The Rise of Genomics and the Promise of Whole Genome Sequencing for Understanding Microbial Foodborne Pathogens

Abstract

Next generation sequencing of pathogens is revolutionizing the science behind clinical diagnostics, epidemiology and the field of microbiology in general. Never before have scientists had access to, and been able to analyze and compare thousands of complete genomic sequences of bacteria, parasites and viruses. This vast amount of genomic data permits a better understanding of virulence traits, adaptability to food manufacturing environments, geographical traceability and transmission to humans, along with a host of other valuable information important to food scientists and regulators. Prior to the very recent (2011) introduction of bench-top, next generation sequencers, sequencing and annotation of complete pathogen genomes took months and was too expensive to be practical on the large scale. Today, through the introduction of a few novel technologies, it is now practical for any facility to sequence a pathogen in 1–2 days at a cost of $100 or less. The widespread availability of small, easy to use, next generation sequencers is resulting in a paradigm shift in the way in which scientists approach the identification and traceability of pathogens in the environment and clinic. A longstanding problem associated with foodborne disease outbreaks is the ability to rapidly identify the food and source of the contamination. Despite the best efforts of food safety experts, the tools available for tracking and tracing foodborne outbreaks are simply too slow and insufficiently resolved to effectively pinpoint the source of the outbreak, resulting in weeks of effort, and in many cases never identifying the source of the contamination. To this end, FDA, in 2012, created an integrated pilot network of state and federal laboratories to use whole genome sequencing to enhance traceback of foodborne pathogens. Known as GenomeTrakr, the network is creating a publically available, global database containing the genetic makeup of thousands of foodborne disease-causing bacteria including Salmonella. At present, WGS impacts food microbiology and regulatory food science in several ways including: (i) support of traceability efforts during foodborne contamination events; (ii) enhanced microbiological workflow; and (iii) quality assurance of food microbiological sampling programs. Taken together, early applications of WGS deployments underscore its extraordinary utility in food safety as well as the potential for complete characterization of bacterial pathogens as they emerge in the food supply.