Molecular Detection of Biological Agents in the Field: Then and Now

Yeh, Kenneth B.; Wood, Hillary; Scullion, Matt; Russell, Joseph A.; Parker, Kyle; Gnade, Bryan T.; Jones, Anthony R.; Whittier, Christopher A.; Mereish, K. A.

doi:10.1128/msphere.00695-19

Cited by 11 publications

(9 citation statements)

References 35 publications

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“…To limit bias, we did not solicit input from respondents whose current positions involve the development, marketing, or sale of qPCR and sequencing instruments or consumables. Previously, Yeh et al discussed a notional qualitative comparison of qPCR and sequencing technologies, according to literature searches and panel feedback [18]. The qualitative comparison included the following evaluation metrics: sensitivity, specificity, reproducibility, ease of use, time to detection, low cost per test, discovery power, scalability, portability, and ruggedness.…”

Section: Methods/background Design Distribution Of Questionnairementioning

confidence: 99%

“…Molecular detection technologies for biological threats in the field and laboratory are well documented [15][16][17]. Yet, while various methods and case histories for deploying field laboratories have been presented [1,[18][19][20], few peer-reviewed publications specify commercially available biodetection systems [21][22][23]. Since the biodefense market and enterprise has evolved following the 2001 anthrax attacks, several marketing references surveying various biological threat detection technologies have been published and presented online [24,25].…”

Section: Introductionmentioning

confidence: 99%

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End-User Perspectives on Using Quantitative Real-Time PCR and Genomic Sequencing in the Field

et al. 2022

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Quantitative real-time PCR and genomic sequencing have become mainstays for performing molecular detection of biological threat agents in the field. There are notional assessments of the benefits, disadvantages, and challenges that each of these technologies offers according to findings in the literature. However, direct comparison between these two technologies in the context of field-forward operations is lacking. Most market surveys, whether published in print form or provided online, are directed to product manufacturers who can address their respective specifications and operations. One method for comparing these technologies is surveying end-users who are best suited for discussing operational capabilities, as they have hands-on experience with state-of-the-art molecular detection platforms and protocols. These end-users include operators in military defense and first response, as well as various research scientists in the public sector such as government and service laboratories, private sector, and civil society such as academia and nonprofit organizations performing method development and executing these protocols in the field. Our objective was to initiate a survey specific to end-users and their feedback. We developed a questionnaire that asked respondents to (1) determine what technologies they currently use, (2) identify the settings where the technologies are used, whether lab-based or field-forward, and (3) rate the technologies according to a set list of criteria. Of particular interest are assessments of sensitivity, specificity, reproducibility, scalability, portability, and discovery power. This article summarizes the findings from the end-user perspective, highlighting technical and operational challenges.

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Section: Methods/background Design Distribution Of Questionnairementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

End-User Perspectives on Using Quantitative Real-Time PCR and Genomic Sequencing in the Field

et al. 2022

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“…When the etiological agent is not known, the pathogen identification must rely on the use of an untargeted screening method by extracting, preparing, and sequencing all of the genomic material in a particular sample at once (Yeh et al, 2019). Even though POC sequencing is not routinely applied for plant pathogens yet, in the last few years, some portable sequencers have been developed that allow to perform amplicon sequencing directly in the field.…”

Section: Poc Sequencingmentioning

confidence: 99%

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

Baldi

Porta

2020

Front. Plant Sci.

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Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.

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“…Tools and associated methods available for One Health-based responses to climate change impacts include both gold standard quantitative real-time PCR (qPCR) and current metagenomics sequencing approaches, which are less biased [13]. Their application can provide increased ability to detect and identify emerging and new pathogens and biological invasion by invasive species that are expected to increase due to climate impact [14,15].…”

Section: Current State Of Sequencing Toolsmentioning

confidence: 99%

Assessing Climate Change Impact on Ecosystems and Infectious Disease: Important Roles for Genomic Sequencing and a One Health Perspective

et al. 2020

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Changes in the Earth’s climate and weather continue to impact the planet’s ecosystems, including the interface of infectious disease agents with their hosts and vectors. Environmental disasters, natural and human-made activities raise risk factors that indirectly facilitate infectious disease outbreaks. Subsequently, changes in habitat, displaced populations, and environmental stresses that affect the survival of species are amplified over time. The recurrence and spread of vector-borne (e.g., mosquito, tick, aphid) human, animal, and plant pathogens to new geographic locations are also influenced by climate change. The distribution and range of humans, agricultural animals and plants, wildlife and native plants, as well as vectors, parasites, and microbes that cause neglected diseases of the tropics as well as other global regions are also impacted. In addition, genomic sequencing can now be applied to detect signatures of infectious pathogens as they move into new regions. Molecular detection assays complement metagenomic sequencing to help us understand the microbial community found within the microbiomes of hosts and vectors, and help us uncover mechanistic relationships between climate variability and pathogen transmission. Our understanding of, and responses to, such complex dynamics and their impacts can be enhanced through effective, multi-sectoral One Health engagement coupled with applications of both traditional and novel technologies. Concerted efforts are needed to further harness and leverage technology that can identify and track these impacts of climate changes in order to mitigate and adapt to their effects.

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Molecular Detection of Biological Agents in the Field: Then and Now

Cited by 11 publications

References 35 publications

End-User Perspectives on Using Quantitative Real-Time PCR and Genomic Sequencing in the Field

End-User Perspectives on Using Quantitative Real-Time PCR and Genomic Sequencing in the Field

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

Assessing Climate Change Impact on Ecosystems and Infectious Disease: Important Roles for Genomic Sequencing and a One Health Perspective

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