Molecular Source Tracking and Molecular Subtyping

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.