Survival of foodborne pathogens in the human upper gastrointestinal tract: Design and analysis of an in vitro model system incorporating gut microbiota and absorption phenomena

Over the past few decades, microbial food safety has received a lot of attention. Yet foodborne infections remain a major burden, worldwide. The primary infection route of foodborne pathogens is through the consumption of contaminated food. Once ingested, incoming pathogens must succumb several antimicrobial barriers along the gastrointestinal tract before reaching an optimal site for attachment and colonization. These gastrointestinal defensive barriers are chiefly composed of (i) gastric acidity, (ii) the intestinal bile acids, (iii) the digestive enzymes, (iv) the mucus and epithelial layer, (v) inflammation, (vi) anaerobiosis and (vii) gut microbiota. Interestingly, the infectious dose of a pathogen has been observed to be highly correlated with its ability to survive the gastrointestinal transit. Moreover, it has been indicated that the food matrix can significantly influence microbial behavior in the gastrointestinal tract, either by protecting or promoting the inhibition of the accompanying pathogens. Typically, the primary method to understand pathogenic behavior in the human gastrointestinal tract is through the generation of quantitative data that mainly relies on digestion studies, with in vivo studies being considered the golden standard. However, over the last years, an increasing interest has been observed in the replacement and/or complementation of these studies with in vitro approaches, given that in vivo methods are often limited by ethical constraints, high costs, and lack of reproducibility and mechanistic information. In this dissertation, the overall objective was to evaluate the influence of food and food digestion on the survival of foodborne pathogens in the human gastrointestinal tract, through an in vitro approach. For this purpose, this dissertation focused on studying the impact of crucial gastrointestinal defensive barriers (physicochemical and microbial), as well as the influence of the food matrix on the behavior of Salmonella Typhimurium and Listeria monocytogenes during in vitro digestion. In conclusion, this dissertation confirmed that both the food and the gastrointestinal barriers of defense strongly affect the survival of foodborne pathogens during food digestion. Additionally, an in vitro digestion model system that is representative for the digestion phenomena that occur in the human upper gastrointestinal tract was developed, optimized and implemented. The overall findings of this research contribute to obtaining deeper knowledge in the behavioral aspects of foodborne pathogens during their encounter with the stressful environment of the human digestive system. This knowledge facilitates a better mode-of-action research that could lead to the development of better strategies for tackling foodborne bacterial pathogens, by (i) the improvement of existing in vitro digestion methods that mimic only a few physiological digestion-related parameters, (ii) the complementation of the current in vivo methods, (iii) acting as a stepping stone for the construction of more sophisticated in vitro digestion model systems that mimic pathogen-host interactions and (iv) the enhancement of the existing infectious dose response assessments.