Chapter 38 : Molecular Source Tracking and Molecular Subtyping

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Molecular subtyping is an instrumental tool for foodborne illness surveillance and outbreak investigation. The term “molecular epidemiology” in the context of foodborne bacteria is usually applied to the subtyping of bacteria that cause foodborne disease and the ways in which such subtyping data contribute to understanding the transmission of those bacteria to humans. Molecular subtyping techniques can be applied to identifying the source of a particular outbreak or to a broader understanding of the role of certain foods or processes in outbreak-related or sporadic infections. Advances in sequencing technology over the last two decades have made whole-genome sequencing (WGS)-based subtyping approaches the method of choice for many foodborne pathogens. Routine application of WGS in laboratory surveillance and monitoring of foodborne pathogens is transforming public health microbiology. With the increasing international trade of food and food animals, it is crucial that molecular subtyping methods for foodborne pathogens be harmonized worldwide to facilitate the rapid comparison of strains isolated in different countries. This method harmonization for comparison is best done in the framework of surveillance networks. The ongoing implementation of WGS provides an unprecedented opportunity to establish universal global standards for subtyping foodborne bacteria that will result in easily exchangeable data and global nomenclature.

Citation: Gerner-Smidt P, Trees E, Carleton H, Katz L, den Bakker H, Deng X. 2019. Molecular Source Tracking and Molecular Subtyping, p 971-988. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch38
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Figure 38.1

MLST correlates strongly with SNP analysis when the number of SNPs is lower than 255. A scatterplot was generated using all allelic distances from wgMLST and SNP distances from SNP analysis for three outbreak clusters. The top left plot shows all pairwise distances, the top right limits the data points to those with <255 SNPs, and the bottom left limits the data points to those of <100. Adapted from reference .

Citation: Gerner-Smidt P, Trees E, Carleton H, Katz L, den Bakker H, Deng X. 2019. Molecular Source Tracking and Molecular Subtyping, p 971-988. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch38
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Table 38.1

Properties of methods commonly used for molecular subtyping of foodborne pathogens

Citation: Gerner-Smidt P, Trees E, Carleton H, Katz L, den Bakker H, Deng X. 2019. Molecular Source Tracking and Molecular Subtyping, p 971-988. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch38

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