A five-minute DNA extraction method for expedited detection of Phytophthora ramorum following prescreening using Phytophthora spp. lateral flow devices

Tomlinson, J. A.; Dickinson, Matthew; Hobden, E.; Robinson, Sandra; Giltrap, P. M.; Boonham, Neil

doi:10.1016/j.mimet.2010.02.006

Cited by 22 publications

(17 citation statements)

References 13 publications

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“…Furthermore, these laboratory methods could be used in conjunction with on-site tests such as Phytophthora spp. LFD (Lane et al 2007;Tomlinson et al 2010) to maximise the overall efficiency and accuracy of testing.…”

Section: Discussionmentioning

confidence: 99%

“…Extraction of DNA from plant material DNA was extracted from aseptically excised samples of plant material using a KingFisher ML instrument (Thermo Scientific, Waltham, MA, USA) as described by Tomlinson et al (2010). Briefly, plant material (typically 200-500 mg) was homogenized in 5 ml of Buffer C1 from the NucleoSpin Plant kit, incubated at 65°C for 30 min and centrifuged for 2 min at 6000 x g. To extract DNA from the clarified lysates, 1 ml Qiagen PB Binding Buffer (Qiagen, Hilden, Germany) and 75 μl Magnesil paramagnetic particles (PMPs) (Promega, Madison, WI, USA) were added and the samples were processed using a KingFisher ML to wash the PMPs three times in 70% ethanol followed by elution of the DNA in 200 μl molecular grade water.…”

Section: Taqman Primer and Probe Designmentioning

confidence: 99%

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Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique

et al. 2011

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Phytophthora kernoviae is a recently described pathogen causing leaf blight, aerial dieback and bleeding cankers on trees and shrubs in parts of Great Britain and Ireland and recently reported in New Zealand. This paper describes the development of a TaqMan real-time PCR assay based on internal transcribed spacer (ITS) sequence to aid diagnosis of this pathogen in culture and in plant material. The assay showed no cross reaction with 29 other Phytophthora species, including the closely related species P. boehmeriae, and detected at least 1.2 pg of P. kernoviae DNA per reaction. A rapid and simple method can be used to extract DNA prior to testing by real-time PCR, and a plant internal control assay can be used to aid interpretation of negative results. A comparison of real-time PCR and plating for 526 plant samples collected in the UK indicated that this assay is suitable for use in routine screening for P. kernoviae.

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Section: Discussionmentioning

confidence: 99%

Section: Taqman Primer and Probe Designmentioning

confidence: 99%

Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique

et al. 2011

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“…Diagnosis is problematic because some Phytophthoras are hard to culture (Hayden et al 2004), taxonomic expertise is lacking and molecular techniques need to be validated. For P. ramorum, there has been much progress in developing molecular tools for rapid and accurate detection (e.g., Kong et al 2004;Bilodeau et al 2009;Tomlinson et al 2010;Vettraino et al 2010). However, given that it cannot be assumed that the latest techniques are adopted immediately by all plant phytosanitary control agents, there is still a question of how reliable realworld plant passporting schemes for this and similar pathogens are (EFSA PLH 2011; Tsopelas et al 2011).…”

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confidence: 99%

Impacts of exotic forest pathogens on Mediterranean ecosystems: four case studies

Garbelotto

Pautasso

2011

Eur J Plant Pathol

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“…If a sample does not test positive by any Phytophthora species, it is likely also not to test positive (and therefore not to be infected) by P. ramorum. In this case, the predictive value of the P. ramorum-specific test will depend not only on the prevalence of P. ramorum, but also on the presence of other Phytophthora species (Tomlinson et al, 2010). Tomlinson et al (2010) argue that Phytophthora species other than P. ramorum are likely to be common for samples coming from plant nurseries, and to be rare for samples coming from confirmed P. ramorum outbreak sites.…”

Section: Additional Information Options To Reduce Likelihood Of Intromentioning

confidence: 99%

Scientific Opinion on the Pest Risk Analysis onPhytophthora ramorumprepared by the FP6 project RAPRA

Rossi¹

2011

EFSA Journal

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The Panel on Plant Health was asked to deliver a scientific opinion on the Pest Risk Analysis on Phytophthora ramorum prepared by the FP6 project RAPRA, taking into account comments by Member States and additional information since RAPRA. P. ramorum is the oomycete causing sudden oak death in the USA and leaf and twig blight/dieback on a range of ornamental species in North America and Europe. Currently P. ramorum is not listed as a harmful organism in Council Directive 2000/29/EC, but the Commission adopted in 2002 provisional emergency measures to prevent introduction into and spread within the EU. Recent large-scale outbreaks in Japanese larch (Larix kaempferi) plantations in the UK and Ireland have worsened the potential consequences in the risk assessment area. However, the Panel concludes that the broad narrative in the RAPRA report stands and supports its conclusion that "There is a risk of further entry (of known or new lineages and/or mating types), establishment and […] impact". It is advisable to avoid introductions of different lineages because of inherent phenotypic differences and the potential for sexual recombination. The Panel supports the management options proposed in the RAPRA report and adds further measures for consideration. Uncertainty remains over the extent to which the association between control measures and gradual reduction in the number of cases in nurseries is causal. The emergency measures have not prevented outbreaks occurring in the natural environment. The many other remaining uncertainties (fitness of progeny, hybridisation with other Phytophthora species, host range and epidemiological role of new hosts, early detection of new outbreaks, understanding of long-range dispersal, structure of plant trade networks, origin of the pathogen) call for further research on P. ramorum across Europe. 4 Editorial changes have been made on pages 51 (acronym PRA removed as it was not in line with the Panel's dictionary as discussed in Appendix 2 of the Guidance on a harmonised framework for pest risk assessment and the identification and evaluation of pest risk management options by EFSA) and 89 (statement which referred to the Panel agreeing with the RAPRA conclusion that "P. ramorum fulfils the criteria of a quarantine pest" was removed as requested by the Panel during adoption of the draft opinion). The changes do not affect the overall conclusions of the opinion. To avoid confusion the original version has been removed from the website. The scope of this Scientific Opinion is the evaluation of the RAPRA report, taking into consideration the comments of Member States as well as additional information published after finalisation of the RAPRA report, or not cited in the RAPRA report. A systematic literature search until March 2011 was carried out. It should be noted that the scientific community is concerned by the shift of P. ramorum to new hosts (with a special focus on the Japanese larch) and its further spread, and therefore new results of ongoing research are constantly be...

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A five-minute DNA extraction method for expedited detection of Phytophthora ramorum following prescreening using Phytophthora spp. lateral flow devices

Cited by 22 publications

References 13 publications

Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique

Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique

Impacts of exotic forest pathogens on Mediterranean ecosystems: four case studies

Scientific Opinion on the Pest Risk Analysis onPhytophthora ramorumprepared by the FP6 project RAPRA

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