Molecular Subtyping and Tracking of Food-Borne Bacterial Pathogens

Abstract

This chapter provides an overview on molecular subtyping methods, including conventional banding-based methods and novel DNA sequence-based methods, to molecularly confirm that isolates belong to a given food-borne bacterial pathogen and to discriminate among isolates belonging to a given food-borne bacterial pathogen. It discusses about molecular subtyping methods which will be grouped into two categories: (i) conventional banding-based or DNA fingerprint-based methods and (ii) DNA sequence-based methods. DNA sequencing of one or more genes or the whole genome, probing the presence of specific repeat sequences, sequence-specific hybridizations, and differentiating allelic types from single-nucleotide polymorphisms (SNPs) represent DNA sequence-based molecular subtyping methods used to differentiate food-borne pathogens. SNP typing assays may be developed to directly target nucleotides that have been shown to discriminate allelic types. Another major advantage of SNP typing over conventional banding-based or other DNA sequence-based molecular subtyping techniques is that SNP genotyping assays can be designed to target slowly accumulated genetic variations in protein-coding genes (e.g., synonymous mutations), providing the most reliable inference of genetic relatedness. In addition, DNA sequence-based subtyping techniques (particularly multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA) typing schemes) are becoming more standardized across laboratories and databases that contain DNA sequenced-based molecular subtyping data continue to rapidly expand. Multiplexed SNP typing assays that differentiate allelic types based on SNPs present within housekeeping genes known to diversify on an evolutionary time scale show great promise to characterize food-borne pathogens.