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Xu Y, Zhang Q, Li Y, Pang X, Cheng N. A 3D-Printed Integrated Handheld Biosensor for the Detection of Vibrio parahaemolyticus. Foods 2024; 13:1775. [PMID: 38891003 PMCID: PMC11171811 DOI: 10.3390/foods13111775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is one of the important seafood-borne pathogens that cause a serious gastrointestinal disorder in humans. Recently, biosensors have attracted serious attention for precisely detecting and tracking risk factors in foods. However, a major consideration when fabricating biosensors is to match the low cost of portable devices to broaden its application. In this study, a 3D-printed integrated handheld biosensor (IHB) that combines RPA-CRISPR/Cas12a, a lateral flow strip (LFS), and a handheld device was developed for the ultrasensitive detection of V. parahaemolyticus. Using the preamplification of RPA on tlh gene of V. parahaemolyticus, a specific duplex DNA product was obtained to activate the trans-cleavage activity of CRISPR/Cas12a, which was then utilized to cleave the ssDNA probe. The ssDNA probe was then detected by the LFS, which was negatively correlated with the content of amplified RPA products of the tlh gene. The IHB showed high selectivity and excellent sensitivity for V. parahaemolyticus detection, and the limit of detection was 4.9 CFU/mL. The IHB also demonstrated great promise for the screening of V. parahaemolyticus in samples and had the potential to be applied to the rapid screening of other pathogen risks for seafood and marine environmental safety.
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Affiliation(s)
- Yuancong Xu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China;
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
| | - Qian Zhang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Yunyi Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Xiaoxu Pang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Nan Cheng
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
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2
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Ji T, Cai Y, Gao Y, Wang G, Miao Y, Gao X. Establishment and application of a rapid visual diagnostic method for Streptococcus agalactiae based on recombinase polymerase amplification and lateral flow strips. Sci Rep 2024; 14:10064. [PMID: 38698011 PMCID: PMC11066032 DOI: 10.1038/s41598-024-56138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
This study aims to establish a rapid diagnostic method for Streptococcus agalactiae (GBS) based on recombinase polymerase amplification (RPA) and lateral flow strips (LFS). The best primer pairs designed by SIP gene were screened according to the basic RPA reaction, then the probe was designed. The reaction condition was optimized based on the color development of the LFS detection line. To ascertain the reaction specificity, 10 common clinical pathogens and 10 clinical specimens of GBS were tested. Furthermore, the reaction sensitivity was assessed by utilizing a tenfold gradient dilution of GBS genomic DNA as templates. RPA-LFS method was compared to the qPCR assay and biochemical culture method for the Kappa consistency test. The RPA-LFS technique was able to complete the amplification process within 30 min and the results were observed on lateral flow strips. The method is highly sensitive, with a minimum detection limit of 1.31 ng for GBS. The RPA-LFS method showed consistent accuracy of results compared to qPCR and the culture-biochemical method. The establishment of this method is conducive to the development of on-site immediate detection, which can provide information for the timely development of a reasonable antimicrobial treatment plan, and has a greater potential for clinical application.
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Affiliation(s)
- Tuo Ji
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Ye Cai
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang Affiliated to Bengbu Medical University, Lianyungang, China
| | - Yuzhi Gao
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Gang Wang
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China.
| | - Yongchang Miao
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China.
| | - Xuzhu Gao
- Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China.
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3
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Ling L, Liang L, Wang H, Lin X, Li C. Real-Time Monitoring on the Chinese Giant Salamander Using RPA-LFD. Int J Mol Sci 2024; 25:4946. [PMID: 38732163 PMCID: PMC11084824 DOI: 10.3390/ijms25094946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The Chinese giant salamander (Andrias davidianus), listed as an endangered species under "secondary protection" in China, faces significant threats due to ecological deterioration and the expansion of human activity. Extensive field investigations are crucial to ascertain the current status in the wild and to implement effective habitat protection measures to safeguard this species and support its population development. Traditional survey methods often fall short due to the elusive nature of the A. davidianus, presenting challenges that are time-consuming and generally ineffective. To overcome these obstacles, this study developed a real-time monitoring method that uses environmental DNA (eDNA) coupled with recombinase polymerase amplification and lateral flow strip (RPA-LFD). We designed five sets of species-specific primers and probes based on mitochondrial genome sequence alignments of A. davidianus and its close relatives. Our results indicated that four of these primer/probe sets accurately identified A. davidianus, distinguishing it from other tested caudata species using both extracted DNA samples and water samples from a tank housing an individual. This method enables the specific detection of A. davidianus genomic DNA at concentrations as low as 0.1 ng/mL within 50 min, without requiring extensive laboratory equipment. Applied in a field survey across four sites in Huangshan City, Anhui Province, where A. davidianus is known to be distributed, the method successfully detected the species at three of the four sites. The development of these primer/probe sets offers a practical tool for field surveying and monitoring, facilitating efforts in population recovery and resource conservation for A. davidianus.
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Affiliation(s)
- Lanxin Ling
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Linyan Liang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Huifang Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaolong Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Chenhong Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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4
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Oslan SNH, Yusof NY, Lim SJ, Ahmad NH. Rapid and sensitive detection of Salmonella in agro-Food and environmental samples: A review of advances in rapid tests and biosensors. J Microbiol Methods 2024; 219:106897. [PMID: 38342249 DOI: 10.1016/j.mimet.2024.106897] [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: 07/19/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Salmonella is as an intracellular bacterium, causing many human fatalities when the host-specific serotypes reach the host gastrointestinal tract. Nontyphoidal Salmonella are responsible for numerous foodborne outbreaks and product recalls worldwide whereas typhoidal Salmonella are responsible for Typhoid fever cases in developing countries. Yet, Salmonella-related foodborne disease outbreaks through its food and water contaminations have urged the advancement of rapid and sensitive Salmonella-detecting methods for public health protection. While conventional detection methods are time-consuming and ineffective for monitoring foodstuffs with short shelf lives, advances in microbiology, molecular biology and biosensor methods have hastened the detection. Here, the review discusses Salmonella pathogenic mechanisms and its detection technology advancements (fundamental concepts, features, implementations, efficiency, benefits, limitations and prospects). The time-efficiency of each rapid test method is discussed in relation to their limit of detections (LODs) and time required from sample enrichment to final data analysis. Importantly, the matrix effects (LODs and sample enrichments) were compared within the methods to potentially speculate Salmonella detection from environmental, clinical or food matrices using certain techniques. Although biotechnological advancements have led to various time-efficient Salmonella-detecting techniques, one should consider the usage of sophisticated equipment to run the analysis by moderately to highly trained personnel. Ultimately, a fast, accurate Salmonella screening that is readily executed by untrained personnels from various matrices, is desired for public health procurement.
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Affiliation(s)
- Siti Nur Hazwani Oslan
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; Food Security Research Laboratory, Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nurul Hawa Ahmad
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Wang R, Zhou R, Meng Y, Zheng J, Lu W, Yang Y, Yang J, Wu Y, Shan W. Specific Detection of Phytophthora parasitica by Recombinase Polymerase Amplification Assays Based on a Unique Multicopy Genomic Sequence. PLANT DISEASE 2024; 108:987-995. [PMID: 37884481 DOI: 10.1094/pdis-04-23-0722-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Phytophthora parasitica is a highly destructive oomycete plant pathogen that is capable of infecting a wide range of hosts including many agricultural cash crops, fruit trees, and ornamental garden plants. One of the most important diseases caused by P. parasitica worldwide is black shank of tobacco. Rapid, sensitive, and specific pathogen detection is crucial for early rapid diagnosis, which can facilitate effective disease management. In this study, we used a genomics approach to identify repeated sequences in the genome of P. parasitica by genome sequence alignment and identified a 203-bp P. parasitica-specific sequence, PpM34, that is present in 31 to 60 copies in the genome. The P. parasitica genome specificity of PpM34 was supported by PCR amplification of 24 genetically diverse strains of P. parasitica, 32 strains representing 12 other Phytophthora species, one Pythium species, six fungal species, and three bacterial species, all of which are plant pathogens. Our PCR and real-time PCR assays showed that the PpM34 sequence was highly sensitive in specifically detecting P. parasitica. Finally, we developed a PpM34-based high-efficiency recombinase polymerase amplification assay, which allowed us to specifically detect as little as 1 pg of P. parasitica total DNA from both pure cultures and infected Nicotiana benthamiana at 39°C using a fluorometric thermal cycler. The sensitivity, specificity, convenience, and rapidity of this assay represent a major improvement for early diagnosis of P. parasitica infection.
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Affiliation(s)
- Rongsheng Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ran Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenqin Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiapeng Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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Huang T, Han Y, Chen Y, Diao Z, Ma Y, Feng L, Wang D, Zhang R, Li J. RLP system: A single-tube two-step approach with dual amplification cascades for rapid identification of EGFR T790M. Anal Chim Acta 2024; 1287:342126. [PMID: 38182396 DOI: 10.1016/j.aca.2023.342126] [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: 09/29/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The detection of cancer gene mutations in biofluids plays a pivotal role in revolutionizing disease diagnosis. The presence of a large background of wild-type sequences poses a challenge to liquid biopsy of tumor mutation genes. Suppressing the detection of wild-type sequences can reduce their interference, however, due to the minimal difference between mutant and wild-type sequences (such as single nucleotide variants differing by only one nucleotide), how to suppress the detection of wild-type sequences to the greatest extent without compromising the sensitivity of mutant sequence detection remains to be explored. SIGNIFICANCE The RLP system addresses the incompatibility between RPA and RT-PCR reactions through a physical separation strategy. Besides, due to the remarkable flexibility of locked nucleic acid probes, the RLP system emerges as a potent tool for detecting mutations across diverse genes. It excels in sensitivity and speed, tolerates plasma matrix, and is cost-effective. This bodes well for advancing the field of precision medicine. RESULTS The recombinase-assisted locked nucleic acid (LNA) probe-mediated dual amplification biosensing platform (namely RLP), which combines recombinase polymerase amplification (RPA) and LNA clamp PCR method in one tube, enabling highly sensitive and selective detection of EGFR T790M mutation under the help of well-designed LNA probes. This technique can quantify DNA targets with a limit of detection (LoD) at the single copy level and identify point mutation with mutant allelic fractions as low as 0.007 % in 45 min. Moreover, RLP has the potential for the direct detection of plasma samples without the need for nucleic acid extraction and the cost of a single test is less than 1USD. Furthermore, the RLP system is a cascading dual amplification reaction conducted in a single tube, which eliminates the risk of cross-contamination associated with opening multiple tubes and ensures the reliability of the results.
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Affiliation(s)
- Tao Huang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.
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Park SB, Zhang Y. Development of Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay to Detect Species-Specific tlh and Pathogenic trh and tdh Genes of Vibrio parahaemolyticus. Pathogens 2024; 13:57. [PMID: 38251364 PMCID: PMC10819497 DOI: 10.3390/pathogens13010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Vibrio parahaemolyticus causes severe gastroenteritis in humans after consuming contaminated raw or undercooked seafood. A species-specific marker, the thermolabile hemolysin (tlh) gene, and two pathogenic markers, thermostable-related hemolysin (trh) and thermostable-direct hemolysin (tdh) genes, have been used to identify V. parahaemolyticus and determine its pathogenicity using both PCR and qPCR assays. To enable testing in field conditions with limited resources, this study aimed to develop a simple and rapid method to detect the species-specific (tlh) and pathogenic (trh and tdh) genes of V. parahaemolyticus using multienzyme isothermal rapid amplification (MIRA) combined with a lateral-flow dipstick (LFD). The amplification of the tlh, trh, and tdh genes could be completed within 20 min at temperatures ranging from 30 to 45 °C (p < 0.05). The test yielded positive results for V. parahaemolyticus but produced negative results for nine Vibrio species and eighteen foodborne pathogenic bacterial species. MIRA-LFD could detect 10 fg of DNA and 2 colony-forming units (CFU) of V. parahaemolyticus per reaction, demonstrating a sensitivity level comparable to that of qPCR, which can detect 10 fg of DNA and 2 CFU per reaction. Both MIRA-LFD and qPCR detected seven tlh-positive results from thirty-six oyster samples, whereas one positive result was obtained using the PCR assay. No positive results for the trh and tdh genes were obtained from any oyster samples using MIRA-LFD, PCR, and qPCR. This study suggests that MIRA-LFD is a simple and rapid method to detect species-specific and pathogenic genes of V. parahaemolyticus with high sensitivity.
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Affiliation(s)
- Seong Bin Park
- Experimental Seafood Processing Laboratory, Coastal Research & Extension Center, Mississippi State University, Pascagoula, MS 39567, USA
| | - Yan Zhang
- Experimental Seafood Processing Laboratory, Coastal Research & Extension Center, Mississippi State University, Pascagoula, MS 39567, USA
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Bai M, Wang Y, Zhang C, Wang Y, Wei J, Liao X, Wang J, Anfossi L, Wang Y. Nanobody-based immunomagnetic separation platform for rapid isolation and detection of Salmonella enteritidis in food samples. Food Chem 2023; 424:136416. [PMID: 37247600 DOI: 10.1016/j.foodchem.2023.136416] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Rapid separation and identification of Salmonella enteritidis (S. enteritidis) in food is of great importance to prevent outbreaks of foodborne diseases. Herein, by using O and H antigens as targets, an epitope-based bio-panning strategy was applied to isolate specific nanobodies towards S. enteritidis. This method constitutes an efficient way to obtain specific antibody fragments and test pairwise nanobodies. On this basis, a double nanobody-based sandwich enzyme-linked immunosorbent assay (ELISA) coupled with immunomagnetic separation (IMS) was developed to rapid enrich and detect S. enteritidis in food. The detection limit of the IMS-ELISA was 3.2 × 103 CFU/mL. In addition, 1 CFU of S. enteritidis in food samples can be detected after 4-h cultivation, which was shortened by 2 h after IMS. The IMS-ELISA strategy could avoid matrix interference and shorten the enrichment culture time, which has great potential for application in monitoring bacterial contamination in food.
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Affiliation(s)
- Mengfan Bai
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yueqi Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Cui Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ye Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Juan Wei
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xingrui Liao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Via Pietro Giuria 7, 10137 Turin, TO, Italy
| | - Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Wu S, Yuan J, Xu A, Wang L, Li Y, Lin J, Yue X, Xi X. A Lab-on-a-Tube Biosensor Combining Recombinase-Aided Amplification and CRISPR-Cas12a with Rotated Magnetic Extraction for Salmonella Detection. MICROMACHINES 2023; 14:830. [PMID: 37421063 DOI: 10.3390/mi14040830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Foodborne pathogenic bacteria threaten worldwide public health, and simple bacterial detection methods are in urgent need. Here, we established a lab-on-a-tube biosensor for simple, rapid, sensitive, and specific detection of foodborne bacteria. METHODS A rotatable Halbach cylinder magnet and an iron wire netting with magnetic silica beads (MSBs) were used for simple and effective extraction and purification of DNA from the target bacteria, and recombinase-aided amplification (RAA) was combined with clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins12a(CRISPR-Cas12a) to amplify DNA and generate fluorescent signal. First, 15 mL of the bacterial sample was centrifuged, and the bacterial pellet was lysed by protease to release target DNA. Then, DNA-MSB complexes were formed as the tube was intermittently rotated and distributed uniformly onto the iron wire netting inside the Halbach cylinder magnet. Finally, the purified DNA was amplified using RAA and quantitatively detected by the CRISPR-Cas12a assay. RESULTS This biosensor could quantitatively detect Salmonella in spiked milk samples in 75 min, with a lower detection limit of 6 CFU/mL. The fluorescent signal of 102 CFU/mL Salmonella Typhimurium was over 2000 RFU, while 104 CFU/mL Listeria monocytogenes, Bacillus cereus, and E. coli O157:H7 were selected as non-target bacteria and had signals less than 500 RFU (same as the negative control). CONCLUSIONS This lab-on-a-tube biosensor integrates cell lysis, DNA extraction, and RAA amplification in one 15 mL tube to simplify the operation and avoid contamination, making it suitable for low-concentration Salmonella detection.
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Affiliation(s)
- Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Jing Yuan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Ai Xu
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinge Xi
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
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10
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Wang J, Wang Y, Liu H, Hu X, Zhang M, Liu X, Ye H, Zeng H. An ultra-sensitive test strip combining with RPA and CRISPR/Cas12a system for the rapid detection of GM crops. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Identification of s9ap used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of Pleurotus eryngii. Mol Biol Rep 2023; 50:621-629. [PMID: 36370299 DOI: 10.1007/s11033-022-07562-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/25/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Pleurotus eryngii is a kind of edible fungi with good quality, and it is popular among consumers. At present, some adulterated edible fungi are available in the market. The rights and interests of consumers can be ensured by establishing a practical edible fungi detection system. Among the existing methods for detecting food adulteration, endogenous reference gene amplification is convenient and reliable. However, no ideal endogenous reference gene is available for P. eryngii. METHODS AND RESULTS In this study, s9ap was screened as an endogenous reference gene through sequence alignment. Qualitative and quantitative PCR analysis of this gene was carried out in one P. eryngii variety and 18 other species. The detection limit of quantitative PCR was 400 pg, and no s9ap amplification products were detected in the 18 other species. CONCLUSIONS This study confirmed that s9ap was an ideal endogenous reference gene for the detection of P. eryngii. This method was also suitable for processed food products.
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Zhou S, Zheng X, Yang Z, Huang Q, Yi J, Su L, Guo B, Xiu Y. Development of Two Recombinase Polymerase Amplification EXO (RPA-EXO) and Lateral Flow Dipstick (RPA-LFD) Techniques for the Rapid Visual Detection of Aeromonas salmonicida. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1094-1109. [PMID: 36192520 DOI: 10.1007/s10126-022-10170-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Aeromonas salmonicida is the pathogen underlying furunculosis, causing a septicemic infection that influences both salmonid and non-salmonid fish. Early diagnosis of these contagions is essential for disease surveillance and prevention, so a rapid and sensitive approach is needed. Herein, a recombinase polymerase amplification EXO (RPA-EXO) assay and RPA with a lateral flow dipstick (RPA-LFD) were produced for testing A. salmonicida. The RPA-EXO and RPA-LFD primer sets were devised based on the conserved fragment sequence of the vapA gene. Then, RPA-EXO and RPA-LFD reaction systems were established, and the reaction temperature and time were optimized. After optimization, the RPA-EXO method was capable of testing A. salmonicida within 10 min, and the RPA-LFD method could detect A. salmonicida in only 5 min. The RPA-EXO and RPA-LFD methods exhibited high specificity with no cross-reaction with other strains. To assess sensitivity, a partial vapA gene was cloned, and serial plasmid dilutions were created ranging from 1 × 106 to 1 × 10-1 copies/μL. The detection limit of RPA-EXO was 1 × 102 copies/μL, and the detection limit of RPA-LFD was 1 copy/μL. For spiked turbot tissue samples, the sensitivity detection of A. salmonicida was 1.2 × 101 CFU/mL and 1.2 CFU/mL by RPA-EXO and RPA-LFD, respectively. In comparative analyses of clinical samples, the diagnostic results of RPA-EXO and RPA-LFD were compared with those of the standard conventional PCR test and showed nearly 100% consistency. Therefore, our RPA-EXO and RPA-LFD assays exhibited excellent specificity and sensitivity, which provided two simple, fast and dependable methods to conduct large-scale field investigations of A. salmonicida in resource-limited settings.
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Affiliation(s)
- Shun Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xujia Zheng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zongrui Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingyuan Yi
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Su
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baoshan Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yunji Xiu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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13
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Park SB, Chang SKC. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay To Detect Hemolysin Gene of Vibrio vulnificus in Oysters. J Food Prot 2022; 85:1716-1725. [PMID: 35435978 DOI: 10.4315/jfp-21-455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/01/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Vibrio vulnificus inhabits estuarine waters around the world and can cause severe infections in people who eat contaminated raw or undercooked oysters. Although current detection methods are sensitive and specific, there are continuous demands for the development of rapid and accurate methods without a trained operator and equipment in the field conditions. Herein, we developed a simple and rapid method by detecting the hemolysin (vvh) gene of V. vulnificus by using recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD). The RPA-LFD could detect 100 fg of DNA (P < 0.05) and 20 CFU of V. vulnificus per reaction within 30 min (P < 0.01) and showed the result with incubation temperature ranges from 30 to 45°C (P < 0.001). The test was specific only to V. vulnificus and was not responsive to 10 other closely related Vibrio species and 18 foodborne pathogenic bacteria. Compared with PCR, quantitative PCR, and colony hybridization assays by using naturally contaminated oyster samples, our RPA-LFD showed the same detection ability as quantitative PCR assay. Therefore, the current RPA-LFD would be a valuable tool to detect V. vulnificus in oysters, especially in field conditions. HIGHLIGHTS
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Affiliation(s)
- Seong Bin Park
- Experimental Seafood Processing Laboratory, Coastal Research and Extension Center, Mississippi State University, Pascagula, Mississippi 39567
| | - Sam K C Chang
- Experimental Seafood Processing Laboratory, Coastal Research and Extension Center, Mississippi State University, Pascagula, Mississippi 39567.,Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi 39762, USA
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14
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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15
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Tan M, Liao C, Liang L, Yi X, Zhou Z, Wei G. Recent advances in recombinase polymerase amplification: Principle, advantages, disadvantages and applications. Front Cell Infect Microbiol 2022; 12:1019071. [PMID: 36519130 PMCID: PMC9742450 DOI: 10.3389/fcimb.2022.1019071] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
After the outbreak of SARS-CoV-2, nucleic acid testing quickly entered people's lives. In addition to the polymerase chain reaction (PCR) which was commonly used in nucleic acid testing, isothermal amplification methods were also important nucleic acid testing methods. Among several common isothermal amplification methods like displaced amplification, rolling circle amplification, and so on, recombinase polymerase amplification (RPA) was recently paid more attention to. It had the advantages like a simple operation, fast amplification speed, and reaction at 37-42°C, et al. So it was very suitable for field detection. However, there were still some disadvantages to RPA. Herein, our review mainly summarized the principle, advantages, and disadvantages of RPA. The specific applications of RPA in bacterial detection, fungi detection, virus detection, parasite detection, drug resistance gene detection, genetically modified food detection, and SARS-CoV-2 detection were also described. It was hoped that the latest research progress on RPA could be better delivered to the readers who were interested in RPA.
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Chatterjee S, Mukhopadhyay S. Recent advances of lateral flow immunoassay components as “point of need”. J Immunoassay Immunochem 2022; 43:579-604. [DOI: 10.1080/15321819.2022.2122063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Susraba Chatterjee
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R.Avenue, Kolkata 700073, West Bengal
| | - Sumi Mukhopadhyay
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R.Avenue, Kolkata 700073, West Bengal
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17
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Wang YL, Zhang X, Wang Q, Liu PX, Tang W, Guo R, Zhang HY, Chen ZG, Han XG, Jiang W. Rapid and visual detection of Staphylococcus aureus in milk using a recombinase polymerase amplification-lateral flow assay combined with immunomagnetic separation. J Appl Microbiol 2022; 133:3741-3754. [PMID: 36073301 DOI: 10.1111/jam.15811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/27/2022]
Abstract
AIMS The aim of this study was to develop a novel approach using lateral flow recombinase polymerase amplification (RPA-LF) combined with immunomagnetic separation (IMS) for the rapid detection of Staphylococcus aureus in milk. METHODS AND RESULTS Under optimum conditions, the average capture efficiency values (CEs) for S. aureus strains (104 CFU ml-1 ) was above 95.0% in PBST and ~80% in milk within 45 min with 0.7 mg immunomagnetic beads. The RPA-LF assay, which comprised DNA amplification via RPA at 39°C for 10 min and visualization of the amplicons through LF strips for 5 min, detected S. aureus within 15 min. The method only detected S. aureus and did not show cross-reaction with other bacteria, exhibiting a high level of specificity. Sensitivity experiments confirmed a detection limit of RPA-LF assay as low as 600 fg reaction-1 for the S. aureus genome (corresponding to approximately 36 CFU of S. aureus), which was about 16.7-fold more sensitive than that of the conventional PCR method. When RPA-LF was used in combination with IMS to detect S. aureus inoculated into artificially contaminated milk, it exhibited a detection limit of approximately 40 CFU reaction-1 . CONCLUSIONS The newly developed IMS-RPA-LF method enabled detection of S. aureus at levels as low as 40 CFU reaction-1 in milk samples without culture enrichment for an overall testing time of only 70 min. SIGNIFICANCE AND IMPACT OF THE STUDY The newly developed IMS-RPA-LF assay effectively combines sample preparation, amplification, and detection into a single platform. Because of its high sensitivity, specificity, and speed, the IMS-RPA-LF assay will have important implications for the rapid detection of S. aureus in contaminated food.
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Affiliation(s)
- Ya-Lei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xin Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Quan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Peng-Xuan Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wei Tang
- Department of Electronic Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai-Yang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhao-Guo Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xian-Gan Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wei Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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18
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Liu S, Zhao K, Huang M, Zeng M, Deng Y, Li S, Chen H, Li W, Chen Z. Research progress on detection techniques for point-of-care testing of foodborne pathogens. Front Bioeng Biotechnol 2022; 10:958134. [PMID: 36003541 PMCID: PMC9393618 DOI: 10.3389/fbioe.2022.958134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022] Open
Abstract
The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.
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Affiliation(s)
- Sha Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Kaixuan Zhao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Meiyuan Huang
- Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Department of Pathology, Central South University, Zhuzhou, China
| | - Meimei Zeng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Wen Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
- *Correspondence: Zhu Chen,
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Li JY, Chen XP, Tie YQ, Sun XL, Zhang RQ, He AN, Nie MZ, Fan GH, Li FY, Tian FY, Shen XX, Feng ZS, Ma XJ. Detection of low-load Epstein-Barr virus in blood samples by enriched recombinase aided amplification assay. AMB Express 2022; 12:71. [PMID: 35689713 PMCID: PMC9188631 DOI: 10.1186/s13568-022-01415-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Epstein-Barr virus (EBV), a common human γ-herpesvirus, infects more than 90% of adults worldwide. The purpose of this study was to establish a novel EBV detection method by combining the recombinase aided amplification (RAA) assay with an initial enrichment step that utilizes magnetic beads coated with a recombinant human mannan-binding lectin (rhMBL, M1 protein). An M1 protein–protein A magnetic bead complex (M1 beads) was prepared and used to achieve separation and enrichment of EBV from blood. After nucleic acid extraction, DNA was amplified by RAA. Using 388 whole blood samples and 1 serum sample, we explored the specificity, sensitivity and applicability of the newly developed detection method and compared it with commercial quantitative real-time polymerase chain reaction (qPCR) following M1 bead enrichment, traditional qPCR and traditional RAA. After enrichment, the positivity rate of EBV was increased from 15.94% to 17.74% by RAA (P < 0.05) and from 7.20% to 15.17% by qPCR (P < 0.05). The viral loads after enrichment were increased by 1.13 to 23.19-fold (P < 0.05). Our data demonstrates that an RAA assay incorporating M1 bead enrichment is a promising tool for detecting low EBV viral loads in blood samples that will facilitate an early response to EBV infection. The RAA with an enrichment step that utilizes magnetic beads coated with M1 protein. A very effective method for detecting low-load virus in blood samples. The first report describing virus detection using this method.
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Affiliation(s)
- Jing-Yi Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yan-Qing Tie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China
| | - Xiu-Li Sun
- Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - An-Na He
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Ming-Zhu Nie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Tian
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
| | - Zhi-Shan Feng
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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20
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Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
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Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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21
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Moon YJ, Lee SY, Oh SW. A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens. Foods 2022; 11:foods11030322. [PMID: 35159473 PMCID: PMC8833899 DOI: 10.3390/foods11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.
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22
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Li J, Zhong Q, Shang MY, Li M, Jiang YS, Zou JJ, Ma SS, Huang Q, Lu WP. Preliminary Evaluation of Rapid Visual Identification of Burkholderia pseudomallei Using a Newly Developed Lateral Flow Strip-Based Recombinase Polymerase Amplification (LF-RPA) System. Front Cell Infect Microbiol 2022; 11:804737. [PMID: 35118011 PMCID: PMC8804217 DOI: 10.3389/fcimb.2021.804737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei is an important infectious disease pathogen that can cause melioidosis. Melioidosis is mainly prevalent in Thailand, northern Australia and southern China and has become a global public health problem. Early identification of B. pseudomallei is of great significance for the diagnosis and prognosis of melioidosis. In this study, a simple and visual device combined with lateral flow strip-based recombinase polymerase amplification (LF-RPA) was developed, and the utility of the LF-RPA assay for identifying B. pseudomallei was evaluated. In order to screen out the optimal primer probe, a total of 16 pairs of specific primers targeting the orf2 gene of B. pseudomallei type III secretion system (T3SS) cluster genes were designed for screening, and F1/R3 was selected as an optimal set of primers for the identification of B. pseudomallei, and parameters for LF-RPA were optimized. The LF-RPA can be amplified at 30-45°C and complete the entire reaction in 5-30 min. This reaction does not cross-amplify the DNA of other non-B. pseudomallei species. The limit of detection (LOD) of this assay for B. pseudomallei genomic DNA was as low as 30 femtograms (fg), which was comparable to the results of real-time PCR. Moreover, 21 clinical B. pseudomallei isolates identified by 16S rRNA gene sequencing were retrospectively confirmed by the newly developed LF-RPA system. Our results showed that the newly developed LF-RPA system has a simple and short time of operation and has good application prospect in the identification of B. pseudomallei.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Laboratory Medicine, Ministry of Education (M.O.E.) Key Laboratory of Laboratory Medicine Diagnostics, Chongqing Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuan-Su Jiang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jia-Jun Zou
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shan-Shan Ma
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
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23
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Feng ZS, Li JY, Zhang JY, Li FY, Guan HX, Zhang RQ, Liu H, Guo Q, Shen XX, Kan B, Ma XJ. Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus. J Microbiol Methods 2022; 193:106404. [PMID: 34990645 DOI: 10.1016/j.mimet.2021.106404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to detect V. parahaemolyticus. The RAA reaction was carried out successfully at 39 °C within 30 min. The sensitivity of the RAA assay was 101 copies/μL using the recombinant plasmid and 10-3 ng/μL using the V. parahaemolyticus strain. In addition, RAA directly detected 7 × 103 CFU/mL of simulated fecal samples and 0.1 CFU/mL after enrichment for 4 h. The sensitivity and specificity of the RAA assay using fecal and fish samples were 100% similar to that of the real-time PCR. We conclude that the RAA assay is an ideal screening method for detecting V. parahaemolyticus due to its rapidity, high accuracy, and simplicity in operation.
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Affiliation(s)
- Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China
| | - Jing-Yi Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing-Yun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Feng-Yu Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hong-Xia Guan
- Wuxi Center for Disease Control and Prevention, Wuxi 214023, Jiangsu, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo255049, Shandong, China
| | - Qi Guo
- Laboratory of Virology, Beijing Key Laboratory ofEtiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing 100020, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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24
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Zhou S, Huang Q, Yu M, Li Y, Zheng X, Xiu Y. Rapid visual detection of Aeromonas salmonicida by loop-mediated isothermal amplification with hydroxynaphthol blue dye. JOURNAL OF FISH DISEASES 2021; 44:1993-2001. [PMID: 34411329 DOI: 10.1111/jfd.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
To make crucial prevention, reduce fish losses and minimize the economic damage of diseases on the fish farm owners, a rapid detection of fish pathogens is mandatory. In this study, a loop-mediated isothermal amplification assay combined with hydroxynaphthol blue dye (LAMP-HNB) was developed and used for the rapid detection of Aeromonas salmonicida that caused significant economic losses in fish farming. Firstly, a pair of outer and inner primers specific for conserved fragment of vapA gene in A. salmonicida were designed and synthesized. Secondly, by optimizing the reaction conditions including reaction temperature, time, Mg2+ concentration, dNTP concentration and primer ratio, a LAMP-HNB assay was successfully established for the detection of A. salmoncida. Thirdly, the assay showed good specificity with no false-positive and false-negative results, and good sensitivity with the detection limit of 3.077 × 10-6 ng/μl, which was 102 times more sensitive than the conventional PCR. Finally, the LAMP-HNB assay was validated by the fish samples inoculated with different concentrations of A. salmoncida. This is the first development of rapid visual detection of A. salmonicida based on LAMP-HNB assay, which has great application prospect and market for diagnostic testing, health certification and active surveillance programmers.
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Affiliation(s)
- Shun Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qing Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Mingming Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Ying Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xujia Zheng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yunji Xiu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
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25
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Ying N, Wang Y, Song X, Yang L, Qin B, Wu Y, Fang W. Lateral flow colorimetric biosensor for detection of Vibrio parahaemolyticus based on hybridization chain reaction and aptamer. Mikrochim Acta 2021; 188:381. [PMID: 34654957 DOI: 10.1007/s00604-021-05031-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is the causative agent for acute hepatopancreatic necrosis disease (AHPND) of shrimp, and it is also a common seafood-borne pathogen for humans. Rapid and accurate identification of V. parahaemolyticus is helpful to diagnose the AHPND and ensure food safety. Common detection methods suffer the deficiency of time-consuming and complexed operation. Based on the increased development of aptamer and our previous study, a new detection assay of V. parahaemolyticus was introduced, in which the aptamer combined with magnetic nanoparticles (MNPs) was the recognizer, hybridization chain reaction (HCR) was the signal amplifier, and lateral flow nucleotide biosensor (LFNB) was the signal exporter. The assay possessed high specificity of distinguishing the target with other bacteria, and the calculated limit of detection was 2.6 × 103 cells. Furthermore, the whole process just needs 67 min, free of thermocycle instruments and signal readout instruments, which means it is suitable for low-resource laboratories or districts.
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Affiliation(s)
- Na Ying
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Yuan Wang
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Xuefeng Song
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Liguo Yang
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Bo Qin
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Yanqing Wu
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China
| | - Wenhong Fang
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, 200090, China.
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26
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Sensitively and quickly detecting Vibrio vulnificus by real time recombinase polymerase amplification targeted to vvhA gene. Mol Cell Probes 2021; 57:101726. [PMID: 33789126 DOI: 10.1016/j.mcp.2021.101726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/28/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022]
Abstract
Vibrio vulnificus (V. vulnificus) is a Gram-negative bacterium living in warm and salty water. This marine bacterium could produce hemolysin (VVH), which often causes serious gastroenteritis or septicemia when people contact to seawater or seafood containing V. vulnificus. Timely diagnosis is regard as essential to disease surveillance. In this paper, we aimed at developing a quick and sensitive method for the detection of Vibrio vulnificus using real time recombinase polymerase amplification (real time RPA). Specific primers and an exo probe were designed on the basis of the vvhA gene sequence available in GenBank. Target DNA could be amplified and labeled with specific fluorophore within 20 min at 38 °C. The method exhibited a high specificity, only detecting Vibrio vulnificus and not showing cross-reaction with other bacteria. The sensitivity of this method was 2 pg per reaction (20 μL) for DNA, or 200 copies per reaction (20 μL) for standard plasmid. The detection limit (LOD) stated as the target level that would be detected 95% of the time and estimated was 1.58 × 102 copies by fit of the probit to the results of 8 replicates in different concentration. For quantitative analysis of the real time RPA, the second order polynomial regression was adopted in our study. The results showed the correlation coefficients were raised above 0.98, which suggested this model might be a better choice for the quantitative analysis of real time RPA compared to the routine linear regression model. For artificially contaminated plasma samples, Vibrio vulnificus could be detected within 16 min by real time RPA at concentration as low as 1.2 × 102 CFU/mL or 2.4 CFU per reaction (20 μL). Thus, the real time RPA method established in this study shows great potential for detecting Vibrio vulnificus in the research laboratory and disease diagnosis.
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27
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Anupama KP, Nayak A, Karunasagar I, Karunasagar I, Maiti B. Evaluation of loop-mediated isothermal amplification assay along with conventional and real-time PCR assay for sensitive detection of pathogenic Vibrio parahaemolyticus from seafood sample without enrichment. Mol Biol Rep 2021; 48:1009-1016. [PMID: 33423185 PMCID: PMC7796815 DOI: 10.1007/s11033-020-06116-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/20/2020] [Indexed: 12/04/2022]
Abstract
The primary reason for foodborne illness is improper seafood safety testing, and hence, an appropriate tool for testing is the key to control the outbreaks. The current study aimed to develop a loop-mediated isothermal amplification (LAMP) assay to detect pathogenic Vibrio parahaemolyticus, important foodborne pathogen, targeting tdh, and trh genes. The specificity of the LAMP assay was good without any false-positive and false-negative results. The assay was highly sensitive and could detect the pathogenic V. parahaemolyticus as low as 1 CFU/reaction in spiked seafood samples and 1 pg of extracted DNA. Out of 62 seafood samples from India’s southwest coastal region tested with LAMP assay, eight (12.9%) were positive for trh, and seven (11.29%) samples were positive tdh gene. LAMP-based on tdh and trh was found to be significantly more sensitive (p < 0.05) than conventional PCR and nearly equal sensitive as real-time PCR (RT-PCR) for the detection of pathogenic V. parahaemolyticus. Our study shows that LAMP assay can be a better approach as a point-of-care (POC) diagnostic tool and could detect pathogenic V. parahaemolyticus on seafood samples directly without enrichment and isolation. The high sensitivity and simplicity make LAMP assay a better alternative method than the conventional method and RT-PCR for the detection of pathogens. LAMP assay can be considered as a good alternative to PCR for the routine detection of pathogenic V. parahaemolyticus in seafood.
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Affiliation(s)
- Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Ashwath Nayak
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India.
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28
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A polymerase chain reaction based lateral flow test strip with propidium monoazide for detection of viable Vibrio parahaemolyticus in codfish. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Wang Z, Cai R, Gao Z, Yuan Y, Yue T. Immunomagnetic separation: An effective pretreatment technology for isolation and enrichment in food microorganisms detection. Compr Rev Food Sci Food Saf 2020; 19:3802-3824. [PMID: 33337037 DOI: 10.1111/1541-4337.12656] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022]
Abstract
The high efficiency and accurate detection of foodborne pathogens and spoilage microorganisms in food are a task of great social, economic, and public health importance. However, the contamination levels of target bacteria in food samples are very low. Owing to the background interference of food ingredients and negative impact of nontarget flora, the establishment of efficient pretreatment techniques is very crucial for the detection of food microorganisms. With the significant advantages of high specificity and great separation efficiency, immunomagnetic separation (IMS) assay based on immunomagnetic particles (IMPs) has been considered as a powerful system for the separation and enrichment of target bacteria. This paper mainly focuses on the development of IMS as well as their application in food microorganisms detection. First, the basic principle of IMS in the concentration of food bacteria is presented. Second, the effect of different factors, including the sizes of magnetic particles (MPs), immobilization of antibody and operation parameters (the molar ratio of antibody to MPs, the amount of IMPs, incubation time, and bacteria concentration) on the immunocapture efficiency of IMPs are discussed. The performance of IMPs in different food samples is also evaluated. Finally, the combination of IMS and various kinds of detection methods (immunology-based methods, nucleic acid-based methods, fluorescence methods, and biosensors) to detect pathogenic and spoilage organisms is summarized. The challenges and future trends of IMS are also proposed. As an effective pretreatment technique, IMS can improve the detection sensitivity and shorten their testing time, thus exhibiting broad prospect in the field of food bacteria detection.
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Affiliation(s)
- Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi, China.,National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi, China
| | - Rui Cai
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi, China.,National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi, China
| | - Zhenpeng Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi, China.,National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi, China.,National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi, China.,National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi, China
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30
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Yang X, Zhao P, Dong Y, Chen S, Shen H, Jiang G, Zhu H, Dong J, Gao S. An isothermal recombinase polymerase amplification and lateral flow strip combined method for rapid on-site detection of Vibrio vulnificus in raw seafood. Food Microbiol 2020; 98:103664. [PMID: 33875195 DOI: 10.1016/j.fm.2020.103664] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Vibrio vulnificus is an important foodborne pathogenic bacterium that mainly contaminates seafood. Rapid and accurate technologies that suitable for on-site detection are critical for effective control of its spreading. Conventional detection methods and polymerase chain reaction (PCR)-based and qPCR-based approaches have application limitations in on-site scenarios. Application of loop-mediated isothermal amplification (LAMP) technology was a good step towards the on-site detection. In this study, a recombinase polymerase amplification (RPA)-based detection method for V. vulnificus was developed combining with lateral flow strip (LFS) for visualized signal. The method targeted the conservative empV gene encoding the extracellular metalloproteinase, and finished detection in 35 min at a conveniently low temperature of 37 °C. It showed good specificity and an excellent sensitivity of 2 copies of the genome or 10-1 colony forming unit (CFU) per reaction, or 1 CFU/10 g in spiked food samples with enrichment. The method tolerated unpurified templates directly from sample boiling, which added the convenience of the overall procedure. Application of the RPA-LFS method for clinical samples showed accurate and consistent detection results compared to bioassay and quantitative PCR. This RPA-LFS combined method is well suited for on-site detection of V. vulnificus.
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Affiliation(s)
- Xiaohan Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research By Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yu Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Shiqi Chen
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, 226007, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, 226007, China
| | - Hai Zhu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China.
| | - Song Gao
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
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31
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Campbell VR, Carson MS, Lao A, Maran K, Yang EJ, Kamei DT. Point-of-Need Diagnostics for Foodborne Pathogen Screening. SLAS Technol 2020; 26:55-79. [PMID: 33012245 DOI: 10.1177/2472630320962003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Foodborne illness is a major public health issue that results in millions of global infections annually. The burden of such illness sits mostly with developing countries, as access to advanced laboratory equipment and skilled lab technicians, as well as consistent power sources, is limited and expensive. Current gold standards in foodborne pathogen screening involve labor-intensive sample enrichment steps, pathogen isolation and purification, and costly readout machinery. Overall, time to detection can take multiple days, excluding the time it takes to ship samples to off-site laboratories. Efforts have been made to simplify the workflow of such tests by integrating multiple steps of foodborne pathogen screening procedures into a singular device, as well as implementing more point-of-need readout methods. In this review, we explore recent advancements in developing point-of-need devices for foodborne pathogen screening. We discuss the detection of surface markers, nucleic acids, and metabolic products using both paper-based and microfluidic devices, focusing primarily on developments that have been made between 2015 and mid-2020.
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Affiliation(s)
- Veronica R Campbell
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
| | - Mariam S Carson
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
| | - Amelia Lao
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
| | - Kajal Maran
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
| | - Eric J Yang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
| | - Daniel T Kamei
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, USA
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32
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Landaverde L, Wong W, Hernandez G, Fan A, Klapperich C. Method for the elucidation of LAMP products captured on lateral flow strips in a point of care test for HPV 16. Anal Bioanal Chem 2020; 412:6199-6209. [PMID: 32488390 PMCID: PMC7266737 DOI: 10.1007/s00216-020-02702-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Loop-mediated amplification (LAMP) is an isothermal amplification technique favored in diagnostics and point-of-care work due to its high sensitivity and ability to run in isothermal conditions. In addition, a visual readout by lateral flow strips (LFS) can be used in conjunction with LAMP, making the assay accessible at the point-of-care. However, the amplicons resulting from a LAMP reaction varied in length and shape, making them undiscernible on a double-stranded DNA intercalating dye stained gel. Standard characterization techniques also do not identify which amplicons specifically bind to the LFS, which generate the visual readout. We aimed to standardize our characterization of LAMP products during assay development by using fluorescein amidite (FAM) and biotin-tagged loop forward and backward primers during assay development. A pvuII restriction enzyme digest is applied to the LAMP products. FAM-tagged bands are directly correlated with the LFS visual readout. We applied this assay development workflow for an HPV 16 assay using both plasmid DNA and clinical samples to demonstrate proof of concept for generalized assay development work.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Winnie Wong
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Gabriela Hernandez
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA.
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Rapid visual detection of Vibrio parahaemolyticus in seafood samples by loop-mediated isothermal amplification with hydroxynaphthol blue dye. World J Microbiol Biotechnol 2020; 36:76. [PMID: 32390085 DOI: 10.1007/s11274-020-02851-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
The detection and monitoring of Vibrio parahaemolyticus pathogen in aquatic foods have become essential for preventing outbreaks. In this study, loop-mediated isothermal amplification (LAMP) assay with the azo dye, hydroxynaphthol blue (HNB) was developed targeting species-specific tlh gene. The assay was carried out on 62 seafood samples that included clam and shrimp and compared with conventional LAMP assay performed with the commonly used fluorescent dye, conventional PCR, and real-time PCR (RT-PCR). Of 62 samples studied for tlh gene, 32 (51.61%) gave positive by HNB-LAMP, which comprised 22 (70.96%) clam samples and 10 (32.25%) shrimp samples. The HNB-LAMP assay was found to be highly sensitive, specific, and superior to conventional PCR (p > 0.05). RT-PCR presented higher sensitivity than HNB-LAMP; however, it has the limitation of being cost-intensive and requiring technical expertise to perform. HNB-LAMP is affordable, rapid, simple, and easy to perform, allowing naked eye visualization.
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