Epigenetically silenced cryptic foodborne pathogens: a silent food safety hazard triggered by host gut signals

Approximately 30-32% of global foodborne outbreaks lack an identified causative agent, a critical surveillance gap driven by traditional taxonomic-based monitoring that fails to detect epigenetically silenced cryptic pathogens. These foodborne commensal strains acquire functional virulence gene clusters via horizontal gene transfer, maintain stable, heritable virulence silencing in food matrices to evade routine detection, and undergo rapid virulence activation upon exposure to host gut-specific signals, triggering unexplained gastrointestinal infections. This critical Mini Review focuses on the unique "silent in food, virulent in host" phenotype, clarifies core prokaryotic epigenetic regulatory mechanisms, dissects unresolved controversies blocking translational application, and proposes actionable research priorities. We emphasize an urgent paradigm shift from taxonomic identification to functional epigenetic risk assessment to mitigate this hidden food safety threat. Unlike existing broad reviews, this work provides phenotype-specific critical analysis to fill a key literature gap for food safety regulation and industrial practice.