Chapter 43 : Molecular Source Tracking and Molecular Subtyping

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Molecular subtyping can be used to study the population structure of a particular bacterial species, to determine the possible evolution of the subject microorganism, or to study the molecular epidemiology of a microbe. The types of methods used for subtyping and the approaches to data analysis and interpretation may vary greatly with the reason for specific subtyping. This chapter focuses almost entirely on subtyping for molecular epidemiology. Molecular epidemiology 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. Perhaps the most easily appreciated reason for molecular subtyping is to facilitate the identification and investigation of foodborne disease outbreaks. Although the focus of this chapter is on molecular methods, it is important to consider them in the context of earlier phenotypic methods such as serotyping, phage typing, biotyping, and antimicrobial susceptibility typing. Most of these phenotypic methods have long and successful histories of use in subtyping for the same purposes for which molecular methods are now used. Although molecular methods typically provide greater strain discrimination than phenotypic methods, this is not always the case, and it is only one reason why molecular methods are generally preferred. In recent years, the main focus of subtyping method development has been on DNA sequence-based methods. Sequence-based approaches to subtyping of bacteria, such as multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA), are already being widely implemented in the surveillance of foodborne infections.

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43
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Figure 43.1

Example of plasmid profile analysis. Each lane contains plasmid DNA extracted from an isolate of ceftriaxone-resistant . In this instance, plasmid DNA was separated by PFGE rather than standard gel electrophoresis for better separation of large plasmids. doi:10.1128/9781555818463.ch43f1

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43
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Image of Figure 43.2
Figure 43.2

PFGE analysis of seven isolates of Berta. (a) Raw data: lanes 2 to 4 and 6 to 9 contain BlnI digests of . Berta genomic DNA, and lanes 1, 5, and 10 contain XbaI digests of a molecular weight standard strain. (b) Analyzed data: dendrogram showing relatedness of . Berta isolates produced using BioNumerics software. doi:10.1128/9781555818463.ch43f2

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43
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Figure 43.3

Example of MLVA of O157:H7 isolates. (a and b) Electropherograms from automated DNA sequencer showing different fragment sizes at three of four sites; (c) dendrogram generated with BioNumerics software showing relatedness of isolates based on data at eight VNTR loci. doi:10.1128/9781555818463.ch43f3

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43
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Figure 43.4

Molecular identification of serotype in by the Luminex platform. The data represent identification of serotype based on reactivity with DNA probes corresponding to specific serotype antigens coupled to fluorescent microspheres. The results are expressed as the ratio of median fluorescent intensity for test versus negative control samples (P/N ratio). (a) Results of the O antigen assay; probes detect sequences specific for common O groups or for serotype Paratyphi A; (b) results of the H antigen assay; probes detect specific H epitopes; (c) interpretation of data based on the Kauffmann-White scheme. (Courtesy J. McQuiston, CDC.) doi:10.1128/9781555818463.ch43f4

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43
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Table 43.1

Properties of methods commonly used for molecular subtyping of foodborne pathogens

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43

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