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Vealan K, Joseph N, Alimat S, Karumbati AS, Thilakavathy K. Lateral flow assay: a promising rapid point-of-care testing tool for infections and non-communicable diseases. ASIAN BIOMED 2023; 17:250-266. [PMID: 38161347 PMCID: PMC10754503 DOI: 10.2478/abm-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The point-of-care testing (POCT) approach has established itself as having remarkable importance in diagnosing various infectious and non-communicable diseases (NCDs). The POCT approach has succeeded in meeting the current demand for having diagnostic strategies that can provide fast, sensitive, and highly accurate test results without involving complicated procedures. This has been accomplished by introducing rapid bioanalytical tools or biosensors such as lateral flow assays (LFAs). The production cost of these tools is very low, allowing developing countries with limited resources to utilize them or produce them on their own. Thus, their use has grown in various fields in recent years. More importantly, LFAs have created the possibility for a new era of incorporating nanotechnology in disease diagnosis and have already attained significant commercial success worldwide, making POCT an essential approach not just for now but also for the future. In this review, we have provided an overview of POCT and its evolution into the most promising rapid diagnostic approach. We also elaborate on LFAs with a special focus on nucleic acid LFAs.
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Affiliation(s)
- Kumaravel Vealan
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang43400, Malaysia
| | - Narcisse Joseph
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang43400, Malaysia
| | - Sharizah Alimat
- Department of Chemistry Malaysia, Ministry of Science, Technology and Innovation, Petaling Jaya46661, Selangor, Malaysia
| | - Anandi S. Karumbati
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore560065, India
| | - Karuppiah Thilakavathy
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang43400, Malaysia
- Malaysian Research Institute on Ageing (MyAgeing), Universiti Putra Malaysia, UPM Serdang43400, Selangor, Malaysia
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Recent advances on the piezoelectric, electrochemical, and optical biosensors for the detection of protozoan pathogens. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Sima N, Dujeancourt-Henry A, Perlaza BL, Ungeheuer MN, Rotureau B, Glover L. SHERLOCK4HAT: A CRISPR-based tool kit for diagnosis of Human African Trypanosomiasis. EBioMedicine 2022; 85:104308. [PMCID: PMC9626900 DOI: 10.1016/j.ebiom.2022.104308] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Background To achieve elimination of Human African Trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense (gHAT), the development of highly sensitive diagnostics is needed. We have developed a CRISPR based diagnostic for HAT using SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) that is readily adaptable to a field-based setting. Methods We adapted SHERLOCK for the detection of T. brucei species. We targeted 7SLRNA, TgSGP and SRA genes and tested SHERLOCK against RNA from blood, buffy coat, dried blood spots (DBS), and clinical samples. Findings The pan-Trypanozoon 7SLRNA and T. b. gambiense-specific TgSGP SHERLOCK assays had a sensitivity of 0.1 parasite/μL and a limit of detection 100 molecules/μL. T. b. rhodesiense-specific SRA had a sensitivity of 0.1 parasite/μL and a limit of detection of 10 molecules/μL. TgSGP SHERLOCK and SRA SHERLOCK detected 100% of the field isolated strains. Using clinical specimens from the WHO HAT cryobank, the 7SLRNA SHERLOCK detected trypanosomes in gHAT samples with 56.1%, 95% CI [46.25–65.53] sensitivity and 98.4%, 95% CI [91.41–99.92] specificity, and rHAT samples with 100%, 95% CI [83.18–100] sensitivity and 94.1%, 95% CI [80.91–98.95] specificity. The species-specific TgSGP and SRA SHERLOCK discriminated between the gambiense/rhodesiense HAT infections with 100% accuracy. Interpretation The 7SLRNA, TgSGP and SRA SHERLOCK discriminate between gHAT and rHAT infections, and could be used for epidemiological surveillance and diagnosis of HAT in the field after further technical development. Funding Institut Pasteur (PTR-175 SHERLOCK4HAT), French Government's Investissement d’Avenir program Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (LabEx IBEID), and Agence Nationale pour la Recherche (ANR-PRC 2021 SherPa).
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Affiliation(s)
- Núria Sima
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, Université Paris Cité, F-75015, Paris, France,Trypanosome Transmission Group, Trypanosome Cell Biology Unit, INSERM U1201 & Department of Parasites and Insect Vectors, Institut Pasteur, Université Paris Sorbonne, Paris, France
| | - Annick Dujeancourt-Henry
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, Université Paris Cité, F-75015, Paris, France
| | - Blanca Liliana Perlaza
- Institut Pasteur, ICAReB Platform (Clinical Investigation & Access to Research Bioresources) of the Center for Translational Science, Paris, France
| | - Marie-Noelle Ungeheuer
- Institut Pasteur, ICAReB Platform (Clinical Investigation & Access to Research Bioresources) of the Center for Translational Science, Paris, France
| | - Brice Rotureau
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, INSERM U1201 & Department of Parasites and Insect Vectors, Institut Pasteur, Université Paris Sorbonne, Paris, France,Parasitology Unit, Institut Pasteur of Guinea, Conakry, Guinea,Corresponding author.
| | - Lucy Glover
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, Université Paris Cité, F-75015, Paris, France,Corresponding author.
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Yalley AK, Ahiatrogah S, Kafintu-Kwashie AA, Amegatcher G, Prah D, Botwe AK, Adusei-Poku MA, Obodai E, Nii-Trebi NI. A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings. Curr Issues Mol Biol 2022; 44:4367-4385. [PMID: 36286015 PMCID: PMC9601131 DOI: 10.3390/cimb44100300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.
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Affiliation(s)
- Akua K. Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Selasie Ahiatrogah
- Department of Obstetrics and Gynaecology, College of Medicine, Pan African University of Life and Earth Sciences Institute, University of Ibadan, Ibadan P.O. Box 22133, Nigeria
| | - Anna A. Kafintu-Kwashie
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Gloria Amegatcher
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Diana Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Akua K. Botwe
- Molecular Biology Unit, Kintampo Health Research Centre, Ghana Health Service, Kintampo P.O. Box 200, Ghana
| | - Mildred A. Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
- Correspondence: ; Tel.: +233-54-827-6424
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Sereno D, Oury B, Geiger A, Vela A, Karmaoui A, Desquesnes M. Isothermal Nucleic Acid Amplification to Detect Infection Caused by Parasites of the Trypanosomatidae Family: A Literature Review and Opinion on the Laboratory to Field Applicability. Int J Mol Sci 2022; 23:7543. [PMID: 35886895 PMCID: PMC9322063 DOI: 10.3390/ijms23147543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
Isothermal amplification of nucleic acids has the potential to be applied in resource-limited areas for the detection of infectious agents, as it does not require complex nucleic purification steps or specific and expensive equipment and reagents to perform the reaction and read the result. Since human and animal infections by pathogens of the Tryponasomatidae family occur mainly in resource-limited areas with scant health infrastructures and personnel, detecting infections by these methodologies would hold great promise. Here, we conduct a narrative review of the literature on the application of isothermal nucleic acid amplification for Trypanosoma and Leishmania infections, which are a scourge for human health and food security. We highlight gaps and propose ways to improve them to translate these powerful technologies into real-world field applications for neglected human and animal diseases caused by Trypanosomatidae.
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Affiliation(s)
- Denis Sereno
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France
| | - Bruno Oury
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France
| | - Anne Geiger
- Centre International de Recherche en Agronomie pour le Développement, Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, 34032 Montpellier, France
| | - Andrea Vela
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de las Américas-Quito, Calle de los Colimes y Avenida De los Granados, Quito 170513, Ecuador
| | - Ahmed Karmaoui
- Bioactives (Health and Environmental, Epigenetics Team), Faculty of Sciences and Techniques, Errachidia (UMI), Moroccan Center for Culture and Sciences, University Moulay Ismail, Meknes 50000, Morocco
| | - Marc Desquesnes
- CIRAD, UMR INTERTRYP, 31076 Toulouse, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34032 Montpellier, France
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Nancy K, Lillian W, Wilkinson M, Claire M, Luna K, Dorcas W, Rosemary G, Japheth L, Christine I, Emily W, Jim K. Optimization of a Loop-Mediated Isothermal Amplification Assay as a Point-of-Care Tool for the Detection of Wuchereria bancrofti in Human Blood in Tana River Delta, Kenya. J Parasitol Res 2021; 2021:6650870. [PMID: 34367688 PMCID: PMC8337116 DOI: 10.1155/2021/6650870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Accurate detection of filarial parasites in humans and vectors is essential for the implementation and evaluation of Global and National Programs to eliminate lymphatic filariasis. Immunological methods to detect infection are available; however, cross-reactivity issues have been reported in most of them. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity and can be used to detect the infections. METHODS In this study, we evaluated loop-mediated isothermal amplification (LAMP) tests to amplify Wuchereria bancrofti DNA in patients' blood. The amplicons were tested by both pH-sensitive dyes for enhanced visual detection and agarose gel electrophoresis. A closed-tube LAMP assay was also evaluated. Cohen's Kappa statistics was used for statistical analysis of the assays. 125 patients consented for blood sampling which were used for clinical analysis of LAMP assays with the PCR method used as the "gold standard." RESULTS The sensitivity of the evaluated Wuchereria bancrofti LAMP was 92.3%, with a specificity of 97.3% and kappa statistics value of 0.84, which is in a strong agreement. CONCLUSION In this study, LAMP assays coupled with fluorescence dye detection have been found to be suitable for diagnosis and monitoring of Wuchereria bancrofti infections in the Kenyan population.
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Affiliation(s)
- Kinyatta Nancy
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Wambua Lillian
- School of Biological Science, University of Nairobi, 30772-00100, Nairobi, Kenya
| | - Mutahi Wilkinson
- School of Biological Science, University of Nairobi, 30772-00100, Nairobi, Kenya
| | - Mugasa Claire
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University Kampala, 7062 Kampala, Uganda
| | - Kamau Luna
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Wachira Dorcas
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Githae Rosemary
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Lusweti Japheth
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Ichugu Christine
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Waigi Emily
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
| | - Kagai Jim
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, P.O. Box 54840-00200, Nairobi, Kenya
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Nucleic Acid-Based Lateral Flow Biosensor for Salmonella Typhi and Salmonella Paratyphi: A Detection in Stool Samples of Suspected Carriers. Diagnostics (Basel) 2021; 11:diagnostics11040700. [PMID: 33919817 PMCID: PMC8070779 DOI: 10.3390/diagnostics11040700] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
A multiplex rapid detection system, based on a PCR-lateral flow biosensor (mPCR-LFB) was developed to identify Salmonella Typhi and Salmonella Paratyphi A from suspected carriers. The lower detection limit for S. Typhi and S. Paratyphi A was 0.16 and 0.08 ng DNA equivalent to 10 and 102 CFU/mL, respectively. Lateral flow biosensor was used for visual detection of mPCR amplicons (stgA, SPAint, ompC, internal amplification control) by labeling forward primers with fluorescein-isothiocyanate (FITC), Texas Red, dinitrophenol (DNP) and digoxigenin (DIG) and reverse primers with biotin. Binding of streptavidin-colloidal gold conjugate with the amplicons resulted in formation of a red color dots on the strip after 15-20 min of sample exposure. The nucleic acid lateral flow analysis of the mPCR-LFB was better in sensitivity and more rapid than the conventional agarose gel electrophoresis. Moreover, the mPCR-LFB showed 100% sensitivity and specificity when evaluated with stools spiked with 100 isolates of Salmonella genus and other bacteria. A prospective cohort study on stool samples of 1176 food handlers in outbreak areas (suspected carriers) resulted in 23 (2%) positive for S. Typhi. The developed assay has potential to be used for rapid detection of typhoid carriers in surveillance program.
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Sereno D, Akhoundi M, Sayehmri K, Mirzaei A, Holzmuller P, Lejon V, Waleckx E. Noninvasive Biological Samples to Detect and Diagnose Infections due to Trypanosomatidae Parasites: A Systematic Review and Meta-Analysis. Int J Mol Sci 2020; 21:E1684. [PMID: 32121441 PMCID: PMC7084391 DOI: 10.3390/ijms21051684] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Unicellular eukaryotes of the Trypanosomatidae family include human and animal pathogens that belong to the Trypanosoma and Leishmania genera. Diagnosis of the diseases they cause requires the sampling of body fluids (e.g., blood, lymph, peritoneal fluid, cerebrospinal fluid) or organ biopsies (e.g., bone marrow, spleen), which are mostly obtained through invasive methods. Body fluids or appendages can be alternatives to these invasive biopsies but appropriateness remains poorly studied. To further address this question, we perform a systematic review on clues evidencing the presence of parasites, genetic material, antibodies, and antigens in body secretions, appendages, or the organs or proximal tissues that produce these materials. Paper selection was based on searches in PubMed, Web of Science, WorldWideScience, SciELO, Embase, and Google. The information of each selected article (n = 333) was classified into different sections and data were extracted from 77 papers. The presence of Trypanosomatidae parasites has been tracked in most of organs or proximal tissues that produce body secretions or appendages, in naturally or experimentally infected hosts. The meta-analysis highlights the paucity of studies on human African trypanosomiasis and an absence on animal trypanosomiasis. Among the collected data high heterogeneity in terms of the I2 statistic (100%) is recorded. A high positivity is recorded for antibody and genetic material detection in urine of patients and dogs suffering leishmaniasis, and of antigens for leishmaniasis and Chagas disease. Data on conjunctival swabs can be analyzed with molecular methods solely for dogs suffering canine visceral leishmaniasis. Saliva and hair/bristles showed a pretty good positivity that support their potential to be used for leishmaniasis diagnosis. In conclusion, our study pinpoints significant gaps that need to be filled in order to properly address the interest of body secretion and hair or bristles for the diagnosis of infections caused by Leishmania and by other Trypanosomatidae parasites.
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Affiliation(s)
- Denis Sereno
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR MIVEGEC IRD, CNRS, 34032 Montpellier, France
| | - Mohammad Akhoundi
- Parasitology-Mycology Department, Avicenne Hospital, AP-HP, 93000 Bobigny, France;
| | - Kourosh Sayehmri
- Psychosocial Injuries Research Center, Department of Biostatistics, Ilam University of Medical Sciences, Ilam 6931851147, Iran;
| | - Asad Mirzaei
- Parasitology Department, Paramedical School, Ilam University of Medical Sciences, Ilam 6931851147, Iran;
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam 6931851147, Iran
| | - Philippe Holzmuller
- CIRAD, UMR ASTRE “Animal, Santé, Territoires, Risques et Ecosystèmes”, F-34398 Montpellier, France;
- ASTRE, CIRAD, INRAE, Université de Montpellier (I-MUSE), 34000 Montpellier, France
| | - Veerle Lejon
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
| | - Etienne Waleckx
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
- Centro de Investigaciones Regionales «Dr Hideyo Noguchi», Universidad autònoma de yucatán, Merida, Yucatán 97000, Mexico
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Newbigging AM, Zhang H, Le XC. Beacon-mediated exponential amplification reaction (BEAR) using a single enzyme and primer. Chem Commun (Camb) 2019; 55:10677-10680. [PMID: 31424057 DOI: 10.1039/c9cc04226a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Beacon-mediated Exponential Amplification Reaction (BEAR) enables isothermal, exponential signal amplification. BEAR uses only a single enzyme and a single primer. Detection of 0.2 amol of a mitochondrial DNA with a point mutation in less than an hour demonstrates an application of the BEAR technique for nucleic acid research.
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Affiliation(s)
- Ashley M Newbigging
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
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Maharana BR, Tewari AK, Saravanan BC, Sudhakar NR. Important hemoprotozoan diseases of livestock: Challenges in current diagnostics and therapeutics: An update. Vet World 2016; 9:487-95. [PMID: 27284225 PMCID: PMC4893720 DOI: 10.14202/vetworld.2016.487-495] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/06/2016] [Indexed: 11/25/2022] Open
Abstract
Hemoprotozoan parasites pose a serious threat to the livestock population in terms of mortality, reduced milk yield and lowered draft power. Diagnosis of these diseases often poses a challenging task. Needless to say that impact of disease in health and productivity is huge though a fair economic assessment on the quantum of economic loss associated is yet to be worked out from India. The diagnosis of hemoprotozoan infections largely depends on various laboratory-based diagnostic methods as the clinical manifestations are often inconspicuous and non-specific. Traditional diagnostic methods rely on microscopical demonstration of infective stages in blood or tissue fluids. However, it is laborious, lesser sensitive, and cannot differentiate between morphologically similar organisms. Recent development in the technologies has opened new avenues for improvement in the accurate diagnosis of parasitic infections. Serological tests are simple, fast but lack specificity. With advent of molecular techniques, as DNA hybridization assays, polymerase chain reaction and its modifications ensure the detection of infection in the latent phase of the disease. Nucleic acid-based assays are highly sensitive, free from immunocompetence and can differentiate between morphologically similar parasites. With the advent of newer diagnostics complemented with traditional ones will be of huge help for targeted selective treatment with better chemotherapeutic agents.
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Affiliation(s)
- Biswa Ranjan Maharana
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Anup Kumar Tewari
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
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Kato CD, Matovu E, Mugasa CM, Nanteza A, Alibu VP. The role of cytokines in the pathogenesis and staging of Trypanosoma brucei rhodesiense sleeping sickness. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2016; 12:4. [PMID: 26807135 PMCID: PMC4722787 DOI: 10.1186/s13223-016-0113-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/06/2016] [Indexed: 12/12/2022]
Abstract
Human African trypanosomiasis due to Trypanosoma brucei rhodesiense is invariably fatal if untreated with up to 12.3 million people at a risk of developing the disease in Sub-Saharan Africa. The disease is characterized by a wide spectrum of clinical presentation coupled with differences in disease progression and severity. While the factors determining this varied response have not been clearly characterized, inflammatory cytokines have been partially implicated as key players. In this review, we consolidate available literature on the role of specific cytokines in the pathogenesis of T. b. rhodesiense sleeping sickness and further discuss their potential as stage biomarkers. Such information would guide upcoming research on the immunology of sleeping sickness and further assist in the selection and evaluation of cytokines as disease stage or diagnostic biomarkers.
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Affiliation(s)
- Charles D. Kato
- />School of Bio-security, Biotechnical & Laboratory Sciences, College of Veterinary Medicine, Animal Resources & Bio-security, Makerere University, P.O BOX 7062, Kampala, Uganda
| | - Enock Matovu
- />School of Bio-security, Biotechnical & Laboratory Sciences, College of Veterinary Medicine, Animal Resources & Bio-security, Makerere University, P.O BOX 7062, Kampala, Uganda
| | - Claire. M. Mugasa
- />School of Bio-security, Biotechnical & Laboratory Sciences, College of Veterinary Medicine, Animal Resources & Bio-security, Makerere University, P.O BOX 7062, Kampala, Uganda
| | - Ann Nanteza
- />School of Bio-security, Biotechnical & Laboratory Sciences, College of Veterinary Medicine, Animal Resources & Bio-security, Makerere University, P.O BOX 7062, Kampala, Uganda
| | - Vincent P. Alibu
- />College of Natural Sciences, Makerere University, P.O. BOX 7062, Kampala, Uganda
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13
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Di Minno G, Perno CF, Tiede A, Navarro D, Canaro M, Güertler L, Ironside JW. Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders. Blood Rev 2016; 30:35-48. [PMID: 26381318 PMCID: PMC7115716 DOI: 10.1016/j.blre.2015.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/11/2015] [Accepted: 07/13/2015] [Indexed: 02/06/2023]
Abstract
The pathogen safety of blood/plasma-derived products has historically been a subject of significant concern to the medical community. Measures such as donor selection and blood screening have contributed to increase the safety of these products, but pathogen transmission does still occur. Reasons for this include lack of sensitivity/specificity of current screening methods, lack of reliable screening tests for some pathogens (e.g. prions) and the fact that many potentially harmful infectious agents are not routinely screened for. Methods for the purification/inactivation of blood/plasma-derived products have been developed in order to further reduce the residual risk, but low concentrations of pathogens do not necessarily imply a low level of risk for the patient and so the overall challenge of minimising risk remains. This review aims to discuss the variable level of pathogenic risk and describes the current screening methods used to prevent/detect the presence of pathogens in blood/plasma-derived products.
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Affiliation(s)
- Giovanni Di Minno
- Dipartimento di Medicina Clinica e Chirurgia, Regional Reference Centre for Coagulation Disorders, Federico II University, Via S. Pansini 5, 80131 Naples, Italy.
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Andreas Tiede
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | - David Navarro
- Department of Microbiology, Microbiology Service, Hospital Clínico Universitario, School of Medicine, University of Valencia, Av Blasco Ibáñez 17, 46010 Valencia, Spain
| | - Mariana Canaro
- Department of Hemostasis and Thrombosis, Son Espases University Hospital, Carretera de Valdemossa, 79, 07120 Palma de Mallorca, Spain
| | - Lutz Güertler
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, University of München, Pettenkofer Str 9A, 80336 Munich, Germany
| | - James W Ironside
- National Creutzfeldt-Jakob Disease Research and Surveillance Unit, School of Clinical Sciences, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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Ang GY, Yu CY, Chan KG, Singh KKB, Chan Yean Y. Development of a dry-reagent-based nucleic acid-sensing platform by coupling thermostabilised LATE-PCR assay to an oligonucleotide-modified lateral flow biosensor. J Microbiol Methods 2015; 118:99-105. [PMID: 26342435 DOI: 10.1016/j.mimet.2015.08.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 01/27/2023]
Abstract
In this study, we report for the first time the development of a dry-reagent-based nucleic acid-sensing platform by combining a thermostabilised linear-after-the-exponential (LATE)-PCR assay with a one-step, hybridisation-based nucleic acid lateral flow biosensor. The nucleic acid-sensing platform was designed to overcome the need for stringent temperature control during transportation or storage of reagents and reduces the dependency on skilled personnel by decreasing the overall assay complexity and hands-on time. The platform was developed using toxigenic Vibrio cholerae as the model organism due to the bacterium's propensity to cause epidemic and pandemic cholera. The biosensor generates result which can be visualised with the naked eyes and the limit of detection was found to be 1pg of pure genomic DNA and 10CFU/ml of toxigenic V. cholerae. The dry-reagent-based nucleic acid-sensing platform was challenged with 95 toxigenic V. cholerae, 7 non-toxigenic V. cholerae and 66 other bacterial strains in spiked stool sample and complete agreement was observed when the results were compared to that of monosialoganglioside (GM1)-ELISA. Heat-stability of the thermostabilised LATE-PCR reaction mixes at different storage temperatures (4-56°C) was investigated for up to 90days. The dry-reagent-based genosensing platform with ready-to-use assay components provides an alternative method for sequence-specific detection of nucleic acid without any cold chain restriction that is associated with conventional molecular amplification techniques.
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Affiliation(s)
- Geik Yong Ang
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Choo Yee Yu
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Kok Gan Chan
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kirnpal Kaur Banga Singh
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Yean Chan Yean
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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Büscher P, Deborggraeve S. How can molecular diagnostics contribute to the elimination of human African trypanosomiasis? Expert Rev Mol Diagn 2015; 15:607-15. [DOI: 10.1586/14737159.2015.1027195] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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African Sleeping Sickness. Sleep Med 2015. [DOI: 10.1007/978-1-4939-2089-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Pritt BS. Molecular Diagnostics in the Diagnosis of Parasitic Infection. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Shiraishi T, Deborggraeve S, Büscher P, Nielsen PE. Sensitive detection of nucleic acids by PNA hybridization directed co-localization of fluorescent beads. ARTIFICIAL DNA, PNA & XNA 2014; 2:60-66. [PMID: 21912728 DOI: 10.4161/adna.2.2.16562] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 06/20/2011] [Indexed: 11/19/2022]
Abstract
We have designed a pair of biotinylated peptide nucleic acid (PNA) probes targeting two sequences in 18S rRNA (from the parasite Trypanosoma brucei) at a distance of 191 nt (corresponding to maximum distance of ca. 60 nm) from each other. The PNA probes were individually bound to (strept)avidin-coated fluorescent beads, differing in size and color [green beads (1 µm) and red beads (5.9 µm)], thereby allowing distinct detection of each PNA probe by conventional fluorescence microscopy. These two PNA beads showed easily detectable co-localization when simultaneously hybridizing to a target nucleic acid. The assay detected the parasite 18S rRNA down to 1.6 fmol while there was no such co-localization visible with human 18S rRNA not containing the PNA targets. Furthermore, the assay showed positive detection with 1.6 ng of total RNA (corresponding to RNA from ca. 300 parasites). Upon further optimization this method may provide a new tool for a diagnosis of Human African Trypanosomiasis (HAT) and it may more generally have applications within diagnostics for (neglected) infectious diseases.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen N, Denmark
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20
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Oriero EC, Jacobs J, Van Geertruyden JP, Nwakanma D, D'Alessandro U. Molecular-based isothermal tests for field diagnosis of malaria and their potential contribution to malaria elimination. J Antimicrob Chemother 2014; 70:2-13. [PMID: 25223973 PMCID: PMC7109677 DOI: 10.1093/jac/dku343] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In countries where malaria transmission has decreased substantially, thanks to the scale-up of control interventions, malaria elimination may be feasible. Nevertheless, this goal requires new strategies such as the active detection and treatment of infected individuals. As the detection threshold for the currently used diagnostic methods is 100 parasites/μL, most low-density, asymptomatic infections able to maintain transmission cannot be detected. Identifying them by molecular methods such as PCR is a possible option but the field deployment of these tests is problematic. Isothermal amplification of nucleic acids (at a constant temperature) offers the opportunity of addressing some of the challenges related to the field deployment of molecular diagnostic methods. One of the novel isothermal amplification methods for which a substantial amount of work has been done is the loop-mediated isothermal amplification (LAMP) assay. The present review describes LAMP and several other isothermal nucleic acid amplification methods, such as thermophilic helicase-dependent amplification, strand displacement amplification, recombinase polymerase amplification and nucleic acid sequence-based amplification, and explores their potential use as high-throughput, field-based molecular tests for malaria diagnosis.
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Affiliation(s)
- Eniyou C Oriero
- Medical Research Council, Banjul, The Gambia Institute of Tropical Medicine, Antwerp, Belgium International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Umberto D'Alessandro
- Medical Research Council, Banjul, The Gambia Institute of Tropical Medicine, Antwerp, Belgium
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Dhama K, Karthik K, Chakraborty S, Tiwari R, Kapoor S, Kumar A, Thomas P. Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review. Pak J Biol Sci 2014; 17:151-66. [PMID: 24783797 DOI: 10.3923/pjbs.2014.151.166] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Diagnosis is an important part in case of animal husbandry as treatment of a disease depends on it. Advancement in molecular biology has generated various sophisticated tools like Polymerase Chain Reaction (PCR), its versions along with pen-side diagnostic techniques. Every diagnostic test however has both advantages and disadvantages; PCR is not an exception to this statement. To ease the odds faced by PCR several non-PCR techniques which can amplify DNA at a constant temperature has become the need of hour, thus generating a variety of isothermal amplification techniques including Nucleic Acid Sequence-Based Amplification (NASBA) along with Self-Sustained Sequence Replication (3SR) and Strand Displacement Amplification (SDA) and Loop mediated isothermal amplification (LAMP) test. LAMP stands out to be a good and effective diagnostic test for empowering in developing countries as it does not require sophisticated equipments and skilled personnel and proves to be cost-effective. Performance of LAMP mainly relies on crafting of six primers (including 2 loop primers) ultimately accelerating the reaction. LAMP amplifies DNA in the process pyrophosphates are formed causing turbidity that facilitates visualisation in a more effective way than PCR. The Bst and Bsm polymerase are the required enzymes for LAMP that does not possess 5'-3' exonuclease activity. Results can be visualized by adding DNA binding dye, SYBR green. LAMP is more stable than PCR and real-time PCR. Non-involvement of template DNA preparation and ability to generate 10(9) copies of DNA are added benefits that make it more effective than NASBA or 3SR and SDA. Thus, it fetches researcher's interest in developing various versions of LAMP viz., its combination with lateral flow assay or micro LAMP and more recently lyophilized and electric (e) LAMP. Availability of ready to use LAMP kits has helped diagnosis of almost all pathogens. LAMP associated technologies however needs to be developed as a part of LAMP platform rather than developing them as separate entities. This review deals with all these salient features of this newly developed tool that has enlightened the world of diagnosis.
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22
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Development of fluorescent nanoparticle-labeled lateral flow assay for the detection of nucleic acids. Biomed Microdevices 2014; 15:751-8. [PMID: 23525961 DOI: 10.1007/s10544-013-9760-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The rapid, specific and sensitive detection of nucleic acids is of utmost importance for the identification of infectious agents, diagnosis and treatment of genetic diseases, and the detection of pathogens related to human health and safety. Here we report the development of a simple and sensitive nucleic acid sequence-based and Ru(bpy)3 (2+)-doped silica nanoparticle-labeled lateral flow assay which achieves low limit of detection by using fluorescencent nanoparticles. The detection of the synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, was utilized to demonstrate this assay. The 30 nm spherical Ru(bpy)3 (2+)-doped silica nanoparticles were prepared in aqueous medium by a novel method recently reported. The nanoparticles were modified by 3-glycidoxypropyl trimethoxysilane in order to conjugate to amine-capped oligonucleotide reporter probes. The fluorescent intensities of the fluorescent assays were quantified on a mictrotiter plate reader using a custom holder. The experimental results showed that the lateral flow fluorescent assay developed was more sensitive compared with the traditional colloidal gold test strips. The limit of detection for the fluorescent lateral flow assay developed is approximately 0.066 fmols as compared to approximately 15 fmols for the colloidal gold. The limit of detection can further be reduced about one order of magnitude when "dipstick" format was used.
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Mugasa CM, Katiti D, Boobo A, Lubega GW, Schallig HD, Matovu E. Comparison of nucleic acid sequence-based amplification and loop-mediated isothermal amplification for diagnosis of human African trypanosomiasis. Diagn Microbiol Infect Dis 2014; 78:144-8. [DOI: 10.1016/j.diagmicrobio.2013.06.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 11/28/2022]
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Deborggraeve S, Büscher P. Recent progress in molecular diagnosis of sleeping sickness. Expert Rev Mol Diagn 2014; 12:719-30. [DOI: 10.1586/erm.12.72] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Cheng Y, Zhao J, Jia H, Yuan Z, Li Z. Ligase chain reaction coupled with rolling circle amplification for high sensitivity detection of single nucleotide polymorphisms. Analyst 2013; 138:2958-63. [PMID: 23535938 DOI: 10.1039/c3an36920j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a highly sensitive and homogeneous assay for the detection of single nucleotide polymorphisms (SNPs) by ligase chain reaction (LCR) coupled with rolling circle amplification (RCA). The LCR probes include one pair of probes and a padlock probe (PLP). In the LCR, one pair of probes composed of X and Y, perfectly hybridize with the upper strand of the target DNA after thermal denaturation. They are then ligated by the thermostable ligase to form the ligation product of XY. At the same time, the PLP hybridizes with the lower strand of the target DNA and are ligated to form the circular PLP (cPLP). After repeated cycles of denaturation, annealing, and ligation, the target DNA is amplified exponentially to generate a large number of XY and cPLPs. Subsequently, RCA is triggered by the cPLP as a template and XY as a primer, producing large numbers of long strand DNA products, which are detected by binding with the fluorescent dye, SYBR Green I, in a homogeneous manner. This method is simple, and avoids the need for detection of the LCR products with labeled probes and complex separation steps. The assay is sensitive and specific enough to detect a 1 fM target DNA molecule. It is possible to accurately determine the allele frequency as low as 1.0%. The LCR coupled with RCA assay extends the application of the LCR and RCA, and provides a new strategy for detecting SNPs as well as nucleic acid analysis, immunoassay, and molecular diagnosis.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding, 071002, P. R. China.
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Roskos K, Hickerson AI, Lu HW, Ferguson TM, Shinde DN, Klaue Y, Niemz A. Simple system for isothermal DNA amplification coupled to lateral flow detection. PLoS One 2013; 8:e69355. [PMID: 23922706 PMCID: PMC3724848 DOI: 10.1371/journal.pone.0069355] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/09/2013] [Indexed: 02/04/2023] Open
Abstract
Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden.
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Affiliation(s)
- Kristina Roskos
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Anna I. Hickerson
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Hsiang-Wei Lu
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Tanya M. Ferguson
- Claremont BioSolutions, Upland, California, United States of America
| | - Deepali N. Shinde
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Yvonne Klaue
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
- * E-mail:
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Human african trypanosomiasis diagnosis in first-line health services of endemic countries, a systematic review. PLoS Negl Trop Dis 2012; 6:e1919. [PMID: 23209860 PMCID: PMC3510092 DOI: 10.1371/journal.pntd.0001919] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/09/2012] [Indexed: 11/19/2022] Open
Abstract
While the incidence of Human African Trypanosomiasis (HAT) is decreasing, the control approach is shifting from active population screening by mobile teams to passive case detection in primary care centers. We conducted a systematic review of the literature between 1970 and 2011 to assess which diagnostic tools are most suitable for use in first-line health facilities in endemic countries. Our search retrieved 16 different screening and confirmation tests for HAT. The thermostable format of the Card Agglutination Test for Trypanosomiasis (CATT test) was the most appropriate screening test. Lateral flow antibody detection tests could become alternative screening tests in the near future. Confirmation of HAT diagnosis still depends on visualizing the parasite in direct microscopy. All other currently available confirmation tests are either technically too demanding and/or lack sensitivity and thus rather inappropriate for use at health center level. Novel applications of molecular tests may have potential for use at district hospital level.
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Huang H, Jin L, Yang X, Song Q, Zou B, Jiang S, Sun L, Zhou G. An internal amplification control for quantitative nucleic acid analysis using nanoparticle-based dipstick biosensors. Biosens Bioelectron 2012. [PMID: 23208096 DOI: 10.1016/j.bios.2012.10.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Quantitative analysis of virus nucleic acids is essential for monitoring the efficacy of medical treatment based on the copy numbers of virus's RNA or DNA in blood. To quantitatively detect virus nucleic acids in blood, here an internal amplification control (IAC) coupled with a nanoparticle-based DNA biosensor was proposed. The IACs with a specific sequence were designed and spiked into serum before nucleic acids extraction. Sequences of the IACs and the targets only differ in the base order of one PCR priming site; thus, the IACs and the targets are identical in Tm, giving the same amplification efficiency during PCR. To visually detect amplicons, a dipstick biosensor based on streptavidin-functionalized nanoparticles is employed. By comparing color densities of a test zone with an IAC zone on the biosensor, the content of the target in serum can be semi-quantitatively analyzed. This approach has achieved the detection of HBV DNA at approximately 100 copies of the pathogen load. The feasibility of this method is demonstrated by successful semi-quantification of pathogen load in 30 clinical samples from HBV-infected patients. These data indicate that the introduction of an IAC and nanoparticle-based dipstick-type biosensor could be a powerful tool in point of care testing (POCT).
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Affiliation(s)
- Huan Huang
- Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
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30
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 483] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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Ang GY, Yu CY, Yean CY. Ambient temperature detection of PCR amplicons with a novel sequence-specific nucleic acid lateral flow biosensor. Biosens Bioelectron 2012; 38:151-6. [PMID: 22705404 DOI: 10.1016/j.bios.2012.05.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/08/2012] [Accepted: 05/15/2012] [Indexed: 12/17/2022]
Abstract
In the field of diagnostics, molecular amplification targeting unique genetic signature sequences has been widely used for rapid identification of infectious agents, which significantly aids physicians in determining the choice of treatment as well as providing important epidemiological data for surveillance and disease control assessment. We report the development of a rapid nucleic acid lateral flow biosensor (NALFB) in a dry-reagent strip format for the sequence-specific detection of single-stranded polymerase chain reaction (PCR) amplicons at ambient temperature (22-25°C). The NALFB was developed in combination with a linear-after-the-exponential PCR assay and the applicability of this biosensor was demonstrated through detection of the cholera toxin gene from diarrheal-causing toxigenic Vibrio cholerae. Amplification using the advanced asymmetric PCR boosts the production of fluorescein-labeled single-stranded amplicons, allowing capture probes immobilized on the NALFB to hybridize specifically with complementary targets in situ on the strip. Subsequent visual formation of red lines is achieved through the binding of conjugated gold nanoparticles to the fluorescein label of the captured amplicons. The visual detection limit observed with synthetic target DNA was 0.3 ng and 1 pg with pure genomic DNA. Evaluation of the NALFB with 164 strains of V. cholerae and non-V. cholerae bacteria recorded 100% for both sensitivity and specificity. The whole procedure of the low-cost NALFB, which is performed at ambient temperature, eliminates the need for preheated buffers or additional equipment, greatly simplifying the protocol for sequence-specific PCR amplicon analysis.
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Affiliation(s)
- Geik Yong Ang
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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Towards Point-of-Care Diagnostic and Staging Tools for Human African Trypanosomiaisis. J Trop Med 2012; 2012:340538. [PMID: 22545057 PMCID: PMC3321554 DOI: 10.1155/2012/340538] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 01/17/2012] [Indexed: 11/18/2022] Open
Abstract
Human African trypanosomiasis is a debilitating disease prevalent in rural sub-Saharan Africa. Control of this disease almost exclusively relies on chemotherapy that should be driven by accurate diagnosis, given the unacceptable toxicity of the few available drugs. Unfortunately, the available diagnostics are characterised by low sensitivities due to the inherent low parasitaemia in natural infections. Demonstration of the trypanosomes in body fluids, which is a prerequisite before treatment, often follows complex algorithms. In this paper, we review the available diagnostics and explore recent advances towards development of novel point-of-care diagnostic tests.
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Fuenzalida L, Prat C, Blanco S, Bas A, Domínguez M, Hernández MÁ, Rodrigo C, Ausina V. Validation of a polymerase chain reaction–oligochromatography test for detection of influenza A (H1N1) 2009 virus. Diagn Microbiol Infect Dis 2012; 72:144-9. [DOI: 10.1016/j.diagmicrobio.2011.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 10/14/2011] [Accepted: 10/25/2011] [Indexed: 10/14/2022]
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Wang Y, Fill C, Nugen SR. Development of chemiluminescent lateral flow assay for the detection of nucleic acids. BIOSENSORS-BASEL 2012; 2:32-42. [PMID: 25585630 PMCID: PMC4263543 DOI: 10.3390/bios2010032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/06/2012] [Accepted: 01/16/2012] [Indexed: 12/02/2022]
Abstract
Rapid, sensitive detection methods are of utmost importance for the identification of pathogens related to health and safety. Herein we report the development of a nucleic acid sequence-based lateral flow assay which achieves a low limit of detection using chemiluminescence. On-membrane enzymatic signal amplification is used to reduce the limit of detection to the sub-femtomol level. To demonstrate this assay, we detected synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, with relevance in human and animal health in sub-Saharan Africa. The intensity of the chemiluminescent signal was evaluated by using a charge-coupled device as well as a microtiter plate reader. We demonstrated that our lateral flow chemiluminescent assay has a very low limit of detection and is easy to use. The limit of detection was determined to be 0.5 fmols of nucleic acid target.
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Affiliation(s)
- Yuhong Wang
- Department of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, MA 01003, USA.
| | - Catherine Fill
- Department of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, MA 01003, USA.
| | - Sam R Nugen
- Department of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, MA 01003, USA.
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Diagnostic accuracy of molecular amplification tests for human African trypanosomiasis--systematic review. PLoS Negl Trop Dis 2012; 6:e1438. [PMID: 22253934 PMCID: PMC3254661 DOI: 10.1371/journal.pntd.0001438] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 10/31/2011] [Indexed: 12/01/2022] Open
Abstract
Background A range of molecular amplification techniques have been developed for the diagnosis of Human African Trypanosomiasis (HAT); however, careful evaluation of these tests must precede implementation to ensure their high clinical accuracy. Here, we investigated the diagnostic accuracy of molecular amplification tests for HAT, the quality of articles and reasons for variation in accuracy. Methodology Data from studies assessing diagnostic molecular amplification tests were extracted and pooled to calculate accuracy. Articles were included if they reported sensitivity and specificity or data whereby values could be calculated. Study quality was assessed using QUADAS and selected studies were analysed using the bivariate random effects model. Results 16 articles evaluating molecular amplification tests fulfilled the inclusion criteria: PCR (n = 12), NASBA (n = 2), LAMP (n = 1) and a study comparing PCR and NASBA (n = 1). Fourteen articles, including 19 different studies were included in the meta-analysis. Summary sensitivity for PCR on blood was 99.0% (95% CI 92.8 to 99.9) and the specificity was 97.7% (95% CI 93.0 to 99.3). Differences in study design and readout method did not significantly change estimates although use of satellite DNA as a target significantly lowers specificity. Sensitivity and specificity of PCR on CSF for staging varied from 87.6% to 100%, and 55.6% to 82.9% respectively. Conclusion Here, PCR seems to have sufficient accuracy to replace microscopy where facilities allow, although this conclusion is based on multiple reference standards and a patient population that was not always representative. Future studies should, therefore, include patients for which PCR may become the test of choice and consider well designed diagnostic accuracy studies to provide extra evidence on the value of PCR in practice. Another use of PCR for control of disease could be to screen samples collected from rural areas and test in reference laboratories, to spot epidemics quickly and direct resources appropriately. A range of molecular amplification techniques has been developed for the diagnosis of HAT, with polymerase chain reaction (PCR) at the forefront. As laboratory strengthening in endemic areas increases, it is expected that the applicability of molecular tests will increase. However, careful evaluation of these tests against the current reference standard, microscopy, must precede implementation. Therefore, we have investigated the published diagnostic accuracy of molecular amplification tests for HAT compared to microscopy for both initial diagnosis as well as for disease staging. Here, PCR tests seem to have an acceptably high specificity and sensitivity for diagnosis of stage I HAT. This conclusion is, however, based on multiple-microscopy based techniques as reference standards, which may have low sensitivity, and a patient population that was not always representative. Future studies should, therefore, first and foremost include those patients for which PCR may become the test of choice. More certainty about the practical value of PCR tests for HAT diagnosis should come from non-accuracy design studies, like feasibility or cost-effectiveness studies.
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Jia H, Chen Z, Wu H, Ye H, Yan Z, Zhou G. Pyrosequencing on templates generated by asymmetric nucleic acid sequence-based amplification (asymmetric-NASBA). Analyst 2011; 136:5229-33. [PMID: 22013588 DOI: 10.1039/c1an15766c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pyrosequencing is an ideal tool for verifying the sequence of amplicons. To enable pyrosequencing on amplicons from nucleic acid sequence-based amplification (NASBA), asymmetric NASBA with unequal concentrations of T7 promoter primer and reverse transcription primer was proposed. By optimizing the ratio of two primers and the concentration of dNTPs and NTPs, the amount of single-stranded cDNA in the amplicons from asymmetric NASBA was found increased 12 times more than the conventional NASBA through the real-time detection of a molecular beacon specific to cDNA of interest. More than 20 bases have been successfully detected by pyrosequencing on amplicons from asymmetric NASBA using Human parainfluenza virus (HPIV) as an amplification template. The primary results indicate that the combination of NASBA with a pyrosequencing system is practical, and should open a new field in clinical diagnosis.
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Affiliation(s)
- Huning Jia
- Department of Analytical Chemistry, China Pharmaceutical University, Nanjing, China.
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Wastling SL, Welburn SC. Diagnosis of human sleeping sickness: sense and sensitivity. Trends Parasitol 2011; 27:394-402. [DOI: 10.1016/j.pt.2011.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/25/2011] [Accepted: 04/28/2011] [Indexed: 11/30/2022]
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LaBarre P, Boyle D, Hawkins K, Weigl B. Instrument-free nucleic acid amplification assays for global health settings. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2011; 8029. [PMID: 25089171 DOI: 10.1117/12.882868] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Many infectious diseases that affect global health are most accurately diagnosed through nucleic acid amplification and detection. However, existing nucleic acid amplification tests are too expensive and complex for most low-resource settings. The small numbers of centralized laboratories that exist in developing countries tend to be in urban areas and primarily cater to the affluent. In contrast, rural area health care facilities commonly have only basic equipment and health workers have limited training and little ability to maintain equipment and handle reagents.1 Reliable electric power is a common infrastructure shortfall. In this paper, we discuss a practical approach to the design and development of non-instrumented molecular diagnostic tests that exploit the benefits of isothermal amplification strategies. We identify modular instrument-free technologies for sample collection, sample preparation, amplification, heating, and detection. By appropriately selecting and integrating these instrument-free modules, we envision development of an easy to use, infrastructure independent diagnostic test that will enable increased use of highly accurate molecular diagnostics at the point of care in low-resource settings.
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Affiliation(s)
- Paul LaBarre
- Diagnostics Group, PATH; 2201 Westlake Avenue; Suite 200; Seattle, WA 98121
| | - David Boyle
- Diagnostics Group, PATH; 2201 Westlake Avenue; Suite 200; Seattle, WA 98121
| | - Kenneth Hawkins
- Diagnostics Group, PATH; 2201 Westlake Avenue; Suite 200; Seattle, WA 98121
| | - Bernhard Weigl
- Diagnostics Group, PATH; 2201 Westlake Avenue; Suite 200; Seattle, WA 98121
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Latent Trypanosoma brucei gambiense foci in Uganda: a silent epidemic in children and adults? Parasitology 2011; 138:1480-7. [PMID: 21554841 DOI: 10.1017/s0031182011000230] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Trypanosoma brucei gambiense sleeping sickness follows a long asymptomatic phase and persists in ancient foci from which epidemic clinical disease arises. A putative focus of T. b. gambiense infections has been identified, initially in mothers and young children, on the Lake Albert shoreline of Western Uganda leading to mass screening of 6207 individuals in September 2008. T. b. gambiense infections were identified by Card Agglutination Test for Trypanosomiasis (CATT) and sub-species-specific PCR although parasitological methods failed to confirm any patent trypanosome infections. In April 2009, CATT positives were re-visited; diagnosis of individuals by CATT and PCR was unstable over the two time points and parasites remained undetected, even using mini Anion Exchange Centrifugation Technique (mAECT). These observations suggest the possibility of a silent focus of disease, where all infected individuals are in a latent stage, and highlight our limited understanding of the local natural history and disease progression of T. b. gambiense in children and adults.
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First evidence that parasite infecting apparent aparasitemic serological suspects in human African trypanosomiasis are Trypanosoma brucei gambiense and are similar to those found in patients. INFECTION GENETICS AND EVOLUTION 2011; 11:1250-5. [PMID: 21530681 DOI: 10.1016/j.meegid.2011.04.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 04/07/2011] [Accepted: 04/11/2011] [Indexed: 11/20/2022]
Abstract
Thanks to its sensitivity and its ease of use in the field, the card agglutination test for trypanosomiasis (CATT) is widely used for serological screening of Trypanosoma brucei gambiense human African trypanosomiasis (HAT). Positive subjects are then examined by microscopy to confirm the disease. However, the CATT exhibits false-positive results raising the question of whether CATT-positive subjects who are not confirmed by microscopic detection of trypanosomes (SERO) are truly exposed to T.b. gambiense infection. For this purpose, we applied microsatellite genotyping on DNA extracted from blood of both HAT confirmed patients and SERO subjects in Guinea and Côte d'Ivoire since microsatellite genotyping has proved useful for the study of T.b. gambiense genetic diversity. Problems of amplification failures raise the question of the sensitivity of microsatellite markers when applied on biological samples especially from SERO subjects for who low blood parasitaemia are suspected. Nevertheless, we have shown that the trypanosomes from SERO individuals that have been genotyped belong to T.b. gambiense group 1 and were identical to those found in HAT patients. These results constitute the first evidences that at least some SERO are indeed infected by T.b. gambiense group 1 and that they may constitute a human reservoir of parasite in HAT foci. Whether these individuals should undergo treatment remains an open question as long as their role in HAT transmission is unknown. Our results strongly recommend the follow-up of such subjects to improve control strategies.
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Rodrigues Ribeiro Teles FS, Pires de Távora Tavira LA, Pina da Fonseca LJ. Biosensors as rapid diagnostic tests for tropical diseases. Crit Rev Clin Lab Sci 2011; 47:139-69. [PMID: 21155631 DOI: 10.3109/10408363.2010.518405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Effective diagnosis of infectious pathogens is essential for disease identification and subsequent adequate treatment, to prevent drug resistance and to adopt suitable public health interventions for the prevention and control of epidemic outbreaks. Particular situations under which medical diagnostics operate in tropical environments make the use of new easy-to-use diagnostic tools the preferred (or even unique) option. These diagnostic tests and devices, usually based on biosensing methods, are being increasingly exploited as promising alternatives to classical, "heavy" lab instrumentation for clinical diagnosis, allowing simple, inexpensive and point-of-care testing. However, in many developing countries the lack of accessibility and affordability for many commercial diagnostic tests remains a major cause of high disease burden in such regions. We present a comprehensive overview about the problems of conventional medical diagnosis of infectious pathologies in tropical regions, while pointing out new methods and analytical tools for in-the-field and decentralized diagnosis of current major infectious tropical diseases. The review includes not only biosensor-based rapid diagnostic tests approved by regulatory entities and already commercialized, but also those at the early stages of research.
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Francois P, Tangomo M, Hibbs J, Bonetti EJ, Boehme CC, Notomi T, Perkins MD, Schrenzel J. Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. ACTA ACUST UNITED AC 2011; 62:41-8. [PMID: 21276085 DOI: 10.1111/j.1574-695x.2011.00785.x] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We evaluated the robustness of loop-mediated isothermal amplification (LAMP) of DNA for bacterial diagnostic applications. Salmonella enterica serovar Typhi was used as the target organism and compared with a real-time quantitative PCR (qPCR) for testing assay performance and reproducibly, as well as the impact of pH and temperature stability. This isothermal amplification method appeared to be particularly robust across 2 pH units (7.3-9.3) and temperature values (57-67 °C). The detection limit was comparable to that observed using optimized home-brew qPCR assays. The specificity of the amplification reaction remained high even at temperatures markedly different from the optimal one. Exposing reagents to the ambient temperature during the preparation of the reaction mixture as well as prolonging times for preparing the amplification reaction did not yield false-positive results. LAMP remained sensitive and specific despite the addition of untreated biological fluids such as stool or urine that commonly inhibit PCR amplification. Whereas the detection of microorganisms from whole blood or a blood-culture medium typically requires extensive sample purification and removal of inhibitors, LAMP amplification remained more sensitive than conventional qPCR when omitting such preparatory steps. Our results demonstrate that LAMP is not only easy to use, but is also a very robust, innovative and powerful molecular diagnostic method for both industrialized and developing countries.
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Affiliation(s)
- Patrice Francois
- Genomic Research Laboratory, University Hospitals of Geneva, Service of Infectious Diseases, Geneva, Switzerland.
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Niemz A, Ferguson TM, Boyle DS. Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol 2011; 29:240-50. [PMID: 21377748 DOI: 10.1016/j.tibtech.2011.01.007] [Citation(s) in RCA: 510] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 01/17/2011] [Accepted: 01/20/2011] [Indexed: 02/05/2023]
Abstract
Nucleic acid testing for infectious diseases at the point of care is beginning to enter clinical practice in developed and developing countries; especially for applications requiring fast turnaround times, and in settings where a centralized laboratory approach faces limitations. Current systems for clinical diagnostic applications are mainly PCR-based, can only be used in hospitals, and are still relatively complex and expensive. Integrating sample preparation with nucleic acid amplification and detection in a cost-effective, robust, and user-friendly format remains challenging. This review describes recent technical advances that might be able to address these limitations, with a focus on isothermal nucleic acid amplification methods. It briefly discusses selected applications related to the diagnosis and management of tuberculosis, HIV, and perinatal and nosocomial infections.
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Affiliation(s)
- Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA.
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Dobigny G, Poirier P, Hima K, Cabaret O, Gauthier P, Tatard C, Costa JM, Bretagne S. Molecular survey of rodent-borne Trypanosoma in Niger with special emphasis on T. lewisi imported by invasive black rats. Acta Trop 2011; 117:183-8. [PMID: 21126503 DOI: 10.1016/j.actatropica.2010.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 11/02/2010] [Accepted: 11/05/2010] [Indexed: 11/24/2022]
Abstract
Invading rodent species can harbor parasites with potential transmission to native rodents and/or humans. To investigate trypanosomes prevalence in rodents, the spleen of 76 rodents from Niger identified by their karyotype was used as a DNA source for Trypanosoma detection using a newly developed qPCR assay. Of the invasive black rat, Rattus rattus, 71% (10/14) were PCR positive as well as 6% (4/62) of native African rodents. Sequences of ~400bp of the SSU rDNA gene identified phylogenetically close Trypanosoma lineages. Trypanosoma lewisi was present in all positive black rats and the sequences displayed 100% similarity with T. lewisi-infected humans in Senegal. T. lewisi was also detected in one Acomys johannis, suggesting a possible transmission to native species. In addition to improved knowledge of Trypanosoma diversity in rodents, our data underscore the introduction of the potentially pathogenic T. lewisi kinetoplastid through the human-mediated invasion of black rats all over West Africa.
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Jacobs RT, Nare B, Phillips MA. State of the art in African trypanosome drug discovery. Curr Top Med Chem 2011; 11:1255-74. [PMID: 21401507 PMCID: PMC3101707 DOI: 10.2174/156802611795429167] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 11/25/2010] [Indexed: 11/22/2022]
Abstract
African sleeping sickness is endemic in sub-Saharan Africa where the WHO estimates that 60 million people are at risk for the disease. Human African trypanosomiasis (HAT) is 100% fatal if untreated and the current drug therapies have significant limitations due to toxicity and difficult treatment regimes. No new chemical agents have been approved since eflornithine in 1990. The pentamidine analog DB289, which was in late stage clinical trials for the treatment of early stage HAT recently failed due to toxicity issues. A new protocol for the treatment of late-stage T. brucei gambiense that uses combination nifurtomox/eflornithine (NECT) was recently shown to have better safety and efficacy than eflornithine alone, while being easier to administer. This breakthrough represents the only new therapy for HAT since the approval of eflornithine. A number of research programs are on going to exploit the unusual biochemical pathways in the parasite to identify new targets for target based drug discovery programs. HTS efforts are also underway to discover new chemical entities through whole organism screening approaches. A number of inhibitors with anti-trypanosomal activity have been identified by both approaches, but none of the programs are yet at the stage of identifying a preclinical candidate. This dire situation underscores the need for continued effort to identify new chemical agents for the treatment of HAT.
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Affiliation(s)
- Robert T. Jacobs
- SCYNEXIS, Inc., Research Triangle Park, North Carolina 27709-2878
| | - Bakela Nare
- SCYNEXIS, Inc., Research Triangle Park, North Carolina 27709-2878
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, Texas 75390-9041
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Barratt JLN, Harkness J, Marriott D, Ellis JT, Stark D. Importance of nonenteric protozoan infections in immunocompromised people. Clin Microbiol Rev 2010; 23:795-836. [PMID: 20930074 PMCID: PMC2952979 DOI: 10.1128/cmr.00001-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There are many neglected nonenteric protozoa able to cause serious morbidity and mortality in humans, particularly in the developing world. Diseases caused by certain protozoa are often more severe in the presence of HIV. While information regarding neglected tropical diseases caused by trypanosomatids and Plasmodium is abundant, these protozoa are often not a first consideration in Western countries where they are not endemic. As such, diagnostics may not be available in these regions. Due to global travel and immigration, this has become an increasing problem. Inversely, in certain parts of the world (particularly sub-Saharan Africa), the HIV problem is so severe that diseases like microsporidiosis and toxoplasmosis are common. In Western countries, due to the availability of highly active antiretroviral therapy (HAART), these diseases are infrequently encountered. While free-living amoebae are rarely encountered in a clinical setting, when infections do occur, they are often fatal. Rapid diagnosis and treatment are essential to the survival of patients infected with these organisms. This paper reviews information on the diagnosis and treatment of nonenteric protozoal diseases in immunocompromised people, with a focus on patients infected with HIV. The nonenteric microsporidia, some trypanosomatids, Toxoplasma spp., Neospora spp., some free-living amoebae, Plasmodium spp., and Babesia spp. are discussed.
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Affiliation(s)
- J L N Barratt
- Department of Microbiology, St. Vincent's Hospital, Darlinghurst 2010, NSW, Australia.
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Matovu E, Mugasa CM, Ekangu RA, Deborggraeve S, Lubega GW, Laurent T, Schoone GJ, Schallig HD, Büscher P. Phase II evaluation of sensitivity and specificity of PCR and NASBA followed by oligochromatography for diagnosis of human African trypanosomiasis in clinical samples from D.R. Congo and Uganda. PLoS Negl Trop Dis 2010; 4:e737. [PMID: 20625557 PMCID: PMC2897845 DOI: 10.1371/journal.pntd.0000737] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 05/20/2010] [Indexed: 12/05/2022] Open
Abstract
Background The polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA) have been recently modified by coupling to oligochromatography (OC) for easy and fast visualisation of products. In this study we evaluate the sensitivity and specificity of the PCR-OC and NASBA-OC for diagnosis of Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense human African trypanosomiasis (HAT). Methodology and Results Both tests were evaluated in a case-control design on 143 HAT patients and 187 endemic controls from the Democratic Republic of Congo (DRC) and Uganda. The overall sensitivity of PCR-OC was 81.8% and the specificity was 96.8%. The PCR-OC showed a sensitivity and specificity of 82.4% and 99.2% on the specimens from DRC and 81.3% and 92.3% on those from Uganda. NASBA-OC yielded an overall sensitivity of 90.2%, and a specificity of 98.9%. The sensitivity and specificity of NASBA-OC on the specimens from DRC was 97.1% and 99.2%, respectively. On the specimens from Uganda we observed a sensitivity of 84.0% and a specificity of 98.5%. Conclusions/Significance The tests showed good sensitivity and specificity for the T. b. gambiense HAT in DRC but rather a low sensitivity for T. b. rhodesiense HAT in Uganda. Diagnosis plays a central role in the control of human African trypanosomiasis (HAT) whose mainstay in disease control is chemotherapy. However, accurate diagnosis is hampered by the absence of sensitive techniques for parasite detection. Without concentrating the blood, detection thresholds can be as high as 10,000 trypanosomes per milliliter of blood. The polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA) are promising molecular diagnostics that generally yield high sensitivity and could improve case detection. Recently, these two tests were coupled to oligochromatography (OC) for simplified and standardized detection of amplified products, eliminating the need for electrophoresis. In this study, we evaluated the diagnostic accuracy of these two novel tests on blood specimens from HAT patients and healthy endemic controls from D.R. Congo and Uganda. Both tests exhibited good sensitivity and specificity compared to the current diagnostic tests and may be valuable tools for sensitive and specific parasite detection in clinical specimens. These standardized molecular test formats open avenues for improved case detection, particularly in epidemiological studies and in disease diagnosis at reference centres.
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Affiliation(s)
- Enock Matovu
- Department of Veterinary Parasitology and Microbiology, Makerere University, Kampala, Uganda.
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Deborggraeve S, Büscher P. Molecular diagnostics for sleeping sickness: what is the benefit for the patient? THE LANCET. INFECTIOUS DISEASES 2010; 10:433-9. [DOI: 10.1016/s1473-3099(10)70077-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Camara M, Camara O, Ilboudo H, Sakande H, Kaboré J, N'Dri L, Jamonneau V, Bucheton B. Sleeping sickness diagnosis: use of buffy coats improves the sensitivity of the mini anion exchange centrifugation test. Trop Med Int Health 2010; 15:796-9. [PMID: 20497407 DOI: 10.1111/j.1365-3156.2010.02546.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To evaluate a modification of the mini anion exchange centrifugation test (mAECT) for the diagnosis of Trypanosoma brucei (T.b.) gambiense human African trypanosomiasis (HAT). To increase its sensitivity, this test uses 350 microl of buffy coat withdrawn from 5 ml of blood instead of blood. METHODS The new protocol was first tested experimentally on serial dilution of trypanosomes and was then further evaluated under field conditions on 57 patients with HAT diagnosed during a medical survey in Guinea. RESULTS Experimentally, the use of buffy coats improved mAECT sensitivity at least five fold and enabled to consistently detect parasites in blood at a concentration of 10 trypanosomes/ml. During the field evaluation, more patients tested positive by mAECT-bc (96.5%) than by mAECT-blood (78.9%, chi(2) = 6.93, P = 0.008) and lymph juice examination (77.2%, chi(2) = 7.67, P = 0.005). Furthermore, the number of parasites per collectors was significantly higher (7.2 vs. 2.6, P = 0.001) when buffy coats were used instead of blood. CONCLUSION The use of the mAECT-bc protocol enabled a significant improvement of HAT parasitological diagnosis in Guinea, without any additional costs. It would deserve to be tested in other T.b. gambiense endemic areas.
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Affiliation(s)
- Mamadou Camara
- Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinée
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Mugasa CM, Deborggraeve S, Schoone GJ, Laurent T, Leeflang MM, Ekangu RA, El Safi S, Saad AFA, Basiye FL, De Doncker S, Lubega GW, Kager PA, Büscher P, Schallig HDFH. Accordance and concordance of PCR and NASBA followed by oligochromatography for the molecular diagnosis of Trypanosoma brucei and Leishmania. Trop Med Int Health 2010; 15:800-5. [PMID: 20487429 DOI: 10.1111/j.1365-3156.2010.02547.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate the repeatability and reproducibility of four simplified molecular assays for the diagnosis of Trypanosoma brucei spp. or Leishmania ssp. in a multicentre ring trial with seven participating laboratories. METHODS The tests are based on PCR or NASBA amplification of the parasites nucleic acids followed by rapid read-out by oligochromatographic dipstick (PCR-OC and NASBA-OC). RESULTS On purified nucleic acid specimens, the repeatability and reproducibility of the tests were Tryp-PRC-OC, 91.7% and 95.5%; Tryp-NASBA-OC, 95.8% and 100%; Leish-PCR-OC, 95.9% and 98.1%; Leish-NASBA-OC, 92.3% and 98.2%. On blood specimens spiked with parasites, the repeatability and reproducibility of the tests were Tryp-PRC-OC, 78.4% and 86.6%; Tryp-NASBA-OC, 81.5% and 89.0%; Leish-PCR-OC, 87.1% and 91.7%; Leish-NASBA-OC, 74.8% and 86.2%. CONCLUSION As repeatability and reproducibility of the tests were satisfactory, further phase II and III evaluations in clinical and population specimens from disease endemic countries are justified.
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Affiliation(s)
- Claire M Mugasa
- Department of Veterinary Parasitology and Microbiology, Makerere University, Kampala, Uganda
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