Saudi Arabia produces a majority of its fruits and vegetables locally in small-scale production farms. These farms utilize groundwater as the main source of irrigation water. The water-regulating authorities in Saudi Arabia rely on traditional culturing methods to monitor coliforms as indicators of microbial contamination. These methods are time-consuming, do not address the sources of contamination, and do not permit assessment on the associated health risk. To address these knowledge gaps, the study investigates the sources of contamination in eight wells northeast of Mecca, Saudi Arabia. The study focuses on the potential impact on groundwater quality due to a nearby chicken farm and urban runoffs from human residential areas. Besides performing conventional methods to determine nutrient content and to enumerate coliforms, quantitative PCR using four host-associated primer sets were used to distinguish microbial contamination from humans and livestock. High-throughput sequencing was also performed to determine the relative abundance of several genera associated with opportunistic pathogens. Bacterial isolates were cultivated from the vegetable samples harvested from these farms, and were characterized for their phylogenetic identities. Lastly, the study collates the information to perform quantitative microbial risk assessment due to ingesting antibiotic-resistant Listeria monocytogenes, Pseudomonas aeruginosa and Enterococcus faecalis in these vegetable samples.

Two studies on potential approaches for processing low-salt, low-fat (LSLF) bologna were completed. In study 1, the effects of three factors, namely salt type (sea salt vs. regular NaCl), NaCl concentration (0.75%, 1.00%, 1.25% and 2.00%) and holding of stuffed batter before cooking (cooked immediately (CI) vs. delayed cooking (DC)), on the quality of LSLF bologna were investigated. There was no difference between salt type for most of the parameters measured. The holding factor significantly improved the water holding capacity (WHC) and texture of bologna samples containing 0.75% NaCl, as shown by lower (p<0.05) expressible moisture. However, holding factor did not affect WHC and instrumental texture of samples with 1.00%, 1.25% or 2.00% NaCl. A NaCl level by hold effect (p<0.05) was observed for texture profile analysis (TPA) in which there was significant improvement in the texture of samples containing 0.75% NaCl that were subjected to DC, but no effect at other NaCl levels. Panelists were able to detect the positive effect (p<0.05) of DC on the texture of samples with 0.75% or 1.00% NaCl. This study showed that DC is effective in improving the texture of bologna samples with extremely low NaCl (0.75%) content. The biggest challenge in this first study was the difficult sample handling experienced during slicing. Since bologna is commonly sold as thin slices, the bologna must be firm enough for ease of slicing. The second study focused on improving bologna firmness by the addition of microbial transglutaminase (MTG), known for its functionality as a protein cross-linker, and of flaxseed meal (FSM), known for its excellent water holding capacity. The physico-chemical and sensory characteristics of 12 treatment combinations (0, 0.15% and 0.30% MTG; 0, 0.5%, 1.0% and 1.5% FSM) were determined. In general, results showed that MTG significantly improved the textural quality of bologna, but resulted in a higher purge loss during storage of vacuum packaged slices. On the other hand, FSM significantly reduced the expressible moisture content and purge loss of the product. In terms of product colour, MTG had no effect but FSM when added to the formulation at level as low as 0.5%, affected the colour as determined by both instrumental and sensory evaluation. The overall results of the project indicated that texture in LSLF bologna is not a major issue, since processing conditions and combinations of ingredients can be manipulated to improve texture. The biggest challenge, however, is in the area of flavour – improving the flavour of low-salt processed meats warrants further research.

Les Escherichia coli entérohémorragiques (EHEC) sont des pathogènes zoonotiques responsables de toxi-infectionsalimentaires pouvant évoluer vers des atteintes potentiellement mortelles chez l’Homme. La survie des EHECet l’expression des gènes de virulence dans l’environnement digestif humain sont des facteurs essentiels dans laphysiopathologie de ces infections mais sont mal connus, essentiellement par manque de modèles d’études adaptés.L’absence de traitement spécifique a conduit à s’intéresser à des moyens préventifs et/ou curatifs alternatifs, commel’utilisation de probiotiques. L’objectif de ce travail de thèse est d’étudier le comportement de souches EHEC dansl’ensemble du tractus digestif et l’influence de souches probiotiques, en utilisant des approches in vitro et in vivocomplémentaires.In vitro, dans le tractus gastro-intestinal supérieur, on observe une mortalité bactérienne dans l’estomac, suivie d’unereprise de croissance dans les parties distales de l’intestin grêle. De plus, la survie des EHEC dépend à la fois de lasouche/sérotype étudié et de la matrice alimentaire dans laquelle les bactéries sont ingérées. En conditions coliqueshumaines simulées, les EHEC sont progressivement éliminés du milieu colique et leurs principaux gènes de virulence(stx1 codant la Shiga-toxine 1 et eae codant l’intimine) sont surexprimés dans les heures suivant l’inoculation dupathogène. L’ajout de levures probiotiques du genre Saccharomyces ne modifie pas la survie du pathogène dansl’environnement colique, que celles-ci soient administrées en traitement « curatif » ou « prophylactique ». Parcontre, l’administration de S. cerevisiae CNCM I-3856 permet (i) de moduler favorablement l’activité fermentairedu microbiote intestinal, en augmentant la production d’acétate et en réduisant celle du butyrate et (ii) de diminuersignificativement l’expression de stx1. Par ailleurs, l’effet du pathogène et des probiotiques sur le microbiote coliqueest individu dépendant, confortant l’hypothèse que des facteurs associés à l’hôte, comme le microbiote, pourraientconditionner l’évolution clinique des infections à EHEC et l’efficacité d’une stratégie probiotique. Enfin, dans unmodèle murin d’anses iléales, l’administration préventive de S. cerevisiae CNCM I-3856 limite significativementl’interaction d’O157:H7 avec les plaques de Peyer et les lésions hémorragiques associées.Ces résultats confirment donc l’intérêt d’une stratégie probiotique dans le contrôle des infections à EHEC. Uneétude plus approfondie du transcriptome du pathogène dans l’environnement digestif humain, en présence ou non deprobiotiques, permettrait de mieux comprendre la physiopathologie des infections à EHEC et les mécanismes associés / The enterohaemorrhagic Escherichia coli (EHEC) are zoonotic pathogens that cause food-borne infection withwhich leads to life-threatening damage in humans. EHEC survival and expression of virulence genes in the humandigestive track are key factors in the pathogenesis of these infections, but little is known, mainly due to lack ofappropriate study models. The absence of specific treatment has led to an interest in preventive and/or alternativemeasures healing, such as the use of probiotics. The objective of this study is the behavior of EHEC strains in theentire digestive tract and the influence of probiotic strains, using in vitro and in vivo complementary approaches.In vitro, in the upper gastrointestinal tract, a bacterial mortality was observed in the stomach, followed bya bacterial resumption in the distal segment of the small intestine. Moreover, survival depends on both theEHEC strain/serotype studied and the food matrix in which the bacteria are ingested. In simulated humancolon conditions, EHEC was progressively eliminated from the bioreactor and the major virulence genes (stx1encoding Shiga-toxin 1 and eae encoding intimin) are overexpressed in the hours following the inoculation ofpathogen. Probiotic yeasts Saccharomyces genus does not modify the survival of the pathogen in the in vitro colonicenvironment, that they be administered in treatment "curative" or "prophylactic". Still, the administration ofS. cerevisiae CNCM I-3856 allows (i) to favorably modulate fermentation activity of the intestinal microbiota, byincreasing the production of acetate and reducing that of butyrate and (ii) reduce significantly the expression ofstx1. Furthermore, the effect of pathogenic and probiotic on colonic microbiota is donor-dependent, supporting thehypothesis that factors associated with the host, as the microbiota could condition the clinical course of EHEC andefficiency a probiotic strategy. Finally, in a murine model of ileal loops, preventive administration of S. cerevisiaeCNCM I-3856 significantly limits the interaction of O157:H7 with the Peyer’s patches and results hemorrhagic lesions.These results confirms the interest of probiotic strategy in controlling EHEC infections. Further transcriptomestudies are warranted for the pathogen in the human digestive environment, with or without probiotics for the betterunderstanding of the pathophysiology of EHEC and so on the mechanisms involved in the antagonistic effect ofprobiotics.