RNA-seq of Pathogen Transcriptomes in Food and Food Associated Environments

Next generation sequencing (NGS) tools are increasingly being recognized for their ability to provide for improved subtyping of foodborne pathogen isolates as well as for metagenomics-based characterization of all DNA present in a given sample; the later approach in particular can provide both intriguing and sometimes potentially misleading information. NGS tools also provide a powerful approach to characterizing all RNA present in a given microbial population exposed to either food relevant environmental conditions or present in an actual food matrix. In these applications, termed “RNA sequencing (RNA-seq)”, NGS provides significant advantages over microarray technologies, which until recently have been predominantly used for characterization of transcriptomes. This presentation will provide examples of how RNA-seq has provided new insights into foodborne pathogen responses to food associated stress conditions and how it has been used to elucidate the physiological state of pathogens in foods. This presentation will also highlight how this information can be translated into improved control strategies using a “precision food safety” type strategy that can custom tailor interventions to different food types and commodities. Ultimately, these approaches may allow us to move to food safety approaches that not just attempt to reduce pathogen numbers in foods, but also will assure a pathogen physiological state that is associated with a reduced public health risk (such as a state that reduces or eliminates production of relevant toxins). In addition to characterization of pathogen transcriptomes, there also is considerable interest in characterization of food meta-transcriptomes, including to address concerns about metagenomics-based detection of genetic material from non-viable organisms. While meta-transcriptomics approaches, alone as well as in combination with metagenomics, have considerable potential for improved characterization of foods and raw materials, including detection of potential food safety and adulteration incidents, considerable additional data and research is needed to develop these tools and to allow for reliable interpretation of results.