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Bacteriocins are antimicrobial protein produced by certain Gram positive and negative bacteria as a defense mechanism against closely related bacteria competing for the same nutrient or in the same niche. The competition for the same nutrient is supported by the fact that bacteriocins have narrow range of effect and only likely to be effective against closely related bacteria for the same scares resources hence a bacteriocin produced by a Gram positive bacteria will be active against a Gram positive pathogens and a bacteriocin produced by a Gram negative bacteria will be active against Gram negative pathogens. This is due to the difference in cell wall composition, they are either bacteriocidal or bacteriostatic Bacteriocins have been used for thousands of years for food preservation unknowingly to man, they are considered advantageous not only to the producing bacteria, but it's now been used by the food industry as a tool to control both spoilage and pathogenic bacteria in food, in a natural manner which is acceptable to the consumer. With a lot of research been carried out on bacteriocins produced by Gram positive bacteria, antagonist to Gram positive food borne pathogens, little is known about bacteriocins produced by Gram negative bacteria which would be active against Gram negative food borne pathogens that predominate in produce. The objective of my research therefore is to screen for antimicrobial antagonist to Gram negative food borne pathogens (Escherichia coli O157:H7 and Salmonella Enteritidis) from produce, to determine an appropriate screening method, to carry out a preliminary characterization of antagonist discovered and also to determine antimicrobial spectrum of antagonist found. Lettuce was screened for antimicrobial antagonist against Gram negative pathogen (Escherichia coli O157:H7 and Salmonella Enteritidis) which were used as indicator strains With over 5000 colonies screen, 1 colony (Serratia plymuthica) was discovered to be antagonistic against these indicator strain. Further screening of cell free extract using the spot test method showed that extract from Serratia plymuthica grown alone in TSBYE showed antagonist activity against indicator strain with a little clearing on the spot of extract dropped. But extract of a co-culture of Serratia plymuthica and either Escherichia coli O157:H7 or Salmonella Enteritidis showed a more obvious clearing around spotted zone, which further indicates antagonism against indicator strains. Preliminary heat test indicates antagonist compound to be heat stable at 60oC for 30mins, 100oC for 30minutes and 60mins and 121oC for 20minites, and antagonist compound possessed antagonist activity against other strains of Escherichia coli when tested.

Verotoxin-producing Escherichia coli (VTEC) of serotype O157:H7 is a pathogen causing illness in humans worldwide. The path and nature of transmission from and among cattle is important knowledge when it comes to preventing cases of disease in humans. Two concepts potentially playing an important role in transmission of VTEC O157:H7 are super-shedding and super-spreading. Super-shedders are individuals (here calves) shedding a high amount of bacteria. Super-spreaders are individuals (here calves) spreading the disease in a higher extent compared to the rest of the population investigated. Little is known about these phenomenons’ effect on transmission as well as the relation between them. Therefore, it is important to investigate this further. The purpose of this master thesis was to get a better understanding of how super-spreaders can be identified. One way to identify super-spreaders and explore the transmission of a pathogen is to investigate molecular data using computational methods. Here, a literature study with a systematic approach was conducted in order to scan the literature for such methods. In this first phase of the master thesis three methods, all constructing transmission trees, were identified as relevant methods for the second phase. These methods are called outbreaker2, phybreak and TransPhylo. In the second phase of the master thesis, 32 whole genome sequences of VTEC O157:H7 collected from four different cattle farms were investigated using the methods outbreaker2 and phybreak. Both methods were able to identify samples infecting more secondary cases compared to the rest of the investigated population. Some of these samples came from the environment, possibly shedding light on the importance of the pathogen's ability to survive outside of the host, and therefore playing an important role in transmission of the disease. The rest of the samples infecting more secondary cases were from calves, and a minority of these were super-shedders. From this the importance of the relation between super-shedders and super-spreaders can neither be confirmed nor denied. Outbreaker2 suggested that the spread of the pathogen is frequently occurring between the four neighbouring farms, while phybreak instead suggested that the spread mostly occurs within the farms. From this, a scenario explaining that the transmission possibly occurs within farms is presented.

For years the issue of food waste has been recognized and quantified; however, food safety issues often go unrecognized as a source of food waste. One objective of this research is to estimate quantities and monetary value of fruits and vegetables implicated in food safety recalls, and thus wasted. Using publicly available data we identified all recalls involving vegetable or fruit commodities contaminated with Listeria monocytogenes, pathogenic E. coli, or Salmonella during 2015-2018. When quantities were provided, monetary value of recalled product was calculated using USDA ERS 2016 average retail prices. Although data limitations only allowed analysis of 17% of the recalls that met the criteria of this study, we estimated an annual loss of 38 million pounds and $61 million in revenue. Overall this shows that food safety issues can result in food waste, therefore mitigation strategies are needed. There are many ways that produce can become contaminated, however contaminated soils are a potential source of produce contamination and treatments to mitigate this risk while maintaining soil health is lacking. Current biofumigation methods that use glucosinolate hydrolysis products in mustard seed meal to control plant pathogens could also be effective against foodborne pathogens in soil. The purpose of this research is to determine the fate of E. coli O157:H7, Salmonella, and L. monocytogenes in soil treated with Brassica spp seed meal and plant material. Seed meals were successful in reducing pathogen concentrations in soil, significant reductions (p < 0.05) of E. coli O157:H7, L. monocytogenes, and Salmonella were observed in soil over 72 hours with the addition of 1.0 and 1.5 g of mustard seed meal. Increasing the seed meal concentration did not significantly (p > 0.05) increase the observed log reduction for L. monocytogenes or Salmonella, reductions ranged from 5.6 – 5.9 log CFU/g. However, for E. coli O157:H7 seed meal concentration was significant (p < 0.05). A 5.7 log CFU/g decrease was observed when 1.5 g of seed meal was used which was larger than 3.5 log CFU/g reduction observed with 1.0 g. Findings suggest that biofumigation with mustard seed meal could potentially be used to reduce E. coli O157:H7, L. monocytogenes, and Salmonella in contaminated soil. However, the use of plant material was not as successful as the use of the processed seed meals. In soil or in the absence of soil Brassica spp. plant material at 10% 15%, and 75% significantly increased E. coli O157:H7, L. monocytogenes, and Salmonella concentrations (p < 0.05). The results of these studies support literature indicating Brassica spp. processed plant products, like seed meals or extracts may be a more effective strategy in reducing human pathogen concentrations in contaminated agricultural soils. While the process of Biofumigation using Brassica spp. cover crops has been successful in eliminating plant pests from agricultural soils, due to its low isothiocyanate release efficiency and reactivity in soil organic matter, it may not be sufficient as a soil decontamination method against human pathogens.

This study focused on evaluating the antimicrobial activity of chlorine dioxide (ClO2) and different plant-based antimicrobials (carvacrol, thymol, and eugenol as bioactive compounds and muscadine extract- ME and blueberry extract- BBE as plant extracts) against selected foodborne pathogens under in vitro conditions and on produce (spinach and blueberries). In addition, bacterial microbiota associated with blueberries and blueberry farm environments from three different regions: Cundinamarca, Colombia; Mississippi, United States; and Guadalajara, Mexico, was determined. Under in vitro conditions, carvacrol and thymol were more effective (lower MICs and MBCs) than eugenol against Salmonella spp., Escherichia coli O157:H7 (MIC=MBC=0.2 mg/ml), and Listeria monocytogenes (MIC=MBC=0.4 mg/ml). Both plant extracts had the same MIC and MBC for Salmonella spp. while BBE had stronger bactericidal effect on Escherichia coli O157:H7 (MBC=150 mg/ml) and ME on L. monocytogenes (MBC=100 mg/ml). ClO2 had stronger bacteriostatic effect on L. monocytogenes (MIC=1 ppm) than on the Gram-negative bacteria (MIC=3 ppm). For the produce study, 300 mg/ml ME exerted the highest (P ≤ 0.05) E. coli O157:H7 reduction (4.5 log CFU/g at day 1) on spinach, and 3 ppm ClO2 + 300 mg/ml ME had the highest (P ≤ 0.05) L. monocytogenes reduction on both (4.5-5.6 log CFU/g). There was a similar (P>0.05) E. coli O157:H7 reduction on blueberries, regardless of antimicrobial treatment. For the microbiota study, Proteobacteria was the most abundant phylum in blueberries, soil, and water, with the exception of fruits from Mexico. Blueberries grown on the different regions shared two predominant genera: Heliorestis (10.5-47.4%) and Thiomonas (5.0-9.1%). Nonetheless, alpha and beta diversity revealed that blueberry microbiota structures were distinctive. PCoA plots revealed that within regions the microbial composition distribution was different (P ≤0.05) among fruits, soil, and water. Based on the results, ME combined with ClO2, could represent an antimicrobial alternative against foodborne pathogens for the produce industry. Furthermore, the study of the microbiota provided a good understanding on the bacterial community profile in blueberries and the blueberry farming environment across regions.

A bifidobacteria mix (nine strains) was evaluated for its effect on the growth and survival of Escherichia coli O157:H7 (ATCC 43890) in 11% NFDM and MRS broth under the optimum growth conditions for E. coli O157:H7 growth (37¡ãC, aerobic). Preliminary experiments were conducted to obtain the growth curves of the 9 strains of bifidobacteria and E. coli O157:H7 and confirm the inhibitory effect of acidity on E. coli O157:H7 (pH of media adjusted to 3.8). Acidapted E. coli O157:H7 showed no difference in resistance toward bifidobacteria (P>0.05) when compared to the non-acid adapted one. Escherichia coli O157:H7 did not survive in the supernatant of the bifodbacteria mix collected after incubation (37¡ãC) with aerobic shaking (8 h). However, the pathogen was able to grow after the pH of the supernatant was adjusted to 6.50 (pH of fresh MRS broth). Results suggest that a high content of bifidobacteria has a strong inhibitory effect on E. coli O157:H7, in part due to the low pH. However, products from bifidobacteria may also exert inhibitory effects.

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