Chapter 5 : Fast and High-Throughput Molecular Typing Methods

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As our understanding of pathogens has expanded and the world’s food supply has become more interconnected, characterization and subtyping of foodborne pathogens have become critically important in monitoring specific foods, performing surveillance for foodborne pathogens, investigating foodborne outbreaks, and understanding the virulence properties of particular lineages or strains. This chapter provides an overview of the molecular subtyping methods most commonly employed, in particular focusing on those methods providing fast and high-throughput analysis of strains. The methods include pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem repeat (VNTR) analysis, DNA microarrays, and mass spectrometry. The heterogeneity that is targeted in the methods falls into three general categories. First, single-nucleotide polymorphisms (SNPs) are single-base changes in one sequence in comparison to another, related sequence. SNPs typically arise through sporadic mutation, so they represent a means of measuring random genetic drift. A large number of SNPs between two sequences may indicate a more distant genetic relationship. Second, some regions of the genome are more likely to change than others; they provide a means of differentiating closely related strains. Examples include variable number tandem repeats and highly polymorphic genes such as some surface structure and virulence genes. Finally, the presence/absence of specific loci can be found in both distantly and closely related strains. The presence of additional sequences in a strain can result from the insertion of a bacteriophage in the chromosome, acquisition of a plasmid, or other horizontal transfer events.

Citation: Fields P, Fitzgerald C, McQuiston J. 2011. Fast and High-Throughput Molecular Typing Methods, p 81-92. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch5
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