[Show abstract][Hide abstract] ABSTRACT: Loop-mediated isothermal AMPlification (LAMP) is an alternative amplification technology which is highly sensitive and less time consuming than conventional PCR-based methods. Three LAMP assays were developed, two for detection of species of symbiotic blue-stain fungi associated with Ips acuminatus, a bark beetle infesting Scots pine (Pinus sylvestris), and an additional assay specific to I. acuminatus itself for use as a control. In common with most bark beetles, I. acuminatus is associated with phytopathogenic blue-stain fungi involved in the process of exhausting tree defenses, which is a necessary step for the colonization of the plant by the insect. However, the identity of the main blue-stain fungus vectored by I. acuminatus was still uncertain, as well as its frequency of association with I. acuminatus under outbreak and non-outbreak conditions. In this study, we employed LAMP technology to survey six populations of I. acuminatus sampled from the Southern Alps. Ophiostoma clavatum was detected at all sampling sites, while O. brunneo-ciliatum, reported in part of the literature as the main blue-stain fungus associated with I. acuminatus, was not detected on any of the samples. These results are consistent with the hypothesis that O. clavatum is the main blue-stain fungus associated with I. acuminatus in the Southern Alps. The method developed in the course of this work provides a molecular tool by which it will be easy to screen populations and derive important data regarding the ecology of the species involved.
Applied and Environmental Microbiology 02/2013; · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Guignardia citricarpa Kiely (anamorph Phyllosticta citricarpa Van der Aa), the causal agent of citrus black spot disease, is subject to phytosanitary restrictions in the EU and USA, such that consignments of citrus are rejected at import if citrus black spot is identified on inspection. Due to the variability of black spot symptoms, positive identification solely on the basis of visual inspection is difficult, especially when lesions lack pycnidia (fruiting bodies of the anamorph Phyllosticta citricarpa). As an aid to visual inspection of symptoms, we have developed a method for detection of G. citricarpa using loop-mediated isothermal amplification (LAMP) which can be used to confirm the presence of G. citricarpa in black spot lesions, including those lacking pycnidia. The LAMP assay can be used to test crude extracts prepared directly from lesions on fruit, and the entire test can be completed in less than 40 min, making it faster than previously described PCR-based methods for detection of G. citricarpa. The method is sufficiently simple to allow deployment of the test in the field, for example in the course of import inspections. Recent years have seen the description of a number of newly recognised species in the genus Phyllosticta that are associated with citrus. As new species emerge, and the taxonomy of the genus is resolved, it will be important to periodically re-evaluate the performance of DNA-based methods for detection of G. citricarpa, including the LAMP assay described here, such that the accuracy of diagnosis can be assured.
European Journal of Plant Pathology 01/2013; 136(2). · 1.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The objective of this study was to develop a rapid, sensitive detection assay for the quarantine pathogen Xanthomonas arboricola pv. pruni, causal agent of stone fruit bacterial spot, an economically important disease of Prunus spp. Unique targets were identified from X. arboricola pv. pruni genomes using a comparative genomics pipeline of other Xanthomonas species, subspecies and pathovars, and used to identify specific diagnostic markers. Loop-mediated isothermal amplification (LAMP) was then applied to these markers to provide rapid, sensitive and specific detection. The method developed showed unrivalled specificity with the 79 tested strains and, in contrast to previously established techniques, distinguished between phylogenetically close subspecies such as X. arboricola pv. corylina. The sensitivity of this test is comparable to that of a previously reported TaqMan™ assay at 103 CFU mL−1, while the unrivalled speed of LAMP technology enables a positive result to be obtained in
Journal of Microbiological Methods 01/2013; 92:332-339. · 2.16 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The causal agents of cassava brown streak disease have recently been identified as Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Primers have been developed for rapid detection of these viruses by reverse transcription loop-mediated isothermal amplification (RT-LAMP). Performance of the RT-LAMP assays compared favourably with published RT-PCR and real-time RT-PCR methods. Furthermore, amplification by RT-LAMP is completed in 40min and does not require thermal cycling equipment. Modification of the RT-LAMP reactions to use labelled primers allowed rapid detection of amplification products using lateral flow devices containing antibodies specific to the incorporated labels, avoiding the need for fluorescence detection or gel electrophoresis.
Journal of virological methods 07/2012; · 2.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A study to investigate the association of phytoplasmas with papaya dieback and citrus decline syndromes in Ethiopia was carried out between July 2009 and February 2010, with sampling performed in major papaya- and citrus-growing areas of the Rift Valley. Samples of plants with symptoms were collected from papaya, citrus and suspected phytoplasma weed hosts and crops in and around the papaya and citrus fields studied. Nested polymerase chain reaction (nested-PCR) was used for initial characterization, using primers that amplify regions of the 16S rRNA and secA genes, and results were then confirmed with rapid real-time group-specific LAMP (loop-mediated isothermal amplification) assays. The results identified the occurrence of a phytoplasma belonging to the stolbur (16SrXII-A) group in papaya plants showing dieback symptoms, whilst no phytoplasmas were found associated with citrus decline. These results contradict previous reports that a 16SrII phytoplasma was associated with both papaya dieback and citrus decline in Ethiopia, but correspond with the association of a 16SrXII phytoplasmas with Nivum-Haamir-Dieback of papaya in Israel and papaya dieback in Australia. No 16SrXII phytoplasmas were found in any of the weeds and potential alternative hosts studied, although 16SrII phytoplasmas were consistently found in Parthenium hysterophorus weed plants. These results indicate that a 16SrXII phytoplasma is associated with papaya dieback in Ethiopia, whilst the causal agent of citrus decline is not a phytoplasma and remains unidentified.
[Show abstract][Hide abstract] ABSTRACT: To develop a sensitive, rapid and simple method for detection of Botrytis cinerea based on loop-mediated isothermal amplification (LAMP) that would be suitable for use outside a conventional laboratory setting.
A LAMP assay was designed based on the intergenic spacer of the B. cinerea nuclear ribosomal DNA (rDNA). The resulting assay was characterized in terms of sensitivity and specificity using DNA extracted from cultures. The assay consistently amplified 65 pg B. cinerea DNA. No cross-reactivity was observed with a range of other fungal pathogens, with the exception of the closely related species Botrytis pelargonii. Use of a novel real-time LAMP platform (the OptiGene Genie I) allowed detection of B. cinerea in infected rose petals, with amplification occurring in <15 min.
The LAMP assay that was developed is suitable for rapid detection of B. cinerea in infected plant material.
The LAMP method combines the sensitivity and specificity of nucleic acid-based methods with simplified equipment and a reduced reaction time. These features make the method potentially suitable for on-site use, where the results of testing could help to inform decisions regarding the storage and processing of commodities affected by B. cinerea, such as cut flowers, fruit and vegetables.
Letters in Applied Microbiology 09/2010; 51(6):650-7. · 1.63 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Rapid and accurate diagnostic tests make an important contribution to programmes to monitor and eradicate infectious diseases that impact animal and plant health. Using foot-and-mouth disease (FMD) and sudden oak death as examples, this review outlines recent progress to develop new field tools for detection of the infectious agents that cause high-impact livestock and plant diseases. The principal driver for this work is to develop tools that can be used locally to assist in decision making. Advances in this area have developed simple-to-use lateral-flow devices for the detection of FMD virus and the genus Phytophthora (including Phytophthora ramorum, the causal agent of sudden oak death and the related pathogen P. kernoviae), as well as new hardware platforms to allow PCR testing for these agents by non-specialists in the field. Although developed for different diseases, the user requirements for rapid diagnostic tools for FMD and sudden oak death share many similarities. Using generic solutions to these challenging problems, it is now possible to imagine a new paradigm for how the collection and testing of samples to monitor the spread of important livestock and plant diseases might be achieved.
[Show abstract][Hide abstract] ABSTRACT: In a direct comparison with established methods for Phytophthora ramorum detection (isolation followed by morphological identification, or conventional DNA extraction followed by TaqMan real-time PCR) a rapid, simplified detection method in which membranes of lateral flow devices (LFDs) are added directly to TaqMan real-time PCR reactions was used to test 202 plant samples collected by plant health inspectors in the field. P. ramorum prevalence within the 202 samples was approximately 40% according to routine testing by isolation or TaqMan real-time PCR. The diagnostic sensitivity and specificity of the rapid detection method were 96.3% and 91.2%, respectively. This method can be used in conjunction with Phytophthora spp. lateral flow devices to reduce the number of samples requiring testing using more laborious conventional methods. The effect of combining prescreening for Phytophthora spp. with P. ramorum-specific tests is discussed in terms of the positive and negative predictive values of species-specific detection when testing samples collected in different inspection scenarios.
Journal of microbiological methods 02/2010; 81(2):116-20. · 2.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: ABSTRACT A method for nucleic-acid-based detection of pathogens in plant material has been developed which comprises a simple and rapid method for extracting DNA on the nitrocellulose membranes of lateral-flow devices, loop-mediated isothermal amplification (LAMP) of target DNA using labeled primers, and detection of the generically labeled amplification products by a sandwich immunoassay in a lateral-flow-device format. Each of these steps can be performed without specialist equipment and is suitable for on-site use, and a result can be obtained in just over an hour. A LAMP assay for the detection of plant DNA (cytochrome oxidase gene) can be used in conjunction with pathogen-specific assays to confirm negative results. The use of this method is demonstrated for the detection of Phytophthora ramorum, the causal agent of sudden oak death and dieback/leaf blight in a range of tree, shrub, and herbaceous species, and the recently described pathogen P. kernoviae.
[Show abstract][Hide abstract] ABSTRACT: A rapid DNA extraction and loop-mediated isothermal amplification (LAMP) procedure was developed and evaluated for the detection of two specific groups of phytoplasmas from infected plant material. Primers based upon the 16–23S intergenic spacer (IGS) region were evaluated in LAMP assays for amplification of group 16SrI (aster yellows group) and group 16SrXXII (Cape St Paul wilt group) phytoplasma strains. DNA could be extracted from leaf material (16SrI phytoplasmas) or coconut trunk borings (16SrXXII phytoplasmas) onto the membranes of lateral flow devices, and small sections of these membranes were then added directly into the LAMP reaction mixture and incubated for 45 min at 65°C. Positive reactions were detected through the hydroxyl napthol blue colorimetric assay within 1 h of the start of DNA extraction, and were confirmed by subsequent agarose gel electrophoresis of the LAMP products. The level of detection was comparable to that obtained by nested PCR using conventional 16S rDNA phytoplasma-specific primers. Furthermore, the assays were specific for the phytoplasmas they were designed to detect – the 16SrI assay only detected 16SrI phytoplasmas and not those from any other phylogenetic groups, whilst the 16SrXXII assay only detected 16SrXXII phytoplasmas. The DNA extractions and LAMP assay are easy to perform, requiring minimal equipment, and may therefore form the basis of a rapid and reliable field-detection system for phytoplasmas.
[Show abstract][Hide abstract] ABSTRACT: A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of African swine fever virus (ASFV). This assay targets the topoisomerase II gene of ASFV and its specificity was confirmed by restriction enzyme digestion of the reaction products. The analytical sensitivity of this ASFV LAMP assay was at least 330 genome copies, and the test was able to detect representative isolates of ASFV (n=38) without cross-reacting with classical swine fever virus. The performance of the LAMP assay was compared with other laboratory tests used for ASF diagnosis. Using blood and tissue samples collected from pigs experimentally infected with ASFV (Malawi isolate), there was good concordance between the LAMP assay and real-time PCR. In addition to detecting the reaction products using either agarose gels or real-time PCR machines, it was possible to visualise dual-labelled biotin and fluorescein ASFV LAMP amplicons using novel lateral flow devices. This assay and detection format represents the first step towards developing a practical, simple-to-use and inexpensive molecular assay format for ASF diagnosis in the field which is especially relevant to Africa where the disease is endemic in many countries.
Journal of virological methods 12/2009; 164(1-2):68-74. · 2.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Phytophthora ramorum is the causal agent of sudden oak death. The pathogen also affects a wide range of tree, shrub, and herbaceous species in natural and landscaped environments as well as plants in the nursery industry. A TaqMan real-time PCR method for the detection of this pathogen in the field has been described previously; this paper describes the development of a number of assays based on this method which have various advantages for use in the field. A scorpion real-time PCR assay that is twice as fast as TaqMan was developed, allowing the detection of P. ramorum in less than 30 min. Also designed was a loop-mediated isothermal amplification (LAMP) assay, which allowed sensitive and specific detection of P. ramorum in 45 min using only a heated block. A positive reaction was identified by the detection of the LAMP product by color change visible to the naked eye.
Applied and Environmental Microbiology 07/2007; 73(12):4040-7. · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Phytophthora ramorum is a recently described pathogen that has resulted in the introduction of emergency European Community phytosanitary legislation in November 2002. The Department of Environment, Food and Rural Affairs Plant Health and Seeds Inspectorate (PHSI) initiated a survey in England and Wales in autumn 2001 to ascertain whether the organism was present. In April 2002, P. ramorum was found for the first time in the UK and for the first time in Europe since the initial reports in the Netherlands and Germany. Following this finding, P. ramorum has been reported mainly on rhododendrons and viburnums but also on a wide range of other ornamental plants in both the UK and other European countries. Effective disease management and implementation of plant health legislation is reliant upon rapid and accurate disease diagnosis based upon recognition of symptoms in the field and identification of the cause by testing. Other diseases and disorders prevent reliable identification of the problem at the time of inspection with typically only 20–30% of samples submitted testing positive for Phytophthora species. This paper describes the evaluation of a direct real-time PCR and a rapid serological assay (lateral flow device) developed by CSL for testing for P. ramorum and Phytophthora spp., respectively.
[Show abstract][Hide abstract] ABSTRACT: ABSTRACT Phytophthora ramorum is a recently described pathogen causing bleeding cankers, dieback, and leaf blight on trees and shrubs in parts of Europe and North America, where the disease is commonly known as sudden oak death. This article describes the development of a single-round real-time polymerase chain reaction (PCR) assay based on TaqMan chemistry, designed within the internal transcribed spacer 1 region of the nuclear ribosomal (nr)RNA gene for detection of P. ramorum in plant material. Unlike previously described methods for the molecular detection of P. ramorum, this assay involves no post amplification steps or multiple rounds of PCR. The assay was found to have a limit of detection of 10 pg of P. ramorum DNA, and could detect P. ramorum in plant material containing 1% infected material by weight within 36 cycles of PCR. The assay also was used to test DNA from 28 other Phytophthora spp. to establish its specificity for P. ramorum. A quick and simple method was used to extract DNA directly from host plant material, and detection of P. ramorum was carried out in multiplex with an assay for a gene from the host plant in order to demonstrate whether amplifiable DNA had been extracted. Amplifiable DNA was extracted from 84.4% of samples, as demonstrated by amplification of host plant DNA. The real-time protocol was used to test 320 plant samples (from 19 different plant species) from which DNA extraction had been successful, and was shown to give results comparable with a traditional isolation technique for diagnosis of P. ramorum in plant material from common U.K. hosts.
[Show abstract][Hide abstract] ABSTRACT: Phytophthora ramorum is a recently described pathogen causing oak mortality (sudden oak death) in forests in coastal areas of California and southern Oregon and dieback and leaf blight in a range of tree, shrub, and herbaceous species in the United States and Europe. Due to the threat posed by this organism, stringent quarantine regulations are in place, which restrict the movement of a number of hosts. Fast and accurate diagnostic tests are required in order to characterize the distribution of P. ramorum, prevent its introduction into pathogen-free areas, and minimize its spread within affected areas. However, sending samples to a laboratory for testing can cause a substantial delay between sampling and diagnosis. A rapid and simple DNA extraction method was developed for use at the point of sampling and used to extract DNAs from symptomatic foliage and stems in the field. A sensitive and specific single-round real-time PCR (TaqMan) assay for P. ramorum was performed using a portable real-time PCR platform (Cepheid SmartCycler II), and a cost-effective method for stabilizing PCR reagents was developed to allow their storage and transportation at room temperature. To our knowledge, this is the first description of a method for DNA extraction and molecular testing for a plant pathogen carried out entirely in the field, independent of any laboratory facilities.
Applied and Environmental Microbiology 12/2005; 71(11):6702-10. · 3.95 Impact Factor