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Chapter 3 : Molecular Detection and Characterization Tools
Authors:
Suresh D. Pillai1,
Everardo Vega2
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Affiliations:
1: Departments of Nutrition and Food Science & Poultry Science, Texas A#x0026;M University, College Station, Texas 77843-2472;
2: Centers for Disease Control and Prevention, Atlanta, GA 30333
Content Type: Monograph
Publication Year:
2007
Category: Environmental Microbiology; Applied and Industrial Microbiology
Book DOI:
10.1128/9781555815769
Chapter DOI:
10.1128/9781555815769.ch3
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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
Figures
Molecular Detection and Characterization Tools
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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
/content/10.1128/9781555815769.ch03.ch03fig01
FIGURE 1
Challenges of detecting low numbers of target organisms in food and environmental samples as compared to clinical samples. org, organisms.
10.1128/9781555815769/f0076-01_thmb.gif
10.1128/9781555815769/f0076-01.gif
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
/content/10.1128/9781555815769.ch03.ch03eqn1
Untitled
10.1128/9781555815769/f0080-01_thmb.gif
10.1128/9781555815769/f0080-01.gif
Untitled
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
/content/10.1128/9781555815769.ch03.ch03fig02
FIGURE 2
The substrate-activity-function-virulence relationships between pathogen characteristics and human health effects (modified from references
39
and
44
).
10.1128/9781555815769/f0083-01_thmb.gif
10.1128/9781555815769/f0083-01.gif
FIGURE 2
The substrate-activity-function-virulence relationships between pathogen characteristics and human health effects (modified from references 39 and 44 ).
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
/content/10.1128/9781555815769.ch03.ch03fig03
FIGURE 3
Interrelationships between food safety, water quality, and environmental microbiology.
10.1128/9781555815769/f0085-01_thmb.gif
10.1128/9781555815769/f0085-01.gif
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
Molecular Detection and Characterization Tools
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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
/content/10.1128/9781555815769.ch03.ch03tab01
Table 1
Partial listing of conventional and real-time PCR-based commercial pathogen detection kits for the food industry
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
/content/10.1128/9781555815769.ch03.ch03tab02
Table 2
Characteristics of contemporary bacterial differentiation methods
a
Table 2
Characteristics of contemporary bacterial differentiation methods a
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