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Kobialka RM, Ceruti A, Roy M, Roy S, Chowdhury R, Ghosh P, Hossain F, Weidmann M, Graf E, Bueno Alvarez J, Moreno J, Truyen U, Mondal D, Chatterjee M, Abd El Wahed A. Portable smartphone-based molecular test for rapid detection of Leishmania spp. Infection 2024; 52:1315-1324. [PMID: 38353873 PMCID: PMC11288998 DOI: 10.1007/s15010-024-02179-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/07/2024] [Indexed: 08/02/2024]
Abstract
PURPOSE Leishmaniasis, caused by the parasite of the genus Leishmania, is a neglected tropical disease which is endemic in more than 60 countries. In South-East Asia, Brazil, and East Africa, it mainly occurs as kala-azar (visceral leishmaniasis, VL), and subsequently as post kala-azar dermal leishmaniasis (PKDL) in a smaller portion of cases. As stated per WHO roadmap, accessibility to accurate diagnostic methods is an essential step to achieve elimination. This study aimed to test the accuracy of a portable minoo device, a small battery-driven, multi-use fluorimeter operating with isothermal technology for molecular diagnosis of VL and PKDL. METHODS Fluorescence data measured by the device within 20 min are reported back to the mobile application (or app) via Bluetooth and onward via the internet to a backend. This allows anonymous analysis and storage of the test data. The test result is immediately returned to the app displaying it to the user. RESULTS The limit of detection was 11.2 genome copies (95% CI) as determined by screening a tenfold dilution range of whole Leishmania donovani genomes using isothermal recombinase polymerase amplification (RPA). Pathogens considered for differential diagnosis were tested and no cross-reactivity was observed. For its diagnostic performance, DNA extracted from 170 VL and PKDL cases, comprising peripheral blood samples (VL, n = 96) and skin biopsies (PKDL, n = 74) from India (n = 108) and Bangladesh (n = 62), was screened. Clinical sensitivity and specificity were 88% and 91%, respectively. CONCLUSION Minoo devices can offer a convenient, cheaper alternative to other molecular diagnostics. Its easy handling makes it ideal for use in low-resource settings to identify parasite burden.
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Affiliation(s)
- Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany.
| | - Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
| | - Madhurima Roy
- Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Sutopa Roy
- Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Rajashree Chowdhury
- Nutrition Research Division, International Centre for Diarrheal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Prakash Ghosh
- Nutrition Research Division, International Centre for Diarrheal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Faria Hossain
- Nutrition Research Division, International Centre for Diarrheal Disease Research Bangladesh, Dhaka, Bangladesh
| | | | | | | | - Javier Moreno
- WHO Collaborating Center for Leishmaniasis, National Center for Microbiology, Instituto de Salud Carlos III, CIBER de Enfermedades Infecciosas-CIBERINFEC, Madrid, Spain
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
| | - Dinesh Mondal
- Nutrition Research Division, International Centre for Diarrheal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Mitali Chatterjee
- Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
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Kumar A, Singh VK, Madhukar P, Tiwari R, Roy R, Rajneesh, Mehrotra S, Sundar S, Kumar R. Evaluation of blood based quantitative PCR as a molecular diagnostic tool for post kala-azar dermal leishmaniasis (PKDL). Mol Biol Rep 2024; 51:716. [PMID: 38824237 DOI: 10.1007/s11033-024-09640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Post kala-azar dermal leishmaniasis (PKDL) is a consequential dermal manifestation of visceral leishmaniasis (VL), serving as a parasite reservoir. The traditional diagnostic approach, which requires an invasive skin biopsy is associated with inherent risks and necessitates skilled healthcare practitioners in sterile settings. There is a critical need for a rapid, less invasive method for Leishmania detection. The main objective of this study was to evaluate and compare the diagnostic efficacy of PCR and qPCR in detecting PKDL, utilizing both skin and blood samples and to assess the utility of blood samples for molecular diagnosis. METHODS AND RESULTS 73 individuals exhibiting clinical symptoms of PKDL and who had tested positive for rK39 rapid diagnostic test (RDT) were enrolled in this study. For the diagnosis of PKDL, both PCR and real-time quantitative PCR (qPCR), employing SYBR Green and TaqMan assays, were performed on blood and skin matched samples. qPCR results using both TaqMan and SYBR Green assay, indicated higher parasite loads in the skin compared to blood, as evident by the Ct values. Importantly, when blood samples were used for PKDL diagnosis by qPCR, an encouraging sensitivity of 69.35% (TaqMan assay) and 79.36% (SYBR Green) were obtained, compared to 8.2% with conventional PCR. CONCLUSION The findings of the study suggest the potential utility of blood for molecular diagnosis by qPCR, offering a less invasive alternative to skin biopsies in field setting for the early detection of parasitaemia in PKDL patients and effective management and control of the disease.
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Affiliation(s)
- Awnish Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Vishal K Singh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Prasoon Madhukar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rahul Tiwari
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Ritirupa Roy
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajneesh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajiv Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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Ghosh P, Chowdhury R, Faisal K, Khan MAA, Hossain F, Rahat MA, Chowdhury MAA, Mithila NT, Kamal M, Maruf S, Nath R, Kobialka RM, Ceruti A, Cameron M, Duthie MS, Wahed AAE, Mondal D. Evaluation of a Point-of-Need Molecular Diagnostic Tool Coupled with Rapid DNA Extraction Methods for Visceral Leishmaniasis. Diagnostics (Basel) 2023; 13:3639. [PMID: 38132223 PMCID: PMC10742398 DOI: 10.3390/diagnostics13243639] [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: 09/18/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
A rapid, cost-effective, and simple nucleic acid isolation technique coupled with a point-of-need DNA amplification assay is a desirable goal for programmatic use. For diagnosis of Visceral Leishmaniasis (VL), Recombinase Polymerase Amplification (RPA) rapid tests for the detection of Leishmania DNA are versatile and have operational advantages over qPCR. To facilitate the delivery of the RPA test at point-of-need for VL diagnosis, we compared two rapid DNA extraction methods, SwiftDx (SX) and an in-house Boil and Spin (BS) method, coupled with RPA amplification, versus more widely used methods for DNA extraction and amplification, namely Qiagen (Q) kits and qPCR, respectively. A total of 50 confirmed VL patients and 50 controls, matched for age and gender, were recruited from Mymensingh, Bangladesh, a region highly endemic for VL. Blood samples were collected from each participant and DNA was extracted using Q, SX and BS methods. Following DNA extraction, qPCR and RPA assays were performed to detect L. donovani in downstream analysis. No significant differences in sensitivity of the RPA assay were observed between DNA extraction methods, 94.00% (95% CI: 83.45-98.75%), 90% (95% CI: 78.19-96.67%), and 88% (95% CI: 75.69-95.47%) when using Q, SX, and BS, respectively. Similarly, using qPCR, no significant differences in sensitivity were obtained when using Q or SX for DNA extraction, 94.00% (95% CI: 83.45-98.75%) and 92.00% (80.77-97.78%), respectively. It is encouraging that RPA and qPCR showed excellent agreement (k: 0.919-0.980) when different extraction methods were used and that the DNA impurities using BS had no inhibitory effect on the RPA assay. Furthermore, significantly higher DNA yields were obtained using SX and BS versus Q; however, a significantly higher parasite load was detected using qPCR when DNA was extracted using Q versus SX. Considering the cost, execution time, feasibility, and performance of RPA assay, rapid extraction methods such as the Boil and Spin technique appear to have the potential for implementation in resource-limited endemic settings. Further clinical research is warranted prior to broader application.
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Affiliation(s)
- Prakash Ghosh
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rajashree Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Khaledul Faisal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Faria Hossain
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Abu Rahat
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Arko Ayon Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Nishad Tasnim Mithila
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Mostafa Kamal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Shomik Maruf
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rupen Nath
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Mary Cameron
- London School of Hygiene and Tropical Medicine, University of London, London WC1E 7HT, UK;
| | | | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Dinesh Mondal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
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Takamiya NT, Rogerio LA, Torres C, Leonel JAF, Vioti G, de Sousa Oliveira TMF, Valeriano KC, Porcino GN, de Miranda Santos IKF, Costa CHN, Costa DL, Ferreira TS, Gurgel-Gonçalves R, da Silva JS, Teixeira FR, De Almeida RP, Ribeiro JMC, Maruyama SR. Parasite Detection in Visceral Leishmaniasis Samples by Dye-Based qPCR Using New Gene Targets of Leishmania infantum and Crithidia. Trop Med Infect Dis 2023; 8:405. [PMID: 37624343 PMCID: PMC10457869 DOI: 10.3390/tropicalmed8080405] [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: 07/03/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Visceral leishmaniasis (VL) is a neglected disease considered a serious public health problem, especially in endemic countries. Several studies have discovered monoxenous trypanosomatids (Leptomonas and Crithidia) in patients with VL. In different situations of leishmaniasis, investigations have examined cases of co-infection between Leishmania spp. and Crithidia spp. These coinfections have been observed in a wide range of vertebrate hosts, indicating that they are not rare. Diagnostic techniques require improvements and more robust tools to accurately detect the causative agent of VL. This study aimed to develop a real-time quantitative dye-based PCR (qPCR) assay capable of distinguishing Leishmania infantum from Crithidia-related species and to estimate the parasite load in samples of VL from humans and animals. The primer LinJ31_2420 targets an exclusive phosphatase of L. infantum; the primer Catalase_LVH60-12060_1F targets the catalase gene of Crithidia. Therefore, primers were designed to detect L. infantum and Crithidia sp. LVH60A (a novel trypanosomatid isolated from VL patients in Brazil), in samples related to VL. These primers were considered species-specific, based on sequence analysis using genome data retrieved from the TriTryp database and the genome assembling of Crithidia sp. LVH60A strain, in addition to experimental and clinical data presented herein. This novel qPCR assay was highly accurate in identifying and quantifying L. infantum and Crithidia sp. LVH60A in samples obtained experimentally (in vitro and in vivo) or collected from hosts (humans, dogs, cats, and vectors). Importantly, the screening of 62 cultured isolates from VL patients using these primers surprisingly revealed that 51 parasite cultures were PCR+ for Crithidia sp. In addition, qPCR assays identified the co-infection of L. infantum with Crithidia sp. LVH60A in two new VL cases in Brazil, confirming the suspicion of co-infection in a previously reported case of fatal VL. We believe that the species-specific genes targeted in this study can be helpful for the molecular diagnosis of VL, as well as for elucidating suspected co-infections with monoxenous-like trypanosomatids, which is a neglected fact of a neglected disease.
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Affiliation(s)
- Nayore Tamie Takamiya
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Caroline Torres
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - João Augusto Franco Leonel
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Geovanna Vioti
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Tricia Maria Ferreira de Sousa Oliveira
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil
| | - Karoline Camila Valeriano
- Ribeirão Preto Medical School, University of São Paulo, FMRP-USP, Ribeirão Preto 14049-900, SP, Brazil
| | | | | | - Carlos H. N. Costa
- Natan Portela Institute of Tropical Diseases, Teresina 64002-510, PI, Brazil
| | | | - Tauana Sousa Ferreira
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - João Santana da Silva
- Fiocruz-Bi-Institutional Translational Medicine Project, Oswaldo Cruz Foundation, Ribeirão Preto 14040-900, SP, Brazil
| | - Felipe Roberti Teixeira
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Roque Pacheco De Almeida
- Department of Medicine, Center for Biology and Health Sciences, Federal University of Sergipe (UFS), Aracaju 49060-108, SE, Brazil
| | - José M. C. Ribeiro
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, NIH/NIAID, Rockville, MD 20892, USA
| | - Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
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A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field. J Clin Virol 2023; 162:105422. [PMID: 36989731 PMCID: PMC9981265 DOI: 10.1016/j.jcv.2023.105422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Background : The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. Objectives : To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. Study design : In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 minutes. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. Results : Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). Conclusion : Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.
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Gauging the skin resident Leishmania parasites through a loop mediated isothermal amplification (LAMP) assay in post-kala-azar dermal leishmaniasis. Sci Rep 2022; 12:18069. [PMID: 36302782 PMCID: PMC9614002 DOI: 10.1038/s41598-022-21497-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/28/2022] [Indexed: 01/24/2023] Open
Abstract
Despite the availability of highly sensitive polymerase chain reaction (PCR)-based methods, the dearth of remotely deployable diagnostic tools circumvents the early and accurate detection of individuals with post-kala-azar dermal leishmaniasis (PKDL). Here, we evaluate a design-locked loop-mediated isothermal amplification (LAMP) assay to diagnose PKDL. A total of 76 snip-skin samples collected from individuals with probable PKDL (clinical presentation and a positive rK39 rapid diagnostic test (RDT)) were assessed by microscopy, qPCR, and LAMP. An equal number of age and sex-matched healthy controls were included to determine the specificity of the LAMP assay. The LAMP assay with a Qiagen DNA extraction (Q-LAMP) showed a promising sensitivity of 72.37% (95% CI: 60.91-82.01%) for identifying the PKDL cases. LAMP assay sensitivity declined when the DNA was extracted using a boil-spin method. Q-qPCR showed 68.42% (56.75-78.61%) sensitivity, comparable to LAMP and with an excellent agreement, whereas the microscopy exhibited a weak sensitivity of 39.47% (28.44-51.35%). When microscopy and/or qPCR were considered the gold standard, Q-LAMP exhibited an elevated sensitivity of 89.7% (95% CI: 78.83-96.11%) for detection of PKDL cases and Bayesian latent class modeling substantiated the excellent sensitivity of the assay. All healthy controls were found to be negative. Notwithstanding the optimum efficiency of the LAMP assay towards the detection of PKDL cases, further optimization of the boil-spin method is warranted to permit remote use of the assay.
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Sereno D, Oury B, Geiger A, Vela A, Karmaoui A, Desquesnes M. Isothermal Nucleic Acid Amplification to Detect Infection Caused by Parasites of the Trypanosomatidae Family: A Literature Review and Opinion on the Laboratory to Field Applicability. Int J Mol Sci 2022; 23:ijms23147543. [PMID: 35886895 PMCID: PMC9322063 DOI: 10.3390/ijms23147543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
Isothermal amplification of nucleic acids has the potential to be applied in resource-limited areas for the detection of infectious agents, as it does not require complex nucleic purification steps or specific and expensive equipment and reagents to perform the reaction and read the result. Since human and animal infections by pathogens of the Tryponasomatidae family occur mainly in resource-limited areas with scant health infrastructures and personnel, detecting infections by these methodologies would hold great promise. Here, we conduct a narrative review of the literature on the application of isothermal nucleic acid amplification for Trypanosoma and Leishmania infections, which are a scourge for human health and food security. We highlight gaps and propose ways to improve them to translate these powerful technologies into real-world field applications for neglected human and animal diseases caused by Trypanosomatidae.
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Affiliation(s)
- Denis Sereno
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France;
- Correspondence:
| | - Bruno Oury
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France;
| | - Anne Geiger
- Centre International de Recherche en Agronomie pour le Développement, Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, 34032 Montpellier, France;
| | - Andrea Vela
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de las Américas-Quito, Calle de los Colimes y Avenida De los Granados, Quito 170513, Ecuador;
| | - Ahmed Karmaoui
- Bioactives (Health and Environmental, Epigenetics Team), Faculty of Sciences and Techniques, Errachidia (UMI), Moroccan Center for Culture and Sciences, University Moulay Ismail, Meknes 50000, Morocco;
| | - Marc Desquesnes
- CIRAD, UMR INTERTRYP, 31076 Toulouse, France;
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34032 Montpellier, France
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de Faria VCS, Gonçalves DU, Soares ARC, Barbosa PH, Saliba JW, de Souza CSA, Cota GF, de Avelar DM. Impact assessment of different DNA extraction methods for non-invasive molecular diagnosis of tegumentary leishmaniasis. Acta Trop 2022; 227:106275. [PMID: 34906549 DOI: 10.1016/j.actatropica.2021.106275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/01/2022]
Abstract
The aim of this study was to evaluate two methods of nucleic acid extraction (spin-column-based method - commercial kit and direct boil - DB) from swab sampling compared to biopsy sampling for the diagnosis of tegumentary leishmaniasis (TL), (cutaneous - CL and mucocutaneous - MCL forms). The impact of these nucleic acid extraction protocols on different types of PCR and LAMP techniques were compared regarding nucleic acid quality, molecular assays accuracy, indirect quantitation, and costs. The evaluated patients were 57 TL cases (36 CL and 21 MCL) and 34 non-cases. Swab samples extracted by the DB method showed a higher DNA degradation rate and worse DNA quality in comparison to the commercial kit. Molecular tests performed on biopsy samples showed identical or higher performance in all analysis, as compared to their own performance on swab samples for TL (CL and MCL). However, only the SSU rRNA TaqMan™ RT-PCR test showed a significant difference between the performance of biopsy and swab samples extracted by commercial kit. The kDNA-cPCR coupled with swab extracted by commercial kit showed the highest accuracy (95.6%) for TL diagnosis. The sensitivity of the LAMP-RT 18S method in swab samples extracted with a commercial kit (82.5%) was close to that found in biopsy samples (86%) for TL diagnosis. The DB extraction method presented the lowest cost. The use of swab as a minimally-invasive sampling method, associated with an efficient nucleic acid extraction protocol, may represent a low-cost alternative for the diagnosis of CL and MCL.
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Khan MAA, Faisal K, Chowdhury R, Nath R, Ghosh P, Ghosh D, Hossain F, Abd El Wahed A, Mondal D. Evaluation of molecular assays to detect Leishmania donovani in Phlebotomus argentipes fed on post-kala-azar dermal leishmaniasis patients. Parasit Vectors 2021; 14:465. [PMID: 34503557 PMCID: PMC8428120 DOI: 10.1186/s13071-021-04961-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Post-kala-azar dermal leishmaniasis (PKDL) caused by Leishmania donovani (LD) is a skin disorder that often appears after treatment of visceral leishmaniasis (VL) patients. PKDL patients are potential reservoirs of LD parasites, which can initiate a new epidemic of anthroponotic VL. Therefore, host infectiousness to its sand fly vector is a critical factor for transmission, and its accurate estimation can facilitate control strategies. At present, conventional microscopy serves as the reference method to detect parasites in its vector. However, low sensitivity of microscopy can be a limiting factor. METHODS In this study, real-time quantitative PCR (LD-qPCR) and recombinase polymerase amplification (LD-RPA) assays were evaluated against microscopy for the detection of LD DNA extracted from live sand flies five days after controlled feeding on PKDL cases. RESULTS The sensitivity of LD-qPCR and LD-RPA assays were found to be 96.43 and 100%, respectively, against microscopy for the selected fed sand flies (n = 28), and an absolute specificity of both molecular tools for apparently unfed sand flies (n = 30). While the proportion of infectious cases among 47 PKDL patients was estimated as 46.81% as defined by microscopic detection of LD in at least one fed sand fly per case, LD-RPA assay evaluation of only the microscopy negative sand flies fed to those 47 PKDL cases estimated an even greater proportion of infectious cases (51.06%). In overall estimation of the infectious cases in retrospective manner, discordance in positivity rate was observed (p < 0.05) between LD-RPA (59.57%) assay and microscopy (46.81%), while LD-RPA had slightly better positivity rate than LD-qPCR (55.32%) as well. CONCLUSIONS Considering the sensitivity, cost, detection time, and field applicability, RPA assay can be considered as a promising single molecular detection tool for investigations pertaining to LD infections in sand flies and/or host infectiousness in PKDL, while it can also be useful in confirmation of microscopy negative sand fly samples.
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Affiliation(s)
- Md Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, An den Tierkliniken 43, 04103, Leipzig, Germany.,Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Khaledul Faisal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Rupen Nath
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Debashis Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, An den Tierkliniken 43, 04103, Leipzig, Germany.
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh. .,Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research Bangladesh, 1212, Dhaka, Bangladesh.
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Sazed SA, Kibria MG, Alam MS. An Optimized Real-Time qPCR Method for the Effective Detection of Human Malaria Infections. Diagnostics (Basel) 2021; 11:736. [PMID: 33919020 PMCID: PMC8142979 DOI: 10.3390/diagnostics11050736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/24/2022] Open
Abstract
Polymerase chain reaction, although an expensive method for the detection of human Plasmodium spp., is still considered the finest for the diagnosis of malaria. The conventional diagnostic PCR is an inexpensive process but consumes a lot of time, reagents and lacks sensitivity. On the other hand, real-time PCR assays currently being used are mostly probe-based expensive methods and sometimes not feasible to detect all the species in a single amplification reaction condition. Here we have established a real-time PCR method that is time and cost effective with a single protocol to detect and distinguish five human Plasmodium species using the existing primers efficiently. The primers used here are being used in the conventional method and the sensitivity as well as specificity of this method has also been immensely improved (100%). The lower limit of detection for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae are 0.064 parasites/µL, 1.6 parasites/µL, and 0.32 parasites/µL respectively and no cross reactivity was observed. Besides, we have analyzed melt curves that can be used for further species confirmation and validation purposes using multiplex systems. This method, therefore, can be considered as an alternative to the existing lineup for molecular diagnosis of malaria in endemic countries.
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Affiliation(s)
| | | | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka 1212, Bangladesh; (S.A.S.); (M.G.K.)
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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A Multi-Country, Single-Blinded, Phase 2 Study to Evaluate a Point-of-Need System for Rapid Detection of Leishmaniasis and Its Implementation in Endemic Settings. Microorganisms 2021; 9:microorganisms9030588. [PMID: 33809332 PMCID: PMC7999011 DOI: 10.3390/microorganisms9030588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
With the advancement of isothermal nucleic acid amplification techniques, detection of the pathogenic DNA in clinical samples at point-of-need is no longer a dream. The newly developed recombinase polymerase amplification (RPA) assay incorporated in a suitcase laboratory has shown promising diagnostic efficacy over real-time PCR in detection of leishmania DNA from clinical samples. For broader application of this point-of-need system, we undertook a current multi-country diagnostic evaluation study towards establishing this technique in different endemic settings which would be beneficial for the ongoing elimination programs for leishmaniasis. For this study purpose, clinical samples from confirmed visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL) patients were subjected to both real-time PCR and RPA assay in Bangladesh, India, and Nepal. Further skin samples from confirmed cutaneous leishmaniasis (CL) patients were also included from Sri Lanka. A total of 450 clinical samples from VL patients, 429 from PKDL patients, 47 from CL patients, and 322 from endemic healthy/healthy controls were under investigation to determine the diagnostic efficacy of RPA assay in comparison to real-time PCR. A comparative sensitivity of both methods was found where real-time PCR and RPA assay showed 96.86% (95% CI: 94.45–98.42) and 88.85% (95% CI: 85.08–91.96) sensitivity respectively in the diagnosis of VL cases. This new isothermal method also exhibited promising diagnostic sensitivity (93.50%) for PKDL cases, when a skin sample was used. Due to variation in the sequence of target amplicons, RPA assay showed comparatively lower sensitivity (55.32%) than that of real-time PCR in Sri Lanka for the diagnosis of CL cases. Except for India, the assay presented absolute specificity in the rest of the sites. Excellent concordance between the two molecular methods towards detection of leishmania DNA in clinical samples substantiates the application of RPA assay incorporated in a suitcase laboratory for point-of-need diagnosis of VL and PKDL in low resource endemic settings. However, further improvisation of the method is necessary for diagnosis of CL.
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One Health and Neglected Tropical Diseases-Multisectoral Solutions to Endemic Challenges. Trop Med Infect Dis 2020; 6:tropicalmed6010004. [PMID: 33383621 PMCID: PMC7838914 DOI: 10.3390/tropicalmed6010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 11/17/2022] Open
Abstract
One Health is defined as an approach to achieve better health outcomes for humans, animals, and the environment through collaborative and interdisciplinary efforts [...].
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Point-Of-Care or Point-Of-Need Diagnostic Tests: Time to Change Outbreak Investigation and Pathogen Detection. Trop Med Infect Dis 2020; 5:tropicalmed5040151. [PMID: 32992688 PMCID: PMC7709694 DOI: 10.3390/tropicalmed5040151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
In the recent years, the progress of international trade and travel has led to an increased risk of emerging infections. Around 75 percent of the pathogens causing these infections are of animal origin. Point-of-care tests (POCT) and point-of-need tests (PONT) have been established in order to directly provide accurate and rapid diagnostics at field level, the patient bed-side or at the site of outbreaks. These assays can help physicians and decision makers to take the right action without delay. Typically, POCT and PONT rely on genomic identification of pathogens or track their immunological fingerprint. Recently, protocols for metagenomic diagnostics in the field have been developed. In this review, we give an overview of the latest developments in portable diagnostic methods. In addition, four mobile platforms for the implementation of these techniques at point-of-care and point-of-need are described. These approaches can provide reliable diagnostics and surveillance, especially in low resource settings as well as at the level of one health.
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