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Zhang J, Chen X, Pan M, Qin Y, Zhao H, Yang Q, Li X, Zeng W, Xiang Z, Wu Y, Duan M, Li X, Wang X, Mazier D, Zhang Y, Zhu W, Sun K, Wu Y, Cui L, Huang Y, Yang Z. Application of a low-cost, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay to detect Plasmodium falciparum imported from Africa. Mol Biochem Parasitol 2022; 252:111529. [PMID: 36374724 PMCID: PMC9890345 DOI: 10.1016/j.molbiopara.2022.111529] [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: 03/22/2022] [Revised: 08/12/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Chinese citizens traveling abroad bring back imported malaria cases to China. Current malaria diagnostic tests, including microscopy and antigen-detecting rapid tests, cannot reliably detect low-density infections. To complement existing diagnostic methods, we aimed to develop a new loop-mediated isothermal amplification (LAMP) assay to detect and identify Plasmodium falciparum in Chinese travelers returning from Africa. METHODS We developed a miniaturized LAMP assay to amplify the actin I gene of P. falciparum. Each reaction consumed only 25% of the reagents used in a conventional LAMP assay and the same amount of DNA templates used in nested PCR. We evaluated this LAMP assay's performance and compared it to microscopy and a nested PCR assay using 466 suspected malaria cases imported from Africa. We assessed the sensitivity of the new LAMP assay using cultured P. falciparum, clinical samples, and a plasmid construct, allowing unprecedented precision when quantifying the limit of detection. RESULTS The new LAMP assay was highly sensitive and detected two more malaria cases than nested PCR. Compared to nested PCR, the sensitivity and specificity of the novel LAMP assay were 100% [95% confidence interval (CI) 98.5-100%] and 99.1% (95% CI 96.7-99.9%), respectively. When evaluated using serial dilutions of the plasmid construct, the detection limit of the new LAMP was as low as 102 copies/μL, 10-fold lower than PCR. The LAMP assay detected 0.01 parasites/μL of blood (equal to 0.04 parasites/μL of DNA) using cultured P. falciparum and 1-7 parasites/μL of blood (4-28 parasites/μL of DNA) in clinical samples, which is as good as or better than previously reported and commercially licensed assays. CONCLUSION The novel LAMP assay based on the P. falciparum actin I gene was specific, sensitive, and cost-effective, as it consumes 1/4 of the reagents in a typical LAMP reaction.
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Affiliation(s)
- Jiaqi Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Zhejiang Provincial Center for Disease Control and Prevention, No.3399 BinSheng Road, Binjiang District, Hangzhou, Zhejiang Province, 310051, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Maohua Pan
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Yucheng Qin
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, Yunnan,China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Dominique Mazier
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Paris, France
| | - Yanmei Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Wenya Zhu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Kemin Sun
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yiman Wu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, MDC84, Tampa, FL 33612, USA
| | - Yaming Huang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China,Correspondence:
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Correspondence:
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Han KT, Han ZY, Zainabadi K. Developing Molecular Surveillance Capacity for Asymptomatic and Drug-Resistant Malaria in a Resource-Limited Setting-Experiences and Lessons Learned. Am J Trop Med Hyg 2022; 107:222-230. [PMID: 35895423 PMCID: PMC9393433 DOI: 10.4269/ajtmh.21-0543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 08/03/2023] Open
Abstract
The COVID-19 pandemic has highlighted the important role molecular surveillance plays in public health. Such capacity however is either weak or nonexistent in many low-income countries. This article outlines a 2-year effort to establish two high-throughput molecular surveillance laboratories in Myanmar for tracking asymptomatic and drug resistant Plasmodium falciparum malaria. The lessons learned from this endeavor may prove useful for others seeking to establish similar molecular surveillance capacity in other resource-limited settings.
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Affiliation(s)
- Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Zay Yar Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York
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3
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Gaber M, Ahmad AA, El-Kady AM, Tolba M, Suzuki Y, Mohammed SM, Elossily NA. Dengue fever as a reemerging disease in upper Egypt: Diagnosis, vector surveillance and genetic diversity using RT-LAMP assay. PLoS One 2022; 17:e0265760. [PMID: 35499983 PMCID: PMC9060354 DOI: 10.1371/journal.pone.0265760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Background
The recent increase in dengue virus (DENV) outbreaks and the absence of an effective vaccine have highlighted the importance of developing rapid and effective diagnostic surveillance tests and mosquito-based screening programs. To establish effective control measures for preventing future DENV transmission, the present study was established to identify the main mosquito vector involved in the dengue fever (DF) outbreak in Upper Egypt in 2016 and detect the diversity of dengue virus serotypes circulating in both humans and vectors.
Methods
We investigated the prevalence of DENV infection and circulating serotypes in the sera of 51 humans clinically suspected of DF and 1800 field-collected Aedes aegypti adult female mosquitoes grouped into 36 pooled samples. Both DENV non-structural protein (NS1) immunochromatographic strip assay and loop-mediated isothermal amplification (LAMP) were used for screening.
Results
Overall, the rate of DENV infection in both human sera and pooled mosquito homogenate was 33.3%, as revealed by rapid dipstick immunochromatographic analysis. However, higher detection rates were observed with RT-LAMP assay of 60.8% and 44.4% for humans and vector mosquitoes, respectively. DENV-1 was the most prevalent serotype in both populations. A combination of two, three, or even four circulating serotypes was found in 87.5% of total positive pooled mosquito samples and 83.87% of DENV-positive human sera.
Conclusion
The study reinforces the evidence of the reemergence of Aedes aegypti in Upper Egypt, inducing an outbreak of DENV. Mosquito-based surveillance of DENV infection is important to elucidate the viral activity rate and define serotype diversity to understand the virus dynamics in the reinfested area. Up to our knowledge, this is the first report of serotyping of DENV infection in an outbreak in Egypt using RT-LAMP assay.
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Affiliation(s)
- Mona Gaber
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Asmaa M. El-Kady
- Department of Parasitology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Mohammed Tolba
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Shereen M. Mohammed
- Department of Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Nahed Ahmed Elossily
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
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Mirahmadi H, Shahrakipour A, Mehravaran A, Rahmati-Balaghaleh M, Zarean M, Etemadi S, Shahraki M, Solgi R. Evaluation of Multiplex/Nested Polymerase Chain Reaction and Loop-Mediated Isothermal Amplification for Malaria Diagnosis in Southeastern Iran. Am J Trop Med Hyg 2022; 106:841-845. [PMID: 35100562 PMCID: PMC8922511 DOI: 10.4269/ajtmh.21-0970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022] Open
Abstract
Malaria is one of the most serious health problems in many countries, including Iran. Accurate diagnosis is important regardless of the elimination status of a country. A cross-sectional study was performed on 105 people who were suspected to be positive for malaria infection in Sistan and Baluchistan, Iran. Blood smears (thin and thick films) were stained with 10% Giemsa. DNA was extracted from the prepared thin and thick films for molecular methods. Multiplex/nested polymerase chain reaction (mn-PCR), loop-mediated isothermal amplification (LAMP), and light microscopy (LM) were compared with nested PCR (nPCR) as a gold standard. Of 105 subjects, 52 (49.5%), 58 (55.2%), 58 (55.2%), and 63 (60%) were positive for malaria by LM, nPCR, mn-PCR, and LAMP, respectively. The sensitivity, specificity, and kappa were 92.1%, 100%, and 0.9 for LAMP and 100%, 100%, and 1 for mn-PCR, respectively. Eight cases of coinfection (Plasmodium vivax and Plasmodium falciparum) that were not detected by LM method were diagnosed by mn-PCR and LAMP. In the present study, the high sensitivity and specificity of LAMP and mn-PCR indicate that these two tests are good alternatives to nPCR for malaria diagnosis.
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Affiliation(s)
- Hadi Mirahmadi
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Azam Shahrakipour
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ahmad Mehravaran
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mansour Rahmati-Balaghaleh
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran;,Cutaneous Leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Iran;,Address correspondence to Rahmat Solgi, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran, E-mail: or Mehdi Zarean, Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
| | - Soodabeh Etemadi
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehdi Shahraki
- Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Rahmat Solgi
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran;,Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran,Address correspondence to Rahmat Solgi, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran, E-mail: or Mehdi Zarean, Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
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5
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Antinori S, Ridolfo AL, Grande R, Galimberti L, Casalini G, Giacomelli A, Milazzo L. Loop-mediated isothermal amplification (LAMP) assay for the diagnosis of imported malaria: a narrative review. LE INFEZIONI IN MEDICINA 2022; 29:355-365. [PMID: 35146340 DOI: 10.53854/liim-2903-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 11/03/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular method to detect malaria recently introduced in the market. LAMP is simple to perform and does not require advanced equipment and training thus satisfying the qualification as a point-of-care diagnostic screening test. In this narrative review, we focus on the role of LAMP for malaria diagnosis in non-endemic settings. We searched PubMed, Embase, Scopus, and Google Scholar, using the following search terms: 'Malaria LAMP' in combination with 'imported malaria' or 'travellers' malaria' or 'non-endemic setting' or 'non-endemic region' or 'malaria screening' or 'malaria diagnosis'. References of each article were also reviewed for possible studies or reports not identified in our search. Overall, 18 studies encompassing 6289 tested samples with 1663 confirmed malaria diagnoses were retrieved. Most of these studies (13/18, 72.2%) were conducted in Europe, and almost half were retrospective. Fourteen studies (77.8%) employed real-time or nested-polymerase chain reaction as the reference method for confirming malaria diagnosis. Sensitivity of LAMP ranged from 93.9 to 100% and specificity from 93.8 to 100% with a negative predictive value of 99.6%-100%. The rate of reported invalid results requiring repeat of the test varied from 0.01% to 5.7%, but they were solved in the majority of cases with a secondary analysis. In non-endemic countries the adoption of LAMP malaria assay as the screening test for malaria diagnosis seems to perform better than conventional methods. However, blood microscopy remains essential to either identify Plasmodium species and quantify parasitaemia and adequately managing malaria cases.
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Affiliation(s)
- Spinello Antinori
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy.,III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Anna Lisa Ridolfo
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Romualdo Grande
- Clinical Microbiology, Virology and Bioemergency, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Laura Galimberti
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Giacomo Casalini
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy
| | - Andrea Giacomelli
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy.,III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Laura Milazzo
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
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6
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Grigg MJ, Lubis IN, Tetteh KKA, Barber BE, William T, Rajahram GS, Tan AF, Sutherland CJ, Noviyanti R, Drakeley CJ, Britton S, Anstey NM. Plasmodium knowlesi detection methods for human infections-Diagnosis and surveillance. ADVANCES IN PARASITOLOGY 2021; 113:77-130. [PMID: 34620386 DOI: 10.1016/bs.apar.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Within the overlapping geographical ranges of P. knowlesi monkey hosts and vectors in Southeast Asia, an estimated 1.5 billion people are considered at risk of infection. P. knowlesi can cause severe disease and death, the latter associated with delayed treatment occurring from misdiagnosis. Although microscopy is a sufficiently sensitive first-line tool for P. knowlesi detection for most low-level symptomatic infections, misdiagnosis as other Plasmodium species is common, and the majority of asymptomatic infections remain undetected. Current point-of-care rapid diagnostic tests demonstrate insufficient sensitivity and poor specificity for differentiating P. knowlesi from other Plasmodium species. Molecular tools including nested, real-time, and single-step PCR, and loop-mediated isothermal amplification (LAMP), are sensitive for P. knowlesi detection. However, higher cost and inability to provide the timely point-of-care diagnosis needed to guide appropriate clinical management has limited their routine use in most endemic clinical settings. P. knowlesi is likely underdiagnosed across the region, and improved diagnostic and surveillance tools are required. Reference laboratory molecular testing of malaria cases for both zoonotic and non-zoonotic Plasmodium species needs to be more widely implemented by National Malaria Control Programs across Southeast Asia to accurately identify the burden of zoonotic malaria and more precisely monitor the success of human-only malaria elimination programs. The implementation of specific serological tools for P. knowlesi would assist in determining the prevalence and distribution of asymptomatic and submicroscopic infections, the absence of transmission in certain areas, and associations with underlying land use change for future spatially targeted interventions.
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Affiliation(s)
- Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia.
| | - Inke N Lubis
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Sumatera Utara, Indonesia
| | - Kevin K A Tetteh
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bridget E Barber
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Gleneagles Medical Centre, Kota Kinabalu, Malaysia
| | - Giri S Rajahram
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Queen Elizabeth Hospital 2, Kota Kinabalu, Malaysia
| | - Angelica F Tan
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Chris J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sumudu Britton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
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Owusu EDA, Campillo A, Daily J, Ding XC. Acceptance and perceived value of non-invasive malaria diagnostic tests in malaria-endemic countries. Malar J 2021; 20:379. [PMID: 34560899 PMCID: PMC8461884 DOI: 10.1186/s12936-021-03911-y] [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: 03/18/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnosis of malaria, using microscopy or rapid diagnostic tests (RDTs), requires the collection of capillary blood. This procedure is relatively simple to perform but invasive and poses potential risks to patients and health workers, arising from the manipulation of potentially infectious bodily fluids. Less or non-invasive diagnostic tests, based on urine, saliva or requiring no sampling, have the potential to generate less discomfort for the patient and to offer simpler and less risky testing procedures that could be safely performed by untrained staff or even self-performed. To explore the potential acceptance and perceived value of such non-invasive tests, an online, international survey was conducted to gather feedback from National Malaria Control Programme (NMCP) representatives. METHODS An online survey comprising nineteen questions, available in English, French or Spanish, was emailed to 300 individuals who work with NMCPs in malaria-endemic countries. Answers were collected between November and December 2017; responses were qualitatively analysed to identify key themes and trends and quantitatively analysed to determine average values stratified by region. RESULTS Responses were received from 70 individuals, from 33 countries. Approximately half of the respondents (52 %) considered current blood-based tests for malaria to be minimally invasive and non-problematic in their setting. For these participants, non-invasive tests would only be of interest if they brought additional performance improvements, as compared with the performance of microscopy and RDTs. Most respondents were of the view that saliva-based (80 %) and urine-based (66 %) tests would be more readily acceptable among children than blood-based tests. Potential use-case scenarios of interest for both saliva- and urine-based tests were ease-of-testing by community health workers, additional surveillance, self-testing, and outbreak investigation. Many respondents (41 %) thought that if saliva-based tests retailed at <$0.50 per unit they could largely replace conventional RDTs, whereas only 25 % of respondents thought a similarly priced urine-based test would do so. CONCLUSIONS Although limited to NMCP stakeholders, this survey indicated that current tests for malaria, based on capillary blood, are generally perceived to be minimally invasive and non-problematic. Non-invasive tests, especially if saliva-based, would be welcome if they could match or out-perform the price and performance of current blood-based tests.
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Affiliation(s)
- Ewurama Dedea Ampadu Owusu
- FIND, Geneva, Switzerland.,Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
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Ultrasensitive Diagnostics for Low-Density Asymptomatic Plasmodium falciparum Infections in Low-Transmission Settings. J Clin Microbiol 2021; 59:JCM.01508-20. [PMID: 33148707 DOI: 10.1128/jcm.01508-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The emergence of multidrug-resistant Plasmodium falciparum malaria in Southeast Asia (SEA) has accelerated regional malaria elimination efforts. Most malaria in this and other low-transmission settings exists in asymptomatic individuals, which conventional diagnostic tests lack the sensitivity to detect. This has led to the development of new ultrasensitive diagnostics that are capable of detecting these low-parasitemia infections. This review summarizes the current status of ultrasensitive technologies, including PCR and loop-mediated isothermal amplification (LAMP)-based methods, as well as a newly developed ultrasensitive rapid diagnostic test (uRDT). The sensitivity, specificity, and field performance of these platforms will be examined, as well as their suitability for use in resource-limited settings to aid in malaria elimination efforts. uRDTs, with their improved sensitivity, are now able to detect approximately half of asymptomatic infections, providing a useful point-of-contact tool for malaria surveillance. The increased sensitivity and high-throughput nature of PCR-based tests make them ideal for screening large populations in places where laboratory capacity exists, and the recent commercialization of malaria LAMP kits should facilitate their adoption as a public health tool in places where such infrastructure is lacking. Finally, recent advances with dried blood spots may enable utilization of the extensive laboratory infrastructure of higher-income countries to assist with molecular surveillance in support of malaria elimination. If malaria is to be eliminated in SEA and other low-endemicity regions, then ultrasensitive diagnostics will likely play a key role in identifying and clearing the vast asymptomatic pool of infections that are common to these regions.
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Performance and Application of Commercially Available Loop-Mediated Isothermal Amplification (LAMP) Kits in Malaria Endemic and Non-Endemic Settings. Diagnostics (Basel) 2021; 11:diagnostics11020336. [PMID: 33670618 PMCID: PMC7922894 DOI: 10.3390/diagnostics11020336] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive molecular tool suitable for use as a near point-of-care test for the diagnosis of malaria. Recent meta-analyses have detailed high sensitivity and specificity of malaria LAMP when compared to microscopy, rapid diagnostic tests, and polymerase chain reaction in both endemic and non-endemic settings. Despite this, the use of malaria LAMP has primarily been limited to research settings to date. In this review, we aim to assess to what extent commercially available malaria LAMP kits have been applied in different settings, and to identify possible obstacles that may have hindered their use from being adopted further. In order to address this, we conducted a literature search in PubMed.gov using the search terms (((LAMP) OR (Loop-mediated isothermal amplification)) AND ((Malaria) OR (Plasmodium))). Focusing primarily on studies employing one of the commercially available kits, we then selected three key areas of LAMP application for further review: the performance and application of LAMP in malaria endemic settings including low transmission areas; LAMP for malaria screening during pregnancy; and malaria LAMP in returning travelers in non-endemic settings.
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Kolluri N, Kamath S, Lally P, Zanna M, Galagan J, Gitaka J, Kamita M, Cabodi M, Lolabattu SR, Klapperich CM. Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for P. falciparum Malaria. Anal Chem 2021; 93:2097-2105. [PMID: 33464825 PMCID: PMC7859932 DOI: 10.1021/acs.analchem.0c03847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
In many countries
targeting malaria elimination, persistent malaria
infections can have parasite loads significantly below the lower limit
of detection (LLOD) of standard diagnostic techniques, making them
difficult to identify and treat. The most sensitive diagnostic methods
involve amplification and detection of Plasmodium DNA by polymerase chain reaction (PCR), which requires expensive
thermal cycling equipment and is difficult to deploy in resource-limited
settings. Isothermal DNA amplification assays have been developed,
but they require
complex primer design, resulting in high nonspecific amplification,
and show a decrease in sensitivity than PCR methods. Here, we have
used a computational approach to design a novel isothermal amplification
assay with a simple primer design to amplify P. falciparum DNA with analytical sensitivity comparable to PCR. We have identified
short DNA sequences repeated throughout the parasite genome to be
used as primers for DNA amplification and demonstrated that these
primers can be used, without modification, to isothermally amplify P. falciparum parasite DNA via strand displacement
amplification. Our novel assay shows a LLOD of ∼1 parasite/μL
within a 30 min amplification time. The assay was demonstrated with
clinical samples using patient blood and saliva. We further characterized
the assay using direct amplicon next-generation sequencing and modified
the assay to work with a visual readout. The technique developed here
achieves similar analytical sensitivity to current gold standard PCR
assays requiring a fraction of time and resources for PCR. This highly
sensitive isothermal assay can be more easily adapted to field settings,
making it a potentially useful tool for malaria elimination.
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Affiliation(s)
- Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Shwetha Kamath
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Mina Zanna
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - James Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Moses Kamita
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Srinivasa Raju Lolabattu
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
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11
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Alfred Compaoré CF, Ilboudo H, Kaboré J, Kaboré JW, Camara O, Bamba M, Sakande H, Koné M, Camara M, Kaba D, Gaston Belem AM, Deborggraeve S, Büscher P, Bucheton B, Lejon V, Jamonneau V. Analytical sensitivity of loopamp and quantitative real-time PCR on dried blood spots and their potential role in monitoring human African trypanosomiasis elimination. Exp Parasitol 2020; 219:108014. [PMID: 33011238 DOI: 10.1016/j.exppara.2020.108014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/19/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
The objective set by WHO to reach elimination of human African trypanosomiasis (HAT) as a public health problem by 2020 is being achieved. The next target is the interruption of gambiense-HAT transmission in humans by 2030. To monitor progress towards this target, in areas where specialized local HAT control capacities will disappear, is a major challenge. Test specimens should be easily collectable and safely transportable such as dried blood spots (DBS). Monitoring tests performed in regional reference centres should be reliable, cheap and allow analysis of large numbers of specimens in a high-throughput format. The aim of this study was to assess the analytical sensitivity of Loopamp, M18S quantitative real-time PCR (M18S qPCR) and TgsGP qPCR as molecular diagnostic tests for the presence of Trypanosoma brucei gambiense in DBS. The sensitivity of the Loopamp test, with a detection limit of 100 trypanosomes/mL, was in the range of parasitaemias commonly observed in HAT patients, while detection limits for M18S and TgsGP qPCR were respectively 1000 and 10,000 trypanosomes/mL. None of the tests was entirely suitable for high-throughput use and further development and implementation of sensitive high-throughput molecular tools for monitoring HAT elimination are needed.
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Affiliation(s)
- Charlie Franck Alfred Compaoré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Hamidou Ilboudo
- Institut de Recherche en Sciences de la Santé, Unité de Recherche Clinique de Nanoro, 11 BP 218, Ouagadougou CMS 11, Burkina Faso
| | - Jacques Kaboré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Justin Windingoudi Kaboré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Oumou Camara
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Mohamed Bamba
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso
| | - Hassane Sakande
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso
| | - Minayégninrin Koné
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa
| | - Mamadou Camara
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Dramane Kaba
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa
| | - Adrien Marie Gaston Belem
- Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Stijn Deborggraeve
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Philippe Büscher
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Bruno Bucheton
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea; Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France
| | - Veerle Lejon
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France
| | - Vincent Jamonneau
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa; Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France.
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12
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Davis CN, Tyson F, Cutress D, Davies E, Jones DL, Brophy PM, Prescott A, Rose MT, Williams M, Williams HW, Jones RA. Rapid detection of Galba truncatula in water sources on pasture-land using loop-mediated isothermal amplification for control of trematode infections. Parasit Vectors 2020; 13:496. [PMID: 32998778 PMCID: PMC7526160 DOI: 10.1186/s13071-020-04371-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fascioliasis caused by the trematodes Fasciola hepatica and F. gigantica, is a global neglected zoonotic disease estimated to cost the livestock industry over €2.5 billion annually. Farm management measures and sustainable use of anthelmintics can, in principle, effectively control trematode infection in livestock and reduce the rate of developing anthelmintic resistance. Previously, we designed an environmental DNA (eDNA) assay to identify a common trematode intermediate host, the freshwater snail Galba truncatula, in water sources to measure specific trematode infection risk areas on pasture-land. To improve this procedure, we now report a loop-mediated isothermal amplification (LAMP) assay to identify G. truncatula eDNA. METHODS A LAMP assay was designed and optimised (e.g. temperature, time duration and primer concentration) to identify G. truncatula DNA. The ability of the LAMP assay to target G. truncatula DNA was identified, and LAMP assay limit of detection was investigated in comparison to conventional PCR. In the field, 48 water samples were collected from stream, ditch and water pool habitats in four locations at two Aberystwyth University farms over a seven week period to investigate the applicability of the LAMP assay for use on eDNA samples, in comparison to conventional PCR. RESULTS The LAMP assay delivered detectable results in 30 min at 63 °C. The assay discriminated between G. truncatula DNA and non-target DNA, presenting a level of DNA detection comparable to conventional PCR. No significant difference was found between the ability of the LAMP and PCR assay to identify G. truncatula eDNA in water samples. Kappa coefficient analysis revealed a moderate level of agreement between LAMP and PCR assays. CONCLUSIONS This study demonstrated that the LAMP assay can detect G. truncatula eDNA in a simple and rapid manner. The LAMP assay may become a valuable tool to determine optimum pasture management for trematode parasite control.
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Affiliation(s)
- Chelsea N Davis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Fiona Tyson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - David Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Emma Davies
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dewi Llyr Jones
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK.,Coleg Cambria, Llysfasi, Ruthin Road, Ruthin, Denbighshire, UK
| | - Peter M Brophy
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Alex Prescott
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael T Rose
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK.,Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, TAS, Australia
| | - Manod Williams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Hefin Wyn Williams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Rhys Aled Jones
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK.
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13
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Ortiz-Prado E, Simbaña-Rivera K, Gómez-Barreno L, Rubio-Neira M, Guaman LP, Kyriakidis NC, Muslin C, Jaramillo AMG, Barba-Ostria C, Cevallos-Robalino D, Sanches-SanMiguel H, Unigarro L, Zalakeviciute R, Gadian N, López-Cortés A. Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review. Diagn Microbiol Infect Dis 2020; 98:115094. [PMID: 32623267 PMCID: PMC7260568 DOI: 10.1016/j.diagmicrobio.2020.115094] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
Coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. The current classification of coronaviruses recognizes 39 species in 27 subgenera that belong to the family Coronaviridae. From those, at least 7 coronaviruses are known to cause respiratory infections in humans. Four of these viruses can cause common cold-like symptoms. Those that infect animals can evolve and become infectious to humans. Three recent examples of these viral jumps include SARS CoV, MERS-CoV and SARS CoV-2 virus. They are responsible for causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the most recently discovered coronavirus disease during 2019 (COVID-19). COVID-19, a respiratory disease caused by the SARS-CoV-2 virus, was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. The rapid spread of the disease has taken the scientific and medical community by surprise. Latest figures from 20 May 2020 show more than 5 million people had been infected with the virus, causing more than 330,000 deaths in over 210 countries worldwide. The large amount of information received daily relating to COVID-19 is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. In order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the SARS CoV-2 Virus and the Coronavirus Diseases 2019 (COVID-19).
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Affiliation(s)
- Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | - Lenin Gómez-Barreno
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | - Mario Rubio-Neira
- Hospital Baca Ortiz, Pediatric and Cardiology Department, Quito, Ecuador.
| | - Linda P Guaman
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador.
| | - Nikolaos C Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de la Americas, Quito, Ecuador.
| | - Claire Muslin
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | | | - Carlos Barba-Ostria
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | | | - Hugo Sanches-SanMiguel
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas (UDLA), Quito, Ecuador.
| | - Luis Unigarro
- Intensive Care Unit, Hospital SOLCA Quito, Quito, Ecuador.
| | - Rasa Zalakeviciute
- Grupo de Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de Las Américas, Quito, Ecuador; Intelligent and Interactive Systems Lab (SI2 Lab) Universidad de Las Américas (UDLA), Quito, Ecuador.
| | - Naomi Gadian
- University of Southampton, Department of Public Health, Southampton, United Kingdome.
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador; Red Latinoamericana de Implementación y Validación de Guías Clínicas Farmacogenómicas (RELIVAF-CYTED), Quito, Ecuador.
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14
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Picot S, Cucherat M, Bienvenu AL. Systematic review and meta-analysis of diagnostic accuracy of loop-mediated isothermal amplification (LAMP) methods compared with microscopy, polymerase chain reaction and rapid diagnostic tests for malaria diagnosis. Int J Infect Dis 2020; 98:408-419. [PMID: 32659450 DOI: 10.1016/j.ijid.2020.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/01/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Diagnosis is a challenging issue for eliminating malaria. Loop-mediated isothermal amplification (LAMP) could be an alternative to conventional methods. This study aimed to evaluate the diagnostic accuracy of LAMP for malaria compared with microscopy, polymerase chain reaction (PCR) and rapid diagnostic tests (RDTs). METHODS AND DESIGN MEDLINE, Web of Science and Scopus were searched from inception to 1 July 2019. Prospective and retrospective, randomised and non-randomised, mono-center and multi-center studies, including symptomatic or asymptomatic patients, that reported one LAMP method and one comparator (microscopy, RDT or PCR) were included. PROSPERO registration number: CRD42017075186. RESULTS Sixty-six studies published between 2006 and 2019 were included, leading to the analysis of 30,641 LAMP tests. The pooled sensitivity of LAMP remained between 96% and 98%, whichever the comparator. The pooled specificity of LAMP was around 95%, but was a little higher if the best PCR studies were considered. The AUC was found to be >0.98, whichever the subgroup of studies was considered. Diagnostic odds ratio (DOR) was found to be around 1000 for all subgroups, except for Plasmodium vivax. CONCLUSION This meta-analysis confirmed that the LAMP method is robust for diagnosing malaria, both in symptomatic and asymptomatic people. Thus, the impact of LAMP for controlling malaria is expected to be important.
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Affiliation(s)
- Stephane Picot
- Malaria Research Unit, SMITh, ICBMS UMR 5246 CNRS-INSA-CPE-Université de Lyon, Campus Lyon-Tech La Doua, 69622 Villeurbanne Cedex, France; Institut de Parasitologie et Mycologie Médicale, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Michel Cucherat
- Service de Pharmacotoxicologie, Hospices Civils de Lyon, Laboratoire de Biométrie et Biologie Évolutive, CNRS, UMR5558, Université Lyon 1, Lyon, France
| | - Anne-Lise Bienvenu
- Malaria Research Unit, SMITh, ICBMS UMR 5246 CNRS-INSA-CPE-Université de Lyon, Campus Lyon-Tech La Doua, 69622 Villeurbanne Cedex, France; Service Pharmacie, Groupement Hospitalier Nord, Hospices Civils de Lyon, France; Service d'Hématologie, Groupement Hospitalier Nord, Hospices Civils de Lyon, France.
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15
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Pasquier G, Azoury V, Sasso M, Laroche L, Varlet-Marie E, Houzé S, Lachaud L, Bastien P, Sterkers Y, Leveque MF. Rapid diagnostic tests failing to detect infections by Plasmodium falciparum encoding pfhrp2 and pfhrp3 genes in a non-endemic setting. Malar J 2020; 19:179. [PMID: 32393251 PMCID: PMC7216663 DOI: 10.1186/s12936-020-03251-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/01/2020] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) detecting the histidine-rich protein 2 (PfHRP2) have a central position for the management of Plasmodium falciparum infections. Yet, variable detection of certain targeted motifs, low parasitaemia, but also deletion of pfhrp2 gene or its homologue pfhrp3, may result in false-negative RDT leading to misdiagnosis and delayed treatment. This study aimed at investigating the prevalence, and understanding the possible causes, of P. falciparum RDT-negative infections at Montpellier Academic Hospital, France. Methods The prevalence of falsely-negative RDT results reported before and after the introduction of a loop-mediated isothermal amplification (LAMP) assay, as part as the malaria screening strategy in January 2017, was analysed. Negative P. falciparum RDT infections were screened for pfhrp2 or pfhrp3 deletion; and exons 2 were sequenced to show a putative genetic diversity impairing PfHRP2 detection. Results The overall prevalence of P. falciparum negative RDTs from January 2006 to December 2018 was low (3/446). Whereas no cases were reported from 2006 to 2016 (0/373), period during which the malaria diagnostic screen was based on microscopy and RDT, prevalence increased up to 4.1% (3/73) between 2017 and 2018, when molecular detection was implemented for primary screening. Neither pfhrp2/3 deletion nor major variation in the frequency of repetitive epitopes could explain these false-negative RDT results. Conclusion This paper demonstrates the presence of pfhrp2 and pfhrp3 genes in three P. falciparum RDT-negative infections and reviews the possible reasons for non-detection of HRP2/3 antigens in a non-endemic setting. It highlights the emergence of falsely negative rapid diagnostic tests in a non-endemic setting and draws attention on the risk of missing malaria cases with low parasitaemia infections using the RDT plus microscopy-based strategy currently recommended by French authorities. The relevance of a novel diagnostic scheme based upon a LAMP assay is discussed.
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Affiliation(s)
- Grégoire Pasquier
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France.,Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | - Vincent Azoury
- Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | - Milène Sasso
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France.,Laboratory of Microbiology, CHU de Nîmes, Nîmes, France
| | - Laëtitia Laroche
- Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | | | - Sandrine Houzé
- Centre National de Référence du Paludisme, APHP, Hôpital Bichat-Claude Bernard, Paris, France
| | - Laurence Lachaud
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France.,Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | - Patrick Bastien
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France.,Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | - Yvon Sterkers
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France.,Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France
| | - Maude F Leveque
- University of Montpellier, CNRS, IRD, UMR MiVEGEC, Montpellier, France. .,Department of Parasitology-Mycology, CHU de Montpellier, Montpellier, France.
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16
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Silva Nunes Bezerra G, Barbosa Júnior WL, Virgínia Batista Vieira A, Xavier AT, Sebastião Da Costa Lima Júnior M, Maria Xavier E, Silva EDD, Cintra Leal N, Medeiros ZMD. Loop-mediated isothermal amplification methods for diagnosis of visceral leishmaniasis ( kala-azar) - a systematic review. Expert Rev Mol Diagn 2020; 20:455-465. [PMID: 32116067 DOI: 10.1080/14737159.2020.1736564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: Visceral leishmaniasis (VL) is a life-threatening infection remaining as one of the most neglected tropical diseases around the world. Despite scientific advances, an accurate diagnosis of VL remains a challenge. Loop-mediated isothermal amplification (LAMP) has emerged as a promising diagnostic tool with the possibility of becoming a point-of-care test to guide VL diagnosis and treatment.Areas covered: We conducted a systematic review assessing LAMP systems for diagnosing VL from 2000 to 2019. We performed structured searches in PubMed, LILACS, Scopus, and Web of Science without language restriction. Two reviewers screened articles, completed the data extraction and assessment of the risk of bias. A qualitative summary of the included studies was performed.Expert opinion: LAMP could be used as a screening test for VL diagnosis, so tissue aspiration could be performed only for those who are LAMP negative. We recommend more studies about the performance of the Loopamp™ Leishmania Detection kit and the Brazilian LAMP assay. Thus, we expect in the future the constitution of an international consortium to share experiences, projects, and other LAMP approaches mainly among researchers and institutions located within VL endemic countries.
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Affiliation(s)
- Gilberto Silva Nunes Bezerra
- Programa De Pós-Graduação Em Ciências Da Saúde, Universidade De Pernambuco (UPE), Recife, Pernambuco, Brasil.,Departamento De Parasitologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brasil
| | - Walter Lins Barbosa Júnior
- Departamento De Parasitologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brasil
| | | | - Amanda Tavares Xavier
- Programa De Pós-Graduação Em Ciências Da Saúde, Universidade De Pernambuco (UPE), Recife, Pernambuco, Brasil
| | | | - Edeneide Maria Xavier
- Programa De Pós-Graduação Em Ciências Da Saúde, Universidade De Pernambuco (UPE), Recife, Pernambuco, Brasil
| | - Elis Dionísio Da Silva
- Departamento De Parasitologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brasil
| | - Nilma Cintra Leal
- Departamento De Microbiologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brasil
| | - Zulma Maria De Medeiros
- Programa De Pós-Graduação Em Ciências Da Saúde, Universidade De Pernambuco (UPE), Recife, Pernambuco, Brasil.,Departamento De Parasitologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brasil
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17
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Hartmeyer GN, Hoegh SV, Skov MN, Kemp M. Use of Loop-Mediated Isothermal Amplification in a Resource-Saving Strategy for Primary Malaria Screening in a Non-Endemic Setting. Am J Trop Med Hyg 2020; 100:566-571. [PMID: 30675835 PMCID: PMC6402892 DOI: 10.4269/ajtmh.18-0496] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Malaria is traditionally diagnosed by blood smear microscopy, which requires continuous resource-demanding training. In areas with only a few cases of malaria, a simple and rapid test that can reliably exclude malaria could significantly reduce the need for microscopy and training. We evaluated whether loop-mediated isothermal amplification (LAMP) for screening malaria parasites could reduce the workload in the diagnosis of malaria. Loop-mediated isothermal amplification was used to analyze 38 ethylene-diamine-tetraacetic acid (EDTA) blood samples from 23 patients who had previously been tested for malaria by microscopy, antigen-based rapid diagnostic test (antigen-RDT), and in-house real-time polymerase chain reaction (RT-PCR). The samples included blood with low-level parasitaemia and samples with discrepancies between the results of the different methods. Loop-mediated isothermal amplification detected malaria parasites in 27 of 28 samples that were positive according to in-house RT-PCR. There were negative microscopy results in 10 of these and negative antigen-RDT results in 11. The sample with a negative LAMP result and positive in-house RT-PCR result was from a patient who had recently been treated for low-level Plasmodium falciparum malaria parasitaemia. We found LAMP to be reliable for malaria screening and suitable for replacing microscopy without loss of performance. The low number of LAMP-positive samples needing microscopy can be handled by a limited number of trained microscopists. The time saved on training and documentation was estimated to be 520 working hours yearly in our laboratory. Using LAMP for primary screening of patient samples, we have made a diagnostic workflow that ensures more reliable, faster, and less resource-demanding diagnosis of malaria.
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Affiliation(s)
- Gitte N Hartmeyer
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit of Clinical Microbiology, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, Odense, Denmark
| | - Silje V Hoegh
- Research Unit of Clinical Microbiology, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, Odense, Denmark
| | - Marianne N Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit of Clinical Microbiology, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, Odense, Denmark
| | - Michael Kemp
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit of Clinical Microbiology, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, Odense, Denmark
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Cheaveau J, Mogollon DC, Mohon MAN, Golassa L, Yewhalaw D, Pillai DR. Asymptomatic malaria in the clinical and public health context. Expert Rev Anti Infect Ther 2019; 17:997-1010. [PMID: 31718324 DOI: 10.1080/14787210.2019.1693259] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Introduction: Historically, the global community has focused on the control of symptomatic malaria. However, interest in asymptomatic malaria has been growing, particularly in the context of malaria elimination.Areas covered: We undertook a comprehensive PubMed literature review on asymptomatic malaria as it relates to detection and elimination with emphasis between 2014 and 2019. Diagnostic tools with a low limit of detection (LOD) have allowed us to develop a more detailed understanding of asymptomatic malaria and its impact. These highly sensitive diagnostics have demonstrated that the prevalence of asymptomatic malaria is greater than previously thought. In addition, it is now possible to detect the malaria reservoir in the community, something that was previously not feasible. Asymptomatic malaria has previously not been treated, but research has begun to examine whether treating individuals with asymptomatic malaria may lead to health benefits. Finally, we have begun to understand the importance of asymptomatic malaria in ongoing transmission.Expert opinion: Therefore, with malaria elimination back on the agenda, asymptomatic malaria can no longer be ignored, especially in light of new ultra-sensitive diagnostic tools.
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Affiliation(s)
- James Cheaveau
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Daniel Castaneda Mogollon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Md Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
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19
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Mohon AN, Getie S, Jahan N, Alam MS, Pillai DR. Ultrasensitive loop mediated isothermal amplification (US-LAMP) to detect malaria for elimination. Malar J 2019; 18:350. [PMID: 31619258 PMCID: PMC6796404 DOI: 10.1186/s12936-019-2979-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
Background Malaria elimination requires diagnostic methods able to detect parasite levels well below what is currently possible with microscopy and rapid diagnostic tests. This is particularly true in surveillance of malaria at the population level that includes so-called “asymptomatic” individuals. Methods The development of the first ultrasensitive loop mediated amplification method capable of detecting malaria from both whole blood and dried blood spots (DBS) is described. The 18S rRNA and corresponding genes that remain stable on DBS for up to 5 months are targeted. Results In the case of Plasmodium falciparum, lower limits of detection of 25 parasite/mL and 50–100 parasite/mL from whole blood and DBS were obtained, respectively. A sensitivity of 97.0% (95% CI 82.5–99.8) and specificity of 99.1% (95% CI 97.6–99.7) was obtained for the detection of all species in asymptomatic individuals from Africa and Asia (n = 494). Conclusion This tool is ideally suited for low middle-income countries where malaria is endemic and ultrasensitive surveillance of malaria is highly desirable for elimination.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada
| | - Sisay Getie
- Department of Medical Parasitology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, P. O. Box: 196, Gondar, Ethiopia
| | - Nusrat Jahan
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Mohammad Shafiul Alam
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Dylan R Pillai
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada. .,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada. .,Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.
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20
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Cheaveau J, Nguyen H, Chow B, Marasinghe D, Mohon AN, Yuan H, Viana G, van Schalkwyk D, Church D, Chan W, Pillai DR. Clinical Validation of a Commercial LAMP Test for Ruling out Malaria in Returning Travelers: A Prospective Diagnostic Trial. Open Forum Infect Dis 2018; 5:ofy260. [PMID: 30465012 PMCID: PMC6239078 DOI: 10.1093/ofid/ofy260] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/08/2018] [Indexed: 12/21/2022] Open
Abstract
The mainstay of malaria diagnosis relies on rapid diagnostic tests (RDTs) and microscopy, both of which lack analytical sensitivity. This leads to repeat testing to rule out malaria. A prospective diagnostic trial of the Meridian illumigene Malaria assay (loop-mediated isothermal amplification [LAMP]) was conducted comparing it with reference microscopy and RDTs (BinaxNOW Malaria) in returning travelers between June 2017 and January 2018. Returning travelers with signs and symptoms of malaria were enrolled in the study. RDTs, microscopy, and LAMP assays were performed simultaneously. A total of 298 patients (50.7% male; mean age, 32.5 years) were enrolled, most visiting friends and relatives (43.3%), presenting with fever (88.9%), not taking prophylaxis (82.9%), and treated as outpatients (84.1%). In the prospective arm (n = 348), LAMP had a sensitivity of 98.1% (95% confidence interval [CI], 90.0%–100%) and a specificity of 97.6% (95% CI, 95.2%–99.1%) vs microscopy. After discrepant resolution with real-time polymerase chain reaction, LAMP had a sensitivity of 100% (95% CI, 93.7%–100%) and a specificity of 100% (95% CI, 98.7%–100%) vs microscopy. After discrepant resolution, RDTs had a sensitivity of 83.3% (95% CI, 58.6%–96.4%) and a specificity of 96.2% (95% CI, 93.2%–98.1%) vs microscopy. When including retrospective specimens (n = 377), LAMP had a sensitivity of 98.8% (95% CI, 93.2%–100%) and a specificity of 97.6% (95% CI, 95.2%–99.1%) vs microscopy, and after discrepant resolution of this set, LAMP had a sensitivity of 100% (95% CI, 95.8%–100%) and a specificity of 100% (95% CI, 98.7%–100%). A cost-benefit analysis of reagents and labor suggests savings of up to USD$13 per specimen using a novel algorithm with LAMP screening.
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Affiliation(s)
- James Cheaveau
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Alberta, Canada
| | - Hong Nguyen
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Barbara Chow
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Dewdunee Marasinghe
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Alberta, Canada.,Laboratório de Pesquisas em Malária, Instituto Evandro Chagas, Levilândia Ananindeua, Pará, Brasil
| | - Hong Yuan
- ProvLab Alberta, Edmonton, Alberta, Canada
| | - Gisele Viana
- Laboratório de Pesquisas em Malária, Instituto Evandro Chagas, Levilândia Ananindeua, Pará, Brasil
| | - Donelly van Schalkwyk
- Department of Immunology & Infection, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Deirdre Church
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Wilson Chan
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Dylan R Pillai
- Clinical Section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Alberta, Canada.,Department Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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21
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Picado A, Cruz I, Redard-Jacot M, Schijman AG, Torrico F, Sosa-Estani S, Katz Z, Ndung’u JM. The burden of congenital Chagas disease and implementation of molecular diagnostic tools in Latin America. BMJ Glob Health 2018; 3:e001069. [PMID: 30364393 PMCID: PMC6195131 DOI: 10.1136/bmjgh-2018-001069] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 11/21/2022] Open
Abstract
It is estimated that between 8000 and 15 000 Trypanosoma cruzi infected babies are born every year to infected mothers in Chagas disease endemic countries. Currently, poor access to and performance of the current diagnostic algorithm, based on microscopy at birth and serology at 8–12 months after delivery, is one of the barriers to congenital Chagas disease (CCD) control. Detection of parasite DNA using molecular diagnostic tools could be an alternative or complement to current diagnostic methods, but its implementation in endemic regions remains limited. Prompt diagnosis and treatment of CCD cases would have a positive clinical and epidemiological impact. In this paper, we analysed the burden of CCD in Latin America, and the potential use of molecular tests to improve access to early diagnosis and treatment of T. cruzi infected newborns.
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Affiliation(s)
- Albert Picado
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Israel Cruz
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Maël Redard-Jacot
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres", Buenos Aires, Argentina
| | - Faustino Torrico
- Faculty of Medicine, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Fundación CEADES, Cochabamba, Bolivia
| | - Sergio Sosa-Estani
- Centro de Investigación de Epidemiología y Salud Pública (CIESP-IECS), CONICET, Buenos Aires, Argentina
- Drugs for Neglected Diseases initiative (DNDi), Rio de Janeiro, Brazil
| | - Zachary Katz
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
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22
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Kollenda H, Hagen RM, Hanke M, Rojak S, Hinz R, Wassill L, Poppert S, Tannich E, Frickmann H. Poor Diagnostic Performance of a Species-Specific Loop-Mediated Isothermal Amplification (LAMP) Platform for Malaria. Eur J Microbiol Immunol (Bp) 2018; 8:112-118. [PMID: 30719327 PMCID: PMC6348705 DOI: 10.1556/1886.2018.00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022] Open
Abstract
Background The objective of this study was to assess an in-house loop-mediated isothermal amplification (LAMP) platform for malaria parasite detection and identification on species level. Methods LAMP primers specific for the human Plasmodium spp., namely, P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, as well as genus-specific primers, were tested against a composite gold standard comprising microscopy from thick and thin blood films, commercial genus-specific Meridian illumigene Malaria LAMP, in-house real-time polymerase chain reaction (PCR), and commercial fast-track diagnostics (FTD) Malaria differentiation PCR. Results Of the 523 blood samples analyzed, the composite gold standard indicated 243 Plasmodium-species-DNA-containing samples (46.5%). Sensitivity and specificity of the analyzed genus- and species-specific LAMP primers were 71.0%–100.0% and 90.8%–100.0%, respectively. The influence of parasitemia was best documented for P. falciparum-specific LAMP with sensitivity values of 35.5% (22/62) for microscopically negative samples containing P. falciparum DNA, 50% (19/38) for parasitemia ≤50/μL, 84% (21/25) for parasitemia ≤500/μL, and 100% (92/92) for parasitemia >500/μL. Conclusions In our hands, performance characteristics of species-specific in-house LAMP for malaria lack reliability required for diagnostic laboratories. The use of the easy-to-apply technique for surveillance purposes may be considered.
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Affiliation(s)
- Hans Kollenda
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy, Munich, Germany
| | - Miriam Hanke
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sandra Rojak
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Department of Infectious Diseases and Tropical Medicine, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Rebecca Hinz
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | | | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Faculty of Medicine, University Basel, Basel, Switzerland
| | - Egbert Tannich
- National Reference Centre for Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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23
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Viana GMR, Silva-Flannery L, Lima Barbosa DR, Lucchi N, do Valle SCN, Farias S, Barbalho N, Marchesini P, Rossi JCN, Udhayakumar V, Póvoa MM, de Oliveira AM. Field evaluation of a real time loop-mediated isothermal amplification assay (RealAmp) for malaria diagnosis in Cruzeiro do Sul, Acre, Brazil. PLoS One 2018; 13:e0200492. [PMID: 29995953 PMCID: PMC6040774 DOI: 10.1371/journal.pone.0200492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022] Open
Abstract
Conventional molecular methods, such as nested polymerase chain reaction (PCR), are very sensitive for detection of malaria parasites, but require advanced laboratory equipment and trained personnel. Real-time loop-mediated isothermal amplification (RealAmp), a loop-mediated isothermal amplification-based molecular tool (LAMP), facilitates rapid target amplification at a single temperature setting, reducing the need for sophisticated equipment. We evaluated the performance of a field-adapted RealAmp assay for malaria diagnosis in Cruzeiro do Sul, Acre State, Brazil, a remote area in Brazil with limited laboratory capabilities. We enrolled 1,000 patients with fever (axillary temperature ≥ 37.5 C) or history of fever in last 24 h presenting for malaria diagnosis from February through June 2015. DNA was extracted from dried blood spots using a boil and spin method (heat treatment) at the sample processing site, and also using commercial kits at a Brazilian national reference laboratory. RealAmp was performed for Plasmodium genus, P. falciparum, and P. vivax identification. In addition, Giemsa-stained blood smears were prepared and examined by two independent well-trained study microscopists. A combination of Real-time PCR and nested PCR was used as reference test. The sensitivity and specificity of RealAmp in the field site laboratory were 94.1% (95% confidence interval [CI]: 90.1–96.8) and 83.9% (95% CI: 81.1–86.4), respectively. The sensitivity and specificity of local microscopy were 87.7% (95% CI: 82.6–91.7) and 98.9% (95% CI: 97.8–99.4), respectively, while study microscopy showed sensitivity of 96.4% (95% CI: 93.0–98.4) and specificity of 98.2% (95% CI: 97.0–99.0). None of the three tests detected 20 P. falciparum and P. vivax mixed infections identified by the reference test. Our findings highlight that it is possible to implement simple molecular tests in facilities with limited resources such as Cruzeiro do Sul in Brazil. RealAmp sensitivity was similar to that of microscopy performed by skilled professionals; both RealAmp and study microscopy performed poorly in detection of mixed infection. Attempts to develop and evaluate simpler molecular tools should continue, especially for the detection of malaria infection in remote areas.
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Affiliation(s)
| | - Luciana Silva-Flannery
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | | | - Naomi Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | | | - Samela Farias
- Secretaria Estadual de Saude do Acre—Hemonúcleo Cruzeiro do Sul. Manuel Terças, Cruzeiro do Sul–Acre—Brasil
| | - Nayara Barbalho
- Secretaria Estadual de Saude do Acre—Hemonúcleo Cruzeiro do Sul. Manuel Terças, Cruzeiro do Sul–Acre—Brasil
| | - Paola Marchesini
- Coordenação Geral do Programa Nacional de Controle da Malária e Doenças Transmitidas pelo Aedes- CGPNCM Setor Comercial Sul, Edifício Principal, Brasília/DF, Brasil
| | - Juliana Chedid Nogaredi Rossi
- Coordenação Geral do Programa Nacional de Controle da Malária e Doenças Transmitidas pelo Aedes- CGPNCM Setor Comercial Sul, Edifício Principal, Brasília/DF, Brasil
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Marinete Marins Póvoa
- Instituto Evandro Chagas–IEC/SVS/MS, S/N° Bairro: Levilândia, Ananindeua, Pará, Brasil
| | - Alexandre Macedo de Oliveira
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Abstract
PURPOSE OF REVIEW Bloodstream infections are a major cause of hospital and ICU admission with high morbidity and mortality; however, early and targeted antimicrobial therapy reduces mortality in high-risk patients. This article focuses on the diagnosis of bloodstream infections by PCR-based approaches at an early stage to enable prompt treatment and prevent organ dysfunction. RECENT FINDINGS PCR systems offering highly multiplexed targeting of bacterial and/or fungal pathogens (in whole blood) offer the best opportunity for clinical impact, as informed decisions can be made within 4-8 h of the blood draw. Although more rapid, these systems are typically associated with lower sensitivity and specificity than postculture detection methods which rely on microbial growth. Additionally, unlike postculture methods, detection directly from blood is not prone to misleading results because of concurrent (or previous) therapy, which limit clinical relevance. SUMMARY Rapid and accurate identification of the cause of sepsis is essential in improving patient outcomes. Early identification of these pathogens by nucleic acid detection assays directly from blood samples remains key to achieving this, particularly if taken at the time of presentation. Selection of the most suitable PCR system is typically influenced by local epidemiology and by the resources of the testing laboratory.
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Peker N, Couto N, Sinha B, Rossen JW. Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches. Clin Microbiol Infect 2018; 24:944-955. [PMID: 29787889 DOI: 10.1016/j.cmi.2018.05.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2018] [Accepted: 05/12/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Bloodstream infections are a major cause of death with increasing incidence and severity. Blood cultures are still the reference standard for microbiological diagnosis, but are rather slow. Molecular methods can be used as add-on complementary assays. They can be useful to speed up microbial identification and to predict antimicrobial susceptibility, applied to direct blood samples or positive blood cultures. AIM To review recent developments in molecular-based diagnostic platforms used for the identification of bloodstream infections, with a focus on assays performed directly on blood samples and positive blood cultures. SOURCES Peer reviewed articles, conference abstracts, and manufacturers' websites. CONTENT We give an update on recent developments of molecular methods in diagnosing BSIs. We first describe the currently available molecular methods to be used for positive blood cultures including: a) in situ hybridization-based methods; b) DNA-microarray-based hybridization technology; c) nucleic acid amplification-based methods; and d) combined methods. Subsequently, molecular methods applied directly to whole blood samples are discussed, including the use of nucleic acid amplification-based methods, T2 magnetic resonance-based methods, and metagenomics for diagnosing BSIs. IMPLICATIONS Advances in molecular-based methods complementary to conventional blood culture diagnostics and antimicrobial stewardship programmes may optimize infection management by allowing rapid identification of pathogens and relevant antimicrobial resistance genes. Rapid diagnosis of the causing microorganism and relevant resistance determinants is important for early administration and modification of appropriate antimicrobial therapy. Ultimately, this may lead to improved quality and cost-effectiveness of health care, as well as reduced antimicrobial resistance selection.
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Affiliation(s)
- N Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - N Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - B Sinha
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands.
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26
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Ibarra-Meneses AV, Cruz I, Chicharro C, Sánchez C, Biéler S, Broger T, Moreno J, Carrillo E. Evaluation of fluorimetry and direct visualization to interpret results of a loop-mediated isothermal amplification kit to detect Leishmania DNA. Parasit Vectors 2018; 11:250. [PMID: 29665825 PMCID: PMC5905109 DOI: 10.1186/s13071-018-2836-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
Background Nucleic acid amplification tests (NAATs) have proven to be advantageous in the diagnosis of leishmaniases, allowing sensitive diagnosis of: (i) cutaneous leishmaniasis in long duration lesions and (ii) visceral leishmaniasis using a less-invasive sample like peripheral blood, in opposition to tissue aspiration required for parasite demonstration by microscopy. Despite their benefits, the implementation of NAATs for leishmaniasis diagnosis at the point-of-care has not been achieved yet, mostly due to the complexity and logistical issues associated with PCR-based methods. Methods In this work, we have evaluated the performance of a ready-to-use loop-mediated isothermal amplification (LAMP) kit using two real time fluorimeters to amplify leishmanial DNA obtained by silica column-based and Boil & Spin protocols. Results The different approaches used to run and interpret the LAMP reactions showed a performance equivalent to PCR and real-time PCR, using spiked and clinical samples. The time to positivity obtained with real-time fluorimetry showed an excellent correlation with both Ct values and parasite load from real-time quantitative PCR. Conclusions The results obtained open the possibility of using a highly stable, ready-to-use LAMP kit for the accurate diagnosis of leishmaniasis at the point-of-care. Furthermore, the feasibility of relating time to positivity, determined with a portable real-time fluorimeter, with the parasite burden could have a wider application in the management of leishmaniasis, such as in treatment efficacy monitoring or as a pharmacodynamics tool in clinical trials.
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Affiliation(s)
- Ana V Ibarra-Meneses
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Israel Cruz
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Carmen Chicharro
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Sánchez
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Sylvain Biéler
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Tobias Broger
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Eugenia Carrillo
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
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27
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Kaur A, Kapil A, Elangovan R, Jha S, Kalyanasundaram D. Highly-sensitive detection of Salmonella typhi in clinical blood samples by magnetic nanoparticle-based enrichment and in-situ measurement of isothermal amplification of nucleic acids. PLoS One 2018; 13:e0194817. [PMID: 29590194 PMCID: PMC5874042 DOI: 10.1371/journal.pone.0194817] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/10/2018] [Indexed: 12/31/2022] Open
Abstract
Enteric fever continues to be a major cause of mortality and morbidity globally, particularly in poor resource settings. Lack of rapid diagnostic assays is a major driving factor for the empirical treatment of enteric fever. In this work, a rapid and sensitive method ‘Miod’ ‘has been developed. Miod includes a magnetic nanoparticle-based enrichment of target bacterial cells, followed by cell lysis and loop-mediated isothermal amplification (LAMP) of nucleic acids for signal augmentation along with concurrent measurement of signal via an in–situ optical detection system. To identify positive/negative enteric fever infections in clinical blood samples, the samples were processed using Miod at time = 0 hours and time = 4 hours post-incubation in blood culture media. Primers specific for the STY2879 gene were used to amplify the nucleic acids isolated from S. typhi cells. A limit of detection of 5 CFU/mL was achieved. No cross-reactivity of the primers were observed against 106 CFU/mL of common pathogenic bacterial species found in blood such as E. coli, P. aeruginosa, S. aureus, A. baumanni, E. faecalis, S. Paratyphi A and K. pneumonia. Miod was tested on 28 human clinical blood samples. The detection of both pre-and post-four-hours incubation confirmed the presence of viable S. typhi cells and allowed clinical correlation of infection. The positive and negative samples were successfully detected in less than 6 hours with 100% sensitivity and specificity.
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Affiliation(s)
- Avinash Kaur
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ravikrishnan Elangovan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Sandeep Jha
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India
| | - Dinesh Kalyanasundaram
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India
- * E-mail: ,
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28
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Kaur H, Sehgal R, Bansal D, Sultan AA, Bhalla A, Singhi SC. Development of Visually Improved Loop Mediated Isothermal Amplification for the Diagnosis of Plasmodium vivax Malaria in a Tertiary Hospital in Chandigarh, North India. Am J Trop Med Hyg 2018; 98:1374-1381. [PMID: 29557335 DOI: 10.4269/ajtmh.17-0857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
More than 80% of the global burden of the Plasmodium vivax is contributed by mainly three countries (India, Indonesia, and Pakistan). Reports from last decades have highlighted the occurrence of severe P. vivax malaria which was earlier considered to be benign. The recent trends of increasing P. vivax-associated morbidity and mortality emphasizes the need for early and accurate diagnosis of P. vivax malaria for the timely management of patients. Microscopy is considered a gold standard but needs experienced laboratory technologists. Over the last few years, Polymerase chain reaction (PCR) is being used as a highly sensitive and specific test but it requires expensive equipment which limits its use in the field. Therefore, in the present study, utility of visually improved loop-mediated isothermal amplification (LAMP) for the detection of P. vivax was evaluated targeting 18SrRNA gene in 145 microscopically confirmed P. vivax and 20 P. vivax negative patients. Sensitivity and specificity of LAMP was assessed with respect to microscopy and multiplex nested PCR (nPCR). Results of the LAMP assay was also correlated with rapid diagnostic test, multiplex nPCR and real-time PCR results. Overall, sensitivity and specificity of P. vivax-specific LAMP compared with microscopy were found to be 100% and 85%, respectively. Furthermore, detection limit for LAMP was found to be 0.8 copies/μL and it was also able to detect three complicated cases of P. vivax which were missed by microscopy. This study showed a LAMP assay to be a rapid and very sensitive method for the early diagnosis of both complicated and uncomplicated P. vivax malaria.
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Affiliation(s)
- Hargobinder Kaur
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Devendra Bansal
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
| | - Ali A Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
| | - Ashish Bhalla
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunit C Singhi
- Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Mukhtar M, Ali SS, Boshara SA, Albertini A, Monnerat S, Bessell P, Mori Y, Kubota Y, Ndung’u JM, Cruz I. Sensitive and less invasive confirmatory diagnosis of visceral leishmaniasis in Sudan using loop-mediated isothermal amplification (LAMP). PLoS Negl Trop Dis 2018; 12:e0006264. [PMID: 29444079 PMCID: PMC5828521 DOI: 10.1371/journal.pntd.0006264] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/27/2018] [Accepted: 01/24/2018] [Indexed: 12/01/2022] Open
Abstract
Background Confirmatory diagnosis of visceral leishmaniasis (VL), as well as diagnosis of relapses and test of cure, usually requires examination by microscopy of samples collected by invasive means, such as splenic, bone marrow or lymph node aspirates. This causes discomfort to patients, with risks of bleeding and iatrogenic infections, and requires technical expertise. Molecular tests have great potential for diagnosis of VL using peripheral blood, but require well-equipped facilities and trained personnel. More user-friendly, and field-amenable options are therefore needed. One method that could meet these requirements is loop-mediated isothermal amplification (LAMP) using the Loopamp Leishmania Detection Kit, which comes as dried down reagents that can be stored at room temperature, and allows simple visualization of results. Methodology/Principal findings The Loopamp Leishmania Detection Kit (Eiken Chemical Co., Japan), was evaluated in the diagnosis of VL in Sudan. A total of 198 VL suspects were tested by microscopy of lymph node aspirates (the reference test), direct agglutination test-DAT (in house production) and rK28 antigen-based rapid diagnostic test (OnSite Leishmania rK39-Plus, CTK Biotech, USA). LAMP was performed on peripheral blood (whole blood and buffy coat) previously processed by: i) a direct boil and spin method, and ii) the QIAamp DNA Mini Kit (QIAgen). Ninety seven of the VL suspects were confirmed as cases by microscopy of lymph node aspirates. The sensitivity and specificity for each of the tests were: rK28 RDT 98.81% and 100%; DAT 88.10% and 78.22%; LAMP-boil and spin 97.65% and 99.01%; LAMP-QIAgen 100% and 99.01%. Conclusions/Significance Due to its simplicity and high sensitivity, rK28 RDT can be used first in the diagnostic algorithm for primary VL diagnosis, the excellent performance of LAMP using peripheral blood indicates that it can be also included in the algorithm for diagnosis of VL as a simple test when parasitological confirmatory diagnosis is required in settings that are lower than the reference laboratory, avoiding the need for invasive lymph node aspiration. Tissue aspiration, either from spleen, bone marrow or lymph node, remains the Gold Standard for parasitological confirmation in patients suspected of visceral leishmaniasis (VL), and is often used for detection of relapses, and as a test of cure. The procedure is invasive, with risks of severe complications, requires skilled personnel to perform, and appropriate facilities to manage severe adverse events, if they occur. These drawbacks can be solved by using sensitive diagnostic test based on peripheral blood. Nucleic acid amplification tests (NAAT) are sensitive for the detection of Leishmania parasites in blood; however, in VL-endemic settings, most NAAT are restricted to well-equipped laboratories. A robust NAAT, Loopamp Leishmania Detection Kit has recently been developed in a collaboration between FIND, Eiken Chemical Co. Ltd., Japan and other partners. We have evaluated this kit in Sudan and obtained a sensitivity of 97.6% and specificity of 99.1%, using DNA obtained from peripheral blood through a simple boil and spin method. Its simplicity and excellent diagnostic performance make this kit ideal for parasitological confirmation of VL in less equipped laboratories.
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Affiliation(s)
- Maowia Mukhtar
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Sababil S. Ali
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Salah A. Boshara
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Audrey Albertini
- Foundation for Innovative New Diagnostics—FIND, Geneva, Switzerland
| | | | - Paul Bessell
- Foundation for Innovative New Diagnostics—FIND, Geneva, Switzerland
| | | | | | | | - Israel Cruz
- Foundation for Innovative New Diagnostics—FIND, Geneva, Switzerland
- * E-mail:
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Lucchi NW, Ndiaye D, Britton S, Udhayakumar V. Expanding the malaria molecular diagnostic options: opportunities and challenges for loop-mediated isothermal amplification tests for malaria control and elimination. Expert Rev Mol Diagn 2018; 18:195-203. [DOI: 10.1080/14737159.2018.1431529] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naomi W. Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Sumudu Britton
- Department of Clinical Tropical Medicine, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Salamin O, Kuuranne T, Saugy M, Leuenberger N. Loop-mediated isothermal amplification (LAMP) as an alternative to PCR: A rapid on-site detection of gene doping. Drug Test Anal 2017; 9:1731-1737. [PMID: 29045058 DOI: 10.1002/dta.2324] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/21/2017] [Accepted: 10/04/2017] [Indexed: 12/21/2022]
Abstract
Innovation in medical research has been diverted at multiple occasions to enhance human performance. The predicted great progress in gene therapy has raised some concerns regarding its misuse in the world of sports (gene doping) for several years now. Even though there is no evidence that gene doping has ever been used in sports, the continuous improvement of gene therapy techniques increases the likelihood of abuse. Therefore, since 2004, efforts have been invested by the anti-doping community and WADA for the development of detection methods. Several nested PCR and qPCR-based strategies exploiting the absence of introns in the transgenic DNA have been proposed for the long-term detection of transgene in blood. Despite their great sensitivity, those protocols are hampered by limitations of the techniques that can be cumbersome and costly. The purpose of this perspective is to describe a new approach based on loop-mediated isothermal amplification (LAMP) for the detection of gene doping. This protocol enables a rapid and simple method to amplify nucleic acids with a high sensitivity and specificity and with a simple visual detection of the results. LAMP is already being used in clinical application for the detection of viruses or mutations. Therefore, this technique has the potential to be further developed for the detection of foreign genetic material in elite athletes. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Olivier Salamin
- Center of Research and Expertise in anti-Doping sciences - REDs, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tiia Kuuranne
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine, Lausanne and Geneva, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Ch. des Croisettes 22, 1066 Epalinges, Switzerland
| | - Martial Saugy
- Center of Research and Expertise in anti-Doping sciences - REDs, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Leuenberger
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine, Lausanne and Geneva, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Ch. des Croisettes 22, 1066 Epalinges, Switzerland
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Rahman SMM, Song HB, Jin Y, Oh JK, Lim MK, Hong ST, Choi MH. Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples. PLoS Negl Trop Dis 2017; 11:e0005995. [PMID: 28991924 PMCID: PMC5648269 DOI: 10.1371/journal.pntd.0005995] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/19/2017] [Accepted: 09/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Clonorchiasis is prevalent in the Far East, and a major health problem in endemic areas. Infected persons may experience, if not treated, serious complications such as bile stone formation, pyogenic cholangitis, and even cholangiocarcinoma. Early diagnosis and treatment are important to prevent serious complications and, therefore, the simple and reliable diagnostic method is necessary to control clonorchiasis in endemic areas, where resources for the diagnosis are limited. METHODOLOGY/PRINCIPLE FINDINGS The loop-mediated isothermal amplification (LAMP) assay has been applied for the detection of Clonorchis sinensis DNA. Six primers targeting eight locations on the cytochrome c oxidase subunit 1 gene of C. sinensis were designed for species-specific amplification using the LAMP assay. The LAMP assay was sensitive enough to detect as little as 100 fg of C. sinensis genomic DNA and the detection limit in 100 mg of stool was as low as one egg. The assay was highly specific because no cross-reactivity was observed with the DNA of other helminths, protozoa or Escherichia coli. Then, LAMP assay was applied to human fecal samples collected from an endemic area of clonorchiasis in Korea. Using samples showing consistent results by both Kato-Katz method and real-time PCR as reference standards, the LAMP assay showed 97.1% (95% CI, 90.1-99.2) of sensitivity and 100% (95% CI, 92.9-100) of specificity. In stool samples with more than 100 eggs per gram of feces, the sensitivity achieved 100%. CONCLUSIONS To detect C. sinensis in human fecal samples, the LAMP assay was applied and achieved high sensitivity and specificity. The LAMP assay can be utilized in field laboratories as a powerful tool for diagnosis and epidemiological survey of clonorchiasis.
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Affiliation(s)
- S. M. Mazidur Rahman
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Korea
| | - Hyun Beom Song
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Korea
| | - Yan Jin
- Department of Microbiology, Dongguk University School of Medicine, Gyeongju, Korea
| | - Jin-Kyoung Oh
- National Cancer Center, Graduate School of Cancer Science and Policy, Goyang, Gyonggi, Korea
| | - Min Kyung Lim
- National Cancer Center, Graduate School of Cancer Science and Policy, Goyang, Gyonggi, Korea
| | - Sung-Tae Hong
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Korea
| | - Min-Ho Choi
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Korea
- * E-mail:
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Loop-mediated isothermal DNA amplification for asymptomatic malaria detection in challenging field settings: Technical performance and pilot implementation in the Peruvian Amazon. PLoS One 2017; 12:e0185742. [PMID: 28982155 PMCID: PMC5628891 DOI: 10.1371/journal.pone.0185742] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/27/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Loop-mediated isothermal DNA amplification (LAMP) methodology offers an opportunity for point-of-care (POC) molecular detection of asymptomatic malaria infections. However, there is still little evidence on the feasibility of implementing this technique for population screenings in isolated field settings. METHODS Overall, we recruited 1167 individuals from terrestrial ('road') and hydric ('riverine') communities of the Peruvian Amazon for a cross-sectional survey to detect asymptomatic malaria infections. The technical performance of LAMP was evaluated in a subgroup of 503 samples, using real-time Polymerase Chain Reaction (qPCR) as reference standard. The operational feasibility of introducing LAMP testing in the mobile screening campaigns was assessed based on field-suitability parameters, along with a pilot POC-LAMP assay in a riverine community without laboratory infrastructure. RESULTS LAMP had a sensitivity of 91.8% (87.7-94.9) and specificity of 91.9% (87.8-95.0), and the overall accuracy was significantly better among samples collected during road screenings than riverine communities (p≤0.004). LAMP-based diagnostic strategy was successfully implemented within the field-team logistics and the POC-LAMP pilot in the riverine community allowed for a reduction in the turnaround time for case management, from 12-24 hours to less than 5 hours. Specimens with haemolytic appearance were regularly observed in riverine screenings and could help explaining the hindered performance/interpretation of the LAMP reaction in these communities. CONCLUSIONS LAMP-based molecular malaria diagnosis can be deployed outside of reference laboratories, providing similar performance as qPCR. However, scale-up in remote field settings such as riverine communities needs to consider a number of logistical challenges (e.g. environmental conditions, labour-intensiveness in large population screenings) that can influence its optimal implementation.
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Detection of Plasmodium Infection by the illumigene Malaria Assay Compared to Reference Microscopy and Real-Time PCR. J Clin Microbiol 2017; 55:3037-3045. [PMID: 28768730 DOI: 10.1128/jcm.00806-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/27/2017] [Indexed: 01/06/2023] Open
Abstract
Malaria is one of the leading causes of infectious disease in travelers returning from the tropics. The diagnosis of malaria is typically performed by examining Giemsa-stained thick and thin peripheral blood smears, which is time consuming, labor intensive, and requires high levels of proficiency. Alternatively, loop-mediated isothermal amplification (LAMP) is a new molecular method, which is rapid, sensitive, and requires less capital equipment and technological training. We conducted a retrospective study comparing two formats of a commercial LAMP assay (Meridian illumigene malaria [M] and malaria Plus [MP]) versus reference microscopy on archived blood specimens (n = 140) obtained from unique returning travelers suspected of having malaria. Discrepant results were resolved by either repeat testing or a laboratory developed ultrasensitive real-time PCR method. On initial testing, the Meridian illumigene M and MP kits had sensitivities of 97.3% (95% confidence interval [CI], 90.7 to 99.7%) and 100.0% (95.1 to 100.0%) and specificities of 93.8% (84.8 to 98.3%) and 91.5% (81.3 to 97.2%), respectively, versus reference microscopy. We project a significant cost reduction in low prevalence settings where malaria is not endemic with LAMP-based malaria screening given the excellent negative predictive value achieved with LAMP.
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Thu AM, Phyo AP, Landier J, Parker DM, Nosten FH. Combating multidrug-resistant Plasmodium falciparum malaria. FEBS J 2017; 284:2569-2578. [PMID: 28580606 PMCID: PMC5575457 DOI: 10.1111/febs.14127] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/09/2017] [Accepted: 06/01/2017] [Indexed: 01/05/2023]
Abstract
Over the past 50 years, Plasmodium falciparum has developed resistance against all antimalarial drugs used against it: chloroquine, sulphadoxine-pyrimethamine, quinine, piperaquine and mefloquine. More recently, resistance to the artemisinin derivatives and the resulting failure of artemisinin-based combination therapy (ACT) are threatening all major gains made in malaria control. Each time resistance has developed progressively, with delayed clearance of parasites first emerging only in a few regions, increasing in prevalence and geographic range, and then ultimately resulting in the complete failure of that antimalarial. Drawing from this repeated historical chain of events, this article presents context-specific approaches for combating drug-resistant P. falciparum malaria. The approaches begin with a context of drug-sensitive parasites and focus on the prevention of the emergence of drug resistance. Next, the approaches address a scenario in which resistance has emerged and is increasing in prevalence and geographic extent, with interventions focused on disrupting transmission through vector control, early diagnosis and treatment, and the use of new combination therapies. Elimination is also presented as an approach for addressing the imminent failure of all available antimalarials. The final drug resistance context presented is one in which all available antimalarials have failed; leaving only personal protection and the use of new antimalarials (or new combinations of antimalarials) as a viable strategy for dealing with complete resistance. All effective strategies and contexts require a multipronged, holistic approach.
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Affiliation(s)
- Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
| | - Jordi Landier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Daniel M Parker
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
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Aydin-Schmidt B, Morris U, Ding XC, Jovel I, Msellem MI, Bergman D, Islam A, Ali AS, Polley S, Gonzalez IJ, Mårtensson A, Björkman A. Field Evaluation of a High Throughput Loop Mediated Isothermal Amplification Test for the Detection of Asymptomatic Plasmodium Infections in Zanzibar. PLoS One 2017; 12:e0169037. [PMID: 28095434 PMCID: PMC5240913 DOI: 10.1371/journal.pone.0169037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/10/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND New field applicable diagnostic tools are needed for highly sensitive detection of residual malaria infections in pre-elimination settings. Field performance of a high throughput DNA extraction system for loop mediated isothermal amplification (HTP-LAMP) was therefore evaluated for detecting malaria parasites among asymptomatic individuals in Zanzibar. METHODS HTP-LAMP performance was evaluated against real-time PCR on 3008 paired blood samples collected on filter papers in a community-based survey in 2015. RESULTS The PCR and HTP-LAMP determined malaria prevalences were 1.6% (95%CI 1.3-2.4) and 0.7% (95%CI 0.4-1.1), respectively. The sensitivity of HTP-LAMP compared to PCR was 40.8% (CI95% 27.0-55.8) and the specificity was 99.9% (CI95% 99.8-100). For the PCR positive samples, there was no statistically significant difference between the geometric mean parasite densities among the HTP-LAMP positive (2.5 p/μL, range 0.2-770) and HTP-LAMP negative (1.4 p/μL, range 0.1-7) samples (p = 0.088). Two lab technicians analysed up to 282 samples per day and the HTP-LAMP method was experienced as user friendly. CONCLUSIONS Although field applicable, this high throughput format of LAMP as used here was not sensitive enough to be recommended for detection of asymptomatic low-density infections in areas like Zanzibar, approaching malaria elimination.
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Affiliation(s)
- Berit Aydin-Schmidt
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Unit of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrika Morris
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xavier C Ding
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Irina Jovel
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mwinyi I Msellem
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, Tanzania
| | - Daniel Bergman
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Atiqul Islam
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Abdullah S Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, Tanzania
| | - Spencer Polley
- Department of Clinical Parasitology, Hospital for Tropical Diseases, University College London Hospitals, NHS Foundation Trust, London, United Kingdom
| | - Iveth J Gonzalez
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Anders Björkman
- Centre for Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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