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Roca-Geronès X, Sala C, Marteles D, Villanueva-Saz S, Riera C, Alcover MM, Fisa R. Genetic Variability in Leishmaniasis-Causing Leishmania infantum in Humans and Dogs from North-East Spain. Animals (Basel) 2024; 14:1796. [PMID: 38929415 PMCID: PMC11200389 DOI: 10.3390/ani14121796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Leishmania infantum is the primary cause of visceral and cutaneous leishmaniasis in the European Mediterranean region. Subspecies-level characterization of L. infantum aids epidemiological studies by offering insights into the evolution and geographical distribution of the parasite and reservoir identity. In this study, conducted in north-east Spain, 26 DNA samples of L. infantum were analyzed, comprising 21 from 10 humans and 5 from 5 dogs. Minicircle kinetoplast DNA (kDNA) polymerase chain reaction assays using primers MC1 and MC2, followed by sequencing, were employed to assess intraspecific genetic variability. Single-nucleotide polymorphism (SNP) analysis detected seven genotypes (G1, G2, G12*-G15*, and G17*), with five being reported for the first time (*). The most prevalent was the newly described G13 (54%), while the other currently identified genotypes were predominantly found in single samples. The in silico restriction fragment length polymorphism (RFLP) method revealed five genotypes (B, F, N, P, and W), one of them previously unreported (W). Genotype B was the most prevalent (85%), comprising three SNP genotypes (G1, G2, and G13), whereas the other RFLP genotypes were associated with single SNP genotypes. These kDNA genotyping methods revealed significant intraspecific genetic diversity in L. infantum, demonstrating their suitability for fingerprinting and strain monitoring.
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Affiliation(s)
- Xavier Roca-Geronès
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Clara Sala
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Diana Marteles
- Animal Pathology Department, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain (S.V.-S.)
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza), 50013 Zaragoza, Spain
| | - Sergio Villanueva-Saz
- Animal Pathology Department, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain (S.V.-S.)
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza), 50013 Zaragoza, Spain
| | - Cristina Riera
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Mª Magdalena Alcover
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Roser Fisa
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
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Gow I, Smith NC, Stark D, Ellis J. Laboratory diagnostics for human Leishmania infections: a polymerase chain reaction-focussed review of detection and identification methods. Parasit Vectors 2022; 15:412. [PMID: 36335408 PMCID: PMC9636697 DOI: 10.1186/s13071-022-05524-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/02/2022] [Indexed: 11/08/2022] Open
Abstract
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.
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Affiliation(s)
- Ineka Gow
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Nicholas C. Smith
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Damien Stark
- Department of Microbiology, St Vincent’s Hospital Sydney, Darlinghurst, NSW 2010 Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
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Ferreira JG, Nascimento F, Marcon GB, de Almeida E, Costa SB. Methods and parameters of melting curve analysis for identification of Leishmania species: A scoping review. ASIAN PAC J TROP MED 2021. [DOI: 10.4103/1995-7645.332807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Conter CC, Mota CA, Dos Santos BA, de Souza Braga L, de Souza Terron M, Navasconi TR, Fernandes ACBS, Demarchi IG, de Castro KRR, Aristides SMA, Lonardoni MVC, Teixeira JJV, Silveira TGV. PCR primers designed for new world Leishmania: A systematic review. Exp Parasitol 2019; 207:107773. [PMID: 31605671 DOI: 10.1016/j.exppara.2019.107773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 01/03/2023]
Abstract
Studies of the primers that were designed to detect New World Leishmania were systematically reviewed to report the characteristics of each target, detection limit, specificity of the primers designed and diagnostic sensibility. The papers identified in the databases PubMed and Web of Science involved 50 studies. Minicircle is the most applied target in molecular research for diagnosis, due to its high sensitivity in detecting Leishmania in different clinical samples, a characteristic that can be partially attributed to the higher number of copies of the minicircle per cell. The other molecular targets shown in this review were less sensitive to diagnostic use because of the lower number of copies of the target gene per cell, but more specific for identification of the subgenus and/or species. The choice of the best target is an important step towards the result of the research. The target allows the design of primers that are specific to the genus, subgenus or a particular species and also imparts sensitivity to the method for diagnosis. The findings of this systematic review provide the advantages and disadvantages of the main molecular targets and primers designed for New World Leishmania, offering information so that the researcher can choose the PCR system best suited to their research need. This is a timely and extremely thorough review of the primers designed for New World Leishmania.
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Affiliation(s)
- Carolina Cella Conter
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | - Camila Alves Mota
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Laís de Souza Braga
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Taísa Rocha Navasconi
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Izabel Galhardo Demarchi
- Department of Clinical Analyses and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
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Nath-Chowdhury M, Sangaralingam M, Bastien P, Ravel C, Pratlong F, Mendez J, Libman M, Ndao M. Real-time PCR using FRET technology for Old World cutaneous leishmaniasis species differentiation. Parasit Vectors 2016; 9:255. [PMID: 27141967 PMCID: PMC4855858 DOI: 10.1186/s13071-016-1531-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/24/2016] [Indexed: 02/06/2023] Open
Abstract
Background Recently, there has been a re-emergence of cutaneous leishmaniasis in endemic countries and an increase in imported cases in non-endemic countries by travelers, workers, expatriates, immigrants, and military force personnel. Old World cutaneous leishmaniasis is caused primarily by Leishmania major, L. tropica and L. aethiopica. Despite their low sensitivity, diagnosis traditionally includes microscopic and histopathological examinations, and in vitro cultivation. Several conventional PCR techniques have been developed for species identification, which are time-consuming and labour-intensive. Real-time PCR using SYBR green dye, although provides rapid detection, may generate false positive signals. Therefore, a rapid and easy method such as a FRET-based real-time PCR would improve not only the turn-around time of diagnosing Old World cutaneous Leishmania species but will also increase its specificity and sensitivity. Methods A FRET-based real-time PCR assay which amplifies the cathepsin L-like cysteine protease B gene encoding a major Leishmania antigen was developed to differentiate L. major, L. tropica, and L. aethiopica in one single step using one set of primers and probes. Assay performance was tested on cutaneous and visceral strains of Leishmania parasite cultures and isolates of other protozoan parasites as well as human biopsy specimen. Results The assay readily differentiates between the three Old World cutaneous leishmaniasis species based on their melting curve characteristics. A single Tm at 55.2 ± 0.5 °C for L. aethiopica strains was distinguished from a single Tm at 57.4 ± 0.2 °C for L. major strains. A double curve with melting peaks at 66.6 ± 0.1 °C and 48.1 ± 0.5 °C or 55.8 ± 0.6 °C was observed for all L. tropica strains. The assay was further tested on biopsy specimens, which showed 100 % agreement with results obtained from isoenzyme electrophoresis and Sanger sequencing. Conclusion Currently, there are no published data on real-time PCR using FRET technology to differentiate between Old World cutaneous Leishmania species. In summary, our assay based on specific hybridization addresses the limitations of previous PCR technology and provides a single step, reliable method of species identification and rapid diagnostic applications.
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Affiliation(s)
- Milli Nath-Chowdhury
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mugundhine Sangaralingam
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Patrick Bastien
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Christophe Ravel
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Francine Pratlong
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Juan Mendez
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Libman
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,J.D. MacLean Centre for Tropical Diseases at McGill University, Montreal, QC, Canada
| | - Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada. .,J.D. MacLean Centre for Tropical Diseases at McGill University, Montreal, QC, Canada.
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Singh S. Changing trends in the epidemiology, clinical presentation, and diagnosis of Leishmania-HIV co-infection in India. Int J Infect Dis 2014; 29:103-12. [PMID: 25449244 DOI: 10.1016/j.ijid.2014.07.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 02/07/2023] Open
Abstract
Following the HIV epidemic, several countries have reported co-infections of Leishmania with HIV. Co-infection with these two pathogens results in rapid disease progression, more severe disease, and a poor response to treatment. A systematic review of the literature from India is presented herein. Since the first case of visceral leishmaniasis (VL) and HIV was published from India in 1999, a number of cases of HIV-Leishmania co-infection have been reported, but the proportion has been low (0.029-0.4%), as also reported in other countries where these two diseases are co-endemic. More than 89 cases of VL-HIV and 10 cases of cutaneous leishmaniasis (CL)-HIV have been published since 1999. Of these latter 10 cases, five had simple CL and five cases manifested with diffuse cutaneous leishmaniasis (DCL). In addition, one case of post-kala-azar mucocutaneous leishmaniasis in a patient with full-blown AIDS has also been reported. In two cases, it could not be ascertained whether they were cases of DCL or post-kala-azar dermal leishmaniasis from the description. Although the first case of VL-HIV co-infection was reported from the sub-Himalayan state of Uttarakhand, most cases have been reported from the VL endemic state of Bihar. HIV-Leishmania is not alarmingly high in India. Most cases were found to have occurred during 1997-2007. After that, the number of new cases decreased. This is most probably due to the low prevalence of HIV in VL and CL endemic regions and to the free supply of highly active antiretroviral therapy for HIV-infected patients.
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Affiliation(s)
- Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India.
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Chaouch M, Fathallah-Mili A, Driss M, Lahmadi R, Ayari C, Guizani I, Ben Said M, BenAbderrazak S. Identification of Tunisian Leishmania spp. by PCR amplification of cysteine proteinase B (cpb) genes and phylogenetic analysis. Acta Trop 2013; 125:357-65. [PMID: 23228525 DOI: 10.1016/j.actatropica.2012.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 11/09/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
Discrimination of the Old World Leishmania parasites is important for diagnosis and epidemiological studies of leishmaniasis. We have developed PCR assays that allow the discrimination between Leishmania major, Leishmania tropica and Leishmania infantum Tunisian species. The identification was performed by a simple PCR targeting cysteine protease B (cpb) gene copies. These PCR can be a routine molecular biology tools for discrimination of Leishmania spp. from different geographical origins and different clinical forms. Our assays can be an informative source for cpb gene studying concerning drug, diagnostics and vaccine research. The PCR products of the cpb gene and the N-acetylglucosamine-1-phosphate transferase (nagt) Leishmania gene were sequenced and aligned. Phylogenetic trees of Leishmania based cpb and nagt sequences are close in topology and present the classic distribution of Leishmania in the Old World. The phylogenetic analysis has enabled the characterization and identification of different strains, using both multicopy (cpb) and single copy (nagt) genes. Indeed, the cpb phylogenetic analysis allowed us to identify the Tunisian Leishmania killicki species, and a group which gathers the least evolved isolates of the Leishmania donovani complex, that was originated from East Africa. This clustering confirms the African origin for the visceralizing species of the L. donovani complex.
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Requena JM, Chicharro C, García L, Parrado R, Puerta CJ, Cañavate C. Sequence analysis of the 3'-untranslated region of HSP70 (type I) genes in the genus Leishmania: its usefulness as a molecular marker for species identification. Parasit Vectors 2012; 5:87. [PMID: 22541251 PMCID: PMC3425316 DOI: 10.1186/1756-3305-5-87] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/08/2012] [Indexed: 12/18/2022] Open
Abstract
Background The Leishmaniases are a group of clinically diverse diseases caused by parasites of the genus Leishmania. To distinguish between species is crucial for correct diagnosis and prognosis as well as for treatment decisions. Recently, sequencing of the HSP70 coding region has been applied in phylogenetic studies and for identifying of Leishmania species with excellent results. Methods In the present study, we analyzed the 3’-untranslated region (UTR) of Leishmania HSP70-type I gene from 24 strains representing eleven Leishmania species in the belief that this non-coding region would have a better discriminatory capacity for species typing than coding regions. Results It was observed that there was a remarkable degree of sequence conservation in this region, even between species of the subgenus Leishmania and Viannia. In addition, the presence of many microsatellites was a common feature of the 3´-UTR of HSP70-I genes in the Leishmania genus. Finally, we constructed dendrograms based on global sequence alignments of the analyzed Leishmania species and strains, the results indicated that this particular region of HSP70 genes might be useful for species (or species complex) typing, improving for particular species the discrimination capacity of phylogenetic trees based on HSP70 coding sequences. Given the large size variation of the analyzed region between the Leishmania and Viannia subgenera, direct visualization of the PCR amplification product would allow discrimination between subgenera, and a HaeIII-PCR-RFLP analysis might be used for differentiating some species within each subgenera. Conclusions Sequence and phylogenetic analyses indicated that this region, which is readily amplified using a single pair of primers from both Old and New World Leishmania species, might be useful as a molecular marker for species discrimination.
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Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid, 28049 Madrid, Spain.
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Khademvatan S, Neisi N, Maraghi S, Saki J. Diagnosis and identification of Leishmania spp. from Giemsa-stained slides, by real-time PCR and melting curve analysis in south-west of Iran. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2012; 105:559-65. [PMID: 22325815 DOI: 10.1179/2047773211y.0000000014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND The aim of present study was describing a real-time PCR assay for the diagnosis and direct identification of Leishmania species on Giemsa-stained slides in south-west of Iran. MATERIALS AND METHODS Altogether, 102 Giemsa-stained slides were collected from different part of south-west of Iran between 2008 and 2011. All the Giemsa-stained slides were examined under light microscope. After DNA extraction, real-time PCR amplification and detection were conducted with fluorescent SYBR Green I. For identification, PCR products were analysed with melting curve analysis. RESULTS One hundred and two archived slides from suspected lesion examined by microscopy and real-time PCR. The sensitivity of the real-time PCR on Giemsa-stained slid was 98% (96/102). The melting curve analysis (T(m)) were 88·3±0·2°C for L. tropica (MHOM/IR/02/Mash10), 86·5±0·2°C for L. major (MHOM/IR/75/ER) and 89·4±0·3°C for L. infantum (MCAN/IR/97/LON 49), respectively. CONCLUSION This study is first report in use of real-time PCR for diagnosis and identification of Leishmania spp. in Iran. Up to now, in Iran, the majority of identification of Leishmania species is restriction fragment length polymorphism (PCR-RFLP) of ITS1 and kinetoplast DNA. Our data showed that Giemsa-stained slides that were stored more than 3 years, can be use for Leishmania DNA extraction and amplification by real-time PCR. Compared to conventional PCR-based methods, the real-time PCR is extremely rapid with results and more samples can be processed at one time.
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Affiliation(s)
- S Khademvatan
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Pita-Pereira D, Lins R, Oliveira MP, Lima RB, Pereira BAS, Moreira OC, Brazil RP, Britto C. SYBR Green-based real-time PCR targeting kinetoplast DNA can be used to discriminate between the main etiologic agents of Brazilian cutaneous and visceral leishmaniases. Parasit Vectors 2012; 5:15. [PMID: 22240199 PMCID: PMC3274473 DOI: 10.1186/1756-3305-5-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 01/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniases control has been hampered by the unavailability of rapid detection methods and the lack of suitable therapeutic and prophylactic measures. Accurate diagnosis, which can distinguish between Leishmania isolates, is essential for conducting appropriate prognosis, therapy and epidemiology. Molecular methods are currently being employed to detect Leishmania infection and categorize the parasites up to genus, complex or species level. Real-time PCR offers several advantages over traditional PCR, including faster processing time, higher sensitivity and decreased contamination risk. RESULTS A SYBR Green real-time PCR targeting the conserved region of kinetoplast DNA minicircles was able to differentiate between Leishmania subgenera. A panel of reference strains representing subgenera Leishmania and Viannia was evaluated by the derivative dissociation curve analyses of the amplified fragment. Distinct values for the average melting temperature were observed, being 78.95 °C ± 0.01 and 77.36 °C ± 0.02 for Leishmania and Viannia, respectively (p < 0.05). Using the Neighbor-Joining method and Kimura 2-parameters, the alignment of 12 sequences from the amplified conserved minicircles segment grouped together L. (V.) braziliensis and L. (V.) shawii with a bootstrap value of 100%; while for L. (L.) infantum and L. (L.) amazonensis, two groups were formed with bootstrap values of 100% and 62%, respectively. The lower dissociation temperature observed for the subgenus Viannia amplicons could be due to a lower proportion of guanine/cytosine sites (43.6%) when compared to species from subgenus Leishmania (average of 48.4%). The method was validated with 30 clinical specimens from visceral or cutaneous leishmaniases patients living in Brazil and also with DNA samples from naturally infected Lutzomyia spp. captured in two Brazilian localities. CONCLUSIONS For all tested samples, a characteristic amplicon melting profile was evidenced for each Leishmania subgenus, corroborating the data from reference strains. Therefore, the analysis of thermal dissociation curves targeting the conserved kinetoplast DNA minicircles region is able to provide a rapid and reliable method to identify the main etiologic agents of cutaneous and visceral leishmaniases in endemic regions of Brazil.
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Affiliation(s)
- Daniela Pita-Pereira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, FIOCRUZ, Pavilhão Leônidas Deane, sala 209, Avenida Brasil 4365, Manguinhos, 21040-360 Rio de Janeiro, RJ, Brazil
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Weirather JL, Jeronimo SMB, Gautam S, Sundar S, Kang M, Kurtz MA, Haque R, Schriefer A, Talhari S, Carvalho EM, Donelson JE, Wilson ME. Serial quantitative PCR assay for detection, species discrimination, and quantification of Leishmania spp. in human samples. J Clin Microbiol 2011; 49:3892-904. [PMID: 22042830 PMCID: PMC3209110 DOI: 10.1128/jcm.r00764-11] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 08/24/2011] [Indexed: 01/04/2023] Open
Abstract
The Leishmania species cause a variety of human disease syndromes. Methods for diagnosis and species differentiation are insensitive and many require invasive sampling. Although quantitative PCR (qPCR) methods are reported for leishmania detection, no systematic method to quantify parasites and determine the species in clinical specimens is established. We developed a serial qPCR strategy to identify and rapidly differentiate Leishmania species and quantify parasites in clinical or environmental specimens. SYBR green qPCR is mainly employed, with corresponding TaqMan assays for validation. The screening primers recognize kinetoplast minicircle DNA of all Leishmania species. Species identification employs further qPCR set(s) individualized for geographic regions, combining species-discriminating probes with melt curve analysis. The assay was sufficient to detect Leishmania parasites, make species determinations, and quantify Leishmania spp. in sera, cutaneous biopsy specimens, or cultured isolates from subjects from Bangladesh or Brazil with different forms of leishmaniasis. The multicopy kinetoplast DNA (kDNA) probes were the most sensitive and useful for quantification based on promastigote standard curves. To test their validity for quantification, kDNA copy numbers were compared between Leishmania species, isolates, and life stages using qPCR. Maxicircle and minicircle copy numbers differed up to 6-fold between Leishmania species, but the differences were smaller between strains of the same species. Amastigote and promastigote leishmania life stages retained similar numbers of kDNA maxi- or minicircles. Thus, serial qPCR is useful for leishmania detection and species determination and for absolute quantification when compared to a standard curve from the same Leishmania species.
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Affiliation(s)
- Jason L. Weirather
- Iowa City VA Medical Center
- Interdisciplinary Graduate Program in Genetics and Departments of Internal Medicine, Microbiology, Biochemistry, and Epidemiology, University of Iowa
| | - Selma M. B. Jeronimo
- Iowa City, Iowa; Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - Mitchell Kang
- Interdisciplinary Graduate Program in Genetics and Departments of Internal Medicine, Microbiology, Biochemistry, and Epidemiology, University of Iowa
| | - Melissa A. Kurtz
- Interdisciplinary Graduate Program in Genetics and Departments of Internal Medicine, Microbiology, Biochemistry, and Epidemiology, University of Iowa
| | - Rashidul Haque
- International Center for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Albert Schriefer
- Immunology Service, Federal University of Bahia, Salvador, Brazil
| | | | | | - John E. Donelson
- Interdisciplinary Graduate Program in Genetics and Departments of Internal Medicine, Microbiology, Biochemistry, and Epidemiology, University of Iowa
| | - Mary E. Wilson
- Iowa City VA Medical Center
- Interdisciplinary Graduate Program in Genetics and Departments of Internal Medicine, Microbiology, Biochemistry, and Epidemiology, University of Iowa
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Molecular approaches for a better understanding of the epidemiology and population genetics ofLeishmania. Parasitology 2010; 138:405-25. [DOI: 10.1017/s0031182010001538] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SUMMARYMolecular approaches are being used increasingly for epidemiological studies of visceral and cutaneous leishmaniases. Several molecular markers resolving genetic differences betweenLeishmaniaparasites at species and strain levels have been developed to address key epidemiological and population genetic questions. The current gold standard, multilocus enzyme typing (MLEE), needs cultured parasites and lacks discriminatory power. PCR assays identifying species directly with clinical samples have proven useful in numerous field studies. Multilocus sequence typing (MLST) is potentially the most powerful phylogenetic approach and will, most probably, replace MLEE in the future. Multilocus microsatellite typing (MLMT) is able to discriminate below the zymodeme level and seems to be the best candidate for becoming the gold standard for distinction of strains. Population genetic studies by MLMT revealed geographical and hierarchic population structure inL. tropica, L. majorand theL. donovanicomplex. The existence of hybrids and gene flow betweenLeishmaniapopulations suggests that sexual recombination is more frequent than previously thought. However, typing and analytical tools need to be further improved. Accessible databases should be created and sustained for integrating data obtained by different researchers. This would allow for global analyses and help to avoid biases in analyses due to small sample sizes.
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Fraga J, Montalvo AM, De Doncker S, Dujardin JC, Van der Auwera G. Phylogeny of Leishmania species based on the heat-shock protein 70 gene. INFECTION GENETICS AND EVOLUTION 2009; 10:238-45. [PMID: 19913110 DOI: 10.1016/j.meegid.2009.11.007] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 11/04/2009] [Accepted: 11/06/2009] [Indexed: 11/29/2022]
Abstract
The 70kDa heat-shock protein (HSP70) is conserved across prokaryotes and eukaryotes, and the protein as well as its encoding gene have been applied in phylogenetic studies of different parasites. In spite of the frequent use of New World Leishmania species identification on the basis of restriction fragment length polymorphisms (RFLP) in the hsp70 gene, it was never sequenced extensively for studying evolutionary relationships. To fill this void we determined the nucleotide sequence of an 1380bp fragment of the coding region commonly used in RFLP analysis, from 43 isolates and strains of different geographic origins. Combination with previously determined sequences amounted to a phylogenetic analysis including 52 hsp70 sequences representing 17 species commonly causing leishmaniasis both in the New and Old World. The genus Leishmania formed a monophyletic group with three distinct subgenera L. (Leishmania), L. (Viannia), and L. (Sauroleishmania). The obtained phylogeny supports the following eight species: L. (L.) donovani, L. (L.) major, L. (L.) tropica, L. (L.) mexicana, L. (V.) lainsoni, L. (V.) naiffi, L. (V.) guyanensis and L. (V.) braziliensis, in some of which subspecies can be recognized: L. (L.) donovani infantum, L. (V.) guyanensis panamensis, and L. (V.) braziliensis peruviana. The currently recognized L. (L.) aethiopica, L. (L.) garnhami, and L. (L.) amazonensis did not form monophyletic clusters. These findings are discussed in relation to results from other genes and proteins, which have to be integrated in order to build a genetically supported taxonomy for the entire genus.
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Affiliation(s)
- Jorge Fraga
- Parasitology Department, Institute of Tropical Medicine Pedro Kouri, La Havana, Cuba
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Laurent T, Van der Auwera G, Hide M, Mertens P, Quispe-Tintaya W, Deborggraeve S, De Doncker S, Leclipteux T, Bañuls AL, Büscher P, Dujardin JC. Identification of Old World Leishmania spp. by specific polymerase chain reaction amplification of cysteine proteinase B genes and rapid dipstick detection. Diagn Microbiol Infect Dis 2008; 63:173-81. [PMID: 19097841 DOI: 10.1016/j.diagmicrobio.2008.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 10/20/2008] [Accepted: 10/27/2008] [Indexed: 11/25/2022]
Abstract
We used the cysteine proteinase B (cpb) gene family of the trypanosomatid genus Leishmania as a target to develop rapid, specific, and easy-to-use polymerase chain reaction (PCR) tests to discriminate Leishmania infantum, Leishmania donovani, Leishmania tropica, Leishmania aethiopica, and Leishmania major. Identification of all 5 Old World species and validation of intraspecies variability are features lacking in other species-specific PCRs. Amplicon analysis was done on agarose gels and was further simplified by using an oligochromatography dipstick to detect L. infantum and L. donovani products. Because the analytical sensitivity is lower than that of certain other species- and genus-specific PCRs, our assays are especially valuable for use on cultured isolates or directly on cryostabilates. As such, they can be implemented by research and health centers having access to culturing, DNA isolation, and PCR.
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Affiliation(s)
- Thierry Laurent
- Department of Parasitology, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
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Seridi N, Belkaid M, Quispe-Tintaya W, Zidane C, Dujardin JC. Application of PCR-RFLP for the exploration of the molecular diversity of Leishmania infantum in Algeria. Trans R Soc Trop Med Hyg 2008; 102:556-63. [DOI: 10.1016/j.trstmh.2008.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 03/03/2008] [Accepted: 03/03/2008] [Indexed: 11/16/2022] Open
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Tupperwar N, Vineeth V, Rath S, Vaidya T. Development of a real-time polymerase chain reaction assay for the quantification of Leishmania species and the monitoring of systemic distribution of the pathogen. Diagn Microbiol Infect Dis 2008; 61:23-30. [DOI: 10.1016/j.diagmicrobio.2007.12.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 12/18/2007] [Indexed: 10/22/2022]
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Bañuls AL, Hide M, Prugnolle F. Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans. ADVANCES IN PARASITOLOGY 2007; 64:1-109. [PMID: 17499100 DOI: 10.1016/s0065-308x(06)64001-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Leishmaniases remain a major public health problem today despite the vast amount of research conducted on Leishmania pathogens. The biological model is genetically and ecologically complex. This paper explores the advances in Leishmania genetics and reviews population structure, taxonomy, epidemiology and pathogenicity. Current knowledge of Leishmania genetics is placed in the context of natural populations. Various studies have described a clonal structure for Leishmania but recombination, pseudo-recombination and other genetic processes have also been reported. The impact of these different models on epidemiology and the medical aspects of leishmaniases is considered from an evolutionary point of view. The role of these parasites in the expression of pathogenicity in humans is also explored. It is important to ascertain whether genetic variability of the parasites is related to the different clinical expressions of leishmaniasis. The review aims to put current knowledge of Leishmania and the leishmaniases in perspective and to underline priority questions which 'leishmaniacs' must answer in various domains: epidemiology, population genetics, taxonomy and pathogenicity. It concludes by presenting a number of feasible ways of responding to these questions.
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Affiliation(s)
- Anne-Laure Bañuls
- Institut de Recherche pour le Développement, UMR CNRS/IRD 2724, Génétique et Evolution des Maladies Infectieuses, IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
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18
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Lukeš J, Mauricio IL, Schönian G, Dujardin JC, Soteriadou K, Dedet JP, Kuhls K, Tintaya KWQ, Jirků M, Chocholová E, Haralambous C, Pratlong F, Oborník M, Horák A, Ayala FJ, Miles MA. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proc Natl Acad Sci U S A 2007; 104:9375-80. [PMID: 17517634 PMCID: PMC1890502 DOI: 10.1073/pnas.0703678104] [Citation(s) in RCA: 291] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis is a geographically widespread severe disease, with an increasing incidence of two million cases per year and 350 million people from 88 countries at risk. The causative agents are species of Leishmania, a protozoan flagellate. Visceral leishmaniasis, the most severe form of the disease, lethal if untreated, is caused by species of the Leishmania donovani complex. These species are morphologically indistinguishable but have been identified by molecular methods, predominantly multilocus enzyme electrophoresis. We have conducted a multifactorial genetic analysis that includes DNA sequences of protein-coding genes as well as noncoding segments, microsatellites, restriction-fragment length polymorphisms, and randomly amplified polymorphic DNAs, for a total of approximately 18,000 characters for each of 25 geographically representative strains. Genotype is strongly correlated with geographical (continental) origin, but not with current taxonomy or clinical outcome. We propose a new taxonomy, in which Leishmania infantum and L. donovani are the only recognized species of the L. donovani complex, and we present an evolutionary hypothesis for the origin and dispersal of the species. The genus Leishmania may have originated in South America, but diversified after migration into Asia. L. donovani and L. infantum diverged approximately 1 Mya, with further divergence of infraspecific genetic groups between 0.4 and 0.8 Mya. The prevailing mode of reproduction is clonal, but there is evidence of genetic exchange between strains, particularly in Africa.
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Affiliation(s)
- Julius Lukeš
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
- Faculty of Biology, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Isabel L. Mauricio
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Gabriele Schönian
- Institute of Microbiology and Hygiene, Charité University Medicine, D-10117 Berlin, Germany
| | - Jean-Claude Dujardin
- Department of Molecular Parasitology, Institute of Tropical Medicine, B-2000 Antwerpen, Belgium
| | - Ketty Soteriadou
- Molecular Parasitology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Jean-Pierre Dedet
- **Laboratoire de Parasitologie, Université Montpellier 1, 34090 Montpellier, France; and
| | - Katrin Kuhls
- Institute of Microbiology and Hygiene, Charité University Medicine, D-10117 Berlin, Germany
| | | | - Milan Jirků
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Eva Chocholová
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Christos Haralambous
- Molecular Parasitology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Francine Pratlong
- **Laboratoire de Parasitologie, Université Montpellier 1, 34090 Montpellier, France; and
| | - Miroslav Oborník
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
- Faculty of Biology, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Aleš Horák
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Michael A. Miles
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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Reithinger R, Dujardin JC. Molecular diagnosis of leishmaniasis: current status and future applications. J Clin Microbiol 2006; 45:21-5. [PMID: 17093038 PMCID: PMC1828971 DOI: 10.1128/jcm.02029-06] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Richard Reithinger
- Clinical Trials Area, Westat, 1441 W. Montgomery Ave., Rockville, MD 20850, USA.
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