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Lee UJ, Oh Y, Kwon OS, Park JM, Cho HM, Kim DH, Kim M. Single-Cell Detection of Erwinia amylovora Using Bio-Functionalized SIS Sensor. SENSORS (BASEL, SWITZERLAND) 2023; 23:7400. [PMID: 37687855 PMCID: PMC10490433 DOI: 10.3390/s23177400] [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: 07/20/2023] [Revised: 08/13/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
Herein, we developed a bio-functionalized solution-immersed silicon (SIS) sensor at the single-cell level to identify Erwinia amylovora (E. amylovora), a highly infectious bacterial pathogen responsible for fire blight, which is notorious for its rapid spread and destructive impact on apple and pear orchards. This method allows for ultra-sensitive measurements without pre-amplification or labeling compared to conventional methods. To detect a single cell of E. amylovora, we used Lipopolysaccharide Transporter E (LptE), which is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane of E. amylovora, as a capture agent. We confirmed that LptE interacts with E. amylovora via LPS through in-house ELISA analysis, then used it to construct the sensor chip by immobilizing the capture molecule on the sensor surface modified with 3'-Aminopropyl triethoxysilane (APTES) and glutaraldehyde (GA). The LptE-based SIS sensor exhibited the sensitive and specific detection of the target bacterial cell in real time. The dose-response curve shows a linearity (R2 > 0.992) with wide dynamic ranges from 1 to 107 cells/mL for the target bacterial pathogen. The sensor showed the value change (dΨ) of approximately 0.008° for growing overlayer thickness induced from a single-cell E. amylovora, while no change in the control bacterial cell (Bacillus subtilis) was observed, or negligible change, if any. Furthermore, the bacterial sensor demonstrated a potential for the continuous detection of E. amylovora through simple surface regeneration, enabling its reusability. Taken together, our system has the potential to be applied in fields where early symptoms are not observed and where single-cell or ultra-sensitive detection is required, such as plant bacterial pathogen detection, foodborne pathogen monitoring and analysis, and pathogenic microbial diagnosis.
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Affiliation(s)
- Ui Jin Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahang-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (U.J.L.); (Y.O.)
| | - Yunkwang Oh
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahang-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (U.J.L.); (Y.O.)
| | - Oh Seok Kwon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea;
- Department of Nano Science and Technology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Nano Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahang-ro, Yuseong-gu, Daejeon 34141, Republic of Korea;
| | - Hyun Mo Cho
- Division of Advanced Instrumentation Institute, Korea Research Institute of Standards and Science (KRISS), 267 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea;
| | - Dong Hyung Kim
- Division of Advanced Instrumentation Institute, Korea Research Institute of Standards and Science (KRISS), 267 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea;
| | - Moonil Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahang-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (U.J.L.); (Y.O.)
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Singh J, Cobb-Smith D, Higgins E, Khan A. Comparative evaluation of lateral flow immunoassays, LAMP, and quantitative PCR for diagnosis of fire blight in apple orchards. JOURNAL OF PLANT PATHOLOGY : AN INTERNATIONAL JOURNAL OF THE ITALIAN PHYTOPATHOLOGICAL SOCIETY 2021; 103:131-142. [PMID: 32904534 PMCID: PMC7456764 DOI: 10.1007/s42161-020-00644-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/26/2020] [Indexed: 05/11/2023]
Abstract
Fire blight remains a serious threat to commercial apple production in the USA and worldwide. Other diseases and spray damage can result in fire blight-like symptoms that can lead to misdiagnosis and affect disease management strategies. Accurate and timely detection of the fire blight pathogen, Erwinia amylovora, is extremely important to deploy appropriate and timely measures to reduce fire blight epidemics in commercial apple orchards. We tested two commercial lateral flow immunoassays (AgriStrip®, and Pocket Diagnostics kit), Loop mediated isothermal amplification (LAMP), and quantitative PCR (qPCR) to diagnose E. amylovora infected samples in lab and field settings. The AgriStrip® and Pocket Diagnostics kits were able to detect actively growing bacteria up to ×106 cfu/ml bacterial concentration. Pocket Diagnostics kit had less specificity and showed positive tests for E. pyrifolia in addition to E. amylovora. The LAMP assay showed high specificity for E. amylovora and was able to detect up to ×103 cfu/ml bacterial concentrations. The qPCR assay was also able to detect bacterial cells up to ×10-3 cfu/ml bacterial concentration with highly specific E. amylovora detection. Grower surveys and comparative cost-benefit analysis indicated that immunoassay kits are less expensive, easier to use, and require less technical expertise for on-site fire blight diagnosis than LAMP and qPCR. However, the choice of a specific diagnostic assay depends on the time, sensitivity, and specificity required for the detection of fire blight and its management.
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Affiliation(s)
- Jugpreet Singh
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
| | - Della Cobb-Smith
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
| | - Elizabeth Higgins
- Eastern NY Commercial Horticulture Program, Cornell Cooperative Extension at Hudson Valley Research Lab, Highland, NY 12528 USA
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
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Cassedy A, Mullins E, O'Kennedy R. Sowing seeds for the future: The need for on-site plant diagnostics. Biotechnol Adv 2020; 39:107358. [DOI: 10.1016/j.biotechadv.2019.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 01/28/2019] [Accepted: 02/21/2019] [Indexed: 01/09/2023]
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Jain A, Sarsaiya S, Wu Q, Lu Y, Shi J. A review of plant leaf fungal diseases and its environment speciation. Bioengineered 2020; 10:409-424. [PMID: 31502497 PMCID: PMC6779379 DOI: 10.1080/21655979.2019.1649520] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
There is increasing difficulty in identifying new plant leaf diseases as a result of environmental change. There is a need to identify the factors influencing the emergence and the increasing incidences of these diseases. Here, we present emerging fungal plant leaf diseases and describe their environmental speciation. We considered the factors controlling for local adaptation associated with environmental speciation. We determined that the advent of emergent fungal leaf diseases is closely connected to environmental speciation. Fungal pathogens targeting the leaves may adversely affect the entire plant body. To mitigate the injury caused by these pathogens, it is necessary to be able to detect and identify them early in the infection process. In this way, their distribution, virulence, incidence, and severity could be attenuated.
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Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi , Guizhou , China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi , Guizhou , China.,Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi , Guizhou , China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi , Guizhou , China
| | - Yuanfu Lu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi , Guizhou , China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi , Guizhou , China
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Tominaga T, Ishii M. Detection of microorganisms with lateral flow test strips. METHODS IN MICROBIOLOGY 2020. [DOI: 10.1016/bs.mim.2019.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Host Range of Bacteriophages Against a World-Wide Collection of Erwinia amylovora Determined Using a Quantitative PCR Assay. Viruses 2019; 11:v11100910. [PMID: 31581574 PMCID: PMC6832558 DOI: 10.3390/v11100910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 01/01/2023] Open
Abstract
Erwinia amylovora is a globally devastating pathogen of apple, pear, and other Rosaceous plants. The use of lytic bacteriophages for disease management continues to garner attention as a possible supplement or alternative to antibiotics. A quantitative productive host range was established for 10 Erwinia phages using 106 wild type global isolates of E. amylovora, and the closely related Erwinia pyrifoliae, to investigate the potential regional efficacy of these phages within a biopesticide. Each host was individually infected with each of the 10 Erwinia phages and phage production after 8 h incubation was measured using quantitative real time PCR (qPCR) in conjunction with a standardized plasmid. PCR amplicons for all phages used in the study were incorporated into a single plasmid, allowing standardized quantification of the phage genome copy number after the infection process. Nine of the tested phages exhibited a broad host range, replicating their genomes by at least one log in over 88% of tested hosts. Also, every Amygdaloideae infecting E. amylovora host was able to increase at least one phage by three logs. Bacterial hosts isolated in western North America were less susceptible to most phages, as the mean genomic titre produced dropped by nearly two logs, and this phenomenon was strongly correlated to the amount of exopolysaccharide produced by the host. This method of host range analysis is faster and requires less effort than traditional plaque assay techniques, and the resulting quantitative data highlight subtle differences in phage host preference not observable with typical plaque-based host range assays. These quantitative host range data will be useful to determine which phages should be incorporated into a phage-mediated biocontrol formulation to be tested for regional and universal control of E. amylovora.
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Fahrentrapp J, Ria F, Geilhausen M, Panassiti B. Detection of Gray Mold Leaf Infections Prior to Visual Symptom Appearance Using a Five-Band Multispectral Sensor. FRONTIERS IN PLANT SCIENCE 2019; 10:628. [PMID: 31156683 PMCID: PMC6529515 DOI: 10.3389/fpls.2019.00628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/26/2019] [Indexed: 05/27/2023]
Abstract
Fungal leaf diseases cause economically important damage to crop plants. Protective treatments help producers to secure good quality crops. In contrast, curative treatments based on visually detectable symptoms are often riskier and less effective because diseased crop plants may develop disease symptoms too late for curative treatments. Therefore, early disease detection prior symptom development would allow an earlier, and therefore more effective, curative management of fungal diseases. Using a five-lens multispectral imager, spectral reflectance of green, blue, red, near infrared (NIR, 840 nm), and rededge (RE, 720 nm) was recorded in time-course experiments of detached tomato leaves inoculated with the fungus Botrytis cinerea and mock infection solution. Linear regression models demonstrate NIR and RE as the two most informative spectral data sets to differentiate pathogen- and mock-inoculated leaf regions of interest (ROI). Under controlled laboratory conditions, bands collecting NIR and RE irradiance showed a lower reflectance intensity of infected tomato leaf tissue when compared with mock-inoculated leaves. Blue and red channels collected higher intensity values in pathogen- than in mock-inoculated ROIs. The reflectance intensities of the green band were not distinguishable between pathogen- and mock infected ROIs. Predictions of linear regressions indicated that gray mold leaf infections could be identified at the earliest at 9 h post infection (hpi) in the most informative bands NIR and RE. Re-analysis of the imagery taken with NIR and RE band allowed to classify infected tissue.
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Affiliation(s)
- Johannes Fahrentrapp
- Institute of Natural Resource Sciences, ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Francesco Ria
- Institute of Natural Resource Sciences, ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Martin Geilhausen
- Institute of Natural Resource Sciences, ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland
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Shin DS, Heo GI, Son SH, Oh CS, Lee YK, Cha JS. Development of an Improved Loop-Mediated Isothermal Amplification Assay for On-Site Diagnosis of Fire Blight in Apple and Pear. THE PLANT PATHOLOGY JOURNAL 2018; 34:191-198. [PMID: 29887775 PMCID: PMC5985645 DOI: 10.5423/ppj.ft.03.2018.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 05/25/2023]
Abstract
Fast and accurate diagnosis is needed to eradicate and manage economically important and invasive diseases like fire blight. Loop-mediated isothermal amplification (LAMP) is known as the best on-site diagnostic, because it is fast, highly specific to a target, and less sensitive to inhibitors in samples. In this study, LAMP assay that gives more consistent results for on-site diagnosis of fire blight than the previous developed LAMP assays was developed. Primers for new LAMP assay (named as DS-LAMP) were designed from a histidine-tRNA ligase gene (EAMY_RS32025) of E. amylovora CFBP1430 genome. The DS-LAMP amplified DNA (positive detection) only from genomic DNA of E. amylovora strains, not from either E. pyrifoliae (causing black shoot blight) or from Pseudomonas syringae pv. syringae (causing shoot blight on apple trees). The detection limit of DS-LAMP was 10 cells per LAMP reaction, equivalent to 104 cells per ml of the sample extract. DS-LAMP successfully diagnosed the pathogens on four fire-blight infected apple and pear orchards. In addition, it could distinguish black shoot blight from fire blight. The Bühlmann-LAMP, developed previously for on-site diagnosis of fire blight, did not give consistent results for specificity to E. amylovora and on-site diagnosis; it gave positive reactions to three strains of E. pyrifoliae and two strains of P. syringae pv. syringae. It also, gave positive reactions to some healthy sample extracts. DS-LAMP, developed in this study, would give more accurate on-site diagnosis of fire blight, especially in the Republic of Korea, where fire blight and black shoot blight coexist.
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Affiliation(s)
- Doo-San Shin
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Gwang-Il Heo
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Soo-Hyeong Son
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Young-Kee Lee
- Department of Agro-food Safety and Crop Protection, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Jae-Soon Cha
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
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DeShields JB, Bomberger RA, Woodhall JW, Wheeler DL, Moroz N, Johnson DA, Tanaka K. On-Site Molecular Detection of Soil-Borne Phytopathogens Using a Portable Real-Time PCR System. J Vis Exp 2018. [PMID: 29553557 PMCID: PMC5931365 DOI: 10.3791/56891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection. This was achieved using a rapid and simple protocol comprising of magnetic bead-based nucleic acid extraction, portable real-time PCR (fluorogenic probe-based assay). The portable real-time PCR approach compared favorably with a laboratory-based system, detecting as few as 100 copies of DNA from Spongospora subterranea. The portable real-time PCR method developed here can serve as an alternative to laboratory-based approaches and a useful on-site tool for pathogen diagnosis.
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Affiliation(s)
| | | | | | | | - Natalia Moroz
- Department of Plant Pathology, Washington State University
| | | | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University;
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Born Y, Fieseler L, Thöny V, Leimer N, Duffy B, Loessner MJ. Engineering of Bacteriophages Y2:: dpoL1-C and Y2:: luxAB for Efficient Control and Rapid Detection of the Fire Blight Pathogen, Erwinia amylovora. Appl Environ Microbiol 2017; 83:e00341-17. [PMID: 28389547 PMCID: PMC5452800 DOI: 10.1128/aem.00341-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
Erwinia amylovora is the causative agent of fire blight, a devastating plant disease affecting members of the Rosaceae Alternatives to antibiotics for control of fire blight symptoms and outbreaks are highly desirable, due to increasing drug resistance and tight regulatory restrictions. Moreover, the available diagnostic methods either lack sensitivity, lack speed, or are unable to discriminate between live and dead bacteria. Owing to their extreme biological specificity, bacteriophages are promising alternatives for both aims. In this study, the virulent broad-host-range E. amylovora virus Y2 was engineered to enhance its killing activity and for use as a luciferase reporter phage, respectively. Toward these aims, a depolymerase gene of E. amylovora virus L1 (dpoL1-C) or a bacterial luxAB fusion was introduced into the genome of Y2 by homologous recombination. The genes were placed downstream of the major capsid protein orf68, under the control of the native promoter. The modifications did not affect viability of infectivity of the recombinant viruses. Phage Y2::dpoL1-C demonstrated synergistic activity between the depolymerase degrading the exopolysaccharide capsule and phage infection, which greatly enhanced bacterial killing. It also significantly reduced the ability of E. amylovora to colonize the surface of detached flowers. The reporter phage Y2::luxAB transduced bacterial luciferase into host cells and induced synthesis of large amounts of a LuxAB luciferase fusion. After the addition of aldehyde substrate, bioluminescence could be readily monitored, and this enabled rapid and specific detection of low numbers of viable bacteria, without enrichment, both in vitro and in plant material.IMPORTANCE Fire blight, caused by Erwinia amylovora, is the major threat to global pome fruit production, with high economic losses every year. Bacteriophages represent promising alternatives to not only control the disease, but also for rapid diagnostics. To enhance biocontrol efficacy, we combined the desired properties of two phages, Y2 (broad host range) and L1 (depolymerase for capsule degradation) in a single recombinant phage. This phage showed enhanced biocontrol and could reduce E. amylovora on flowers. Phage Y2 was also genetically engineered into a luciferase reporter phage, which transduces bacterial bioluminescence into infected cells and allows detection of low numbers of viable target bacteria. The combination of speed, sensitivity, and specificity is superior to previously used diagnostic methods. In conclusion, genetic engineering could improve the properties of phage Y2 toward better killing efficacy and sensitive detection of E. amylovora cells.
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Affiliation(s)
- Yannick Born
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
- Agroscope, Research Division Plant Protection, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Valentin Thöny
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Nadja Leimer
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
| | - Brion Duffy
- Agroscope, Research Division Plant Protection, Wädenswil, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland
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López-Soriano P, Noguera P, Gorris MT, Puchades R, Maquieira Á, Marco-Noales E, López MM. Lateral flow immunoassay for on-site detection of Xanthomonas arboricola pv. pruni in symptomatic field samples. PLoS One 2017; 12:e0176201. [PMID: 28448536 PMCID: PMC5407831 DOI: 10.1371/journal.pone.0176201] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/06/2017] [Indexed: 02/03/2023] Open
Abstract
Xanthomonas arboricola pv. pruni is a quarantine pathogen and the causal agent of the bacterial spot disease of stone fruits and almond, a major threat to Prunus species. Rapid and specific detection methods are essential to improve disease management, and therefore a prototype of a lateral flow immunoassay (LFIA) was designed for the detection of X. arboricola pv. pruni in symptomatic field samples. It was developed by producing polyclonal antibodies which were then combined with carbon nanoparticles and assembled on nitrocellulose strips. The specificity of the LFIA was tested against 87 X. arboricola pv. pruni strains from different countries worldwide, 47 strains of other Xanthomonas species and 14 strains representing other bacterial genera. All X. arboricola pv. pruni strains were detected and cross-reactions were observed only with four strains of X. arboricola pv. corylina, a hazelnut pathogen that does not share habitat with X. arboricola pv. pruni. The sensitivity of the LFIA was assessed with suspensions from pure cultures of three X. arboricola pv. pruni strains and with spiked leaf extracts prepared from four hosts inoculated with this pathogen (almond, apricot, Japanese plum and peach). The limit of detection observed with both pure cultures and spiked samples was 104 CFU ml-1. To demonstrate the accuracy of the test, 205 samples naturally infected with X. arboricola pv. pruni and 113 samples collected from healthy plants of several different Prunus species were analyzed with the LFIA. Results were compared with those obtained by plate isolation and real time PCR and a high correlation was found among techniques. Therefore, we propose this LFIA as a screening tool that allows a rapid and reliable diagnosis of X. arboricola pv. pruni in symptomatic plants.
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Affiliation(s)
- Pablo López-Soriano
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Patricia Noguera
- Instituto Universitario de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, València, Spain
| | - María Teresa Gorris
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Rosa Puchades
- Instituto Universitario de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, València, Spain
| | - Ángel Maquieira
- Instituto Universitario de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, València, Spain
| | - Ester Marco-Noales
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - María M. López
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
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Khater M, de la Escosura-Muñiz A, Merkoçi A. Biosensors for plant pathogen detection. Biosens Bioelectron 2016; 93:72-86. [PMID: 27818053 DOI: 10.1016/j.bios.2016.09.091] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/15/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
Abstract
Infectious plant diseases are caused by pathogenic microorganisms such as fungi, bacteria, viruses, viroids, phytoplasma and nematodes. Worldwide, plant pathogen infections are among main factors limiting crop productivity and increasing economic losses. Plant pathogen detection is important as first step to manage a plant disease in greenhouses, field conditions and at the country boarders. Current immunological techniques used to detect pathogens in plant include enzyme-linked immunosorbent assays (ELISA) and direct tissue blot immunoassays (DTBIA). DNA-based techniques such as polymerase chain reaction (PCR), real time PCR (RT-PCR) and dot blot hybridization have also been proposed for pathogen identification and detection. However these methodologies are time-consuming and require complex instruments, being not suitable for in-situ analysis. Consequently, there is strong interest for developing new biosensing systems for early detection of plant diseases with high sensitivity and specificity at the point-of-care. In this context, we revise here the recent advancement in the development of advantageous biosensing systems for plant pathogen detection based on both antibody and DNA receptors. The use of different nanomaterials such as nanochannels and metallic nanoparticles for the development of innovative and sensitive biosensing systems for the detection of pathogens (i.e. bacteria and viruses) at the point-of-care is also shown. Plastic and paper-based platforms have been used for this purpose, offering cheap and easy-to-use really integrated sensing systems for rapid on-site detection. Beside devices developed at research and development level a brief revision of commercially available kits is also included in this review.
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Affiliation(s)
- Mohga Khater
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain; On leave from Agricultural Research Center (ARC), Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Alfredo de la Escosura-Muñiz
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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14
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Lau HY, Wang Y, Wee EJH, Botella JR, Trau M. Field Demonstration of a Multiplexed Point-of-Care Diagnostic Platform for Plant Pathogens. Anal Chem 2016; 88:8074-81. [PMID: 27403651 DOI: 10.1021/acs.analchem.6b01551] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Effective disease management strategies to prevent catastrophic crop losses require rapid, sensitive, and multiplexed detection methods for timely decision making. To address this need, a rapid, highly specific and sensitive point-of-care method for multiplex detection of plant pathogens was developed by taking advantage of surface-enhanced Raman scattering (SERS) labeled nanotags and recombinase polymerase amplification (RPA), which is a rapid isothermal amplification method with high specificity. In this study, three agriculturally important plant pathogens (Botrytis cinerea, Pseudomonas syringae, and Fusarium oxysporum) were used to demonstrate potential translation into the field. The RPA-SERS method was faster, more sensitive than polymerase chain reaction, and could detect as little as 2 copies of B. cinerea DNA. Furthermore, multiplex detection of the three pathogens was demonstrated for complex systems such as the Arabidopsis thaliana plant and commercial tomato crops. To demonstrate the potential for on-site field applications, a rapid single-tube RPA/SERS assay was further developed and successfully performed for a specific target outside of a laboratory setting.
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Affiliation(s)
- Han Yih Lau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Eugene J H Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane QLD 4072, Australia
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15
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Elkins RB, Temple TN, Shaffer CA, Ingels CA, Lindow SB, Zoller BG, Johnson KB. Evaluation of Dormant-Stage Inoculum Sanitation as a Component of a Fire Blight Management Program for Fresh-Market Bartlett Pear. PLANT DISEASE 2015; 99:1147-1152. [PMID: 30695942 DOI: 10.1094/pdis-10-14-1082-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
From 2010 to 2013, the efficacy of copper-based inoculum sanitation as a component of fire blight management programs was evaluated in commercial pear orchards located in northern California. Forty-one 4-ha sections of orchard were split into two equal-sized plots, with the orchardist applying horticultural oil alone to one plot and horticultural oil plus a fixed copper bactericide to the other plot. These treatments were timed to begin just prior to and finish at the "green tip" phenological stage, which occurs about 5 weeks before full bloom. During bloom, flower samples were collected from the plots and subjected to a loop-mediated isothermal DNA amplification (LAMP) assay for specific detection of Erwinia amylovora. Overall, epiphytic populations of E. amylovora on flowers were detected rarely at midbloom (6% of samples) but commonly at petal fall (44% of samples). In three of four seasons, E. amylovora detection in flower samples at a given bloom stage was significantly suppressed in copper-plus-oil-treated plots compared with oil-only plots. All orchards also received antibiotic treatments during the bloom period and, perhaps as a consequence, the development of fire blight was sporadic and not affected significantly by the copper treatment in any season. The pathogen detection data indicate that copper sanitation may add value to a fire blight management program by delaying the increase of epiphytic populations of E. amylovora in flowers to the late stages of the bloom period, at which time the number of susceptible flowers declines rapidly.
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Affiliation(s)
- Rachel B Elkins
- Lake County Cooperative Extension, University of California, Lakeport 95453-5405
| | - Todd N Temple
- Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331-2902
| | - Carolyn A Shaffer
- Lake County Cooperative Extension, University of California, Lakeport
| | - Chuck A Ingels
- Sacramento County Cooperative Extension, University of California, Sacramento 95827-3823
| | - Steven B Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102
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16
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Chen A, Yang S. Replacing antibodies with aptamers in lateral flow immunoassay. Biosens Bioelectron 2015; 71:230-242. [PMID: 25912679 DOI: 10.1016/j.bios.2015.04.041] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 12/30/2022]
Abstract
Aptamers have been identified against various targets as a type of chemical or nucleic acid ligand by systematic evolution of ligands by exponential enrichment (SELEX) with high sensitivity and specificity. Aptamers show remarkable advantages over antibodies due to the nucleic acid nature and target-induced structure-switching properties and are widely used to design various fluorescent, electrochemical, or colorimetric biosensors. However, the practical applications of aptamer-based sensing and diagnostics are still lagging behind those of antibody-based tests. Lateral flow immunoassay (LFIA) represents a well established and appropriate technology among rapid assays because of its low cost and user-friendliness. The antibody-based platform is utilized to detect numerous targets, but it is always hampered by the antibody preparation time, antibody stability, and effect of modification on the antibody. Seeking alternatives to antibodies is an area of active research and is of tremendous importance. Aptamers are receiving increasing attention in lateral flow applications because of a number of important potential performance advantages. We speculate that aptamer-based LFIA may be one of the first platforms for commercial use of aptamer-based diagnosis. This review first gives an introduction to aptamer including the selection process SELEX with its focus on aptamer advantages over antibodies, and then depicts LFIA with its focus on aptamer opportunities in LFIA over antibodies. Furthermore, we summarize the recent advances in the development of aptamer-based lateral flow biosensing assays with the aim to provide a general guide for the design of aptamer-based lateral flow biosensing assays.
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Affiliation(s)
- Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
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17
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Pletzer D, Stahl A, Oja AE, Weingart H. Role of the cell envelope stress regulators BaeR and CpxR in control of RND-type multidrug efflux pumps and transcriptional cross talk with exopolysaccharide synthesis in Erwinia amylovora. Arch Microbiol 2015; 197:761-72. [DOI: 10.1007/s00203-015-1109-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 01/31/2023]
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18
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Hodgetts J, Johnson G, Perkins K, Ostoja-Starzewska S, Boonham N, Mumford R, Dickinson M. The development of monoclonal antibodies to the secA protein of Cape St. Paul wilt disease phytoplasma and their evaluation as a diagnostic tool. Mol Biotechnol 2014; 56:803-13. [PMID: 24845751 DOI: 10.1007/s12033-014-9759-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Partial recombinant secA proteins were produced from six different phytoplasma isolates representing five 16Sr groups and the expressed, purified recombinant (partial secA) protein from Cape St. Paul wilt disease phytoplasma (CSPWD, 16SrXXII) was used to immunise mice. Monoclonal antibodies (mAbs) were selected by screening hybridoma supernatants for binding to the recombinant proteins. To characterise the binding to proteins from different phytoplasmas, the antibodies were screened by ELISA and western blotting, and epitope mapping was undertaken. Eight different mAbs with varying degrees of specificity against recombinant proteins from different phytoplasma groups were selected. Western blotting revealed that the mAbs bind to proteins in infected plant material, two of which were specific for phytoplasmas. ELISA testing of infected material, however, gave negative results suggesting that either secA was not expressed at sufficiently high levels, or conformational changes of the reagents adversely affected detection. This work has shown that the phytoplasma secA gene is not a suitable antibody target for routine detection, but has illustrated proof of principle for the methodology.
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Affiliation(s)
- Jennifer Hodgetts
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK,
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19
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Coyne S, Litomska A, Chizzali C, Khalil MNA, Richter K, Beerhues L, Hertweck C. Control of Plant Defense Mechanisms and Fire Blight Pathogenesis through the Regulation of 6-Thioguanine Biosynthesis inErwinia amylovora. Chembiochem 2014; 15:373-6. [DOI: 10.1002/cbic.201300684] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 01/20/2023]
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20
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Bühlmann A, Dreo T, Rezzonico F, Pothier JF, Smits THM, Ravnikar M, Frey JE, Duffy B. Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites. Environ Microbiol 2013; 16:2112-25. [PMID: 24112873 DOI: 10.1111/1462-2920.12289] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/14/2013] [Indexed: 01/08/2023]
Abstract
Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple-Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region.
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Affiliation(s)
- Andreas Bühlmann
- Plant Protection Division, Agroscope Changins-Wädenswil Research Station ACW, CH-8820, Wädenswil, Switzerland
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21
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22
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Bühlmann A, Pothier JF, Rezzonico F, Smits THM, Andreou M, Boonham N, Duffy B, Frey JE. Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. J Microbiol Methods 2012; 92:332-9. [PMID: 23275135 DOI: 10.1016/j.mimet.2012.12.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022]
Abstract
Several molecular methods have been developed for the detection of Erwinia amylovora, the causal agent of fire blight in pear and apple, but none are truly applicable for on-site use in the field. We developed a fast, reliable and field applicable detection method using a novel target on the E. amylovora chromosome that we identified by applying a comparative genomic pipeline. The target coding sequences (CDSs) are both uniquely specific for and all-inclusive of E. amylovora genotypes. This avoids potential false negatives that can occur with most commonly used methods based on amplification of plasmid gene targets, which can vary among strains. Loop-mediated isothermal AMPlification (LAMP) with OptiGene Genie II chemistry and instrumentation proved to be an exceptionally rapid (under 15 min) and robust method for detecting E. amylovora in orchards, as well as simple to use in the plant diagnostic laboratory. Comparative validation results using plant samples from inoculated greenhouse trials and from natural field infections (of regional and temporal diverse origin) showed that our LAMP had an equivalent or greater performance regarding sensitivity, specificity, speed and simplicity than real-time PCR (TaqMan), other LAMP assays, immunoassays and plating, demonstrating its utility for routine testing.
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Affiliation(s)
- Andreas Bühlmann
- Agroscope Changins-Wädenswil Research Station ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland
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23
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Rezzonico F, Braun-Kiewnick A, Mann RA, Rodoni B, Goesmann A, Duffy B, Smits THM. Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora. MOLECULAR PLANT PATHOLOGY 2012; 13:975-984. [PMID: 22583486 PMCID: PMC6638724 DOI: 10.1111/j.1364-3703.2012.00807.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Comparative genomic analysis revealed differences in the lipopolysaccharide (LPS) biosynthesis gene cluster between the Rubus-infecting strain ATCC BAA-2158 and the Spiraeoideae-infecting strain CFBP 1430 of Erwinia amylovora. These differences corroborate rpoB-based phylogenetic clustering of E. amylovora into four different groups and enable the discrimination of Spiraeoideae- and Rubus-infecting strains. The structure of the differences between the two groups supports the hypothesis that adaptation to Rubus spp. took place after species separation of E. amylovora and E. pyrifoliae that contrasts with a recently proposed scenario, based on CRISPR data, in which the shift to domesticated apple would have caused an evolutionary bottleneck in the Spiraeoideae-infecting strains of E. amylovora which would be a much earlier event. In the core region of the LPS biosynthetic gene cluster, Spiraeoideae-infecting strains encode three glycosyltransferases and an LPS ligase (Spiraeoideae-type waaL), whereas Rubus-infecting strains encode two glycosyltransferases and a different LPS ligase (Rubus-type waaL). These coding domains share little to no homology at the amino acid level between Rubus- and Spiraeoideae-infecting strains, and this genotypic difference was confirmed by polymerase chain reaction analysis of the associated DNA region in 31 Rubus- and Spiraeoideae-infecting strains. The LPS biosynthesis gene cluster may thus be used as a molecular marker to distinguish between Rubus- and Spiraeoideae-infecting strains of E. amylovora using primers designed in this study.
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Affiliation(s)
- Fabio Rezzonico
- Agroscope Changins-Wädenswil ACW, Plant Protection Division, Swiss National Competence Centre for Fire Blight, CH-8820 Wädenswil, Switzerland
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24
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De Boer SH, López MM. New grower-friendly methods for plant pathogen monitoring. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:197-218. [PMID: 22607454 DOI: 10.1146/annurev-phyto-081211-172942] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.
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Affiliation(s)
- Solke H De Boer
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, PE, C1A 5T1 Canada.
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