Application of Quantitative PCR in the Diagnosis and Evaluating Treatment Efficacy of Leishmaniasis

Molecular diagnosis of visceral leishmaniasis from blood samples using different genetic markers: A simple, sensitive and less invasive diagnostic approach

Visceral leishmaniasis (VL), or kala-azar, is a deadly disease with high fatality rates if diagnosis and treatment are delayed. Diagnosis is often delayed due to symptoms that mimic other conditions. Sample isolation and diagnostic procedures are labor-intensive and time-consuming. Rapid immunochromatographic tests cannot differentiate active cases from past infections. In the present study we investigated the utility of peripheral blood samples for molecular diagnosis of VL. Whole genomic DNA from the erythrocyte fraction of blood from VL and cutaneous leishmaniasis (CL) suspected patients was used for PCR using multiple markers (k-DNA, ITS-Ⅰ, and 18s rRNA). PCR amplification of k-DNA, ITS-Ⅰ, and 18s rRNA genes yielded positive results in VL symptomatic patients. However, the same PCR approach with peripheral blood samples from CL patients was not significant. Hence, peripheral blood samples can effectively distinguish active VL cases through PCR using multiple markers, offering a less invasive and labor-intensive diagnostic alternative.

Advances and Challenges in the Diagnosis of Leishmaniasis

Leishmaniasis remains a significant public health challenge, particularly in endemic regions with limited resources. Traditional diagnostic methods, including microscopy, culture, and serology, though widely utilized, often suffer from limitations such as variable  sensitivity, time delays, and the need for specialized infrastructure. Some of these limitations have been addressed with the emergence of molecular diagnostic techniques. Quantitative PCR (q-PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) assays have improved  the diagnostic sensitivity and specificity, enabling species identification and detection of asymptomatic infections. Further, nanodiagnostics and portable sequencing technologies such as the MinION™, along with lab-on-chip platforms, are revolutionizing the diagnostic landscape of leishmaniasis by offering point-of-care (POC) options for remote settings and field-based diagnosis. This review provides an in-depth analysis of these cutting-edge advances, discusses their application in resource-constrained settings, and evaluates their potential to reshape the future of leishmaniasis diagnosis and management.

qPCR as a Tool for the Diagnosis of Visceral and Cutaneous Leishmaniasis: A Systematic Review and Meta-Analysis

INTRODUCTION

Ensuring accuracy in the diagnosis of leishmaniasis is crucial due to the myriad of potential differential diagnoses. Given the inherent limitations of serological techniques, real-time polymerase chain reaction (qPCR) emerges as a superior alternative. Furthermore, parasitological methods, conventionally regarded as the gold standard owing to their high specificity, encounter challenges concerning sensitivity and invasiveness for patients. In this context, the present study aims to assess, via meta-analysis, the performance of qPCR in diagnosing visceral and cutaneous leishmaniasis.

METHOD

This meta-analysis encompassed studies published between January 2011 and December 2022, sourced from six databases (PubMed, LILACS, Scopus, Scielo, EMBASE, and Web of Science), utilizing the keywords "qPCR," "molecular diagnosis," and "leishmaniasis." Epidemiological studies focusing on the efficacy of qPCR for leishmaniasis diagnosis were included. Data such as study demographics, geographic locations, sampling techniques, and the number of positive qPCR results were aggregated and analyzed to derive overall positivity rates, sensitivity, and specificity values associated with qPCR. Heterogeneity analysis was conducted on the data to select appropriate models, and the collective efficacy data of qPCR were illustrated in forest plots.

RESULTS

Fifty-four studies met all inclusion criteria. The positivity rates for human visceral and cutaneous leishmaniasis were 27.07% (95% CI: 17.81-36.33%) and 60.40% (95% CI: 30.23-90.57%), respectively. In cases of visceral leishmaniasis in dogs, cats, and wild animals, the positivity rates were 26.55% (95% CI: 21.40-31.70%), 0.92% (95% CI: 0.09-1.75%), and 28.98% (95% CI: 21.86-35.10%), respectively. Analysis of the selected studies revealed high overall sensitivity and specificity values achieved with qPCR, at 91.08% (95% CI: 81.77-100.39%) and 98.08% (95% CI: 97.13-99.03%), respectively.

CONCLUSION

This study indicates that qPCR is a highly sensitive and specific tool, adequately suitable for the diagnosis of human visceral and cutaneous leishmaniasis, as well as visceral leishmaniasis in animals.

"High specificity of PCR in diagnosing mucocutaneous leshminiasis: a systematic review and meta analysis"

BACKGROUND

Mucocutaneous leishmaniasis (MCL) is a severe form of leishmaniasis causing chronic and destructive lesions. Accurate diagnosis is crucial for effective treatment. Traditional methods, such as the Montenegro skin test is delayed hypersensitivity test. Polymerase chain reaction (PCR) has emerged as a superior diagnostic tool for detecting Leishmania DNA, offering higher sensitivity and specificity.

METHODOLOGY

This meta-analysis adhered to PRISMA guidelines and included studies focusing exclusively on the diagnostic accuracy of PCR for MCL. A comprehensive literature search was conducted across multiple databases. Inclusion criteria mandated studies with relevant diagnostic accuracy metrics, while those mixing other forms of leishmaniasis or lacking a control group were excluded. Quality was assessed using the STARD checklist, and ensuring a low risk of bias assessed through QUADAS-2 tool.

RESULTS

Eight studies were included, showing PCR sensitivity ranging from 50% to 97.1% and consistently high specificity, often reaching 100%. The studies demonstrated a low risk of bias and applicability concerns, supporting the robustness of the findings. Heterogeneity was substantial, necessitating a random-effects model for pooled estimates.

INTERPRETATIONS

This analysis confirms PCR's high specificity for MCL diagnosis, despite variable sensitivity. Compared to previous meta-analyses, this study's focus on MCL exclusively provides a more targeted evaluation. Future research should aim to standardize PCR protocols and explore non-invasive sampling techniques to enhance diagnostic accuracy and patient comfort, ultimately improving clinical outcomes for MCL patients.

From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases

Infectious diseases impose a significant burden on global health systems due to high morbidity and mortality rates. According to the World Health Organization, millions die from infectious diseases annually, often due to delays in accurate diagnosis. Traditional diagnostic methods in clinical microbiology, primarily culture-based techniques, are time-consuming and may fail with hard-to-culture pathogens. Molecular biology advancements, notably the polymerase chain reaction (PCR), have revolutionized infectious disease diagnostics by allowing rapid and sensitive detection of pathogens' genetic material. PCR has become the gold standard for many infections, particularly highlighted during the COVID-19 pandemic. Following PCR, next-generation sequencing (NGS) has emerged, enabling comprehensive genomic analysis of pathogens, thus facilitating the detection of new strains and antibiotic resistance tracking. Innovative approaches like CRISPR technology are also enhancing diagnostic precision by identifying specific DNA/RNA sequences. However, the implementation of these methods faces challenges, particularly in low- and middle-income countries due to infrastructural and financial constraints. This review will explore the role of molecular diagnostic methods in infectious disease diagnosis, comparing their advantages and limitations, with a focus on PCR and NGS technologies and their future potential.

Visceral Leishmaniasis in a Twin Pregnancy: A Case Report and Review of the Literature

Visceral leishmaniasis (VL), often referred to as kala-azar, is quite rare in developed countries during pregnancy. Only few studies have evaluated its impact on perinatal outcome. It is caused primarily by Leishmania donovani or Leishmania infantum and presents with a wide spectrum of clinical manifestations from cutaneous ulcers to multisystem disease. Differential diagnosis is challenging as symptoms and signs are insidious, mimicking other diseases. Misdiagnosis can result in severe adverse perinatal outcomes, even maternal/neonatal death. Early treatment with liposomal amphotericin-B (LAmB) is currently the first choice with adequate effectiveness. We report a rare case of VL in a twin pregnancy with onset at the second trimester, presenting with periodic fever with rigors, right flank pain, and gradual dysregulation of all three cell lines. The positive rK39 enzyme-linked immunosorbent assay test confirmed the diagnosis. Treatment with LAmB resulted in clinical improvement within 48 h and in the delivery of two late-preterm healthy neonates with no symptoms or signs of vertical transmission. The one-year follow-up, of the mother and the neonates, was negative for recurrence. To our knowledge, this is the first reported case of VL in a twin pregnancy, and consequently treatment and perinatal outcome are of great importance.

Clinical and laboratory characterization of cutaneous leishmaniasis in Chinese migrant workers returned from Iraq

BACKGROUND

Imported cutaneous leishmaniasis (CL) is a growing problem with increasing global travel to endemic areas. Returned travelers with CL are easy to be misdiagnosed and mistreated due to the lack of awareness for the disease to the physicians in non-endemic region that may lead to unfavorable outcome. Our study intends to summarize the characteristics of Leishmania infection imported from Iraq, so as to help Chinese physicians diagnose and treat the disease. All CL patients were treated with intralesional injection of antimony.

METHODS

The definitive diagnosis of CL is based on the parasite identification by microscopic examination directly on lesion smear or parasite culture, PCR amplification of Leishmania-specific internal transcribed spacer 1 (ITS-1). The phylogenetic analysis, the immunopathological examination and the cytokine detection were proceeded after the diagnosis.

RESULTS

We have identified 25 CL cases in migrant Chinese workers returned from Iraq for the first time with L. major as the major species of infected Leishmania parasite. Clinical features of the Iraq-imported CL include the history of skin exposure to sandflies bite and the lesions mostly on the exposed limbs. More ulcerative wet lesion was observed than nodular dry lesion. PCR is not only used to detect Leishmania parasite with high sensitivity, but also to identify the species of infected parasite through sequencing the amplified Leishmania-specific ITS-1 gene. The phylogenetic analysis based on the amplified ITS-1 sequences revealed that the infected Leishmania was closed related to the species and strains endemic in Iraq. The immunopathological examination revealed the T-cell filtrated cellular immune response with less B cells and NK cells involved. The cytokine profile measured in the skin lesion also confirmed the Th1 cellular response with higher expression levels of IFN-γ, IL-6 and IL-8. The skin lesions in CL patients were healed after being treated locally with antimony.

CONCLUSIONS

The clinical and parasitological features of these Chinese CL cases imported from Iraq provide useful information for the diagnosis and treatment of CL that is not commonly seen in Chinese local population.

Assessment of pan-Leishmania detection by recombinase polymerase amplification assay

The spread of vector habitats along with increasing human mobility can introduce atypical Leishmania species and hence can challenge existing diagnostic practices for rapid detection of active infection with species outside the narrow target range. Here we assessed the pan-Leishmania detection ability of isothermal recombinase polymerase amplification (RPA) assays targeting 18S rRNA gene, cathepsin L-like cysteine proteinase B (Cpb) gene, and kinetoplast minicircle DNA (kDNA) regions. While the lowest limit of detection of the 18S rRNA-RPA and Cpb-RPA assays were estimated as 12 and 17 standard DNA molecules, respectively, both assays could amplify genomic DNA of 7 pathogenic Leishmania species. Evaluation of 18S rRNA-RPA and our previously developed kDNA-RPA assays on 70 real-time PCR-positive leishmaniasis samples of varying pathologies resulted in sensitivity rates of 35.71% and 88.57%, respectively, while the combined sensitivity was 98.57%. Combinatorial application of 18S rRNA-RPA and kDNA-RPA assays can be recommended for further diagnostic assessments.

Blood parasite load by qPCR as therapeutic monitoring in visceral leishmaniasis patients in Brazil: a case series study

Background:

This study aimed to describe the kinetics of Leishmania parasite load determined using kinetoplast DNA (kDNA)-based quantitative polymerase chain reaction (qPCR) in visceral leishmaniasis (VL) patients.

Methods:

Parasite load in blood was assessed by qPCR at five time points, up to 12 months post-diagnosis. Sixteen patients were followed up.

Results:

A significant reduction in the parasite load was observed after treatment (P < 0.0001). One patient had an increased parasite load 3 months post-treatment and relapsed clinically at month six.

Conclusions:

We have described the use of kDNA-based qPCR in the post-treatment follow-up of VL cases.

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.

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Qualitative and quantitative PCR-based tests are widely used in both diagnostics and research to assess the prevalence of disease-causing pathogens in veterinary medicine. The efficacy of these tests, usually measured in terms of sensitivity and specificity, is critical in confirming or excluding a clinical diagnosis. We undertook a meta-analysis to assess the inherent value of published PCR diagnostic approaches used to confirm and quantify bacteria and viruses associated with bovine respiratory disease (BRD) in cattle. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A thorough search of nine electronic databases (Web of Science, EBSCOhost, Cambridge journals online, ProQuest, PubMed, Sage journals online, ScienceDirect, Wiley online library and MEDLINE) was undertaken to find studies that had reported on the use of PCR and/or qPCR for the detection and/or quantification of BRD associated organisms. All studies meeting the inclusion criteria for reporting quantitative PCR for identification of BRD associated microorganisms were included in the analysis. Studies were then assessed on the applications of the Minimum Information for Publication of Quantitative Real-Time PCR Experiment (MIQE) and PCR primer/probe sequences were extracted and tested for in silico specificity using a high level of stringency. Fourteen full-text articles were included in this study. Of these, 79% of the analysed articles did not report the application of the MIQE guidelines in their study. High stringency in silico testing of 144 previously published PCR primer/probe sequences found many to have questionable specificity. This review identified a high occurrence of primer/probe sequences with a variable in silico specificity such that this may have implications for the accuracy of reporting. Although this analysis was only applied to one specific disease state, identification of animals suspected to be suffering from bovine respiratory disease, there appears to be more broadly a need for veterinary diagnostic studies to adopt international best practice for reporting of quantitative PCR diagnostic data to be both accurate and comparable between studies and methodologies.

Establish an allele-specific real-time PCR for Leishmania species identification

Background

Leishmaniasis is a serious neglected tropical disease that may lead to life-threatening outcome, which species are closely related to clinical diagnosis and patient management. The current Leishmania species determination method is not appropriate for clinical application. New Leishmania species identification tool is needed using clinical samples directly without isolation and cultivation of parasites.

Methods

A probe-based allele-specific real-time PCR assay was established for Leishmania species identification between Leishmania donovani and L. infantum for visceral leishmaniasis (VL) and among L. major, L. tropica and L. donovani/L. infantum for cutaneous leishmaniasis (CL), targeting hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and spermidine synthase (SPDSYN) gene with their species-specific single nucleotide polymorphisms (SNPs). The limit of detection of this assay was evaluated based on 8 repeated tests with intra-assay standard deviation < 0.5 and inter-assay coefficients of variability < 5%. The specificity of this assay was tested with DNA samples obtained from Plasmodium falciparum, Toxoplasma gondii, Brucella melitensis and Orientia tsutsugamushi. Total 42 clinical specimens were used to evaluate the ability of this assay for Leishmania species identification. The phylogenetic tree was constructed using HGPRT and SPDSYN gene fragments to validate the performance of this assay.

Results

This new method was able to detect 3 and 12 parasites/reaction for VL and CL respectively, and exhibited no cross-reaction with P. falciparum, T. gondii, B. melitensis, O. tsutsugamushi and non-target species of Leishmania. Twenty-two samples from VL patients were identified as L. donovani (n = 3) and L. infantum (n = 19), and 20 specimens from CL patients were identified as L. major (n = 20), providing an agreement of 100% compared with sequencing results. For further validation, 29 sequences of HGPRT fragment from nine Leishmania species and 22 sequences from VL patients were used for phylogenetic analysis, which agreed with the results of this new method. Similar results were obtained with 43 sequences of SPDSYN fragment from 18 Leishmania species and 20 sequences from CL patients.

Conclusions

Our assay provides a rapid and accurate tool for Leishmania species identification which is applicable for species-adapted therapeutic schedule and patient management.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-00992-y.

Precision Medicine in Control of Visceral Leishmaniasis Caused by L. donovani

Precision medicine and precision global health in visceral leishmaniasis (VL) have not yet been described and could take into account how all known determinants improve diagnostics and treatment for the individual patient. Precision public health would lead to the right intervention in each VL endemic population for control, based on relevant population-based data, vector exposures, reservoirs, socio-economic factors and other determinants. In anthroponotic VL caused by L. donovani, precision may currently be targeted to the regional level in nosogeographic entities that are defined by the interplay of the circulating parasite, the reservoir and the sand fly vector. From this 5 major priorities arise: diagnosis, treatment, PKDL, asymptomatic infection and transmission. These 5 priorities share the immune responses of infection with L. donovani as an important final common pathway, for which innovative new genomic and non-genomic tools in various disciplines have become available that provide new insights in clinical management and in control. From this, further precision may be defined for groups (e.g. children, women, pregnancy, HIV-VL co-infection), and eventually targeted to the individual level.

Clinical and laboratory characteristics of hemophagocytic lymphohistiocytosis induced by Leishmania infantum infection

Background

Visceral leishmaniasis (VL) could progress to secondary hemophagocytic lymphohistiocytosis (HLH), which is a rare but life-threatening condition with poor prognosis. So far, the clinical and laboratory characteristics of VL associated HLH have not been well elucidated.

Method and findings

In this study, we retrospectively analyzed the clinical and laboratory profiles between 17 patients with VL associated HLH and 27 patients with VL alone admitted at the Beijing Friendship Hospital, Capital Medical University from May 2016 to March 2021. In addition to the identification of Leishmania infection, hemophagocytosis was identified in bone marrow in the most cases of VL associated HLH (15/17). The patients with VL associated HLH had higher chances of bleeding, hepatomegaly, thrombocytopenia, hypertriglyceridemia, hyperferritinemia, hypofibrinogenemia, elevated secretion of soluble IL-2 receptor or lower NK cell activity compared to patients with VL only. Furthermore, patients with VL associated HLH had higher inflammation status associated with higher levels of Th1 (TNF-α, IFN-γ, IL-1beta, IL-6, IL-8, IL-12p70), Th2 (IL-4) and Th17 cytokines (IL-17, IL-23) in the peripheral blood, and higher parasite load (qPCR and parasite culture). All 27 VL cases were totally recovered after being treated with Sodium Stibogluconate, five of the 17 patients with VL associated HLH died even after timely treatment with anti-parasite and immunosuppressive chemotherapy.

Conclusion

Without appropriate treatment, visceral leishmaniosis could develop to secondary HLH. The parasite culturing and qPCR detection of bone marrow samples facilitates the diagnosis of VL associated HLH in addition to other findings of HLH. Prompt treatment with anti-Leishmania and immunosuppressive chemotherapy is critical to reduce the mortality of VL associated HLH.

Hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening syndrome characterized by pro-inflammatory cytokine secretion, hyperinflammatory and multiple organ damages. Visceral leishmaniasis (VL) is a well-known cause of infection associated HLH and result in fatal consequence. However, it is not well characterized for the clinical and laboratory features of the visceral leishmaniasis associated HLH. In this study, we presented that, compared to the VL alone, patients with VL associated HLH had higher chances of bleeding, hepatomegaly, thrombocytopenia, hypertriglyceridemia, hyperferritinemia, hypofibrinogenemia, elevated secretion of soluble IL-2 receptor or lower NK cell activity. Moreover, patients with VL associated HLH also had higher levels of Th1, Th2 and Th17 cytokines in the sera and had higher parasite load in the bone marrow specimen. More cases with VL associated HLH had hepatosplenomegaly with iron overload in the magnetic resonance imaging. In the therapeutic strategy, besides the anti-Leishmania treatment, anti-inflammatory therapy to reduce cytokine storm and excessive immune responses facilitated the remission in the VL associated HLH cases.