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Chapter 3 : Molecular Detection and Characterization Tools

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Molecular Detection and Characterization Tools, Page 1 of 2

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Abstract:

This chapter discusses the technological advances and the current limitations of DNA- and RNA-based methods from a “food perspective.” Consequently, the focus of the chapter is on the application and utility of these methods to detect and characterize microorganisms in foods. The discussion is on the context of whether specific methods can be used to identify the types of microbial contaminants, the extent of contamination, and the possible sources of contamination. A key driving force in the development of new-generation detection and characterization tools is the extraordinary amount of genomic and proteomic information that is now publicly available. The criticality of regulatory pressure in catalyzing the commercialization of molecular detection tools is evident when one compares the availability of commercial kits for the food industry to that for the drinking water industry. A majority of the molecular detection methods, however, only provide qualitative information about the presence or absence of specific pathogens. Paradigm-shifting changes in sequencing technologies have improved the sequencing of organisms, which, in turn, has greatly benefited microbial molecular detection technologies such as gene amplification and probe-based technologies. Improved surveillance and tracking studies will lead to the identification of many of these pathogens that could be classified as emerging or reemerging pathogens. The current 16S rRNA gene-based fingerprinting method (termed riboprinting), though automated and sophisticated, is still far from being as discriminatory as pulsed-field gel electrophoresis (PFGE).

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3

Key Concept Ranking

Nucleic Acid Amplification Techniques
0.7421161
Antimicrobial Susceptibility Testing
0.54393697
Environmental Microbiology
0.5385053
Random Amplified Polymorphic DNA
0.4524714
Restriction Fragment Length Polymorphism
0.4524714
0.7421161
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FIGURE 1

Challenges of detecting low numbers of target organisms in food and environmental samples as compared to clinical samples. org, organisms.

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3
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Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3
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FIGURE 2

The substrate-activity-function-virulence relationships between pathogen characteristics and human health effects (modified from references and ).

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3
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FIGURE 3

Interrelationships between food safety, water quality, and environmental microbiology.

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3
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Tables

Generic image for table
Table 1

Partial listing of conventional and real-time PCR-based commercial pathogen detection kits for the food industry

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3
Generic image for table
Table 2

Characteristics of contemporary bacterial differentiation methods

Citation: Pillai S, Vega E. 2007. Molecular Detection and Characterization Tools, p 65-91. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch3

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