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Jaroenram W, Teerapittayanon S, Suvannakad R, Pengpanich S, Kampeera J, Arunrut N, Dangtip S, Sirithammajak S, Tondee B, Khumwan P, Japakasetr S, Leaungwutiwong P, Chatnuntawech I, Kiatpathomchai W. Enhancing efficiency in detection of COVID-19 through AI-driven colorimetric isothermal detection with multiplex primers. Diagn Microbiol Infect Dis 2024; 110:116446. [PMID: 39096664 DOI: 10.1016/j.diagmicrobio.2024.116446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/27/2024] [Accepted: 07/14/2024] [Indexed: 08/05/2024]
Abstract
COVID-19 has afflicted millions of lives worldwide. Although there are many rapid methods to detect it based on colorimetric loop-mediated isothermal amplification, there remains room for improvement. This study aims to 1) integrate multiple primers into a singleplex assay to enhance the diagnostic sensitivity, and 2) utilize a high-throughput smartphone-operatable AI-driven color reading tool to enable a rapid result analysis. This setup can improve the sensitivity by 10-100 times and can analyze approximately 6700 samples per minute. The assay is simpler than RT-qPCR, with a turnaround time of less than 75 min. It can detect various types of SARS-CoV-2 by targeting 3 genes, increasing the likelihood that it will remain effective even if the virus undergoes mutations in any single target gene. In summary, it affords potential for adaptation to detection of new/re-emerging diseases with the visual readout for maximum assay simplicity and AI-operated mode for large-scale testing.
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Affiliation(s)
- Wansadaj Jaroenram
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Surat Teerapittayanon
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Rapheephat Suvannakad
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sukanya Pengpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Jantana Kampeera
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Narong Arunrut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sirintip Dangtip
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sarawut Sirithammajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Benyatip Tondee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Pakapreud Khumwan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | | | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Itthi Chatnuntawech
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Wansika Kiatpathomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand.
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Arunrut N, Jitrakorn S, Tondee B, Saksmerprome V, Kiatpathomchai W. Real-time triplex loop-mediated isothermal amplification (LAMP) using a turbidimeter for detection of shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV). JOURNAL OF AQUATIC ANIMAL HEALTH 2024; 36:205-219. [PMID: 38923038 DOI: 10.1002/aah.10218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/24/2023] [Accepted: 02/19/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVE The World Organization for Animal Health still regulates the infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp. The existing disease identification approach is time consuming, necessitates expensive equipment, and requires specialized expertise, thereby limiting the accessibility of shrimp disease screening on farms. Loop-mediated isothermal amplification (LAMP) is recognized for its ability to detect inhibitory substances with high sensitivity and specificity. METHODS We developed a real-time triplex LAMP assay that combines the simplicity of point-of-care testing with the accuracy of a turbidimeter. Using a set of three LAMP primers, our technology enables rapid DNA amplification in a single reaction within 45 min and with a low detection limit (10 copies/reaction). RESULT We tested 192 shrimp samples from different sources and demonstrated the clinical utility of our method, achieving 100% specificity (95% confidence interval = 93.40-100.00%), 100% sensitivity (97.36-100.00%), and 100% accuracy (98.10-100.00%) in detecting IHHNV DNA, with a high Cohen's kappa value (1) compared to the standard quantitative polymerase chain reaction assay. CONCLUSION The high technology readiness level of our method makes it a versatile platform for any real-time LAMP assay, and its low cost and simplicity make it well suited for fast deployment and use in shrimp farming.
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Affiliation(s)
- Narong Arunrut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sarocha Jitrakorn
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Benyatip Tondee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Vanvimon Saksmerprome
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wansika Kiatpathomchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
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Wang S, Song H, Wang T, Xue H, Fei Y, Xiong X. Recent advancements with loop-mediated isothermal amplification (LAMP) in assessment of the species authenticity with meat and seafood products. Crit Rev Food Sci Nutr 2024:1-22. [PMID: 38494899 DOI: 10.1080/10408398.2024.2329979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Species adulteration or mislabeling with meat and seafood products could negatively affect the fair trade, wildlife conservation, food safety, religion aspect, and even the public health. While PCR-based methods remain the gold standard for assessment of the species authenticity, there is an urgent need for alternative testing platforms that are rapid, accurate, simple, and portable. Owing to its ease of use, low cost, and rapidity, LAMP is becoming increasingly used method in food analysis for detecting species adulteration or mislabeling. In this review, we outline how the features of LAMP have been leveraged for species authentication test with meat and seafood products. Meanwhile, as the trend of LAMP detection is simple, rapid and instrument-free, it is of great necessity to carry out end-point visual detection, and the principles of various end-point colorimetry methods are also reviewed. Moreover, with the aim to enhance the LAMP reaction, different strategies are summarized to either suppress the nonspecific amplification, or to avoid the results of nonspecific amplification. Finally, microfluidic chip is a promising point-of-care method, which has been the subject of a great deal of research directed toward the development of microfluidic platforms-based LAMP systems for the species authenticity with meat and seafood products.
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Affiliation(s)
- Shihui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hongwei Song
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Tianlong Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Lamalee A, Saiyudthong S, Changsen C, Kiatpathomchai W, Limthongkul J, Naparswad C, Sukphattanaudomchoke C, Chaopreecha J, Senapin S, Jaroenram W, Buates S. End-point rapid detection of total and pathogenic Vibrio parahaemolyticus ( tdh+ and/or trh1+ and/or trh2+) in raw seafood using a colorimetric loop-mediated isothermal amplification-xylenol orange technique. PeerJ 2024; 12:e16422. [PMID: 38188160 PMCID: PMC10771086 DOI: 10.7717/peerj.16422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/17/2023] [Indexed: 01/09/2024] Open
Abstract
Background Vibrio parahaemolyticus is the leading cause of bacterial seafood-borne gastroenteritis in humans worldwide. To ensure seafood safety and to minimize the occurrence of seafood-borne diseases, early detection of total V. parahaemolyticus (pathogenic and non-pathogenic strains) and pathogenic V. parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) is required. This study further improved a loop-mediated isothermal amplification (LAMP) assay using xylenol orange (XO), a pH sensitive dye, to transform conventional LAMP into a one-step colorimetric assay giving visible results to the naked eye. LAMP-XO targeted rpoD for species specificity and tdh, trh1, and trh2 for pathogenic strains. Multiple hybrid inner primers (MHP) of LAMP primers for rpoD detection to complement the main primer set previously reported were designed by our group to maximize sensitivity and speed. Methods Following the standard LAMP protocol, LAMP reaction temperature for rpoD, tdh, trh1, and trh2 detection was first determined using a turbidimeter. The acquired optimal temperature was subjected to optimize six parameters including dNTP mix, betaine, MgSO4, Bst 2.0 WarmStart DNA polymerase, reaction time and XO dye. The last parameter was done using a heat block. The color change of the LAMP-XO result from purple (negative) to yellow (positive) was monitored visually. The detection limits (DLs) of LAMP-XO using a 10-fold serial dilution of gDNA and spiked seafood samples were determined and compared with standard LAMP, PCR, and quantitative PCR (qPCR) assays. Subsequently, the LAMP-XO assay was validated with 102 raw seafood samples and the results were compared with PCR and qPCR assays. Results Under optimal conditions (65 °C for 75 min), rpoD-LAMP-XO and tdh-LAMP-XO showed detection sensitivity at 102 copies of gDNA/reaction, or 10 folds greater than trh1-LAMP-XO and trh2-LAMP-XO. This level of sensitivity was similar to that of standard LAMP, comparable to that of the gold standard qPCR, and 10-100 times higher than that of PCR. In spiked samples, rpoD-LAMP-XO, tdh-LAMP-XO, and trh2-LAMP-XO could detect V. parahaemolyticus at 1 CFU/2.5 g spiked shrimp. Of 102 seafood samples, LAMP-XO was significantly more sensitive than PCR (P < 0.05) for tdh and trh2 detection and not significantly different from qPCR for all genes determined. The reliability of tdh-LAMP-XO and trh2-LAMP-XO to detect pathogenic V. parahaemolyticus was at 94.4% and 100%, respectively. Conclusions To detect total and pathogenic V. parahaemolyticus, at least rpoD-LAMP-XO and trh2-LAMP-XO should be used, as both showed 100% sensitivity, specificity, and accuracy. With short turnaround time, ease, and reliability, LAMP-XO serves as a better alternative to PCR and qPCR for routine detection of V. parahaemolyticus in seafood. The concept of using a one-step LAMP-XO and MHP-LAMP to enhance efficiency of diagnostic performance of LAMP-based assays can be generally applied for detecting any gene of interest.
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Affiliation(s)
- Aekarin Lamalee
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Soithong Saiyudthong
- Institute of Food Research and Product Development, Kasetsart University, Bangkok, Thailand
| | - Chartchai Changsen
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jitra Limthongkul
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chanita Naparswad
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Jarinya Chaopreecha
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Saengchan Senapin
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wansadaj Jaroenram
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sureemas Buates
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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