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Paenkaew S, Poommouang A, Pradit W, Chomdej S, Nganvongpanit K, Siengdee P, Buddhachat K. Feasibility of implementing RPA coupled with CRISPR-Cas12a (RPA-Cas12a) for Hepatozoon canis detection in dogs. Vet Parasitol 2024; 331:110298. [PMID: 39217761 DOI: 10.1016/j.vetpar.2024.110298] [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: 05/22/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Hepatozoonosis, caused by the protozoan Hepatozoon canis, is a prevalent blood disease affecting owned and stray dogs and cats. The prevalence of these parasites among companion animals in Thailand remains poorly understood. Diagnosing the old-world form of the disease is challenging due to the wide range of nonspecific clinical signs and the reliance on finding low levels of Hepatozoon gamonts in blood smears for conventional diagnosis. PCR demonstrates high specificity and sensitivity but it requires sophisticated instrumentation. Therefore, we established recombinase polymerase amplification (RPA) coupled with Cas12a for H. canis detection based on 18S rRNA. Our findings showed that RPA-Cas12a using gRNA_H was highly specific to H. canis, without yielding positives for other pathogen species including Babesia species. Even in cases of co-infection, RPA-Cas12a only detected positives in samples containing H. canis. This approach detected minimal amounts of H. canis18S rRNA-harboring plasmid at 10 copies per reaction, whereas plasmid-spiked canine blood enabled detection at a minimal amount of 100 copies per reaction. The performance of RPA-Cas12a was validated by comparing it with quantitative PCR-high resolution melting analysis (qPCR-HRM) and sequencing based on 35 canine blood samples. RPA-Cas12a demonstrated precision and accuracy values of 94 % and 90 %, respectively comparable to qPCR-HRM. Overall, these results indicate that RPA-Cas12a serves as a promising tool for H. canis detection as indicated by comparable performance to qPCR-HRM and is suitable for implementation in small animal hospitals or clinics due to its minimal resource requirements, thereby contributing to effective diagnosis and treatment for infected dogs.
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Affiliation(s)
- Suphaporn Paenkaew
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Anocha Poommouang
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Puntita Siengdee
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Innovation and Technology for Detection and Advanced Materials (ITDAM), Naresuan University, Phitsanulok 65000, Thailand.
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Duan J, Ma H, Wang W, Li Y, Shi X, Chen X, Kageyama K, Yan Y, Li M. A rapid quarantine approach for the pathogenic and invasive Phytophthora species associated with imported fruits in China. PEST MANAGEMENT SCIENCE 2024. [PMID: 39073206 DOI: 10.1002/ps.8340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Phytophthora spp. represent a pivotal genus of plant pathogens with a global distribution, exerting significant deleterious effects on food safety and forestry ecosystems. Numerous pathogenic and invasive Phytophthora species, introduced through imported fruits, have been frequently detected at Chinese ports. With the rise in global trade activities, the plant quarantine of imported fruits is becoming increasingly important but challenging. Fast, simple, and labor-saving techniques are necessary and anticipated. RESUITS A polymerase chain reaction restriction fragment length polymorphism capillary electrophoresis (PCR-RFLP-CE) technology-based quarantine approach was developed for 16 Phytophthora species associated with the imported fruits in China. The Ypt1 gene, exhibiting abundant interspecific variations, was selected as the marker gene for PCR. The restriction endonuclease AluI was proven to be capable and compatible in simultaneously separating different Phytophthora species during CE. By combining with a fast and efficient DNA extraction kit, the developed PCR-RFLP-CE technique was successfully applied to identify Phytophthora species in artificially infested fruits. CONCLUSION We provide a quick, practical, and high-throughput detection approach for hazardous and invasive Phytophthora species associated with imported fruits in China. This strategy can give good convenience and technological support for carrying out massive quarantine activities at Chinese ports. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jiaying Duan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haiting Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wenxin Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yaling Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyu Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaowei Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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3
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Tan M, Liang L, Liao C, Zhou Z, Long S, Yi X, Wang C, Wei C, Cai J, Li X, Wei G. A rapid and ultra-sensitive dual readout platform for Klebsiella pneumoniae detection based on RPA-CRISPR/Cas12a. Front Cell Infect Microbiol 2024; 14:1362513. [PMID: 38994004 PMCID: PMC11236598 DOI: 10.3389/fcimb.2024.1362513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
The bacterium Klebsiella pneumoniae (Kp) was the primary pathogen of hospital-acquired infection, but the current detection method could not rapidly and conveniently identify Kp. Recombinase polymerase amplification (RPA) was a fast and convenient isothermal amplification technology, and the clustered regularly interspaced short palindromic repeats (CRISPR) system could rapidly amplify the signal of RPA and improve its limit of detection (LOD). In this study, we designed three pairs of RPA primers for the rcsA gene of Kp, amplified the RPA signal through single-strand DNA reporter cleavage by CRISPR/Cas12a, and finally analyzed the cleavage signal using fluorescence detection (FD) and lateral flow test strips (LFTS). Our results indicated that the RPA-CRISPR/Cas12a platform could specifically identify Kp from eleven common clinical pathogens. The LOD of FD and LFTS were 1 fg/μL and 10 fg/μL, respectively. In clinical sample testing, the RPA-CRISPR/Cas12a platform was consistent with the culture method and qPCR method, and its sensitivity and specificity were 100% (16/16) and 100% (9/9), respectively. With the advantages of detection speed, simplicity, and accuracy, the RPA-CRISPR/Cas12a platform was expected to be a convenient tool for the early clinical detection of Kp.
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Affiliation(s)
- Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Shaoping Long
- Department of Clinical Laboratory, Baise People's Hospital, Guangxi, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Chunfang Wang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Caiheng Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
| | - Jinyuan Cai
- School of Food and Chemical Engineering, Liuzhou Institute of Technology, Guangxi, China
| | - Xuebin Li
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Guangxi, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Guangxi, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Guangxi, China
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Li Z, Feng W, Zhu Z, Lu S, Lin M, Dong J, Wang Z, Liu F, Chen Q. Cas-OPRAD: a one-pot RPA/PCR CRISPR/Cas12 assay for on-site Phytophthora root rot detection. Front Microbiol 2024; 15:1390422. [PMID: 38903797 PMCID: PMC11188302 DOI: 10.3389/fmicb.2024.1390422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Phytophthora sojae is a devastating plant pathogen that causes soybean Phytophthora root rot worldwide. Early on-site and accurate detection of the causal pathogen is critical for successful management. In this study, we have developed a novel and specific one-pot RPA/PCR-CRISPR/Cas12 assay for on-site detection (Cas-OPRAD) of Phytophthora root rot (P. sojae). Compared to the traditional RPA/PCR detection methods, the Cas-OPRAD assay has significant detection performance. The Cas-OPRAD platform has excellent specificity to distinguish 33 P. sojae from closely related oomycetes or fungal species. The PCR-Cas12a assay had a consistent detection limit of 100 pg. μL-1, while the RPA-Cas12a assay achieved a detection limit of 10 pg. μL-1. Furthermore, the Cas-OPRAD assay was equipped with a lateral flow assay for on-site diagnosis and enabled the visual detection of P. sojae on the infected field soybean samples. This assay provides a simple, efficient, rapid (<1 h), and visual detection platform for diagnosing Phytophthora root rot based on the one-pot CRISPR/Cas12a assay. Our work provides important methods for early and accurate on-site detection of Phytophthora root rot in the field or customs fields.
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Affiliation(s)
- Zhiting Li
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Zaobing Zhu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Shengdan Lu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Jiali Dong
- Sanya Institute of China Agricultural University, Sanya, China
| | - Zhixin Wang
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Fuxiu Liu
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
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Dong J, Feng W, Lin M, Chen S, Liu X, Wang X, Chen Q. Comparative Evaluation of PCR-Based, LAMP and RPA-CRISPR/Cas12a Assays for the Rapid Detection of Diaporthe aspalathi. Int J Mol Sci 2024; 25:5773. [PMID: 38891961 PMCID: PMC11172161 DOI: 10.3390/ijms25115773] [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: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Southern stem canker (SSC) of soybean, attributable to the fungal pathogen Diaporthe aspalathi, results in considerable losses of soybean in the field and has damaged production in several of the main soybean-producing countries worldwide. Early and precise identification of the causal pathogen is imperative for effective disease management. In this study, we performed an RPA-CRISPR/Cas12a, as well as LAMP, PCR and real-time PCR assays to verify and compare their sensitivity, specificity and simplicity and the practicality of the reactions. We screened crRNAs targeting a specific single-copy gene, and optimized the reagent concentrations, incubation temperatures and times for the conventional PCR, real-time PCR, LAMP, RPA and Cas12a cleavage stages for the detection of D. aspalathi. In comparison with the PCR-based assays, two thermostatic detection technologies, LAMP and RPA-CRISPR/Cas12a, led to higher specificity and sensitivity. The sensitivity of the LAMP assay could reach 0.01 ng μL-1 genomic DNA, and was 10 times more sensitive than real-time PCR (0.1 ng μL-1) and 100 times more sensitive than conventional PCR assay (1.0 ng μL-1); the reaction was completed within 1 h. The sensitivity of the RPA-CRISPR/Cas12a assay reached 0.1 ng μL-1 genomic DNA, and was 10 times more sensitive than conventional PCR (1.0 ng μL-1), with a 30 min reaction time. Furthermore, the feasibility of the two thermostatic methods was validated using infected soybean leaf and seeding samples. The rapid, visual one-pot detection assay developed could be operated by non-expert personnel without specialized equipment. This study provides a valuable diagnostic platform for the on-site detection of SSC or for use in resource-limited areas.
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Affiliation(s)
- Jiali Dong
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Shuzhe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaozhen Liu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaodan Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
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Meng JN, Xu ZK, Li PR, Zeng X, Liu Y, Xu ZL, Wang J, Ding Y, Shen X. Universal and Naked-Eye Diagnostic Platform for Emetic Bacillus cereus Based on RPA-Assisted CRISPR/Cas12a. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8823-8830. [PMID: 38578074 DOI: 10.1021/acs.jafc.3c06744] [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: 04/06/2024]
Abstract
Emetic Bacillus cereus (B. cereus), which can cause emetic food poisoning and in some cases even fulminant liver failure and death, has aroused widespread concern. Herein, a universal and naked-eye diagnostic platform for emetic B. cereus based on recombinase polymerase amplification (RPA)-assisted CRISPR/Cas12a was developed by targeting the cereulide synthetase biosynthetic gene (cesB). The diagnostic platform enabled one-pot detection by adding components at the bottom and cap of the tube separately. The visual limit of detection of RPA-CRISPR/Cas12a for gDNA and cells of emetic B. cereus was 10-2 ng μL-1 and 102 CFU mL-1, respectively. Meanwhile, it maintained the same sensitivity in the rice, milk, and cooked meat samples even if the gDNA was extracted by simple boiling. The whole detection process can be finished within 40 min, and the single cell of emetic B. cereus was able to be recognized through enrichment for 2-5 h. The good specificity, high sensitivity, rapidity, and simplicity of the RPA-assisted CRISPR/Cas12a diagnostic platform made it serve as a potential tool for the on-site detection of emetic B. cereus in food matrices. In addition, the RPA-assisted CRISPR/Cas12a assay is the first application in emetic B. cereus detection.
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Affiliation(s)
- Jing-Nan Meng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ze-Ke Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Peng-Ru Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xi Zeng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Guangzhou Institute of Food Inspection, Guangzhou 510410, China
| | - Yingju Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
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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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Sun X, Lei R, Zhang H, Chen W, Jia Q, Guo X, Zhang Y, Wu P, Wang X. Rapid and sensitive detection of two fungal pathogens in soybeans using the recombinase polymerase amplification/CRISPR-Cas12a method for potential on-site disease diagnosis. PEST MANAGEMENT SCIENCE 2024; 80:1168-1181. [PMID: 37874890 DOI: 10.1002/ps.7847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Diaporthe aspalathi and Diaporthe caulivora are two of the fungal pathogens causing soybean stem canker (SSC) in soybean, which is one of the most widespread diseases in soybean growing regions and can cause 100% loss of yield. Current methods for the detection of fungal pathogens, including morphological identification and molecular detection, are mostly limited by the need for professional laboratories and staff. To develop a detection method for potential on-site diagnosis for two of the fungal pathogens causing SSC, we designed a rapid assay combining recombinase polymerase amplification (RPA) and CRISPR-Cas12a-based diagnostics to specifically detect D. aspalathi and D. caulivora. RESULTS The translation elongation factor 1-alpha gene was employed as the target gene to evaluate the specificity and sensitivity of this assay. The RPA/CRISPR-Cas12a system has excellent specificity to distinguish D. aspalathi and D. caulivora from closely related species. The sensitivities of RPA/CRISPR-Cas12a-based fluorescence detection and lateral flow assay for D. aspalathi and D. caulivora are 14.5 copies and 24.6 copies, respectively. This assay can detect hyphae in inoculated soybean stems at 12 days after inoculation and has a recovery as high as 86% for hyphae-spiked soybean seed powder. The total time from DNA extraction to detection was not more than 60 min. CONCLUSION The method developed for rapid detection of plant pathogens includes DNA extraction with magnetic beads or rapid DNA extraction, isothermal nucleic acid amplification at 39 °C, CRISPR-Cas12a cleavage reaction at 37 °C, and lateral flow assay or endpoint fluorescence visualization at room temperature. The RPA and CRISPR-Cas12a reagents can be preloaded in the microcentrifuge tube to simplify the procedures in the field. Both RPA and CRISPR-Cas12a reaction can be realized on a portable incubator, and the results are visualized using lateral flow strips or portable flashlight. This method requires minimal equipment and operator training, and has promising applications for rapid on-site disease screening, port inspection, or controlling fungal pathogen transmission in crop. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiwen Sun
- Chinese Academy of Inspection and Quarantine, Beijing, China
- Shenyang Agricultural University, Shenyang, China
| | - Rong Lei
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | | | - Wujian Chen
- Technical Center of Hangzhou Customs, Hangzhou, China
| | - Qianwen Jia
- School of Life and Health, Dalian University, Dalian, China
| | - Xing Guo
- School of Life and Health, Dalian University, Dalian, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Pinshan Wu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xinyi Wang
- School of Life and Health, Dalian University, Dalian, China
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Wang R, Li B, Shi M, Zhao Y, Lin J, Chen Q, Liu P. Rapid Visual Detection of Peronophythora litchii on Lychees Using Recombinase Polymerase Amplification Combined with Lateral Flow Assay Based on the Unique Target Gene Pl_101565. PLANTS (BASEL, SWITZERLAND) 2024; 13:555. [PMID: 38498516 PMCID: PMC10891779 DOI: 10.3390/plants13040555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
Downy blight, caused by Peronophythora litchii, is a destructive disease that impacts lychee fruit throughout the pre-harvest, post-harvest, and transportation phases. Therefore, the prompt and precise identification of P. litchii is crucial for the effective management of the disease. A novel gene encoding a Rh-type ammonium transporter, Pl_101565, was identified in P. litchii through bioinformatic analysis in this study. Based on this gene, a coupled recombinase polymerase amplification-lateral flow (RPA-LF) assay for the rapid visual detection of P. litchii was developed. The assay has been shown to detect P. litchii accurately, without cross-reactivity to related pathogenic oomycetes or fungi. Moreover, it can be performed effectively within 15 to 25 min at temperatures ranging from 28 to 46 °C. Under optimized conditions, the RPA-LF assay could detect as low as 1 pg of P. litchii genomic DNA in a 25 μL reaction system. Furthermore, the RPA-LF assay successfully detected P. litchii in infected lychee samples within a 30 min timeframe. These attributes establish the RPA-LF assay as a rapid, sensitive, and specific method for diagnosing P. litchii early; it is particularly suitable for applications in resource-limited settings.
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Affiliation(s)
- Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
| | - Benjin Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
| | - Mingyue Shi
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
| | - Yumei Zhao
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
| | - Jinlong Lin
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
| | - Qinghe Chen
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572000, China;
| | - Peiqing Liu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (R.W.); (B.L.); (M.S.); (Y.Z.); (J.L.)
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Trippa D, Scalenghe R, Basso MF, Panno S, Davino S, Morone C, Giovino A, Oufensou S, Luchi N, Yousefi S, Martinelli F. Next-generation methods for early disease detection in crops. PEST MANAGEMENT SCIENCE 2024; 80:245-261. [PMID: 37599270 DOI: 10.1002/ps.7733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniela Trippa
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Riccardo Scalenghe
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | | - Stefano Panno
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Davino
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Chiara Morone
- Regione Piemonte - Phytosanitary Division, Torino, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Palermo, Italy
| | - Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicola Luchi
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, Florence, Italy
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
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11
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Hu S, Yan C, Yu H, Zhang Y, Zhang CQ. Establishment of the Recombinase Polymerase Amplification-Lateral Flow Dipstick Detection Technique for Fusarium oxysporum. PLANT DISEASE 2023; 107:2665-2672. [PMID: 36774580 DOI: 10.1094/pdis-12-22-2841-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum causes crown rot, wilt, root rot, and many other major plant diseases worldwide. During the progression of strawberry crown rot disease, the pathogen is transmitted from the mother plant to the seedling through the stolon, with obvious characteristics of latent infection. Therefore, rapid and timely detection of F. oxysporum is important for efficient disease management. In this study, a recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) detection technique was developed for the rapid detection of F. oxysporum on strawberry plants by targeting the CYP51C gene, which is unique to Fusarium spp. Because this RPA-LFD detection technique was highly specific to F. oxysporum, other Fusarium and non-Fusarium fungi were not detected. The optimal reaction temperature and time for this technique were 39°C and 8 min, respectively. The detection limit was 1 pg of F. oxysporum genomic DNA in a 50-μl reaction system. A total of 46 strawberry plants with or without crown rot symptoms collected from Jiande, Changxing, and Haining in Zhejiang Province were further assessed for F. oxysporum infection using both RPA-LFD and traditional tissue isolation techniques. The RPA-LFD test showed that 32 of the 46 strawberry plants tested were positive for F. oxysporum, while in the traditional isolation technique, F. oxysporum was isolated from 30 of the 46 strawberry plants. These results suggest that our established RPA-LFD method is rapid, sensitive, and highly specific in detecting F. oxysporum infection in strawberry plants.
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Affiliation(s)
- Shuodan Hu
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chenyi Yan
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Hong Yu
- Research Institute for the Agriculture Science of Hangzhou, Hangzhou 310013, China
| | - Yu Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chuan-Qing Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
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Saetang J, Sukkapat P, Palamae S, Singh P, Senathipathi DN, Buatong J, Benjakul S. Multiplex PCR-Lateral Flow Dipstick Method for Detection of Thermostable Direct Hemolysin ( TDH) Producing V. parahaemolyticus. BIOSENSORS 2023; 13:698. [PMID: 37504096 PMCID: PMC10377466 DOI: 10.3390/bios13070698] [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: 05/18/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Vibrio parahaemolyticus is usually found in seafood and causes acute gastroenteritis in humans. Therefore, a detection method of pathogenic V. parahaemolyticus is necessary. Multiplex PCR combined with lateral flow dipstick (LFD) assay was developed to detect pathogenic V. parahaemolyticus. Biotin-, FAM-, and Dig-conjugated primers targeting thermolabile hemolysin (TLH) and thermostable direct hemolysin (TDH) genes were used for multiplex PCR amplification. The condition of the method was optimized and evaluated by agarose gel electrophoresis and universal lateral flow dipstick. The specificity assay was evaluated using strains belonging to seven foodborne pathogen species. The sensitivity of the method was also evaluated using DNA in the concentration range of 0.39-100 ng/reaction. The artificial spiking experiment was performed using 10 g of shrimp samples with an enrichment time of 0, 4, and 8 h with 101, 102, and 103 CFU of V. parahaemolyticus. The developed multiplex PCR-LFD assay showed no non-specific amplification with a limit of the detection of 0.78 ng DNA/reaction visualized by agarose gel electrophoresis and 0.39 ng DNA with LFD assay. The artificial spiking experiment demonstrated that this method could detect pathogenic V. parahaemolyticus at 10 CFU/10 g shrimp samples following a 4 h of enrichment. Multiplex PCR-LFD assay was therefore established for detecting pathogenic V. parahaemolyticus with high sensitivity and specificity and might be a useful tool to develop a detection kit used in the food safety sector.
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Affiliation(s)
- Jirakrit Saetang
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Phutthipong Sukkapat
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Suriya Palamae
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Prashant Singh
- Department of Nutrition, and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA
| | - Deep Nithun Senathipathi
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Jirayu Buatong
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
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13
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Yilmaz S, Batuman O. Development of a reverse transcription recombinase polymerase amplification combined with lateral flow assay for equipment-free on-site field detection of tomato chlorotic spot virus. Virol J 2023; 20:136. [PMID: 37349823 PMCID: PMC10288760 DOI: 10.1186/s12985-023-02097-w] [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: 04/11/2023] [Accepted: 06/11/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Tomato chlorotic spot virus (TCSV) is an economically important, thrips-transmitted, emerging member of the Orthotospovirus genus that causes significant yield loss mainly in tomatoes, but also in other vegetable and ornamental crops. Disease management of this pathogen is often challenging due to the limited availability of natural host resistance genes, the broad host range of TCSV, and the wide distribution of its thrips vector. Point-of-care detection of TCSV with a rapid, equipment-free, portable, sensitive, and species-specific diagnostic technique can provide prompt response outside the laboratory, which is critical for preventing disease progression and further spread of the pathogen. Current diagnostic techniques require either laboratory-dependent or portable electronic equipment and are relatively time-consuming and costly. RESULTS In this study, we developed a novel technique for reverse-transcription recombinase polymerase amplification combined with lateral flow assay (RT-RPA-LFA) to achieve a faster and equipment-free point-of-care detection of TCSV. The RPA reaction tubes containing crude RNA are incubated in the hand palm to obtain sufficient heat (∼36 °C) for the amplification without the need for equipment. Body-heat mediated RT-RPA-LFA is highly TCSV-specific with a detection limit as low as ∼6 pg/μl of total RNA from TCSV-infected tomato plants. The assay can be performed in 15 min in the field. CONCLUSION To the best of our knowledge, this is the first equipment-free, body-heat-mediated RT-RPA-LFA technique developed to detect TCSV. Our new system offers a time-saving advantage for the sensitive and specific diagnostic of TCSV that local growers and small nurseries in low-resource settings can use without skilled personnel.
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Affiliation(s)
- Salih Yilmaz
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL, 34142, USA
| | - Ozgur Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL, 34142, USA.
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Guo Y, Xia H, Dai T, Liu T. RPA-CRISPR/Cas12a mediated isothermal amplification for visual detection of Phytophthora sojae. Front Cell Infect Microbiol 2023; 13:1208837. [PMID: 37305413 PMCID: PMC10250720 DOI: 10.3389/fcimb.2023.1208837] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Phytophthora sojae is among the most devastating pathogens of soybean (Glycine max) and severely impacts soybean production in several countries. The resulting disease can be difficult to diagnose and other Phytophthora species can also infect soybean. Accurate diagnosis is important for management of the disease caused by P. sojae. Methods In this study, recombinase polymerase amplification (RPA) in combination with the CRISPR/Cas12a system were used for detection of P. sojae. The assay was highly specific to P. sojae. Results The test results were positive for 29 isolates of P. sojae, but negative for 64 isolates of 29 Phytophthora species, 7 Phytopythium and Pythium species, 32 fungal species, and 2 Bursaphelenchus species. The method was highly sensitive, detecting as little as 10 pg.µL-1 of P. sojae genomic DNA at 37°C in 20 min. The test results were visible under UV light and readout coming from fluorophores. In addition, P. sojae was detected from natural inoculated hypocotyls of soybean seedlings using this novel assay. The rapidity and accuracy of the method were verified using 30 soybean rhizosphere samples. Discussion In conclusion, the RPA-CRISPR/Cas12a detection assay developed here is sensitive, efficient, and convenient, and has potential for further development as a kit for monitoring root rot of soybean in the field.
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Affiliation(s)
- Yufang Guo
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hongming Xia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingli Liu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, China
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15
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Wang Y, Niu J, Sun M, Li Z, Wang X, He Y, Qi J. Rapid and Sensitive Detection of Streptococcus iniae in Trachinotus ovatus Based on Multienzyme Isothermal Rapid Amplification. Int J Mol Sci 2023; 24:ijms24097733. [PMID: 37175440 PMCID: PMC10178759 DOI: 10.3390/ijms24097733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023] Open
Abstract
Infectious diseases caused by Streptococcus iniae lead to massive death of fish, compose a serious threat to the global aquaculture industry, and constitute a risk to humans who deal with raw fish. In order to realize the early diagnosis of S. iniae, and control the outbreak and spread of disease, it is of great significance to establish fast, sensitive, and convenient detection methods for S. iniae. In the present study, two methods of real-time MIRA (multienzyme isothermal rapid amplification, MIRA) and MIRA-LFD (combining MIRA with lateral flow dipsticks (LFD)) for the simA gene of S. iniae were established, which could complete amplification at a constant temperature of 42 °C within 20 min. Real-time MIRA and MIRA-LFD assays showed high sensitivity (97 fg/μL or 7.6 × 102 CFU/mL), which were consistent with the sensitivity of real-time PCR and 10 times higher than that of PCR with strong specificity, repeatability simplicity, and rapidity for S. iniae originating from Trachinotus ovatus. In summary, real-time MIRA and MIRA-LFD provide effective ways for early diagnosis of S. iniae in aquaculture, especially for units in poor conditions.
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Affiliation(s)
- Yifen Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jingjing Niu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
| | - Minmin Sun
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ziyi Li
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiangyuan Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yan He
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jie Qi
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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Roumani F, Barros-Velázquez J, Garrido-Maestu A, Prado M. Real-time PCR, and Recombinase Polymerase Amplification combined with SYBR Green I for naked-eye detection, along with Propidium Monoazide (PMA) for the detection of viable patulin-producing fungi in apples and by-products. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109347] [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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17
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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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Singh R, Kumar K, Purayannur S, Chen W, Verma PK. Ascochyta rabiei: A threat to global chickpea production. MOLECULAR PLANT PATHOLOGY 2022; 23:1241-1261. [PMID: 35778851 PMCID: PMC9366070 DOI: 10.1111/mpp.13235] [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: 12/11/2021] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 06/01/2023]
Abstract
UNLABELLED The necrotrophic fungus Ascochyta rabiei causes Ascochyta blight (AB) disease in chickpea. A. rabiei infects all aerial parts of the plant, which results in severe yield loss. At present, AB disease occurs in most chickpea-growing countries. Globally increased incidences of A. rabiei infection and the emergence of new aggressive isolates directed the interest of researchers toward understanding the evolution of pathogenic determinants in this fungus. In this review, we summarize the molecular and genetic studies of the pathogen along with approaches that are helping in combating the disease. Possible areas of future research are also suggested. TAXONOMY kingdom Mycota, phylum Ascomycota, class Dothideomycetes, subclass Coelomycetes, order Pleosporales, family Didymellaceae, genus Ascochyta, species rabiei. PRIMARY HOST A. rabiei survives primarily on Cicer species. DISEASE SYMPTOMS A. rabiei infects aboveground parts of the plant including leaves, petioles, stems, pods, and seeds. The disease symptoms first appear as watersoaked lesions on the leaves and stems, which turn brown or dark brown. Early symptoms include small circular necrotic lesions visible on the leaves and oval brown lesions on the stem. At later stages of infection, the lesions may girdle the stem and the region above the girdle falls off. The disease severity increases at the reproductive stage and rounded lesions with concentric rings, due to asexual structures called pycnidia, appear on leaves, stems, and pods. The infected pod becomes blighted and often results in shrivelled and infected seeds. DISEASE MANAGEMENT STRATEGIES Crop failures may be avoided by judicious practices of integrated disease management based on the use of resistant or tolerant cultivars and growing chickpea in areas where conditions are least favourable for AB disease development. Use of healthy seeds free of A. rabiei, seed treatments with fungicides, and proper destruction of diseased stubbles can also reduce the fungal inoculum load. Crop rotation with nonhost crops is critical for controlling the disease. Planting moderately resistant cultivars and prudent application of fungicides is also a way to combat AB disease. However, the scarcity of AB-resistant accessions and the continuous evolution of the pathogen challenges the disease management process. USEFUL WEBSITES https://www.ndsu.edu/pubweb/pulse-info/resourcespdf/Ascochyta%20blight%20of%20chickpea.pdf https://saskpulse.com/files/newsletters/180531_ascochyta_in_chickpeas-compressed.pdf http://www.pulseaus.com.au/growing-pulses/bmp/chickpea/ascochyta-blight http://agriculture.vic.gov.au/agriculture/pests-diseases-and-weeds/plant-diseases/grains-pulses-and-cereals/ascochyta-blight-of-chickpea http://www.croppro.com.au/crop_disease_manual/ch05s02.php https://www.northernpulse.com/uploads/resources/722/handout-chickpeaascochyta-nov13-2011.pdf http://oar.icrisat.org/184/1/24_2010_IB_no_82_Host_Plant https://www.crop.bayer.com.au/find-crop-solutions/by-pest/diseases/ascochyta-blight.
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Affiliation(s)
- Ritu Singh
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
| | - Kamal Kumar
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Department of Plant Molecular BiologyUniversity of Delhi (South Campus)New DelhiIndia
| | - Savithri Purayannur
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Weidong Chen
- Grain Legume Genetics and Physiology Research Unit, USDA Agricultural Research Service, and Department of Plant PathologyWashington State UniversityPullmanWashingtonUSA
| | - Praveen Kumar Verma
- Plant Immunity LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
- Plant Immunity Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
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19
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [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] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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20
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Zhao M, Wang X, Wang K, Li Y, Wang Y, Zhou P, Wang L, Zhu W. Recombinant polymerase amplification combined with lateral flow strips for the detection of deep-seated Candida krusei infections. Front Cell Infect Microbiol 2022; 12:958858. [PMID: 36004333 PMCID: PMC9394440 DOI: 10.3389/fcimb.2022.958858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
The incidence of Candida infections in intensive care units (ICU) has significantly increased in recent years, and these infections have become one of the most serious complications threatening the lives of ICU patients. The proportion of non-Candida albicans infections, such as Candida krusei and Candida glabrata infections, which are resistant to fluconazole, is increasing each year. Early identification of the strains causing Candida infections is important for the timely implementation of targeted treatments to save patients’ lives. However, the current methods of direct microscopy, culture, and histopathology, as well as other diagnostic methods, have many shortcomings, such as their low sensitivity and long assay times; therefore, they cannot meet the needs for early clinical diagnosis. Recombinant polymerase amplification (RPA) is a promising isothermal amplification technique that can be performed without sophisticated instruments and equipment, and is suitable for use in resource-poor areas. RPA combined with lateral flow strips (LFS) can be used to rapidly amplify and visualize target genes within 20 min. In this study, RPA-LFS was used to amplify the internal transcribed spacer 2 (ITS2) region of C. krusei. The primer-probe design was optimized by introduction of base mismatches (probe modification of five bases) to obtain a specific and sensitive primer-probe combination for the detection of clinical specimens. Thirty-five common clinical pathogens were tested with RPA-LFS to determine the specificity of the detection system. The RPA-LFS system specifically detected C. krusei without cross-reaction with other fungi or bacteria. A gradient dilution of the template was tested to explore the lower limit of detection and sensitivity of the assay. The sensitivity was 10 CFU/50 µL per reaction, without interference from genomic DNA of other species. The RPA-LFS and qPCR assays were performed on 189 clinical specimens to evaluate the detection performance of the RPA-LFS system. Seventy-six specimens were identified as C. krusei, indicating a detection rate of 40.2%. The results were consistent with those of qPCR and conventional culture methods. The RPA-LFS system established in our study provides a reliable molecular diagnostic method for the detection of C. krusei, thus meeting the urgent need for rapid, specific, sensitive, and portable clinical field testing.
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Affiliation(s)
- Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xizhen Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Kun Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yuanyuan Li
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Ping Zhou
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Lei Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Wenjun Zhu
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
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21
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Wang L, Xu A, Zhou P, Zhao M, Xu C, Wang Y, Wang K, Wang F, Miao Y, Zhao W, Gao X. Rapid Detection of Candida tropicalis in Clinical Samples From Different Sources Using RPA-LFS. Front Cell Infect Microbiol 2022; 12:898186. [PMID: 35873165 PMCID: PMC9301490 DOI: 10.3389/fcimb.2022.898186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Candida tropicalis is one of the few Candida species besides Candida albicans that is able to produce true hyphae. At present, the commonly used clinical methods for the identification of this organism are traditional fungal culture, CTB staining, and color development. Polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) are also used to identify this fungus. Since the course of C. tropicalis infection progresses rapidly, there is an urgent need for rapid, sensitive, real-time field assays to meet the needs of clinical diagnosis. Recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) can rapidly amplify and visualize target genes within 20 min, and by pre-processing samples from different sources, the entire process can be controlled within 30 min. In this study, RPA-LFS was used to amplify the internal transcribed spacer-2 (ITS2) gene of C. tropicalis, and primer-probe design was optimized by introducing base mismatches to obtain a specific and sensitive primer-probe combination for clinical sample detection. LFS assay for 37 common clinical pathogens was performed, sensitivity and specificity of the detection system was determined, reaction temperature and time were optimized, and 191 actual clinical samples collected from different sources were tested to evaluate the detection performance of the established RPA-LFS system to provide a reliable molecular diagnostic method for the detection of C. tropicalis, the results show that the RPA-LFS system can specifically detect C. tropicalis without cross-reacting with other fungi or bacterial, with a sensitivity of 9.94 CFU/µL, without interference from genomic DNA of other species, at an optimal reaction temperature of 39°C, and the whole reaction process can be controlled within 20 min, and to meet the clinical need for rapid, sensitive, real-time, and portable field testing.
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Affiliation(s)
- Lei Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Aiguo Xu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Ping Zhou
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Chenglai Xu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Kun Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Fang Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yongchang Miao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Weiguo Zhao, ; Yongchang Miao, ; Xuzhu Gao,
| | - Weiguo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- *Correspondence: Weiguo Zhao, ; Yongchang Miao, ; Xuzhu Gao,
| | - Xuzhu Gao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Weiguo Zhao, ; Yongchang Miao, ; Xuzhu Gao,
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22
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Li N, Wang L, Wang F, Chen H, Tao S, Zhu Q, Liu L, Liang W, Ma F. Rapid Detection of Klebsiella pneumoniae Carrying Virulence Gene rmpA2 by Recombinase Polymerase Amplification Combined With Lateral Flow Strips. Front Cell Infect Microbiol 2022; 12:877649. [PMID: 35663473 PMCID: PMC9160666 DOI: 10.3389/fcimb.2022.877649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022] Open
Abstract
Highly virulent Klebsiella pneumoniae often causes invasive infections with high morbidity and mortality rates, posing an immense clinical challenge. Rapid and accurate detection of pathogenic bacteria is of great significance for treatment and preventive control. Conventional detection by polymerase chain reaction (PCR) is limited by a dependence on laboratory equipment and professional staff. Recombinase polymerase amplification (RPA) combined with a lateral flow strip (LFS) can rapidly amplify and visualize target genes in a short period of time. The aim of this study was to develop an RPA-LFS technique for detection of the K. pneumoniae virulence gene rmpA2. Primers were designed against conserved sequences specific to the virulence gene, and primer probe design was optimized by introducing base substitution to obtain a specific and sensitive primer-probe combination for clinical detection. We tested 65 actual samples collected from clinics to evaluate the performance of the newly established RPA-LFS system in comparison with conventional PCR methods and qPCR methods. The RPA-LFS assay was performed at for 25 min a constant temperature of 37°C, and results could be observed without instrumentation. The system could specifically identify highly virulent K. pneumoniae carrying the virulence gene rmpA2 with a minimum detection limit of 10−1 ng/μL and 10 copies/μL. For the 65 clinical samples tested, The RPA-LFS assay results were in complete agreement with the qPCR results and PCR results. The RPA-LFS assay provides a rapid, accurate, and simple method for identification of highly virulent K. pneumoniae carrying rmpA2.
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Affiliation(s)
- Na Li
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- Department of Medical Laboratory, Bengbu Medical College, Bengbu, China
| | - Lei Wang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Fang Wang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
| | - Huimin Chen
- Department of Central Laboratory, Lianyungang Second People’s Hospital affiliated to Jiangsu University, Lianyungang, China
| | - Shuan Tao
- Department of Central Laboratory, Lianyungang Second People’s Hospital affiliated to Jiangsu University, Lianyungang, China
| | - Qing Zhu
- Lianyungang Second People’s Hospital affiliated to Xuzhou Medical University, Lianyungang, China
| | - Liping Liu
- Lianyungang Second People’s Hospital affiliated to Xuzhou Medical University, Lianyungang, China
| | - Wei Liang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- *Correspondence: Wei Liang, ; Fang Ma,
| | - Fang Ma
- Department of Medical Laboratory, Bengbu Medical College, Bengbu, China
- *Correspondence: Wei Liang, ; Fang Ma,
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23
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A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives. J Microbiol Methods 2022; 196:106477. [DOI: 10.1016/j.mimet.2022.106477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
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24
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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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25
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Zhou Q, Liu Y, Wang Z, Wang H, Zhang X, Lu Q. Rapid On-Site Detection of the Bursaphelenchus xylophilus Using Recombinase Polymerase Amplification Combined With Lateral Flow Dipstick That Eliminates Interference From Primer-Dependent Artifacts. FRONTIERS IN PLANT SCIENCE 2022; 13:856109. [PMID: 35371187 PMCID: PMC8971978 DOI: 10.3389/fpls.2022.856109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/17/2022] [Indexed: 05/03/2023]
Abstract
The pine wood nematode (PWN), Bursaphelenchus xylophilus, is one of the most lethal nematode species, which causes pine wilt disease (PWD), a devastating forest disease. To date, no effective methods have been developed to control the disease; hence, rapid precise detection of B. xylophilus is of great significance. Traditional molecular diagnostic methods are time-consuming and require sophisticated instruments or skilled operators, which are unavailable in resource-limited settings. A specific, sensitive, and field-applicable diagnostic method is urgently needed. In this study, we developed a diagnostic method using recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) for the rapid on-site detection of B. xylophilus. The false-positive signals from primer-dependent artifacts were eliminated using a probe, and base substitutions were included in the primer and probe. The entire detection process for the RPA-LFD assay can be completed under 38°C within approximately 30 min, including 15 min for crude nematode genomic DNA (gDNA) extraction and master mix preparation, 15 min for the RPA-LFD assay. This assay displayed high specificity toward B. xylophilus and showed no cross-reactions with closely related species, including Bursaphelenchus mucronatus and Bursaphelenchus doui. The sensitivity of this assay had a detection limit as low as 1 pg of B. xylophilus purified genomic DNA. Furthermore, the application of the RPA-LFD assay in simulated spiked pinewood samples showed accurate detection results. The RPA-LFD assay in this study successfully detected B. xylophilus in less than 30 min, providing a novel alternative for the simple, sensitive, and specific detection of B. xylophilus and showed potential for B. xylophilus point-of-care testing (POCT) in resource-limited areas or in field.
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Affiliation(s)
| | | | | | | | | | - Quan Lu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China
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26
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Li M, Guo Q, Liang M, Zhao Q, Lin T, Gao H, Hieno A, Kageyama K, Zhang X, Cui L, Yan Y, Qiang Y. Population Dynamics, Effective Soil Factors, and LAMP Detection Systems for Phytophthora Species Associated with Kiwifruit Diseases in China. PLANT DISEASE 2022; 106:846-853. [PMID: 34661453 DOI: 10.1094/pdis-04-21-0852-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: 06/13/2023]
Abstract
China has the largest area of kiwifruit production in the world. Pathogens associated with root diseases of kiwi trees have not been investigated extensively. In this research, three Phytophthora species, Phytophthora cactorum, Phytophthora cinnamomi, and Phytophthora lateralis, which are pathogenic to kiwi trees in the main planting areas of China, were studied. The population densities of these species in 128 soil samples from 32 kiwi orchards in 2017 and 2018 were measured using multiplex real-time quantitative PCR based on the ras-related protein gene Ypt1. P. cactorum was the most widely distributed of the three species in orchards of the Zhouzhi and Meixian prefectures. We used redundancy analysis to examine soil factors in the kiwi orchards to understand their effects on the population densities of the Phytophthora species. The redundancy analysis indicated that soil temperature and pH were significantly correlated with the abundance of P. cactorum and P. cinnamomi. In addition, two loop-mediated isothermal amplification detection systems for P. cactorum were developed based on the tigA gene. The color-change detection system proved to be accurate, sensitive, and faster than quantitative PCR. The results of this study, along with the loop-mediated isothermal amplification detection systems, will be of great use in the control of Phytophthora diseases for the production of kiwifruits in China.
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Affiliation(s)
- Mingzhu Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Han Gao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Xin Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Langjun Cui
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yaping Yan
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yi Qiang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
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27
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Chen S, Yuan H, Yan X. Rapid visual detection of benzimidazole resistance in Botrytis cinerea by recombinase polymerase amplification combined with a lateral flow dipstick. PEST MANAGEMENT SCIENCE 2022; 78:821-830. [PMID: 34719103 DOI: 10.1002/ps.6697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/24/2021] [Accepted: 10/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Benzimidazole resistance in Botrytis cinerea is related to point mutations in the target β-tubulin gene (TUB2). Three mutations (E198A, E198K, E198V) at codon 198 account for most of the resistant strains. A rapid on-site diagnostic assay would be useful to detect the presence and monitor further spread of this resistance mechanism. RESULTS A recombinase polymerase amplification combined with lateral flow detection (RPA-LFD) method was established for the rapid detection of methyl benzimidazole carbamate (MBC) resistance in B. cinerea. Based on the three mutations at TUB2 codon 198, three sets of RPA-LFD primers were designed, and each of these primer sets was able to specifically amplify the DNA containing its corresponding mutation; no amplification was detected with other mutated or wild-type DNA. The assay was optimized for specificity and sensitivity and was shown to detect the presence of 2 × 102 copies μl-1 of target DNA per reaction within 10 min. DNA from eight other common fungal species of small fruit did not yield a signal. The system worked well over a wide range of temperatures from 25 to 45°C. Crude DNA obtained from boiled mycelium and conidia of symptomatic fruit could be used as templates, which simplified the assay process. CONCLUSION This study developed a novel assay based on RPA-LFD for the rapid and equipment-free detection of MBC-resistant isolates. In combination with a simple DNA extraction method, the assay could detect B. cinerea MBC-resistant isolates even without specialized equipment within 30 min. Considering its specificity, stability and simplicity, the RPA-LFD assay could be a promising tool for rapid on-site diagnosis of fungicide-resistant isolates. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Shuning Chen
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huizhu Yuan
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojing Yan
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Hu YQ, Huang XH, Guo LQ, Shen ZC, LV LX, Li FX, Zhou ZH, Zhang DF. Rapid and Visual Detection of Vibrio parahaemolyticus in Aquatic Foods Using blaCARB-17 Gene-Based Loop-Mediated Isothermal Amplification with Lateral Flow Dipstick (LAMP-LFD). J Microbiol Biotechnol 2021; 31:1672-1683. [PMID: 34489378 PMCID: PMC9705909 DOI: 10.4014/jmb.2107.07022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/22/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Abstract
Vibrio parahaemolyticus is recognized as one of the most important foodborne pathogens responsible for gastroenteritis in humans. The blaCARB-17 gene is an intrinsic β-lactamase gene and a novel species-specific genetic marker of V. parahaemolyticus. In this study, a loop-mediated isothermal amplification (LAMP) assay combined with a lateral flow dipstick (LFD) was developed targeting this blaCARB-17 gene. The specificity of LAMP-LFD was ascertained by detecting V. parahaemolyticus ATCC 17802 and seven other non-V. parahaemolyticus strains. Finally, the practicability of LAMP-LFD was confirmed by detection with V. parahaemolyticus-contaminated samples and natural food samples. The results showed that the optimized reaction parameters of LAMP are as follows: 2.4 mmol/l Mg2+, 0.96 mmol/l dNTPs, 4.8 U Bst DNA polymerase, and an 8:1 ratio of inner primer to outer primer, at 63°C for 40 min. The optimized reaction time of the LFD assay is 60 min. Cross-reactivity analysis with the seven non-V. parahaemolyticus strains showed that LAMP-LFD was exclusively specific for V. parahaemolyticus. The detection limit of LAMP-LFD for V. parahaemolyticus genomic DNA was 2.1 × 10-4 ng/μl, corresponding to 630 fg/reaction and displaying a sensitivity that is 100-fold higher than that of conventional PCR. LAMP-LFD in a spiking study revealed a detection limit of approximately 6 CFU/ml, which was similar with conventional PCR. The developed LAMP-LFD specifically identified the 10 V. parahaemolyticus isolates from 30 seafood samples, suggesting that this LAMP-LFD may be a suitable diagnostic method for detecting V. parahaemolyticus in aquatic foods.
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Affiliation(s)
- Yuan-qing Hu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China,Corresponding authors Y.Q. Hu Phone: +86 596 2528735 Fax: +86 596 2528735 E-mail:
| | - Xian-hui Huang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China
| | - Li-qing Guo
- Zhangzhou Center for Disease Control and Prevention, Zhangzhou 363000, P.R. China
| | - Zi-chen Shen
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China
| | - Lin-xue LV
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China
| | - Feng-xia Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China
| | - Zan-hu Zhou
- Comprehensive Technical Service Center, Zhangzhou Customs, Zhangzhou 363000, P.R. China
| | - Dan-feng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, P.R. China,
D.F. Zhang E-mail:
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112424. [PMID: 34834787 PMCID: PMC8621059 DOI: 10.3390/plants10112424] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.
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Arocha Rosete Y, To H, Evans M, White K, Saleh M, Trueman C, Tomecek J, Van Dyk D, Summerbell RC, Scott JA. Assessing the Use of DNA Detection Platforms Combined with Passive Wind-Powered Spore Traps for Early Surveillance of Potato and Tomato Late Blight in Canada. PLANT DISEASE 2021; 105:3610-3622. [PMID: 34743538 DOI: 10.1094/pdis-12-20-2695-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative PCR (qPCR), loop-mediated amplification (LAMP), and lateral flow strip-based recombinase polymerase amplification (RPA-LFS) assays were assessed for early detection of Phytophthora infestans, the global causal agent of potato and tomato late blight, on passive wind-powered spore traps known as Spornados. Spore traps were deployed in potato and tomato fields during the 2018, 2019, and 2020 growing seasons in the provinces of Alberta, British Columbia, Manitoba, Prince Edward Island, and Ontario. All assays used DNA extracts from Spornado cassette membranes targeting the P. infestans nuclear ribosomal internal transcribed spacer. A total of 1,003 Spornado samples were qPCR tested, yielding 115 positive samples for P. infestans spores. In further assessment of these samples, LAMP detected P. infestans in 108 (93.9%) of 115 qPCR positive samples, and RPA-LFS detected it in 103 (89.6%). None of the assays showed cross-reaction with other Phytophthora species or pathogenic fungi known to infect potato and tomato. The qPCR detected ≤1 fg of P. infestans DNA, and LAMP and RPA-LFS amplified 10 fg in as little as 10 min. All assays detected P. infestans before the first report of late blight symptoms in commercial potato or tomato fields within each region or province. The combination of Spornado passive samplers with qPCR, LAMP, or RPA-LFS proved a valuable spore trapping system for early surveillance of late blight in potato and tomato. Both LAMP and RPA-LFS showed potential as alternative approaches to qPCR for in-field monitoring of P. infestans.
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Affiliation(s)
| | - Henry To
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | - Martin Evans
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | | | | | - Cheryl Trueman
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Joseph Tomecek
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Dennis Van Dyk
- Ontario Ministry of Agriculture, Food and Rural Affairs, Guelph, Ontario, Canada
| | - Richard C Summerbell
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
| | - James A Scott
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
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Mansotra R, Vakhlu J. Comprehensive account of present techniques for in-field plant disease diagnosis. Arch Microbiol 2021; 203:5309-5320. [PMID: 34410444 DOI: 10.1007/s00203-021-02529-7] [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: 01/28/2021] [Revised: 07/19/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
The early detection of plant pathogens is an appropriate preventive strategy for the management of crop yield and quality. For this reason, effective diagnostic techniques and tools, which are simple, specific, rapid and economic, are needed to be developed. Although several such technologies have been developed still most of them suffer one or the other limitation. Major limitations of the widely used diagnostic methods are requirement of trained staff and laboratory setup. Development of point-of-care diagnostic devices (handy portable devices) that require no specialized staff and can directly be used in fields is need of the hour. The aim of this review is to compile the information on current promising techniques that are in use for plant-pathogen diagnosis. Additionally, it focuses on the latest in-field pathogen diagnostic techniques with associated advantages and limitations.
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Affiliation(s)
- Ritika Mansotra
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - Jyoti Vakhlu
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, India.
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Rapid Identification of Salmo salar Using a Combined Isothermal Recombinase Polymerase Amplification–Lateral Flow Strip Approach. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02128-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Song Z, Yang X, Zhang X, Luan M, Guo B, Liu C, Pan J, Mei S. Rapid and Visual Detection of Meloidogyne hapla Using Recombinase Polymerase Amplification Combined with a Lateral Flow Dipstick Assay. PLANT DISEASE 2021; 105:2697-2703. [PMID: 33267643 DOI: 10.1094/pdis-06-20-1345-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The northern root-knot nematode, Meloidogyne hapla, is a biotrophic parasite that infects many crops and causes severe economic losses worldwide. Rapid and accurate detection of M. hapla is crucial for disease forecasting and control. We developed a recombinase polymerase amplification combined with a lateral flow dipstick (RPA-LFD) assay for rapid detection of M. hapla. The primers and probe were designed based on the effector gene 16D10 sequence and were highly specific to M. hapla. The RPA reaction was performed at a wide range of temperatures from 25 to 45°C within 5 to 25 min, and the amplicon was visualized directly on the LFD within 5 min. The detection limits of the RPA-LFD assay were 10-3 females and 10-2 second-stage juveniles/0.5 g of soil, which was 10 times more sensitive than the conventional PCR assay. In addition, the RPA-LFD assay can detect M. hapla from infested plant roots and soil samples, and the entire detection process can be completed within 1.5 h. These results indicate that the RPA-LFD assay is a simple, rapid, specific, sensitive, and visual method that can be used for rapid detection of M. hapla in the field and in resource-limited conditions.
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Affiliation(s)
- Zhiqiang Song
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Xiaowei Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Bing Guo
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Chunjie Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Jiangpeng Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Shiyong Mei
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
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Wu X, Pan J, Zhu X, Hong C, Hu A, Zhu C, Liu Y, Yang K, Zhu L. MS 2 device: smartphone-facilitated mobile nucleic acid analysis on microfluidic device. Analyst 2021; 146:3823-3833. [PMID: 34121097 DOI: 10.1039/d1an00367d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mobile sensing based on the integration of microfluidic devices and smartphones, so-called MS2 technology, has enabled many applications over recent years and continues to stimulate growing interest in both research communities and industries. In particular, MS2 technology has been proven to be able to be applied to molecular diagnostic analysis and can be implemented for basic research and clinical testing. However, the currently reported MS2-based nucleic acid analysis system has limited use in practical applications, because it is not integrated with quantitative PCR, multiplex PCR, and isothermal amplification functions, and lacks temperature control, image acquisition and real-time processing units with excellent performance. To provide a more universal and powerful platform, we here developed a novel MS2 device by integrating a thermocycler, a multi fluorescence detection unit, a PCR chip, an isothermal chip, and a smartphone. The MS2 device was approximately 325 mm (L) × 200 mm (W) × 200 mm (H) in volume and only 5 kg in weight, and showed an average power consumption of about 38.4 W. The entire nucleic acid amplification and analysis could be controlled through a self-made smartphone App. The maximum heating and cooling rates were 5 °C s-1 and 4 °C s-1, respectively. The entire PCR could be completed within 65 min. The temperature uniformity was less than 0.1 °C. Besides, the temperature stability over time (30 min) was within ±0.04 °C. Four optical channels were integrated (FAM, HEX, TAMRA, and ROX) on the MS2 device. In particular, the PCR-based detection sensitivity reached 1 copy per μL, and the amplification efficiency was calculated to be 106.8%. Besides, the MS2 device also was compatible with multiplex PCR and isothermal amplification. In short, the MS2 device showed performance consistent with that of traditional commercial equipment. Thus, the MS2 device provides an easy and integrated experimental platform for molecular diagnostic-related research and potential medical diagnostic applications.
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Affiliation(s)
- Xiaosong Wu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China. and University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei 230026, PR China
| | - Jingyu Pan
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Xinchao Zhu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China. and University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei 230026, PR China
| | - Chenggang Hong
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Anzhong Hu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Cancan Zhu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Yong Liu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Ke Yang
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Ling Zhu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid. Mol Cell Probes 2021; 58:101746. [PMID: 34102255 DOI: 10.1016/j.mcp.2021.101746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, Republic of Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea.
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Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics. PLANTS 2021; 10:plants10030435. [PMID: 33668762 PMCID: PMC7996204 DOI: 10.3390/plants10030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/26/2022]
Abstract
Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.
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Zhao N, Jia L, Che J, He X, Zhang B. Novel molecular marker for RAA-LFD visual detection of Cynoglossus semilaevis sex. Anim Reprod Sci 2021; 226:106713. [PMID: 33549888 DOI: 10.1016/j.anireprosci.2021.106713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
Due to the significant sex dimorphism, Cynoglossus semilaevis has long been a species of research interest in the field of artificial sex manipulation. The existence of pseudo-males both in the natural habitat and aquaculture enterprises also is indicative of the importance for identification of the genetic sex in this species. In the present study, there was elucidation of a novel molecular marker for utilizing the recombinase aided amplification-lateral flow dipstick (RAA-LFD) visual system to identify the genetic sex of C. semilaevis. This 533 bp novel marker is a differential single copy fragment between the Z and W chromosome of C. semilaevis and exists only in the W chromosome. After primer designing and probe labeling, this marker has been utilized in a RAA isothermal amplification system. There were 49 C. semilaevis specimens evaluated for genetic sex identification using both PCR-agarose gel electrophoresis based InDel marker detection and the novel RAA-LFD system. The results from conducting evaluations with the two methods were consistent in all samples. Also, results from sensitivity analysis with use of the RAA-LFD system indicated the detection system was effective and reliable from 108 copy number to 101. With use of the RAA reaction, there was only need to utilize a constant temperature of 37 ℃ for specific DNA amplification within 30 min. The combination use of RAA with LFD resulted in more efficient and convenient sex determination with there being a lesser technical threshold.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai, 201306, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, 300457, China
| | - Jinyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, 300457, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin, 300457, China.
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Lu X, Xu H, Song W, Yang Z, Yu J, Tian Y, Jiang M, Shen D, Dou D. Rapid and simple detection of Phytophthora cactorum in strawberry using a coupled recombinase polymerase amplification-lateral flow strip assay. PHYTOPATHOLOGY RESEARCH 2021; 3:12. [PMID: 34127941 PMCID: PMC8189726 DOI: 10.1186/s42483-021-00089-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 05/22/2023]
Abstract
UNLABELLED Phytophthora cactorum is a devastating pathogen that infects a wide range of plants and causes Phytophthora rot disease, which has resulted in great economic losses in crop production. Therefore, the rapid and practicable detection of P. cactorum is important for disease monitoring and forecasting. In this study, we developed a lateral flow recombinase polymerase amplification (LF-RPA) assay for the sensitive visual detection of P. cactorum. Specific primers for P. cactorum were designed based on the ras-related protein gene Ypt1; all 10 P. cactorum isolates yielded positive detection results, whereas no cross-reaction occurred in related oomycete or fungal species. The detection limit for the LF-RPA assay was 100 fg of genomic DNA under optimized conditions. Combined with a simplified alkaline lysis method for plant DNA extraction, the LF-RPA assay successfully detected P. cactorum in naturally diseased strawberry samples without specialized equipment within 40 min. Thus, the LF-RPA assay developed in this study is a rapid, simple, and accurate method for the detection of P. cactorum, with the potential for further application in resource-limited laboratories. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42483-021-00089-8.
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Affiliation(s)
- Xinyu Lu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Heng Xu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wen Song
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zitong Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jia Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuee Tian
- Department of Plant Protection, Henan University of Science and Technology, Luoyang, 471000 China
| | - Min Jiang
- Pingyi County Forestry Development Center, Linyi, 273300 China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
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Fang W, Cai Y, Zhu L, Wang H, Lu Y. Rapid and Highly Sensitive Detection of Toxigenic Vibrio cholerae Based on Recombinase-Aided Amplification Combining with Lateral Flow Assay. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01909-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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40
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Lu X, Zheng Y, Zhang F, Yu J, Dai T, Wang R, Tian Y, Xu H, Shen D, Dou D. A Rapid, Equipment-Free Method for Detecting Phytophthora infestans in the Field Using a Lateral Flow Strip-Based Recombinase Polymerase Amplification Assay. PLANT DISEASE 2020; 104:2774-2778. [PMID: 32924873 DOI: 10.1094/pdis-01-20-0203-sc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Late blight, caused by the oomycete Phytophthora infestans, is a major constraint on the production of potatoes and tomatoes as well as a constant threat to global food security. An early diagnostic tool is important for the effective management of late blight in the field. Here, in combination with a simplified DNA extraction method, we developed a lateral flow strip-based recombinase polymerase amplification (LF-RPA) assay for the rapid, equipment-free detection of P. infestans. This assay targets the Ras-related protein (Ypt1) gene and can be performed over a wide range of temperatures (25 to 45°C). All 12 P. infestans isolates yielded positive detection results using the LF-RPA assay, and no cross-reaction occurred with related oomycetes or fungal species. With this assay, the detection limit was 500 fg of genomic DNA in optimized conditions. Furthermore, by combining a simplified polyethylene glycol-NaOH method for extracting DNA from plant samples, the entire LF-RPA assay enabled the detection of P. infestans within 30 min with no specialized equipment. When applied to field samples, it successfully detected P. infestans in naturally diseased potato plants from eight different fields in China. Therefore, the LF-RPA assay is simple, rapid, and cost-effective and has potential for further development as a kit for diagnosing late blight in resource-limited settings or even on-site.
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Affiliation(s)
- Xinyu Lu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zheng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Dai
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Rongbo Wang
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yuee Tian
- Department of Plant Protection, Henan University of Science and Technology, Luoyang 471000, China
| | - Heng Xu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Wu H, Zhao P, Yang X, Li J, Zhang J, Zhang X, Zeng Z, Dong J, Gao S, Lu C. A Recombinase Polymerase Amplification and Lateral Flow Strip Combined Method That Detects Salmonella enterica Serotype Typhimurium With No Worry of Primer-Dependent Artifacts. Front Microbiol 2020; 11:1015. [PMID: 32655504 PMCID: PMC7324538 DOI: 10.3389/fmicb.2020.01015] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
On-site detection demands are quickly increasing to control foodborne pathogenic bacteria along with the long food supply chains. Combining the isothermal recombinase polymerase amplification (RPA) with lateral flow strips (LFSs) is a promising molecular detection approach for the short reaction time, low isothermal condition, and simple and "instrument-free" procedure. However, the method comes with a non-negligible intrinsic risk of the primer-dependent artifacts. In this study, with an important foodborne pathogenic bacterium Salmonella enterica serotype Typhimurium (S. Typhimurium) as the model, system measures including the careful selection of primers targeting unique virulence genes, use of a probe in the RPA reaction, introducing base substitutions with specific guidelines in the primer and probe sequences, and analyzing and screening the primer-probe complex formation were taken to eliminate the primer-dependent artifacts. The measures were strictly tested for the efficacy, and the standardized method was able to specifically detect S. typhimurium within 30 min at 42°C without any interference of probe-primer signals. The established RPA-LFS method shared high sensitivity with the detection limit of 1 CFU/μl of unpurified culture. Our study provided practical measures for the prevention of false positive signals from primer-dimers or primer-probe complexes when using the RPA-LFS method in pathogen detections, and also established a readily applicable method for S. Typhimurium detection.
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Affiliation(s)
- Huahua Wu
- 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, China
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research by Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - 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, China
| | - Juan Li
- Wuhan Institute for Food and Cosmetic Control, Wuhan, China
| | - Jingyu Zhang
- Department of Animal Science, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Xun Zhang
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Zihan Zeng
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, 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, China
| | - Song Gao
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Chen Lu
- 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, China
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PHYCI_587572: An RxLR Effector Gene and New Biomarker in A Recombinase Polymerase Amplification Assay for Rapid Detection of Phytophthora cinnamomi. FORESTS 2020. [DOI: 10.3390/f11030306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Phytophthora cinnamomi is a devastating pathogen causing root and crown rot and dieback diseases of nearly 5000 plant species. Accurate and rapid detection of P. cinnamomi plays a fundamental role within the current disease prevention and management programs. In this study, a novel effector gene PHYCI_587572 was found as unique to P. cinnamomi based on a comparative genomic analysis of 12 Phytophthora species. Its avirulence homolog protein 87 (Avh87) is characterized by the Arg-Xaa-Leu-Arg (RxLR) motif. Avh87 suppressed the pro-apoptotic protein BAX- and elicitin protein INF1-mediated cell death of Nicotiana benthamiana. Furthermore, a recombinase polymerase amplification-lateral flow dipstick detection assay targeting this P. cinnamomi-specific biomarker was developed. While successfully detected 19 P. cinnamomi isolates of a global distribution, this assay lacked detection of 37 other oomycete and fungal species, including P. parvispora, a sister taxon of P. cinnamomi. In addition, it detected P. cinnamomi from artificially inoculated leaves of Cedrus deodara. Moreover, the RPA-LFD assay was found to be more sensitive than a conventional PCR assay, by detecting as low as 2 pg of genomic DNA in a 50-µL reaction. It detected P. cinnamomi in 13 infested soil samples, while the detection rate was 46.2% using PCR. Results in this study indicated that PHYCI_587572 is a unique biomarker for detecting P. cinnamomi. Although PHYCI_587572 was identified as an effector gene based on the RxLR motif of Avh87 and the avirulence activity on Nicotiana, its exact genetic background and biological function on the natural hosts of P. cinnamomi warrant further investigations.
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Dong Y, Zhao P, Chen L, Wu H, Si X, Shen X, Shen H, Qiao Y, Zhu S, Chen Q, Jia W, Dong J, Li J, Gao S. Fast, simple and highly specific molecular detection of Vibrio alginolyticus pathogenic strains using a visualized isothermal amplification method. BMC Vet Res 2020; 16:76. [PMID: 32131821 PMCID: PMC7057676 DOI: 10.1186/s12917-020-02297-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Background Vibrio alginolyticus is an important pathogen that has to be closely monitored and controlled in the mariculture industry because of its strong pathogenicity, quick onset after infection and high mortality rate in aquatic animals. Fast, simple and specific methods are needed for on-site detection to effectively control outbreaks and prevent economic losses. The detection specificity towards the pathogenic strains has to be emphasized to facilitate pointed treatment and prevention. Polymerase chain reaction (PCR)-based molecular approaches have been developed, but their application is limited due to the requirement of complicated thermal cycling machines and trained personnel. Results A fast, simple and highly specific detection method for V. alginolyticus pathogenic strains was established based on isothermal recombinase polymerase amplification (RPA) and lateral flow dipsticks (LFD). The method targeted the virulence gene toxR, which is reported to have good coverage for V. alginolyticus pathogenic strains. To ensure the specificity of the method, the primer-probe set of the RPA system was carefully designed to recognize regions in the toxR gene that diverge in different Vibrio species but are conserved in V. alginolyticus pathogenic strains. The primer-probe set was determined after a systematic screening of amplification performance, primer-dimer formation and false positive signals. The RPA-LFD method was confirmed to have high specificity for V. alginolyticus pathogenic strains without any cross reaction with other Vibrio species or other pathogenic bacteria and was able to detect as little as 1 colony forming unit (CFU) per reaction without DNA purification, or 170 fg of genomic DNA, or 6.25 × 103 CFU/25 g in spiked shrimp without any enrichment. The method finishes detection within 30 min at temperatures between 35 °C and 45 °C, and the visual signal on the dipstick can be directly read by the naked eye. In an application simulation, randomly spiked shrimp homogenate samples were 100% accurately detected. Conclusions The RPA-LFD method developed in this study is fast, simple, highly specific and does not require complicated equipment. This method is applicable for on-site detection of V. alginolyticus pathogenic strains for the mariculture industry.
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Affiliation(s)
- 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
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research by Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Li 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
| | - Huahua Wu
- 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
| | - Xinxin Si
- 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
| | - Xin Shen
- 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
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, 226007, China
| | - Shanyuan Zhu
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, 225300, China
| | - Qiong Chen
- Wuhan Institute for Food and Cosmetic Control, Wuhan, 430000, China
| | - Weiwei Jia
- 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.
| | - Juan Li
- Wuhan Institute for Food and Cosmetic Control, Wuhan, 430000, China.
| | - Song Gao
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
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