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Chapter 2.3.4 : Field Application of Pathogen Detection Technologies

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Abstract:

Many of the principles underlying rapid detection methods are derived from methods for environmental microbiology, but there is a dearth of literature describing and evaluating field-based detection systems. Thus, the aims of this chapter are to: 1) summarize the different kinds of commercially available sampling kits and field-based biological detectors; 2) highlight some of the continued challenges of sample preparation to stimulate new research towards minimizing the impact of inhibitors on PCR-based detection systems; 3) describe our general rationale and statistically-based approach for instrument evaluation; 4) provide statistical and spatial guidelines for developing valid sampling plans; and 5) summarize some current needs and emerging technologies. This information is presented both to highlight the state of the field, and to also highlight major questions that students may wish to consider investigating further. Where possible we will cite studies that have been conducted and published either in traditional peer-reviewed or other literature (e.g., AOAC International Methods).

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Image of FIGURE 1
FIGURE 1

Example of a real-time PCR reaction where PCR inhibitors either block product detection completely, or cause the estimate to be extended and thereby underestimate the starting copy number for the template DNA. doi:10.1128/9781555818821.ch2.3.4.f1

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Image of FIGURE 2
FIGURE 2

Example of a real-time PCR reaction where too much template was added to the sample. Initially fluorescence increases as expected, but both the initial quantity and amount of accumulating template squelches fluorescence. doi:10.1128/9781555818821.ch2.3.4.f2

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Image of FIGURE 3
FIGURE 3

Number of independent tests required to meet test performance criteria. ** A one-sided score confidence interval. doi:10.1128/9781555818821.ch2.3.4.f3

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Image of FIGURE 4
FIGURE 4

Symbols show distribution of “multiple increment” samples where sample location is randomly allocated (Visual Sample Planner software; ) and samples for each symbol within a plot are pooled for analysis. Inset table is an example of the coordinate output, where coordinates can be arranged randomly or systematically for the confidence interval estimation module. doi:10.1128/9781555818821.ch2.3.4.f4

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Image of FIGURE 5
FIGURE 5

Left panel illustrates an example of how a room can be mapped and shown in three dimensions with sample locations (white circles; = 10). Right panel shows how sample area polygons can be overlaid on Google Earth imagery and sample sites subsequently mapped to location ( = 50 random points within systematic grids in this case). Images such as that shown here can be easily calibrated for scale. Produced using VSP software ( ). doi:10.1128/9781555818821.ch2.3.4.f5

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
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Tables

Generic image for table
TABLE 1

Overview of products for sampling and detection of potential biothreats ( )

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
Generic image for table
TABLE 2

Predicted mechanisms of inhibition and outcomes for seven inhibitors added to a standardized qPCR reaction

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4
Generic image for table
TABLE 3

Sampling goals and sample selection strategies with some options that are available in Visual Sample Planner ( )

Citation: Straub T, Call D, Bruckner-Lea C, Colburn H, Baird C, Bartholomew R, Ozanich R, Jarman K. 2016. Field Application of Pathogen Detection Technologies, p 2.3.4-1-2.3.4-17. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.4

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