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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOP TECHNOLOGIES TO PROTECT AIR QUALITY, MAINTAIN PRODUCTION EFFICIENCY & ENHANCE USE OF MANURE FROM SOUTHN GREAT PLAINS BEEF & DAIRY AG

Location: Renewable Energy and Manure Management Research

Title: Application of amplicon length polymorphism to differentiate amongst closely related strains of bacteria

Author
item Rice, William

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: August 15, 2010
Publication Date: December 15, 2010
Citation: Rice, W.C. 2010. Application of amplicon length polymorphism to differentiate amongst closely related strains of bacteria. In: Vilas, A.M., editor. Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology, Volume 2. Badajoz, Spain: Formatex Research Center. p. 1509-1516.

Interpretive Summary: The incidence of food-borne illnesses from pathogenic bacteria (e.g. Escherichia coli (E. coli) and Salmonella spp) remains relatively constant despite the use of various abatement practices for reducing them. Methods to rapidly find and tell the difference between closely related pathogens are needed to identify the sources of food-borne illnesses. A method using DNA markers was developed that resulted in high discrimination amongst pathogenic E coli and Salmonella spp. The application of amplicon length polymorphism (ALP) represents a novel genome-based molecular method to detect, identify, and confirm the source of an outbreak. Amplicon length polymorphism can discriminate among related strains of pathogens to the same or to a higher degree of resolution than pulsed field gel electrophoresis (PFGE), while also reducing both the time and expense required to confirm the source that is responsible for the food-borne illness. The theory underlying ALP and its ability to tell the difference among closely related pathogens such as E. coli and Salmonella spp. is described in the book chapter. In principle, ALP can be applied to tell the difference among any group of closely related strains of bacteria. Since nearly 1100 microbial and archaeal genomes have been completely sequenced, with several hundred other sequencing projects underway, the ALP method should have widespread application.

Technical Abstract: The incidence of food-borne illnesses from pathogenic bacteria (e.g. Escherichia coli and Salmonella spp) remains relatively constant despite the use of various abatement practices for reducing them. Methods to rapidly detect and discriminate between closely related pathogens are required to identify sources of food-borne illnesses. Pulsed field gel electrophoresis (PFGE) is currently considered the 'gold standard' molecular method for sub typing pathogens by the Centers for Disease Control and Prevention (CDC). The PFGE method requires four days to complete, thus slowing identification of a disease source. Application of amplicon length polymorphism (ALP) represents a novel genome-based molecular method to detect, identify, and confirm the source of an outbreak. ALP can discriminate amongst related strains of pathogens to the same or to a higher degree of resolution than PFGE, while also reducing both the time and expense required to confirm the source responsible for the food-borne illness. The theory underlying ALP and its ability to differentiate amongst closely related pathogens, such as Escherichia coli and Salmonella spp. will be described. In principle, ALP can be applied to differentiate any group of closely related strains of bacteria. Since nearly 1100 microbial and archaeal genomes have been completely sequenced, with several hundred other sequencing projects underway, the ALP method should have widespread applicability.

Last Modified: 4/16/2014
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