Chapter 4 : Molecular Subtyping, Source Tracking, and Food Safety

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This chapter focuses on the application of molecular subtyping methods for identifying and tracing sources of microbial pathogens in food and food-borne human diseases. It should be noted, however, that in addition to the food-borne pathogens, harmless or nonpathogenic microorganisms can also contaminate the food supply and contribute to spoilage. These microbes are generally part of the natural microbiota of raw foods and food products, which serves as an ideal growth medium for many organisms with nearly neutral pH, high water activity, and richness in nutrients. If left unchecked, growth of these harmless microorganisms on foods results in off odors and flavors and, ultimately, in an inedible food product. Many of the methods developed to inhibit the growth of nonpathogenic microbes in foods also restrict the growth of food-borne pathogens. The major advantage of pulsed-field gel electrophoresis (PFGE) profiling is that the technique can be widely applied to different bacterial species and is relatively simple and straightforward to perform in the laboratory. Outbreak investigation and epidemiological tracing have been the primary incentives encouraging the development of the PulseNet and FoodNet national systems for food-borne disease surveillance. In the future, the authors expect to see the application of new molecular genotyping systems with rapid throughput, such as those based on single-nucleotide polymorphisms, to generate high-quality genotypic data for microbial source tracking.

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 1

Reported cases of food-borne illness in 2004 for 10 FoodNet sites (California, Colorado, Connecticut, Georgia, Maryland, Minnesota, New Mexico, New York, Oregon, and Tennessee).

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 2

PFGE patterns of O157:H7. Lanes 1, 6, and 10 represent isolate G5244, which is a standard strain used to characterize molecular size. Lanes 3 and 9 represent isolates from cases involved in a single cluster. Lanes 2, 4, 7, and 8 represent isolates from other sporadic cases of disease. Lane 5 is an additional molecular size standard ( ). Copyright © 1997, Massachusetts Medical Society. All rights reserved.

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 3

(A) Sources of water pollution addressed by microbial source tracking. (B) Sources of food contamination in the food chain addressed by microbial subtyping.

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 4

Routes of transmission for serotype Enteritidis ( ). (Reprinted from the Volume 89, no. 5, 2006. Copyright 2006 by AOAC International.)

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 5

O157:H7 outbreaks in the United States from 1982 to 2002 ( ). axis is number of outbreaks.

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Figure 6

Estimated number of cases of salmonellosis attributed to domestic and imported food sources based on a Bayesian model ( ).

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Table 1

Bacterial, viral, and parasitic agents that contribute to the burden of food-borne illness in the United States

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4
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Table 2

Summary of potential advantages and disadvantages of some of the alternative subtyping methods for food-borne pathogens

Citation: Whittam T, Bergholz T. 2007. Molecular Subtyping, Source Tracking, and Food Safety, p 93-136. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch4

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