Biosurveillance of forest insects: part II—adoption of genomic tools by end user communities and barriers to integration

Bilodeau, Pierre; Roe, Amanda D.; Bilodeau, Guillaume J.; Blackburn, Gwylim S.; Cui, Mingming; Cusson, Michel; Doucet, Daniel; Griess, Verena C.; Lafond, Valentine; Nilausen, Chelsea; Paradis, Gregory; Porth, Ilga; Prunier, Julien; Srivastava, Vivek; Stewart, Don; Torson, Alex S.; Tremblay, Émilie D.; Uzunovic, Adnan; Yemshanov, Denys; Hamelin, Richard

doi:10.1007/s10340-018-1001-1

Cited by 24 publications

(35 citation statements)

References 68 publications

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“…Despite the advantages that metabarcoding may offer to insect surveillance programs, uptake of new diagnostic tools into operational use depends on more than just the cost-effectiveness of the tool, but also on factors such as ease of use, accuracy, reproducibility, and perceived usefulness to the end users, as well as compatibility with existing policy frameworks [46, 47]. With the introduction of the World Trade Organisation Agreement on the Application of Sanitary and Phytosanitary measures (SPS) came new obligations for exporting nations to demonstrate freedom of a geographic area from particular pests using scientifically rigorous surveillance practices [48].…”

Section: Introductionmentioning

confidence: 99%

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

et al. 2019

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Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations.DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.

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Section: Introductionmentioning

confidence: 99%

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

et al. 2019

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“…Accurate detection of invasive pathogens is a hallmark of efficient prevention and integrated pest management programs [42,43]. In some instance assessing pathogen viability may even be more crucial.…”

Section: Discussionmentioning

confidence: 99%

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

et al. 2020

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Wood and wood products can harbor microorganisms that can raise phytosanitary concerns in countries importing or exporting these products. To evaluate the efficacy of wood treatment on the survival of microorganisms of phytosanitary concern the method of choice is to grow microbes in petri dishes for subsequent identification. However, some plant pathogens are difficult or impossible to grow in axenic cultures. A molecular methodology capable of detecting living fungi and fungus-like organisms in situ can provide a solution. RNA represents the transcription of genes and can become rapidly unstable after cell death, providing a proxy measure of viability. We designed and used RNA-based molecular diagnostic assays targeting genes essential to vital processes and assessed their presence in wood colonized by fungi and oomycetes through reverse transcription and real-time polymerase chain reaction (PCR). A stability analysis was conducted by comparing the ratio of mRNA to gDNA over time following heat treatment of mycelial cultures of the Oomycete Phytophthora ramorum and the fungus Grosmannia clavigera. The real-time PCR results indicated that the DNA remained stable over a period of 10 days post treatment in heat-treated samples, whereas mRNA could not be detected after 24 hours for P. ramorum or 96 hours for G. clavigera. Therefore, this method provides a reliable way to evaluate the viability of these pathogens and offers a potential way to assess the effectiveness of existing and emerging wood treatments. This can have important phytosanitary impacts on assessing both timber and non-timber forest products of commercial value in international wood trade.

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“…Numerous molecular diagnostic tools have been developed in recent years for use in clinical settings, and there has been a push to apply similar tools to invasive species management. In particular, there are opportunities to use genomic tools for invasive species biosurveillance (e.g., for managing forest pests; Bilodeau et al 2018;Roe et al 2018). The use of deoxyribonucleic acid (DNA) for invasive species identification is well-established (Lyal and Miller 2019, this issue), but limited in application because relatively few species have been genetically sequenced and profiled in open access information systems, including GenBank, the National Institute of Health (NIH) annotated collection of all publicly available gene sequences (Benson et al 2013), or the other international databases with which GenBank interfaces (https://www.ncbi.nlm.nih.gov/genbank, accessed 30 October 2019).…”

Section: Genetic Detectionmentioning

confidence: 99%

Technology innovation: advancing capacities for the early detection of and rapid response to invasive species

et al. 2019

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The 2016-2018 National Invasive Species Council (NISC) Management Plan and Executive Order 13751 call for US federal agencies to foster technology development and application to address invasive species and their impacts. This paper complements and draws on an Innovation Summit, review of advanced biotechnologies applicable to invasive species management, and a survey of federal agencies that respond to these high-level directives. We provide an assessment of federal government capacities for the early detection of and rapid response to invasive species (EDRR) through advances in technology application; examples of emerging technologies for the detection, identification, reporting, and response to invasive species; and guidance for fostering further advancements in applicable technologies. Throughout the paper, we provide examples of how federal agencies are applying technologies to improve programmatic effectiveness and cost-efficiencies. We also highlight the outstanding technology-related needs identified by federal agencies to overcome barriers to enacting EDRR. Examples include improvements in research facility infrastructure, data mobilization across a wide range of invasive species parameters (from genetic to landscape scales), promotion of and support for filling key gaps in technological capacity (e.g., portable, field-ready devices with automated capacities), and greater investments in technology prizes and challenge competitions.

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Biosurveillance of forest insects: part II—adoption of genomic tools by end user communities and barriers to integration

Cited by 24 publications

References 68 publications

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

Technology innovation: advancing capacities for the early detection of and rapid response to invasive species

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