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Ghosh P, Chowdhury R, Faisal K, Khan MAA, Hossain F, Rahat MA, Chowdhury MAA, Mithila NT, Kamal M, Maruf S, Nath R, Kobialka RM, Ceruti A, Cameron M, Duthie MS, Wahed AAE, Mondal D. Evaluation of a Point-of-Need Molecular Diagnostic Tool Coupled with Rapid DNA Extraction Methods for Visceral Leishmaniasis. Diagnostics (Basel) 2023; 13:3639. [PMID: 38132223 PMCID: PMC10742398 DOI: 10.3390/diagnostics13243639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
A rapid, cost-effective, and simple nucleic acid isolation technique coupled with a point-of-need DNA amplification assay is a desirable goal for programmatic use. For diagnosis of Visceral Leishmaniasis (VL), Recombinase Polymerase Amplification (RPA) rapid tests for the detection of Leishmania DNA are versatile and have operational advantages over qPCR. To facilitate the delivery of the RPA test at point-of-need for VL diagnosis, we compared two rapid DNA extraction methods, SwiftDx (SX) and an in-house Boil and Spin (BS) method, coupled with RPA amplification, versus more widely used methods for DNA extraction and amplification, namely Qiagen (Q) kits and qPCR, respectively. A total of 50 confirmed VL patients and 50 controls, matched for age and gender, were recruited from Mymensingh, Bangladesh, a region highly endemic for VL. Blood samples were collected from each participant and DNA was extracted using Q, SX and BS methods. Following DNA extraction, qPCR and RPA assays were performed to detect L. donovani in downstream analysis. No significant differences in sensitivity of the RPA assay were observed between DNA extraction methods, 94.00% (95% CI: 83.45-98.75%), 90% (95% CI: 78.19-96.67%), and 88% (95% CI: 75.69-95.47%) when using Q, SX, and BS, respectively. Similarly, using qPCR, no significant differences in sensitivity were obtained when using Q or SX for DNA extraction, 94.00% (95% CI: 83.45-98.75%) and 92.00% (80.77-97.78%), respectively. It is encouraging that RPA and qPCR showed excellent agreement (k: 0.919-0.980) when different extraction methods were used and that the DNA impurities using BS had no inhibitory effect on the RPA assay. Furthermore, significantly higher DNA yields were obtained using SX and BS versus Q; however, a significantly higher parasite load was detected using qPCR when DNA was extracted using Q versus SX. Considering the cost, execution time, feasibility, and performance of RPA assay, rapid extraction methods such as the Boil and Spin technique appear to have the potential for implementation in resource-limited endemic settings. Further clinical research is warranted prior to broader application.
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Affiliation(s)
- Prakash Ghosh
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rajashree Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Khaledul Faisal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Faria Hossain
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Abu Rahat
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Arko Ayon Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Nishad Tasnim Mithila
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Mostafa Kamal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Shomik Maruf
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rupen Nath
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Mary Cameron
- London School of Hygiene and Tropical Medicine, University of London, London WC1E 7HT, UK;
| | | | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Dinesh Mondal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
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Wang XF, Chen WQ, Guo JL, Peng C, Chen XY, Xu XL, Wei W, Yang L, Ca J, Xu JF. A Fast, Visual, and Instrument-free Platform Involving Rapid DNA Extraction, Chemical Heating, and Recombinase Aided Amplification for On-Site Nucleic Acid Detection. Front Bioeng Biotechnol 2021; 9:764306. [PMID: 34881235 PMCID: PMC8645684 DOI: 10.3389/fbioe.2021.764306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The nucleic acid-based technique has been widely utilized in many fields including for on-site detection. However, traditional molecular detection techniques encounter limitations like relying on instruments, time consuming or complex operation, and cannot meet the demands of on-site testing. In this study, a rapid DNA extraction method (RDEM), recombinase aided amplification (RAA), and chemical heating packet (CHP) are integrated and termed as RRC platform for on-site detection of nucleic acid. For demonstration purposes, SHZD32-1 (a new transgenic soybean line from China) was detected using the novel platform to demonstrate its feasibility and capability for on-site detection. Using the RDEM, high-quality DNA appropriate for molecular detection was quickly extracted in 3–5 min. The heat energy generated by CHP was met the temperature requirements of RAA. Using the RRC platform, the whole detection process can be accomplished within only 30 min, and the results can be visually detected with glasses under blue light. No special or expensive instrument was needed for the detection process. This study provides a novel approach for on-site detection of nucleic acids besides providing valuable insight on related future research.
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Affiliation(s)
- Xiao Fu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Wen Qiang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,College of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Jian Li Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Xiao Yun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Xiao Li Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Ca
- College of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Jun Feng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
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Yu J, Shen D, Dai T, Lu X, Xu H, Dou D. Rapid and equipment-free detection of Phytophthora capsici using lateral flow strip-based recombinase polymerase amplification assay. Lett Appl Microbiol 2019; 69:64-70. [PMID: 31021437 DOI: 10.1111/lam.13166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 11/30/2022]
Abstract
Phytophthora capsici is an important oomycete pathogen that causes devastating diseases in various crops. Methods for the rapid detection of P. capsici are important for disease control and eradication programmes. Here, we developed an assay based on lateral flow strip-based recombinase polymerase amplification (LF-RPA) for the rapid and equipment-free detection of P. capsici. The specific primers and a probe were designed using the sequence of Ypt1, and the optimal assay conditions were 40°C for 20 min. The specificity of the assay was verified using closely related oomycetes and fungal species, and its detection limit was 10 pg of genomic DNA. In combination with a simple DNA extraction method, the LF-RPA assay enabled detection of P. capsici in diseased pepper samples without specialized equipment within 30 min. Consequently, the LF-RPA assay developed in this study enables rapid and equipment-free detection of P. capsici and has potential for further development as a diagnostic kit for application in the field or in resource-limited laboratories. SIGNIFICANCE AND IMPACT OF THE STUDY: We developed a novel assay based on lateral flow strip-based recombinase polymerase amplification (LF-RPA) for the rapid and equipment-free detection of Phytophthora capsici. In combination with a simple DNA extraction method, the LF-RPA assay detected P. capsici in field samples without specialized equipment within 30 min. The assay has potential for further development as a diagnostic kit for application in the field or in resource-limited laboratories.
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Affiliation(s)
- J Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - D Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - T Dai
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - X Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - H Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - D Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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