119.4/-1476 kcal/mol. Overall, the aforementioned designed vaccine constructs were found appropriate for including in self-assembly protein nanoparticles (SAPN) for further study in developing cutting-edge precision vaccine against VL in short duration with cost-effective manner.

Genome based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach

Visceral leishmaniasis (VL) is a dreadful protozoan disease caused by Leishmania donovani that severely affects huge populations in tropical and sub-tropical regions. The present study reports an unbiased genome based screening of 4 potent vaccine antigens against 8023 L. donovani proteins by following the criteria of presence of signal peptides, GPI-anchors and ≤1 transmembrane helix using advanced bioinformatics tools viz. SignalP4.0, PredGPI and TMHMM2.0, respectively. They are designated as genome based predicted signal peptide antigens (GBPSPA). The antigenicity/immunogenicity of chosen vaccine antigens (GBPSPA) with 4 randomly selected known leishmanial antigens (RSKLA) was compared by simulation study employing C-ImmSim software for human immune responses. This revealed better immunological responses. These antigens were further evaluated for the presence of B- and T-cell epitopes using immune epitope database (IEDB) based recommended consensus method of MHC class I and II tools. It was found to forecast CD4⁺ and CD8⁺ T-cell responses in genetically diverse human population worldwide as well as different endemic regions through IEDB based predicted population coverage (PPC) analysis tool. The worldwide percent PPC value of combined (HLA class I and II) epitope ensemble forecast was found to be 99.98, 99.96 and 50.04, respectively for GBPSPA, RSKLA and experimentally known epitopes (EKE) of L. donovani. Therefore, these potential antigens/epitope ensembles could favor the design of prospective and novel vaccine constructs like self-assembled epitopes as nano vaccine formulations against VL. Overall, the present study will serve as a model framework that might improve the effectiveness of designed vaccine against L. donovani and other related pathogens.

Leishmania cytochrome b gene sequence polymorphisms in southern Iran: relationships with different cutaneous clinical manifestations

Background

Cutaneous leishmaniasis (CL) caused by Leishmania species, is a geographically extensive disease that infects humans and animals. CL is endemic in half of the 31 provinces of Iran, with 29,201 incidence cases reported in Fars province from 2010 to 2015. CL is polymorphic and may result in lesions characterized by different clinical features. Parasite genetic diversity is proposed to be one of the factors affecting the clinical outcome and lesion characteristics in CL patients. However, there is still very limited data regarding the genetic variation of Leishmania spp. based on the sequencing of Cytochrome b (Cyt b) gene.

Methods

All patients originated from endemic regions in Fars province. The amplification of the Cyt b gene from isolates of 100 patients with disparate clinical forms of CL was accomplished using Nested-PCR. Sequence analysis of the amplified Cyt b was used to scrutinize the genetic variations among Leishmania isolates and connect the results with clinical pictures. The clinical demonstrations were basically of two types, typical and atypical lesions. Molecular phylogenetic tree was constructed using the Neighbor-Joining method, with species/strains from this study compared to species/strains from other geographical regions.

Results

Leishmania major was identified as the predominant infecting Leishmania spp. (86% of cases), with the remainder of cases being infected by Leishmania tropica. Clinical examination of patients revealed 12 different clinical CL forms. Among Leishmania samples analyzed, five distinct haplotypes were recognized: three in L. major and two in L. tropica. We found a correlation between clinical outcomes and Cyt b sequence variation of Leishmania spp. involved. Moreover, we observed a higher presence of polymorphisms in L. major compared with L. tropica. This difference may be due to the different eco-epidemiologies of both species, with L. tropica being an anthroponosis compared to L. major, which is a zoonosis.

Conclusions

The sequence analysis of Cyt b gene from 25 L. major and L. tropica strains demonstrated genetic variability of L. major and L. tropica causing CL in southern Iran, and a feasible connection amid the genetic heterogeneity of the parasite, geographical source and clinical appearance of the disease in human was detected.

Cutaneous Manifestations of Human and Murine Leishmaniasis

The leishmaniases are diseases caused by pathogenic protozoan parasites of the genus Leishmania. Infections are initiated when a sand fly vector inoculates Leishmania parasites into the skin of a mammalian host. Leishmania causes a spectrum of inflammatory cutaneous disease manifestations. The type of cutaneous pathology is determined in part by the infecting Leishmania species, but also by a combination of inflammatory and anti-inflammatory host immune response factors resulting in different clinical outcomes. This review discusses the distinct cutaneous syndromes described in humans, and current knowledge of the inflammatory responses associated with divergent cutaneous pathologic responses to different Leishmania species. The contribution of key hematopoietic cells in experimental cutaneous leishmaniasis in mouse models are also reviewed and compared with those observed during human infection. We hypothesize that local skin events influence the ensuing adaptive immune response to Leishmania spp. infections, and that the balance between inflammatory and regulatory factors induced by infection are critical for determining cutaneous pathology and outcome of infection.

Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review

Background

The outcome of leishmaniasis is an interplay between Leishamania and the host. Identifying contributory host genetic factors is complicated by the variability in phenotype, ethnicity and parasite species. Leishmaniasis is caused exclusively by L. donovani in Sri Lanka with localized cutaneous leishmaniasis (LCL) being the predominant form. We report here an association study of human leucocyte antigen (HLA) class I and II genes with LCL in Sri Lanka, the first on HLA associations in cutaneous leishmaniasis in a South Asian population.

Methods

An existing DNA repository of 200 each of patients and controls was typed for HLA-DQ by PCR-SSP. Next generation sequencing-based typing for HLA-A, HLA-B and HLA-DRB1 alleles was done in a subset of 280 samples. Association tests were performed on 28,489 genotyped and imputed SNPs spanning a region of 1.4 Mb across the HLA genes. To compare our results with similar studies, we carried out a systematic review to document all HLA associations reported to-date for cutaneous and muco-cutaneous leishmaniasis.

Results

DRB1*04 DQB1*02 (P = 0.03; Pc = 0.09), DRB1*07 DQB1*02 (P = 0.03; Pc = 0.09) haplotypes were absent in patients. B*07 (P = 0.007; Pc = 0.13; OR = 0.36; 95 % CI = 0.17–0.77) allele and DRB1*15 DQB1*06 (P = 0.00; Pc < 0.01; OR = 0.3; 95 % CI = 0.2–.0.6) haplotype were over represented in controls and DRB1*15 (P = 0.002; Pc = 0.01) allele was over represented in patients. Two SNPs (rs281864595/rs1050517) in the antigen recognition region of HLA-B, comprised a haplotype more frequent in controls (P = 0.04). The alleles identified by the systematic review to predispose or to protect from cutaneous/mucocutaneous leishmaniasis remained highly heterogeneous in different populations studied.

Conclusions

Our preliminary findings suggest a role for some class I and class II HLA genes in determining predisposition to LCL in this population which should be corroborated with further studies. The systematic review reiterates this need, as the purported susceptibility or protection gained by certain HLA alleles or haplotypes has rarely been independently verified.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1626-8) contains supplementary material, which is available to authorized users.