Host-specific Genetic Markers of Fecal Bacteria for Fecal Source Tracking in Food and Water

Fecal pollution in food and water is the major cause of disease outbreaks, so accurate identification of this fecal pollution in these locations is critical to prevent such outbreaks. Fecal source tracking (FST) is an effective tool to identify the sources (human vs. animal) of any particular instance of fecal pollution. Many FST technologies were developed over the past two decades and used mainly to monitor and manage water quality, but their applications have recently attracted more attention in food systems. With the great advances of technologies in DNA sequencing and related bioinformatic tools, a significant number of novel genetic markers of fecal indicator bacteria (FIB) have been identified to be associated with particular host species, and thus, suitable for FST. The host-specific genetic markers were originally limited to 16S rDNA sequences of FIB, which are relatively conserved. Novel genetic markers include genes of the host-bacterium interaction and intervening sequences within the 16S- and 23S-rDNA of fecal bacteria. However, most of the genetic markers were only evaluated in laboratory settings, and their compete values in the monitoring and management of food and water safety need further assessments in the field.