Development of a Highly Sensitive Nested PCR and Its Application for the Diagnosis of Cutaneous Leishmaniasis in Sri Lanka.
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SUBMITTER: De Silva NL
PROVIDER: S-EPMC9145043 | biostudies-literature | 2022 May
REPOSITORIES: biostudies-literature
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Development of a Highly Sensitive Nested PCR and Its Application for the Diagnosis of Cutaneous Leishmaniasis in Sri Lanka.
De Silva Nirmitha Lalindi NL De Silva Viraji Nefertiti Hiromel VNH Deerasinghe Arachchige Theja Hemapala ATH Rathnapala Upeksha Lakmini UL Itoh Makoto M Takagi Hidekazu H Weerasooriya Mirani Vasanthamala MV Kato Hirotomo H Yahathugoda Thishan Channa TC
Microorganisms 20220509 5
The recent surge in cutaneous leishmaniasis (CL) in Sri Lanka has rendered clinical diagnosis difficult; thus, laboratory confirmation is indispensable. A modified (two novel inner primers to detect CL caused by Leishmania donovani) nested Internal Transcribed Spacer-1 (ITS1) PCR-Restriction Fragment Length Polymorphism (RFLP) method was developed and tested. The sensitivity of the modified nested PCR was tested using serial dilutions (103 to 10−2) of the DNA extract of a cultured L. donovani DD ...[more]
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Project description:To investigate the relationship of cutaneous leishmaniasis isolates from Sri Lanka to known species, we performed DNA sequencing and microsatellite analyses. We identified Leishmania donovani as the agent of Sri Lanka cutaneous leishmaniasis and showed that these parasites are closely related to those causing visceral leishmaniasis in the Indian subcontinent.
| S-EPMC2725894 | biostudies-literature
Project description:BackgroundHuman leishmaniasis is one of the major parasitic diseases with worldwide distribution. Sri Lanka is a recently established focus of leishmaniasis caused by a variant Leishmania donovani. Early case detection and management is a main approach identified for L. donovani control in the regional leishmaniasis elimination drive. Usefulness of light microscopy and in-vitro culture are limited in chronic, atypical or treated lesions though timely and accurate detection of all light microscopy/in-vitro culture negative cases of all forms of leishmaniasis is necessary for treatment. Timely treatment is important to minimize risk for death in visceral disease and undesired sequelae of long standing infection and illness on both patients and community. We described a 100% sensitive, Leishmania spp. specific modified version of a nested PCR (Mo-STNPCR) that also minimizes carry over and cross contaminations while facilitate investigation of light microscopy and in-vitro culture negative clinically suggestive cases of leishmaniasis.MethodsLeishmania DNA was amplified using previously published P221: 5'-GGTTCCTTTCCTGATTTACG-3' and P332: 5'-GGCCGGTAAAGGCCGAATAG-3'outer primers followed by a nested reaction using P223: 5'-TCCCATCGCAACCTCGGTT-3' and P333: 5'-AAGCGGGCGCGGTGCTG-3' inner primers that by passes the requirement of tube handling between the two steps of the conventional nested PCR. Leishmania DNA was detected in a range of infected tissue material. Infected material from patients with cutaneous leishmaniasis (n = 30), visceral leishmaniasis (n = 10) and from a control group including patients with non-leishmanial skin diseases (n = 10), other systemic diseases (n = 10) and healthy individuals (n = 10) were examined with Mo-STNPCR. Results were further compared with those of light microscopy and in-vitro culture.ResultsMo-STNPCR method was 100% sensitive and 100% specific for diagnosis of leishmaniasis. Light microscopy and in-vitro culture were positive in 75.0% (n = 30/40) and 72.5% (n = 29/40) samples respectively where combined results of them gave 87.5% (n = 35/40) sensitivity. Mo-STNPCR did not cross react with control samples. Furthermore, Mo-STNPCR reduces the risk of cross-contaminations and carry over contaminations since the full reaction is carried out without opening the tubes. Per patient cost was calculated as 22 USD while the same was 3 and 6 USD for light microscopy and in-vitro culture respectively.ConclusionMo-STNPCR method is a useful tool in detecting leishmaniasis in minority of cases that go undetected by first line investigations.
| S-EPMC6631494 | biostudies-literature
Project description:BackgroundLeishmaniasis is a neglected tropical vector-borne disease, which is on the rise in Sri Lanka. Spatiotemporal and risk factor analyses are useful for understanding transmission dynamics, spatial clustering and predicting future disease distribution and trends to facilitate effective infection control.MethodsThe nationwide clinically confirmed cutaneous leishmaniasis and climatic data were collected from 2001 to 2019. Hierarchical clustering and spatiotemporal cross-correlation analysis were used to measure the region-wide and local (between neighboring districts) synchrony of transmission. A mixed spatiotemporal regression-autoregression model was built to study the effects of climatic, neighboring-district dispersal, and infection carryover variables on leishmaniasis dynamics and spatial distribution. Same model without climatic variables was used to predict the future distribution and trends of leishmaniasis cases in Sri Lanka.ResultsA total of 19,361 clinically confirmed leishmaniasis cases have been reported in Sri Lanka from 2001-2019. There were three phases identified: low-transmission phase (2001-2010), parasite population buildup phase (2011-2017), and outbreak phase (2018-2019). Spatially, the districts were divided into three groups based on similarity in temporal dynamics. The global mean correlation among district incidence dynamics was 0.30 (95% CI 0.25-0.35), and the localized mean correlation between neighboring districts was 0.58 (95% CI 0.42-0.73). Risk analysis for the seven districts with the highest incidence rates indicated that precipitation, neighboring-district effect, and infection carryover effect exhibited significant correlation with district-level incidence dynamics. Model-predicted incidence dynamics and case distribution matched well with observed results, except for the outbreak in 2018. The model-predicted 2020 case number is about 5,400 cases, with intensified transmission and expansion of high-transmission area. The predicted case number will be 9115 in 2022 and 19212 in 2025.ConclusionsThe drastic upsurge in leishmaniasis cases in Sri Lanka in the last few year was unprecedented and it was strongly linked to precipitation, high burden of localized infections and inter-district dispersal. Targeted interventions are urgently needed to arrest an uncontrollable disease spread.
| S-EPMC8099137 | biostudies-literature
Project description:BackgroundThere is limited knowledge about the stigma associated with cutaneous leishmaniasis (CL) in Sri Lanka. To ensure that leishmaniasis researchers focus on CL-associated stigma, we provide an evidence-based framework that can be used in future research.MethodsWe conducted a systematic review on CL-associated stigma using international evidence and carried out a multimethod qualitative study in the Anuradhapura district in Sri Lanka. Based on that, we identified manifestations of stigma, drivers and facilitators that we synthesised to develop a conceptual framework on CL-associated stigma.ResultsOur framework consists of drivers, facilitators and self-stigma experienced by people with CL. Stigma drivers included fear, misbeliefs and misconceptions about CL; the belief that wounds are disfiguring; the treatment burden and implied blame. Facilitators that reduced stigma included knowledge of the curability of CL and awareness that CL is not contagious. The nature of social interactions in rural communities enhanced stigma formation. We identified various enacted, felt and internalised stigma experiences of people with CL.ConclusionsWe developed a conceptual framework of the stigma associated with CL that can be used to develop targeted interventions to increase CL awareness, address stigma and improve the quality of life for CL patients.
| S-EPMC11375585 | biostudies-literature
Project description:BackgroundLeishmaniasis is a neglected tropical disease that affects countries in the developing world. In Sri Lanka, cutaneous leishmaniasis is the most common form of the disease. It is prevalent in dry and intermediate zones, mostly associated with rural settings. Understanding basic risk factors is critical in the management of the disease with effective interventions. This study is focused on assessing the demographic, socioeconomic and landscape factors associated with leishmaniasis in Kurunegala District, Sri Lanka.MethodsA descriptive cross-sectional study was conducted. Households of the past patients and randomly selected households, which had no history of leishmaniasis cases were interviewed. The clinical, socioeconomic, demographic, landscape and awareness-related data were obtained using a pre-tested, interviewer-administered questionnaire.ResultsA total of 101 patients and a similar number of controls were included in the study. All the patients had the cutaneous form of the disease. Housewives and personnel with monthly incomes less than Rs. 10,000 (56.76 USD) were 3.9- and 9.5-times more prone to the disease, respectively, according to multivariate analysis. Presence of decaying garbage, termite hills, unclear areas, wet soil and gardening areas were always associated with the increased odds of acquiring the disease.ConclusionsDemographic factors do not play a pivotal role in the prevalence of leishmaniasis in the area. Housewives, inhabitants with low incomes and individuals who live in areas with conditions suitable for sand fly breeding and resting are major groups with a higher risk of infection. Special attention must be given in raising awareness and environmental management in control activities.
| S-EPMC7216469 | biostudies-literature
Project description:Sri Lanka is a recent focus having Leishmania donovani induced cutaneous leishmaniasis (CL) as the main clinical entity. A separate clinical entity within profile of CL was described in this study. Laboratory confirmed cases of CL (n= 950, 2002-2014) were analysed. Most lesions showed known classical developmental stages of CL (CCL) observed in other CL endemic settings while few cases (13%, 122/950) showed atypical skin manifestations (ACL). Clinical, geographical, and treatment response patterns of ACL were different from those of CCL. ACL was mainly found among males (68.0%), in 21-40 year age group (51.6%), and reported delayed treatment seeking (23.5% vs 16.3% in CCL), more nonclassical onset (lesions other than acne form <1cm sized papules), (12.1 vs 2.7%, P<0.05.), more head and neck lesions (41.5%. vs 27.2%), more large lesions (>4cm), (18.6 vs 9.9%), and poor laboratory positivity rates (65.6% vs 88.2%) when compared to CCL. When compared to lesions reporting a typical onset, lesions reporting nonclassical onset were more likely to develop ACL later on (50.1% vs 10.7%). As compared to lesions on limbs, those on head and neck and trunk were more likely to be ACL (7.0%, 16.3%, and 22.8%, respectively, P<0.05). ACL features were not age or gender dependent. Highest proportion within ACL category (32.8%) and small proportion of CCL (10.1%) originated from less leishmaniasis prevalent areas (other regions) (P<0.05). North reported more ACL than South (15.9% vs 7.4%). A total of 95 CL cases with a significant travel history were further analyzed. Residents of other regions when acquired infection from North or South developed more ACL than residents in North or South (60.9% vs 15.9% and 42.9% vs 7.4% respectively). Patients in other regions when travelled to North developed more ACL than when they travelled to South (60.9%, 42.9%). ACL and CCL required an average of 18 doses over 16.7 months and 10 doses over 12 weeks, respectively, to achieve a complete clinical cure. Underlying host immunological factors, parasite strain variations and regional variations of both could be underlying etiologies. Established independent transmission within less leishmaniasis prevalent regions combined with an unusual clinical picture leading to poor clinical suspicion and low laboratory confirmation rate will pose potential difficulties in early case detection in these highly populated and commercialized areas. This in turn will further facilitate silent and high disease transmission.
| S-EPMC6556790 | biostudies-literature
Project description:Among the most central questions in Leishmania research is why some species remain in the skin dermis at the site of infection by the sand fly vector whereas other species migrate to visceral organs where they cause fatal visceral leishmaniasis. Although L. donovani is the species typically responsible for visceral leishmaniasis, an atypical L. donovani strain is the etiologic agent for cutaneous leishmaniasis in Sri Lanka. To identify molecular determinants for visceral disease, we have analysed the phenotype and genotype of two L. donovani clinical isolates from Sri Lanka where one isolate was derived from a cutaneous leishmaniasis patient (CL) and the other from a visceral leishmaniasis patient (VL). These isolates cause dramatically different pathology when introduced into mice; notably the CL isolate has lost the ability to survive in visceral organs while the VL isolate was highly virulent in visceral organs of BALB/c mice. Whole genome sequencing of the CL and VL isolates revealed that these genomes were very similar as there were no gene deletions and few individual gene amplifications. Indels resulting in frame shifts and loss/gain of stop codons resulted in 13 distinct pseudogenes present in each of the CL and VL isolates. There were 154 non-synonymous SNPs specific to the CL isolate and 193 non-synonymous SNPs specific to the VL isolate. Genome wide gene expression analysis revealed several transcript level differences, including the A2 virulence gene resulting in higher expression of A2 proteins in the VL isolate than in the CL isolate. Genotypic variations relevant to pathology and tropism in Leishmania can be interrogated by reverse genetics. Experimentally increasing A2 expression in the CL isolate through gene transfer significantly increased itM-bM-^@M-^Ys ability to survive in the spleen of BALB/c mice and conversely, down-regulating A2 expression in the VL isolate abrogated attenuated its survival in BALB/c mice. These observations reveal that there are relatively few genetic differences between the CL and VL isolates apart from the A2 genes, but collectively these have profound effects on human disease and experimentally infected mice. 6 Samples in total, 3 each from VL and CL causing isolates were analyzed by Splice Leader RNASeq. These three samples from each of the isolates were grown to form one of the following three lifestages, Promastigotes, Macrophage derived Amastigotes, Axenic Amastigotes.
2013-12-31 | E-GEOD-48475 | biostudies-arrayexpress
Project description: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.
| S-EPMC7223001 | biostudies-literature
Project description:Leishmaniasis is a tropical infectious disease affecting some of the world's most economically disadvantaged and resource-poor regions. Cutaneous leishmaniasis (CL) is the most common out of the three clinical types of Leishmaniasis. Since 1904 this disease has been endemic in Sri Lanka. CL is considered a disfiguring stigmatising disease with a higher psychosocial burden. However, there needs to be a more in-depth, holistic understanding of the psychosocial burden of this disease, both locally and internationally. An in-depth understanding of the disease burden beyond morbidity and mortality is required to provide people-centred care. We explored the psychosocial burden of CL in rural Sri Lanka using a complex multimethod qualitative approach with community engagement and involvement. Data collection included participant observation, an auto-ethnographic diary study by community researchers with post-diary interviews, and a Participant Experience Reflection Journal (PERJ) study with post-PERJ interviews with community members with CL. The thematic analysis revealed three major burden-related themes on perceptions and reflections on the disease: wound, treatment, and illness-experience related burden. Fear, disgust, body image concerns, and being subjected to negative societal reactions were wound-related. Treatment interfering with day-to-day life, pain, the time-consuming nature of the treatment, problems due to the ineffectiveness of the treatment, and the burden of attending a government hospital clinic were the treatment-related burdens. Anxiety/worry due to wrongly perceived disease severity and negative emotions due to the nature of the disease made the illness experience more burdensome. Addressing the multifaceted psychosocial burden is paramount to ensure healthcare seeking, treatment compliance, and disease control and prevention. We propose a people-centred healthcare model to understand the contextual nature of the disease and improve patient outcomes.
| S-EPMC10826957 | biostudies-literature
Project description:Among the most central questions in Leishmania research is why some species remain in the skin dermis at the site of infection by the sand fly vector whereas other species migrate to visceral organs where they cause fatal visceral leishmaniasis. Although L. donovani is the species typically responsible for visceral leishmaniasis, an atypical L. donovani strain is the etiologic agent for cutaneous leishmaniasis in Sri Lanka. To identify molecular determinants for visceral disease, we have analysed the phenotype and genotype of two L. donovani clinical isolates from Sri Lanka where one isolate was derived from a cutaneous leishmaniasis patient (CL) and the other from a visceral leishmaniasis patient (VL). These isolates cause dramatically different pathology when introduced into mice; notably the CL isolate has lost the ability to survive in visceral organs while the VL isolate was highly virulent in visceral organs of BALB/c mice. Whole genome sequencing of the CL and VL isolates revealed that these genomes were very similar as there were no gene deletions and few individual gene amplifications. Indels resulting in frame shifts and loss/gain of stop codons resulted in 13 distinct pseudogenes present in each of the CL and VL isolates. There were 154 non-synonymous SNPs specific to the CL isolate and 193 non-synonymous SNPs specific to the VL isolate. Genome wide gene expression analysis revealed several transcript level differences, including the A2 virulence gene resulting in higher expression of A2 proteins in the VL isolate than in the CL isolate. Genotypic variations relevant to pathology and tropism in Leishmania can be interrogated by reverse genetics. Experimentally increasing A2 expression in the CL isolate through gene transfer significantly increased it’s ability to survive in the spleen of BALB/c mice and conversely, down-regulating A2 expression in the VL isolate abrogated attenuated its survival in BALB/c mice. These observations reveal that there are relatively few genetic differences between the CL and VL isolates apart from the A2 genes, but collectively these have profound effects on human disease and experimentally infected mice.
2013-12-31 | GSE48475 | GEO