Finding specific gene sequences in a DNA extract from foodstuffs or cultural enrichments can have many meanings. Modern DNA sequencing and bioinformatics allow the determination of specific genes (e.g., targeted bacterial microbiomes) or total DNA sequences (metagenomes) in matrices including food, which has not been culturally enriched. This new paradigm of food analysis brings us to question whether finding a specific gene sequence should be considered, [a] a true-positive or viable pathogen; [b] an indicator of the potential for viable organisms; [c] a history of past pathogen contamination; or [d] DNA from non-viable cells.  Zero tolerance rules for Listeria monocytogenes and Escherichia coli O157 are predicated on evidence from finding a specific DNA amplicon and/or culturing and isolation of the target organism. In early days of PCR tests, based on presence/absence of a specific PCR amplicon and not a defined sequence, the dilemma of PCR positive/culture negative samples was addressed and seemingly rectified. But, since some pathogens appear to be ubiquitous within food production environments, what does finding their DNA signature in a microbiome or metagenome mean?  Does merely finding a sequence constitute a basis for action? Will we reach a point in which zero tolerance rules lose meaning as we are able to analyze effectively larger sample sizes just from their DNA extract; thereby, increasing chances of finding pathogens in a production environment? Should we begin transitioning from zero tolerance pathogen rules to quantitative standards?  These are key questions, in the early days, of applying genomics to microbial food analysis.  Here we discuss the implications of using microbiomes beyond straight presence/absence PCR. The emphasis of this symposium will be on how genomic technologies could potentially call into question the meaning of zero tolerance and finding pathogen sequences.  A successful outcome will provide guidance for practitioners of microbiomics for industry and regulatory problems.

Presentations