Performance of a universal PCR assay to identify different Leishmania species causative of Old World cutaneous leishmaniasis

A High Resolution Melting Analysis (HRM) PCR assay for the detection and identification of Old World Leishmania species

BACKGROUND

Cutaneous Leishmaniases (CL), highly endemic in Africa and Mediterranean region, are caused by different Leishmania parasite species. Accurate species identification is crucial for effective diagnosis, treatment, and control of these diseases, but traditionally relies on DNA-based methods. High Resolution Melting analysis PCR (HRM PCR) provides rapid results and precise differentiation based on nucleotide variations. We hypothesized that the Strumpellin gene of Leishmania could serve as an effective target for developing a HRM PCR method for the rapid and efficient detection and identification of Leishmania species in CL diagnosis.

METHODOLOGY

The Strumpellin gene was investigated in Trypanosomatidae family using bioinformatics and phylogenetic approaches to explore its evolutionary conservation and suitability for HRM PCR. HRM PCR target and primers were selected and validated on 73 different Leishmania DNAs. The analytical limit of detection was assessed, and the performance for detecting and identifying parasites in 38 cutaneous lesions aspirates was compared to Direct Examination (DE) and ITS1-PCR RFLP methods.

FINDINGS

The developed HRM PCR assay accurately identified promastigote DNAs of L. donovani/L. infantum, L. major, L. aethiopica, L. turanica, L. arabica, L. tarentolae and 3 genotypes of L. tropica. Differentiation was achievable with as little as a single nucleotide difference occurring within or between species. HRM profile interpretations were consistent with sequencing results of the HRM PCR target and identification by ITS1-PCR RFLP. The assay could detect the equivalent of 24 Leishmania parasites. In a small-scale sample, we brought proof of principle demonstration the HRM could detect and identify Leishmania in human cutaneous samples. In comparison to DE, the sensitivity and specificity of the HRM PCR assay on human cutaneous samples were 88% and 84.62%, respectively, while the ITS1-PCR assay evaluation parameters were 84% and 92.31%. Statistical analysis confirmed good correlation among the three tests, with both molecular methods providing congruent parasite identification. Notably, in three samples, only the HRM PCR assay was able to assign them to L. infantum or L. tropica.

CONCLUSIONS

The HRM PCR assay is a valuable tool for the detection and identification of Old World Leishmania species. Its integration into molecular diagnostic algorithms for CL or in eco-epidemiological studies holds promise for improving disease management and control.

Molecular Diagnosis of Human Cutaneous Leishmaniasis and Identification of the Causative Leishmania Species in Iran: A Narrative Review

Cutaneous leishmaniasis (CL) is a common form of leishmaniasis in underdeveloped countries. Although CL tends to be self-limiting, it can cause significant scars and may progress to more severe manifestations. Additionally, Leishmania species vary in susceptibility to the available treatments. The selection of treatment and clinical outcome of CL depend on the accurate determination of the Leishmania species. This mini-review aims to provide an overview of the molecular diagnosis techniques such as PCR-based assays, nucleic acid sequence-based amplification, and loop-mediated isothermal amplification utilized in the identification of Leishmania species in Iran.

Rapid detection, quantification and speciation of Leishmania using real-time PCR and DNA sequencing at the rRNA Internal Transcribed Spacer 2

The ability to discriminate infection between closely related Leishmania species within the Viannia species complex, specifically L. braziliensis, L. guyanensis and L. panamensis is critical to inform the clinical diagnosis and determine the most efficacious treatment modality. We designed a nested primer set targeting the rRNA Internal Transcribed Spacer 2 (ITS2), located on Chromosome 27, to distinguish among all human infective Leishmania species. Separate nested and single primer pairs were developed for conventional and quantitative PCR approaches respectively. Species-specific single nucleotide polymorphisms and indels located within the PCR products were identified by Sanger sequencing. This single locus approach provides a sensitive and specific platform to identify the species of Leishmania causing infection.

Cytokines signatures and susceptibility to cutaneous leishmaniasis in patients from Sistan and Baluchestan province of Iran

BACKGROUND

Cutaneous leishmaniasis (CL) is a complex, multifactorial disease that results from environmental factors such as parasite polymorphism, phlebotomine vectors, and host genetic factors. Some studies have identified specific genetic factors that may be associated with cutaneous leishmaniasis. The objective of this research was to resolve the association of 8 cytokine polymorphisms, including TNF-α -308 A/G (rs 1800629), TNF-α -238 A/G (rs 361525), TGF-β1 -509 T/C (rs 1800469), TGF-β1+ 915 G/C (rs 1800471), IFN-γ -874 T/A (rs 2430561), IFN-γ -179 G/A (rs 2069709), IL-10 -819 C/T (rs 1800871), and IL-10 -592 A/C (rs 1800872) with susceptibility to CL.

METHODS

A total of 152 patients with designated CL and 100 healthy controls were selected from those referred to Sistan and Baluchestan hospitals. CL was diagnosed by microscopic examination of Giemsa-stained samples and culture. Leishmania species were identified using ITS2 gene PCR amplification with universal primers. Genetic polymorphism was determined by the ARMS PCR method on extracted genomic DNA of individuals. Eight SNPs cytokines were genotyped.

RESULTS

Most of the Genotypic and allelic frequency comparisons between patients with CL and healthy subjects showed no difference, except 3. Individual SNP analysis showed highest association of TGF-β1 -509 (rs1800469) -CC genotype (P = 0.03, OR = 7.05, 95 % CI = 3.3-15) with 5.7-fold increase, IFN-γ -874 (rs 2430561) -AA genotype (P = 0.04, OR = 4.72, 95 % CI = 1.6-14) with 4.2-fold increase, and IL10 -819 (rs1800871) -CC genotype (P = 0.05, OR = 3.63, 95 % CI = 2.5-5.3) with 1.9-fold increase, with CL. Odds ratios (ORs) and 95 % confidence intervals (CIs) were evaluated to assess the association power.

CONCLUSION

Our results conclude that rs1800469 (TGF-β1), rs2430561 (INF-γ), and rs1800872 (IL10) polymorphisms are associated with CL in southeastern Iranian people.

A Novel Multiplex LAMP Assay for the Rapid and Accurate Diagnosis of Visceral Leishmaniasis Caused by Leishmania infantum from Iran

Visceral leishmaniosis (VL) is one of the neglected tropical diseases despite being responsible for serious clinical symptoms, some of which lead to fatal outcomes. Thus, there is a need to apply accurate, rapid, and specific diagnostic measurements in order to control the disease and reduce the mortality rate. We aimed to develop and validate a multiplex LAMP assay for the diagnosis of VL caused by Leishmania infantum (L. infantum). Moreover, a thorough assessment was conducted to determine the effectiveness of multiplex LAMP in identifying various Leishmania species, such as Leishmania tropica (L. tropica) and Leishmania major (L. major) in comparison to Leishmania infantum (L. infantum). The diagnostic performance of the multiplex LAMP method for VL was compared to each LAMP assay, real-time polymerase chain reaction (RT-qPCR), and nested PCR technique. Two separated primers were set and used in a multiplex LAMP assay which was designed based on the ITS2 (internal transcribed spacer II) and were selected on the basis of conserved and high copy number region. Multiplex LAMP primers were designed using an online tool available at https://www.primerexplorer.jp/e. The alignment was performed using MEGA5, and the primers were further adjusted utilizing GENE Runner software. All molecular methods were tested on the serial dilution of cloned plasmid containing ITS region from standard strains of L. infantum, L. tropica, and L. major. Moreover, multiplex LAMP assay was evaluated and compared based on both standard strains and 55 clinical samples from humans as well as dogs. Various approaches were applied to interpret the multiplex LAMP reaction which deciphered a higher sensitivity when compared to the RT-qPCR for L. infantum (one copy number of plasmid, equal to 0.85 femtograms (fg) of plasmid concentration, and 0.004 parasite DNA per μL) detection while these three standard strains of Leishmania were confirmed to contain 40 DNA copies using RT-qPCR. Additionally, the multiplex LAMP detection limit was approximately equivalent to RT-qPCR for L. major and L. tropica, which included 0.342 picograms (pg) and 342 femtograms (fg) of plasmid concentration, 4 × 103 and 4 × 102 copy number of plasmid, and 17.1 and 1.71 parasite DNA per μL for L. major and L. tropica, respectively. Nested PCR exhibited a lower detection limit for L. infantum of 4 × 106 plasmid copy number compared to multiplex LAMP and RT-qPCR. Multiplex LAMP has the potential for accurate and rapid detection of infectious disease, successful treatment, and finding and monitoring asymptomatic cases, especially in low-income countries.

The efficacy of AuNP-probe conjugate nanobiosensor in non-amplification and amplification forms for the diagnosis of leishmaniasis

Nanobiosensor platforms have emerged as convenient and promising approaches with remarkable efficacy for the diagnosis of infectious diseases. Gold nanoparticles (AuNPs) have been widely used due to numerous advantageous properties such as optical, electrical, physicochemical and great biomolecules binding capabilities. This study aimed to apply AuNP-Probe Conjugate for the detection of Leishmania spp., using colorimetric and amplification methods targeting parasitic ITS2 fragment. The first method was carried out by hybridization of 10µL of DNA with 4 µL of probe and addition of 5 µL of 0.2 N HCl (non-amplification method). Second method was followed by polymerase chain reaction (PCR) amplification using thiolated primer, 5 µL of AuNP and 5 µL of 0.2 N HCl. The appearance of red and purple colors indicated positive and negative results, respectively. The minimum of detection for non-amplification and amplification methods for three strains of Leishmania namely L. major, L. tropica and L. infantum were determined to be 32 fg/µL and 16 fg/µL, respectively. Sensitivity for detection of visceral leishmaniasis (VL) for non-amplification and amplification methods included 96% and 100%, respectively and for cutaneous leishmaniasis (CL) included 98% and 100%, respectively. The results of this investigation revealed that sensitivity of amplification method was the same as RT-qPCR, while that of non-amplification method was lower. However, this method was promising because of no need for any equipment, high specificity, enough sensitivity, low cost and rapidity (less than 30 min) to complete after genomic DNA extraction.

Laboratory diagnostics for human Leishmania infections: a polymerase chain reaction-focussed review of detection and identification methods

Leishmania infections span a range of clinical syndromes and impact humans from many geographic foci, but primarily the world's poorest regions. Transmitted by the bite of a female sand fly, Leishmania infections are increasing with human movement (due to international travel and war) as well as with shifts in vector habitat (due to climate change). Accurate diagnosis of the 20 or so species of Leishmania that infect humans can lead to the successful treatment of infections and, importantly, their prevention through modelling and intervention programs. A multitude of laboratory techniques for the detection of Leishmania have been developed over the past few decades, and although many have drawbacks, several of them show promise, particularly molecular methods like polymerase chain reaction. This review provides an overview of the methods available to diagnostic laboratories, from traditional techniques to the now-preferred molecular techniques, with an emphasis on polymerase chain reaction-based detection and typing methods.

Involvement of tryparedoxin peroxidase (TryP) and trypanothione reductase (TryR) in antimony unresponsive of Leishmania tropica clinical isolates of Iran

Clinical resistance to pentavalent antimonial compounds has long been recognized as a major problem in the treatment of human leishmaniasis. Trypanothione metabolism, the main form of thiol, has shown to play a central role in antimony resistance of laboratory-generated resistant Leishmania spp. and field-isolated resistant L. donovani; but the mechanism of antimony resistance in the clinical isolates of L. tropica causing anthroponotic cutaneous leishmaniasis (ACL) is less studied. Patients were selected among confirmed positive ACL cases who referred to Pasteur Institute of Iran, Tehran, from endemic regions of north-east and south of Iran. L. tropica clinical isolates were collected from patients who were either treatment-responsive (MAS=S1 to S5) or unresponsive (MAR=R1 to R4) to Glucantime® (meglumine antimoniate=MA). Isolates were tested for sensitivity to trivalent antimony (SbIII) in promastigotes and to pentavalent antimony (SbV) in intracellular amastigotes stages. Intracellular thiol levels were assayed and trypanothione-dependent components, including trypanothione reductase (TR) and tryparedoxin peroxidase I (TryP) were analysed at protein level and enzymatic activity in isolates. The MAR isolates had an approximate two fold increase in the levels of intracellular thiols (P< 0.05) accompanied by an average 5-10 fold increase in in vitro resistance to antimony. TryP was amplified at the protein level in all MAR strains as compared to the MAS strains (range: 2.8-5.6 fold). All MAR isolates metabolized H₂O₂ at higher rates than MAS isolates (8.55±0.75 nmol/min/mg vs. 3.14±0.36 nmol/min/mg) (P< 0.05). In addition, levels of TryR protein were also markedly elevated in 3 out of 4 MAR isolates (range: 2.2-4.1 fold). This was accompanied by overexpressed TryR activity (mean level of 46.83±2.43 for extracts of MAR vs. 20.98±3.02 for MAS strains) (P< 0.05). Elevated levels of TryP, active enzyme in peroxide detoxification, were observed in MAR parasites resulting in an increased metabolism of H₂O₂. TryR activity was overexpressed on average in extracts of MAR strains, but not in all isolates. Enhanced anti-oxidant defenses through thiol metabolism may play a significant role in clinical resistance of ACL patients to Glucantime.

Differential inflammatory responses associated with Leishmania major and L tropica in culture

BACKGROUND

Anthroponotic cutaneous leishmaniasis (ACL) due to Leishmania tropica and zoonotic CL (ZCL) due to L major have different clinical and epidemiological features.

OBJECTIVES

To determine whether pro-inflammatory cytokines are involved in diverse pathogenicity of Leishmania species causing CL.

PATIENTS/METHODS

The capacity of L major/L tropica to modulate expression of IL-1β, IL-8 (CXCL8), IFN-γ, TNF-α and MCP-1 (CCL2) in peripheral blood mononuclear cells (PBMCs) and monocyte-derived macrophages (MDMs) was evaluated by real-time RT-PCR technique.

RESULTS

PBMCs from both ZCL and ACL cases expressed significantly higher IFN-γ (P < .001) and TNF-α (P < .05) compared with healthy controls (HC). PBMCs from ACL patients expressed significantly higher IL-1β and IL-8 compared with ZCL patients and HC when stimulated with live L major or L tropica promastigotes (P < .001). After 4 and 10 hours, L major-infected MDMs expressed significantly higher IFN-γ (P < .05), and after 10 hours, L tropica-infected MDMs expressed significantly higher IL-1β, IFN-γ and IL-8 compared with noninfected cells (P < .05).

CONCLUSIONS

This study shows differential parasite-mediated stimulations of the inflammatory response with L major vs L tropica ex vivo. Pro-inflammatory cytokines particularly IL-8 (CXCL8) and IL-1β might contribute in diverse clinical features of CL such as longer duration of lesion persistence in ACL patients.

Evaluation of a kDNA-Based qPCR Assay for the Detection and Quantification of Old World Leishmania Species

The parasite protozoan Leishmania, the causative agent of leishmaniasis, includes two subgenera of medical interest: Leishmania (Leishmania) and Leishmania (Viannia). Parasite species detection and characterization is crucial to choose treatment protocols and to monitor the disease evolution. Molecular approaches can speed up and simplify the diagnostic process. In particular, several molecular assays target the mitochondrial DNA minicircle network (kDNA) that characterizes the Leishmania genus. We previously proposed a qPCR assay targeting kDNA, followed by high resolution melt (HRM) analysis (qPCR-ML) to distinguish L. (L.) infantum and L. (L.) amazonensis from L. Viannia species. Successively, this assay has been integrated with other qPCR assays, to differentiate L. (L.) infantum, L. (L.) amazonensis and L. (L.) mexicana. In this work, we tested the applicability of our qPCR-ML assay on L. (L.) donovani, L. (L.) major, L. (L.) tropica and L. (L.) aethiopica, showing that the qPCR-ML assay can also amplify Old World species, different from L. (L.) infantum, with good quantification limits (1 × 10^-4-1 × 10^-6 ng/pcr tube). Moreover, we evaluated 11 L. (L.) infantum strains/isolates, evidencing the variability of the kDNA minicircle target molecules among the strains/isolates of the same species, and pointing out the possibility of quantification using different strains as reference. Taken together, these data account for the consideration of qPCR-ML as a quantitative pan-Leishmania assay.

Laboratory Diagnosis of Cutaneous and Visceral Leishmaniasis: Current and Future Methods

Leishmaniasis is a neglected tropical disease with two main clinical forms: cutaneous and visceral leishmaniasis. Diagnosis of leishmaniasis is still a challenge, concerning the detection and correct identification of the species of the parasite, mainly in endemic areas where the absence of appropriate resources is still a problem. Most accessible methods for diagnosis, particularly in these areas, do not include the identification of each one of more than 20 species responsible for the disease. Here, we summarize the main methods used for the detection and identification of leishmaniasis that can be performed by demonstration of the parasite in biological samples from the patient through microscopic examination, by in vitro culture or animal inoculation; by molecular methods through the detection of parasite DNA; or by immunological methods through the detection of parasite antigens that may be present in urine or through the detection of specific antibodies against the parasite. Potential new methods that can be applied for laboratory diagnosis of leishmaniasis are also discussed.

Multilocus sequence typing analysis of Leishmania clinical isolates from cutaneous leishmaniasis patients of Iran

Cutaneous leishmaniasis (CL) is mainly caused by L. major and L. tropica in Old World and might be represented as typical skin lesion(s) or sometimes as a spectrum of atypical manifestations. We applied multilocus sequence typing (MLST) to explore genetic variations of Leishmania strains isolated from atypical vs. typical CL patients from Iran. A PCR-sequencing was performed for seven housekeeping genes (g6pd, mpi, asat, icd, 6pgd, fh, and trys) and genetic diversity indices and phylogenetic relationships were analyzed. A total of 41 isolates of L. major (28/41) and L. tropica (13/41) from 21 (51.2%) atypical CL and 20 (48.8%) typical CL cases were included. A set of additional sequences of 41 strains of 17 species of Leishmania were retrieved from databases. Different SNP variations were detected and the highest rate of heterozygous sites was found in g6pd and 6pgd genes (6 sites) for L. tropica and in asat and 6pgd genes (7 sites) for L. major strains. All strains were clustered into 58 unique sequence types (STs) including 17 STs related to 41 strains of Leishmania of this study. Concatenated tree clustered all strains in 6 main clades (A to F) including L. major (clade D) and L. tropica (clade B) strains. Two strains of L. major (codes 28 and 42) with highest nucleotide variations were more close to L. tropica and were grouped in Clade B. All of the STs were related in clonal complexes by using eBURST with the prediction of founder genotypes. A high rate of genetic variations and heterozygocity was evident in L. tropica and L. major strains; nevertheless, there was no significant difference in the diversity of Leishmania strains between typical CL and atypical CL groups. This study represents the first successful application of MLST approach to L. tropica and L. major strains in Iran.