Fresh and fresh-cut tomatoes have been associated with numerous outbreaks of salmonellosis in recent years. While the exact routes of contamination are unknown, high pressure processing (HPP) is being evaluated as a post harvest treatment to eliminate Salmonella enterica from tomatoes. The objectives of the study were to determine the potential for of HPP to reduce S. enterica serovars Newport, Javiana, Braenderup and Anatum (clinical isolates from tomato outbreaks) in tryptic soy broth (TSB) and to determine the effect of HPP to reduce the most pressure resistant S. enterica serovar from fresh diced and whole tomatoes. Five ml portions of broth containing 8 log CFU/ml of one of the four serovars (nalidixic acid resistant) were packaged in sterile stomacher bags and subjected to one of three different pressures (350, 450, or 550 MPa) for 120s. Samples were enumerated by surface plating onto tryptic soy agar supplemented with 50 ppm nalidixic acid (TSAN) and incubated at 35°C for 48 hours. The most pressure resistant S. enterica serovar evaluated was Braenderup. Subjecting the broth culture to 350, 450 and 550 MPa resulted in a 4.53, 5.74 and 7.09 log reduction in S. Braenderup, respectively. Diced tomatoes (150g) and whole red round tomatoes (150g; packaged in 350ml of 1% CaCl2) were inoculated with S. Braenderup, to obtain 6 log CFU/g throughout the sample and subjected to the same pressure treatments as described above. After HPP, diced tomatoes were homogenized for 1 minute and then plated on TSAN. Whole tomatoes were surface sampled, and then homogenized for 1 minute. Surface and homogenate samples were plated on TSAN supplemented with 1% pyruvic acid (TSANP). Significant reductions of S. Braenderup concentrations in diced tomatoes (P < 0.05) were seen after processing at 350 (0.46 CFU/g), 450 (1.44 log CFU/g), and 550 MPa (3.67 log CFU/g). In whole tomatoes, significant reductions (P < 0.05) were also seen at 350 (1.41 log CFU/g), 450 (2.25 log CFU/g) and 550 MPa (3.35 log CFU/g). There were no differences in visual appearance between fresh and HPP diced and whole tomatoes. HPP may be an effective post harvest strategy to reduce low levels of S. enterica contamination in diced tomatoes. / Master of Science in Life Sciences

L'émergence de la résistance aux antibiotiques représente un risque grandissant, tant au niveau de la santé animale qu'humaine. Afin de répondre à cette problématique, plusieurs options sont présentement à l'étude par la communauté scientifique, dont l'utilisation de phages comme une alternative ou un complément aux antibiotiques. Avant que ces virus bactériens ne soient une solution viable à long terme, plusieurs défis devront être relevés, dont la production optimale des phages ainsi que leur conservation et distribution. Il est également essentiel de bien comprendre le fonctionnement de ces virus et leurs interactions avec les bactéries afin de limiter l'émergence de bactéries résistantes aux phages. Le phage de Salmonella S16, un phage virulent ayant un large spectre lytique, a été étudié afin de maximiser le rendement lors de sa production. Des titres supérieurs à 1x10¹⁰ UFP/mL ont pu être obtenus de manière constante en variant la charge virale, la charge bactérienne et la multiplicité d'infection. L'atomisation des phages S16 et Felix-O1 a par la suite été réalisée afin d'obtenir une poudre concentrée de phages, facilitant l'entreposage et la distribution de ces derniers. Ensuite, des bactéries résistantes aux phages ont été générées via un cocktail de trois phages virulents (Felix-O1, 16-19 et 9 heidelberg). Les génomes de ces bactéries mutantes ont par la suite été séquencés et analysés dans le but d'identifier le mécanisme utilisé par Salmonella pour se protéger contre l'infection par ces phages. Finalement, une interaction phage-hôte peu connue, la pseudolysogénie, a été observée et analysée chez le phage S16. L'analyse protéomique via la spectrométrie de masse a permis de déterminer trois protéines du phage qui sont surexprimées lors de la pseudolysogénie comparativement à un cycle d'infection normal. Ces protéines phagiques pourraient être reliées à la régulation ou au mécanisme menant à la pseudolysogénie. / The emergence of antibiotic resistance in several pathogenic bacteria is currently a significant risk, both in animal and human health. To manage this issue, several options are currently being explored by the scientific community, including the use of phages as alternatives or complements to antibiotics. Before those bacterial viruses are seen as a long-term viable option, several challenges remain, including the optimization of phage production as well as their conservation and distribution. It is also critical to understand how these viruses work and how they interact with their bacterial hosts to limit the emergence of phage-resistant bacteria. The Salmonella phage S16, a virulent phage with a broad host range, was studied to maximize its yield during production. Titers greater than 1x10¹⁰ PFU/mL were routinely obtained by varying the viral load, the bacterial load, and the multiplicity of infection. Spray drying of phages S16 and Felix-O1 was then carried out to manufacture a concentrated phage powder, facilitating storage and distribution. Then, phage resistant Salmonella bacteria were generated using a cocktail of three virulent phages (Felix-O1, 16-19 and 9 heidelberg). The genome of these bacterial mutants was sequenced and analyzed to better understand the mechanism used by Salmonella to protect itself against phage infection. Finally, a poorly described phage-host interaction phenomenon, the pseudolysogeny, has been observed with phage S16. Proteomic analysis via mass spectrometry identified three phage proteins that are overexpressed during pseudolysogeny compared to a normal lytic cycle. These proteins could be linked to the regulation, or the mechanism involved in pseudolysogeny.

Raw produce has frequently been identified as the source of bacterial pathogens that can cause human illnesses, including listeriosis and salmonellosis. Microbial pathogens may attach and form biofilms on raw fruit surfaces and can be difficult to remove. A cavitation process (formation of bubbles in water) was studied for its effectiveness for removal and inactivation of Listeria monocytogenes and Salmonella Newport from the surfaces of fresh Roma tomatoes and cantaloupes. Individual fruit were separately inoculated with each pathogen, then submerged in a water tank and treated with a bubble flow through an air stone using one airflow rate (0 – 14 liters/min.) for up to 60 sec. As air flow increased, pathogen reduction increased up to 1.2 log CFU/fruit greater than with water alone (no bubbles). Additional pathogen reduction in the tank water (organisms detached from the fruit) was observed with the bubble treatments. Therefore, these bubble streams can be used to enhance the detachment of bacteria from fruit surfaces and to inactivate a proportion of these detached microorganisms. Additionally, recoveries of Salmonella from inoculated Roma tomatoes and cantaloupe were determined for treatment water that contained 50 or 150 ppm sodium hypochlorite. The combination of cavitation and chlorine resulted in greater efficacy of inactivating the pathogen in treatment water, but not in removing this organism from the fruit surfaces. The physical force of a bubble stream on raw produce can effectively reduce and inactivate surface bacteria, and has the potential to reduce antimicrobial chemical and water use in post-harvest packing operations. / Master of Science in Life Sciences / Every year, one in six Americans will have been affected by a foodborne illness, many of which are caused by bacteria found on the surface of fresh fruits and vegetables. Most of these bacteria are removed with the help of a water wash with or without chlorine added. Nevertheless, microorganisms, including bacterial pathogens, may attach and form biofilms on raw fruit surfaces and can be difficult to remove. For this research, a cavitation process (formation of bubbles in water) was studied for its effectiveness for removal and inactivation of <i>Listeria monocytogenes</i> and <i>Salmonella</i> Newport from the surfaces of fresh Roma tomatoes and cantaloupes. Individual fruit were separately spiked with each pathogen, then submerged in a water tank and treated with a bubble flow through an air stone using one airflow rate (up to 14 liters air per minute) for 30 or 60 seconds. As air flow increased, the number of bacteria was reduced by up to 94% more bacteria per fruit than when using water alone (no bubbles). Additional bacteria reduction in the tank water (organisms detached from the fruit) was observed with the bubble treatments. Therefore, these bubble streams can be used to enhance the detachment of bacteria from fruit surfaces and to kill or injure some of these detached microorganisms. Additionally, recoveries of <i>Salmonella</i> from inoculated Roma tomatoes and cantaloupe were determined for treatment water that contained 50 or 150 parts per million sodium hypochlorite (chlorine solution). The combination of cavitation bubbles and chlorine showed a greater ability for inactivating these bacteria in the tank water, but not in removing this organism from the fruit surfaces. The physical force of a bubble stream on raw produce can effectively reduce and inactivate surface bacteria, and this process could reduce the amount of water or chemicals used to process fresh fruits and vegetables, while ensuring that these foods will not cause people to get sick upon eating.

Salmonella enterica spp. enterica est un pathogène omniprésent responsable de toxi-infection alimentaire pouvant potentiellement être mortelle pour l’humain. Afin de déclencher une infection, le pathogène doit survivre aux conditions stressantes rencontrées lors de son passage dans le tractus gastro-intestinal humain et coordonner l'expression de plusieurs facteurs de virulence. L’objectif de cette thèse est d’étudier le comportement de différentes souches de S. enterica dans le tractus gastro-intestinal humain en utilisant des approches in vitro. Les souches ont été sélectionnées en fonction de leur potentiel de virulence et de leur origine (clinique, alimentaire, animale, environnementale). En simulant le tractus gastro-intestinal supérieur avec le modèle in vitro TIM-1, une mortalité bactérienne est observée en compte viable dans l'estomac comparé aux résultats au PMA-qPCR. Cette différence suggère la présence de cellules viables mais non cultivables dans l’estomac. Une reprise de croissance est par la suite observée dans le duodénum et l’iléon. Après le passage dans le TIM-1, toutes les souches ont bien survécu, mais la survie de S. enterica dépendait de sa virulence. En effet, les souches de virulence élevée avaient significativement une survie plus élevée que celles de faible virulence. En condition iléale simulée dans le modèle PolyfermS, S. enterica est progressivement éliminée du milieu durant les douze premières heures, mais certaines souches maintiennent leur présence avec le lavage continu après 24 h. Les souches de S. enterica varient donc dans leur capacité à coloniser le système en présence du microbiote iléal. Par ailleurs, l’ajout de S.enterica n’a eu aucun impact sur la composition du microbiote iléale ou sur son activité métabolique. S. enterica ne peut utiliser le système immunitaire pour provoquer une dysbiose dans ce modèle, ce qui limite les mécanismes compétitifs. L’exposition des souches de S. enterica à une digestion gastro-intestinale en présence du microbiote iléal a induit l'expression de facteurs de virulence liés à l'adhésion et au gène ssaB du SPI-2, malgré l'absence de tissus hôtes. Cette induction était plus importante pour les souches à virulence élevée que pour les souches à faible virulence. Ces résultats approfondissent les connaissances sur le comportement de S. enterica dans le tractus gastro-intestinal humain pour pouvoir établir des stratégies de prévention contre ce microorganisme pathogène et pour mieux gérer le risque lié à Salmonella. / Salmonella enterica subsp. enterica is a ubiquitous pathogen responsible for food-borne infection, potentially life-threatening to humans. In order to trigger infection, the pathogen must survive the stressful conditions of the human gastrointestinal tract and coordinate the expression of several virulence factors in response to this environment. The objective of this thesis is to study the behavior of S. enterica in the human gastrointestinal tract using in vitro approaches. S. enterica strains were selected according to their virulence potential and their origin (clinical, food, animal and environmental). By simulating the upper gastrointestinal tract with the in vitro model TIM-1, bacterial mortality was observed by viable count in the stomach, compared to PMA-qPCR results. This difference suggests the presence of viable but non-cultivable cells. A resumption of growth was subsequently observed in the duodenum and the ileum. After passage through the TIM-1, all strains survived but high virulence S. enterica strains had significantly higher survival than low virulence strains. In simulated ileal conditions in the PolyfermS model, S. enterica was gradually eliminated from the medium during the first twelve hours. After 24 h, most strains maintained their presence with continuous wash-out. S.enterica strains vary in their capacity to colonize the system in the presence of the ileal microbiota. Furthermore, S. enterica had no impact on the composition of the ileal microbiota or on its metabolicactivity. S. enterica cannot use the immune system to induce dysbiosis in this model, limiting the competitive mechanisms. The exposure of S. enterica strains to gastrointestinal digestion in the presence of ileal microbiota induced expression of virulence factors linked to adhesion and SPI-2 gene (ssaB), despite the absence of host tissues. This induction was greater for high virulence strains than low virulence strains.These results deepen our knowledge on the behavior of S. enterica in the human gastrointestinal tract, in order to establish prevention strategies against the pathogen and to better manage the risk linked to Salmonella.

Memoria para optar al Título Profesional de Médico Veterinario / Los serotipos de Salmonella tradicionalmente se han clasificado mediante métodos serológicos que determinan antígenos somáticos y flagelares específicos. Sin embargo, este método diagnóstico es caro y tarda mucho tiempo en dar un resultado ya que requiere implementar una batería de anticuerpos para detectar los más de 2.500 serotipos de Salmonella enterica que se han identificado. Por otra parte, la identificación molecular de los genes responsables de la expresión de antígenos flagelares son más rápidos y más sensibles que la identificación serológica. Es por esto que, en la presente memoria se implementaron pruebas de PCR para identificar S. enterica serotipos Typhimurium y Hadar, ambas incluidas en un plan nacional de control de Salmonella en establecimientos comerciales de aves. Se analizaron 135 cepas, 50 correspondientes a S. Typhimurium, 50 a S. Hadar y 35 enterobacterias como controles negativos. Estas cepas, previamente serotipificadas en el Instituto de Salud Pública (ISP), fueron sometidas a la prueba de PCR para determinar si existen diferencias de diagnóstico entre ambas técnicas. Del total de cepas analizadas, sólo 46 cepas de S. Typhimurium dieron positivas a la prueba de PCR y cuatro dieron negativas, mientras que las 50 cepas de S. Hadar dieron positivas a las dos pruebas de PCR. Las 35 enterobacterias dieron negativas a las 3 pruebas de PCR. De acuerdo a los resultados obtenidos en el estudio, la detección de antígenos mediante serotipificación y PCR para las cepas de S. Typhimurium fue menor al esperado (92%), a diferencia de lo que ocurrió con las cepas de S. Hadar en que hubo 100% de acuerdo entre ambas técnicas, sugiriendo que esta prueba de detección de Salmonella es posible reemplazarla por los métodos tradicionales de identificación y así poder acelerar el diagnóstico de esta bacteria de gran importancia para la salud pública

Manifiesta que el cuy es una especie de producción que se ve afectada principalmente por Salmonella Typhimurium, la cual expresa factores de virulencia codificados por diferentes genes, que, en conjunto, cumplen funciones coordinadas para llevar a cabo la patogenia y desarrollar la enfermedad. Por ello, el presente estudio evaluó la presencia de 10 genes codificantes de diversos factores de virulencia de importancia biológica de un total de 100 aislados de Salmonella Typhimurium, compuestos por 90 cepas procedentes de cuyes enfermos y 10 cepas procedentes de cuyes aparentemente sanos, confirmados en estudios previos. El ADN de los aislados fue extraído y analizado mediante la técnica de PCR múltiple, para evaluar la presencia de los genes spvB, spiA, cdtB, sipB, tolC, sitC, lpfC, sifA, sopB y pefA, obteniéndose un patrón genético similar, con frecuencias de detección variables mayores al 60%, tanto en aislados de cuyes sanos como enfermos, excepto el gen cdtB, el cual no fue detectado; concluyéndose que no existe diferencia entre los factores de virulencia presentes en cepas de Salmonella Typhimurium aisladas de cuyes enfermos y cuyes aparentemente sanos; sin embargo, debe tenerse en cuenta el potencial peligro que representan los animales portadores dentro de la producción. / Universidad Nacional Mayor de San Marcos (Lima). Vicerrectorado de Investigación y Posgrado Perú. Ministerio de la Producción. Programa Nacional de Innovación para la Competitividad y Productividad (Innóvate Perú) / Tesis

Wong Yin Wai. / Thesis submitted in: June 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 82-93). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iii / 摘要 --- p.v / Table of Content --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Taxonomy of salmonellae --- p.1 / Chapter 1.2 --- Clinical significance --- p.2 / Chapter 1.3 --- Treatment of Salmonella infections --- p.4 / Chapter 1.4 --- Global and local prevalence of Salmonella --- p.5 / Chapter 1.5 --- Antimicrobial Susceptibilities --- p.8 / Chapter 1.5.1 --- Salmonella Typhimurium --- p.8 / Chapter 1.5.2 --- Other salmonellae --- p.9 / Chapter 1.5.3 --- Emergence of quinolone-resistant salmonellae --- p.9 / Chapter 1.6 --- Mechanisms of β-lactam resistance --- p.10 / Chapter 1.6.1 --- Enzymatic deactivation of β-lactam antibiotics --- p.10 / Chapter 1.6.2 --- Modifications of normal PBPs --- p.11 / Chapter 1.6.3 --- Alternative routes of peptidoglycan synthesis --- p.12 / Chapter 1.6.4 --- Impermeability and active efflux system --- p.12 / Chapter 1.7 --- Classification and nomenclature of β-lactamases --- p.13 / Chapter 1.7.1 --- Functional classification --- p.13 / Chapter 1.7.2 --- Molecular classification --- p.15 / Chapter 1.7.3 --- Nomenclature of β-lactamases --- p.16 / Chapter 1.8 --- β-Lactamases in salmonellae --- p.17 / Chapter 1.8.1 --- Salmonella Typhimurium --- p.17 / Chapter 1.8.2 --- Other salmonellae --- p.18 / Chapter 1.9 --- Methods for the characterization of β-lactamases --- p.18 / Chapter 1.9.1 --- Isoelectric focusing (IEF) --- p.19 / Chapter 1.9.2 --- β-Lactamase activity assays --- p.20 / Chapter 1.9.3 --- Hybridization with DNA probes --- p.20 / Chapter 1.9.4 --- Amplification of β-lactamase genes by polymerase chain reaction (PCR) --- p.21 / Chapter 1.9.5 --- Polymerase chain reaction - Single strand conformational polymorphism (PCR-SSCP) analysis --- p.23 / Chapter 1.9.6 --- Gene sequencing --- p.23 / Chapter 1.10 --- Objectives --- p.25 / Chapter 2 --- Materials and Methods --- p.26 / Chapter 2.1 --- Bacterial Strains --- p.26 / Chapter 2.1.1 --- Identification of salmonellae --- p.26 / Chapter 2.1.2 --- Antibiotics and chemicals used --- p.26 / Chapter 2.1.3 --- Antimicrobial susceptibility testing --- p.28 / Chapter 2.2 --- Localization of β-lactamase genes --- p.30 / Chapter 2.2.1 --- Transferability study --- p.30 / Chapter 2.3 --- Characterization of β-lactamases --- p.31 / Chapter 2.3.1 --- Extraction of crude β-lactamases --- p.31 / Chapter 2.3.2 --- Isoelectric focusing (IEF) --- p.31 / Chapter 2.4 --- Molecular characterization of β-lactamase genes --- p.33 / Chapter 2.4.1 --- Detection of TEM-type β-lactamase genes using polymerase chain reaction (PCR) --- p.33 / Chapter 2.4.2 --- Detection of OXA-type β-lactamase gene using PCR --- p.36 / Chapter 2.4.3 --- Detection of TEM mutations by polymerase chain reaction 一 single strand conformational polymorphism (PCR-SSCP) analysis --- p.37 / Chapter 2.4.4 --- Detection of OXA mutations by PCR-SSCP analysis --- p.38 / Chapter 2.4.5 --- Sequencing of β-lactamase genes --- p.39 / Chapter 2.4.5.1 --- Preparation of sequencing template --- p.39 / Chapter 2.4.5.2 --- Sequencing reaction --- p.39 / Chapter 2.4.5.3 --- Preparation of sequencing gel --- p.40 / Chapter 2.4.5.4 --- Silver staining of the sequencing gel --- p.41 / Chapter 2.5 --- Relatedness of ampicillin-resistant S. Typhimurium --- p.42 / Chapter 2.5.1 --- Pulsed field gel electrophoresis (PFGE) --- p.42 / Chapter 2.5.2 --- Cluster analysis --- p.44 / Chapter 3 --- Results --- p.46 / Chapter 3.1 --- Bacterial Strains --- p.46 / Chapter 3.1.1 --- Antimicrobial susceptibilities --- p.46 / Chapter 3.2 --- Characterization of β-lactamases by isoelectric focusing --- p.52 / Chapter 3.3 --- Characterization of β-lactamase genes --- p.53 / Chapter 3.3.1 --- Transferability of β-lactamase genes --- p.53 / Chapter 3.3.2 --- Detection of OXA-type β-lactamase gene by polymerase chain reaction (PCR) --- p.53 / Chapter 3.3.3 --- Detection of OXA-type mutations by polymerase chain reaction- single strand conformational polymorphism (PCR-SSCP) analysis --- p.56 / Chapter 3.3.4 --- Detection of TEM-type β-lactamase gene by PCR --- p.56 / Chapter 3.3.5 --- Detection of TEM-type mutations by PCR-SSCP analysis --- p.56 / Chapter 3.3.6 --- Sequencing of β-lactamase genes --- p.61 / Chapter 3.3.7 --- Pulsed-field gel electrophoresis --- p.64 / Chapter 4 --- Discussion --- p.67 / Chapter 4.1 --- Antimicrobial susceptibilities of S. Typhimurium in Hong Kong --- p.67 / Chapter 4.2 --- Transferability of resistance --- p.69 / Chapter 4.3 --- β-Lactamases of S. Typhimurium --- p.70 / Chapter 4.4 --- DNA sequence of β-lactamase genes --- p.72 / Chapter 4.5 --- Relatedness of ampicillin-resistant S. Typhimurium --- p.73 / Chapter 4.6 --- Methods for the characterization of β-lactamases --- p.75 / Chapter 4.7 --- Significance of this study --- p.78 / Chapter 4.8 --- Conclusions --- p.79 / Chapter 4.9 --- Further studies --- p.80 / References --- p.83

by Koo Ching Irene. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 105-118). / Abstract also in Chinese. / Acknowledgments --- p.i / Abstract --- p.ii / Content --- p.iv / List of tables --- p.viii / List of figures --- p.x / Chapter Chapter 1: --- Introduction --- p.1 / Chapter A. --- Classification of salmonellae --- p.1 / Chapter B. --- Salmonellae enterica ser Enteritidis --- p.4 / Chapter C. --- Global increase in the prevalence of S. Enteritidis --- p.6 / Chapter D. --- Susceptibility of S. Enteritidis to antimicrobial agents --- p.13 / Chapter E. --- Methods for the epidemiological typing of S. Enteritidis --- p.17 / Chapter 1. --- Phenotypic methods --- p.17 / Chapter (1) --- Biotyping --- p.17 / Chapter (2) --- Antibiotic resistance pattern --- p.18 / Chapter (3) --- Phage typing --- p.18 / Chapter (4) --- Characterization of plasmids --- p.19 / Chapter a. --- Resistance plasmids --- p.20 / Chapter b. --- Transferability of plasmids --- p.20 / Chapter c. --- Incompatibility --- p.21 / Chapter 2. --- Molecular methods --- p.21 / Chapter (1) --- Plasmid analysis --- p.21 / Chapter a. --- Plasmid profile --- p.22 / Chapter b. --- Plasmid fingerprinting --- p.22 / Chapter (2) --- Chromosomal DNA fingerprinting --- p.24 / Chapter a. --- Restriction fragment length polymorphism (RFLP) of chromosomal DNA --- p.25 / Chapter b. --- Pulsed-field gel electrophoresis (PFGE) --- p.25 / Chapter c. --- Hybridization with specific gene probes --- p.26 / Chapter d. --- Ribotyping --- p.27 / Chapter e. --- Insertion sequence IS200 fingerprinting --- p.29 / Chapter (3) --- Polymerase chain reaction (PCR) --- p.30 / Chapter 3. --- Other --- p.32 / Chapter (1) --- Lipopoly saccharide (LPS) analysis --- p.32 / Chapter (2) --- "Whole cell protein profile analysis, fatty acid profile analysis, multilocus enzyme electrophoresis and Fourier-transform injfrared spectroscopy" --- p.33 / Chapter F. --- Epidemiology of S. Enteritidis in different parts of the world --- p.34 / Chapter G. --- Objectives --- p.35 / Chapter Chapter 2: --- Materials and Methods --- p.36 / Materials --- p.36 / Methods --- p.38 / Chapter A. --- Identification --- p.38 / Chapter 1. --- Biochemical tests --- p.38 / Chapter 2. --- Serotyping --- p.38 / Chapter B. --- Antimicrobial susceptibility testing --- p.39 / Chapter C. --- Characterization of β-lactamases --- p.39 / Chapter 1. --- Extraction of β-lactamases --- p.39 / Chapter 2. --- Determination of isoelectric points (pIs) --- p.41 / Chapter D. --- Characterization ofplasmids --- p.42 / Chapter 1. --- Genetic studies --- p.42 / Chapter (1) --- Transferability of resistance plasmids --- p.42 / Chapter (2) --- Mobilization of resistances --- p.43 / Chapter 2. --- Molecular studies --- p.44 / Chapter (1) --- Plasmid profile analysis --- p.44 / Chapter a. --- Plasmid extraction --- p.44 / Chapter b. --- Agarose gel electrophoresis --- p.45 / Chapter (2) --- Plasmid DNA fingerprinting --- p.45 / Chapter a. --- Preparation of pure plasmid DNA --- p.46 / Chapter b. --- Preparation of individual plasmid from strains harbouring more than one plasmid --- p.46 / Chapter c. --- Restriction endonuclease digestion of plasmid DNA --- p.47 / Chapter E. --- Total DNA fingerprinting --- p.47 / Chapter 1. --- Total DNA preparation --- p.48 / Chapter 2. --- Restriction endonuclease digestion of total DNA --- p.48 / Chapter 3. --- Ribotyping --- p.49 / Chapter (1) --- Restriction enzyme digestion of total DNA --- p.49 / Chapter (2) --- Transfer of DNA fragments to solid support --- p.49 / Chapter (3) --- Reverse transcription of rRNA into cDNA and labelling of cDNA --- p.50 / Chapter (4) --- Hybridization --- p.50 / Chapter (5) --- Detection of hybridized fragments --- p.51 / Chapter 4. --- AP-PCR (Arbitrary primed-PCR) --- p.51 / Chapter F. --- Experimental design --- p.52 / Chapter Chapter 3: --- Results --- p.54 / Chapter A. --- Prevalence of S. Enteritidis in the Prince of Wales Hospital --- p.54 / Chapter B. --- Antimicrobial susceptibilities --- p.58 / Chapter C. --- β-lactamases produced by β-lactam-resistant S. Enteritidis --- p.66 / Chapter D. --- Plasmid profile analysis --- p.66 / Chapter E. --- Characterization of resistance plasmids --- p.69 / Chapter F. --- Plasmid fingerprinting --- p.72 / Chapter G. --- Total DNA fingerprinting --- p.76 / Chapter H. --- Ribotyping --- p.82 / Chapter I. --- AP-PCR --- p.85 / Chapter J. --- "Correlation of plasmid analysis, total DNA fingerprinting, ribotyping and AP-PCR results" --- p.88 / Chapter Chapter 4: --- Discussion --- p.91 / Chapter A. --- Prevalence of S. Enteritidis --- p.91 / Chapter B. --- Susceptibilities of S. Enteritidis to antimicrobial agents --- p.92 / Chapter C. --- Evaluation of methods for epidemiological typing of S. Enteritidis --- p.94 / Chapter D. --- Molecular epidemiology of S. Enteritidis in Hong Kong --- p.99 / Chapter E. --- Areas for future research --- p.102 / References --- p.105 / Appendix --- p.119

Foodborne diseases are one among the diseases with high morbidity and mortality rate. The concern is raised with the emergence of pathogenic strains that are resistant to the available set of antibiotics. Conventional regimens fail to treat the infections caused by these pathogens prolonging the sickness leading to increased morbidity and mortality. The situation can get further complicated with the dietary intake of the host. Of late it has been understood that the dietary flavonoids play an important role in regulating the immune system. Curcumin, a pigment from turmeric, is one among such bioflavonoid with an immunomodulatory potential. Curcumin has been a front-line topic of mainstream scientific research for a variety of diseases from cancer to Alzheimer’s to infectious diseases. Curcumin being considered as a spicy panacea is not a remedy for all diseases. Its ability to act differentially as an antioxidant or pro-oxidant can be either beneficial or harmful for the host. It exhibits antioxidant properties at concentrations achievable in the body; this can make the host vulnerable to infections due to the suppression of innate immune responses. Curcumin also suppresses the type 1 immune response, which might lead to alleviation of type 1 immune response disorders. However, the inhibition of type 1 immune response might invite infections with opportunistic pathogens. We have chosen curcumin to assess the effect of diet on the regulation of pathogenesis of Salmonella along with few medically important pathogens like Yersinia enterocolitica, Staphylococcus aureus, Shigella flexneri and Listeria monocytogenes. The thesis is divided into five chapters. As the main focus of the thesis is on Salmonella, in Chapter 1 we introduce diverse aspects of curcumin and the basic biology of Salmonella. Initially the properties of curcumin, the molecule of interest are introduced followed by brief overview to Salmonella biology and pathogenesis. Various activities of curcumin dealing with the variety of diseases are discussed. Further, the introduction to the intricate underlying mechanisms and the functional determinants of curcumin is given. The subsequent sections give an overview of different phases of Salmonella pathogenesis and the molecular mechanisms of Salmonella virulence and host defense. Towards the end of the chapter we discuss the strength, limitations and the distinctive characteristics of the murine model of typhoid fever. Curcumin has gained immense importance for its vast therapeutic and prophylactic applications. Its anti-bacterial effect has been demonstrated in bacteria, like B. subtilis, H. pylori and E. coli. Contrary to this, the results of the Chapter 2 reveals that curcumin at a nontoxic concentration to both host and pathogen, regulates the defense pathways of Salmonella enterica serovar Typhimurium (S. Typhimurium) to enhance its pathogenicity. In a murine model of typhoid fever, we observed higher bacterial load in reticuloendothelial organs when infected with curcumin-treated Salmonella. Curcumin increased the resistance of S. Typhimurium against antimicrobial agents like antimicrobial peptides, reactive oxygen and nitrogen species. It up-regulated the genes involved in resistance against antimicrobial peptides - pmrD and pmrHFIJKLM and genes with antioxidant function - mntH, sodA and sitA. We implicate that the iron chelation property of curcumin has a role in regulating mntH and sitA. Interestingly, we see that the curcumin-mediated modulation of pmr genes is through the PhoPQ two-component regulatory system (TCS). Curcumin downregulates SPI-1 genes required for entry into epithelial cells and upregulates SPI-2 genes required for intracellular survival, through PhoPQ TCS. Thus, this common regulator (PhoPQ) could explain curcumin's mode of action. Another important factor for the pathogen’s success is its ability to counteract the action of antibiotics. Almost all the bactericidal antibiotics act via production of reactive oxygen species in the bacteria. Curcumin has anti-oxidant property that might interfere with the action of antibiotics. Ciprofloxacin is a commonly used anti-typhoidal drug. It kills the bacteria by inhibiting DNA replication and increasing reactive oxygen species in bacterial cell. In Chapter 3 we present the results obtained after the investigation of the interference of curcumin with the anti-bacterial action of ciprofloxacin against Salmonella. We found that curcumin indeed increased the proliferation of Salmonella Typhi and Salmonella Typhimurium in ciprofloxacin treated macrophages by reducing the ciprofloxacin-induced reactive oxygen species. It also inhibited ciprofloxacin mediated DNA damage and the resultant SOS response and filamentation. However, curcumin was unable to rescue the ciprofloxacin induced gyrase inhibition. The reduced antibiotic (ciprofloxacin) efficacy against Salmonella by curcumin might aggravate the disease. Thus, the results of chapter 1 and 2 urge us to rethink the indiscriminate use of curcumin especially during Salmonella outbreaks. Bacteria modulate its virulence determinants in response to the environmental cues. Salmonella being a foodborne pathogen has a very likely chance of getting exposed to turmeric and hence curcumin. In Chapter 4 we have assessed the modulation of motility of S. Typhimurium, an important virulence determinant, by curcumin. We show that curcumin reduced the motility of the S. Typhimurium by decreasing the flagellar density around it. Surprisingly, this was achieved without affecting the expression of the flagellin gene and protein. Curcumin physically adhered to the flagella making it fragile and breaking it into fragments. This can hinder bacterial motility, chemotaxis, adherence and invasion into the host cells. However, aflagellate bacteria are hypervirulent as is the case with our experimental results with curcumin treated bacteria. Curcumin regulates myriad of bacterial (Salmonella) activities increasing its pathogenicity. Curcumin is known to regulate the host defenses in response to the disease. In Chapter 5 we have sought to address the effect of curcumin treatment of host cells on the outcome of infection by different pathogens. Pathogens have evolved different strategies to evade the host innate immune system, one of them being avoiding lysosome mediated degradation. Pathogens like Salmonella, Yersinia, Mycobacterium and Staphylococcus have acquired molecular machinery to inhibit the fusion of the pathogen containing vacuole with lysosomes and multiply within the vacuole whereas other pathogens like Shigella, Listeria and Rickettsia escape into and multiply in the cytosol. In our study we show that pretreatment of macrophage with curcumin increased the fold proliferation of S. Typhimurium, S. aureus and Y. enterocolitica whereas decreased that of S. flexneri and L. monocytogenes. From the results obtained, we can state that curcumin differentially regulates the pathogenesis of vacuolar and cytosolic pathogen. We hypothesized that curcumin pretreatment stabilizes the membrane of pathogen containing vacuole retarding the lysis of the phagolysosome harboring the cytosolic pathogen and hence facilitating its clearance. We indeed observed that the membrane stabilizing effect of curcumin led to increased fusion of cytosolic pathogen with the lysosome, decreasing its proliferation in the cells. As the vacuolar pathogens have an inherent ability to inhibit this fusion, they proliferate better in curcumin treated cells. In a nutshell curcumin can have multiple and sometimes unexpected effects not only on a pathogen’s potential to successfully cause infection but also on the host’s ability to counter it. A brief summary of the study that does not directly deal with the modulation of bacterial pathogenesis by curcumin is included in the Appendix. In this study a novel, simple, sensitive and efficient PCR based assay was devised to detect Salmonella contamination in milk, fruit juice and ice-cream without any pre-enrichment.

A aplicação de métodos de tipificação baseados na caracterização fenotípica e genotípica em vários pontos da cadeia de produção de suínos pode ser uma importante ferramenta para identificar a principal fonte de contaminação por Salmonella sp. A partir disso, o trabalho propôs tipificar uma coleção de 97 amostras de Salmonella enterica subsp. enterica ser. Typhimurium (ST) isolada de suínos levados ao abate em três diferentes frigoríficos no Rio Grande do Sul, por meio de fagotipificação, hibridização com IS200, resistência a antimicrobianos, amplificação da região spvR, amplificação de sequências repetitivas (rep-PCR) e PFGE. Paralelamente, os isolados de ST foram avaliados frente a dois desinfetantes (amônia quaternária e iodofor) pela técnica da diluição em tubo. Os isolados foram classificados em 12 fagotipos distintos, sendo o DT177 o mais freqüentemente identificado. Houve o predomínio de um padrão único de hibridização com o IS200 e em apenas três isolados, a região spvR foi detectada. Um alto número de amostras resistentes à tetraciclina, sulfonamida e estreptomicina foi encontrado, sendo o perfil de resistência relacionado ao frigorífico de origem dos isolados. No rep-PCR, usando seqüências iniciadoras para REP e ERIC, um único padrão de bandas foi gerado entre os isolados de ST. A análise por PFGE mostrou doze diferentes padrões de bandas. Sessenta e quatro isolados apresentaram um padrão idêntico no PFGE. Todas amostras foram inibidas pelo composto quaternário de amônio, na concentração recomendada pelo fabricante e numa concentração inferior à indicada. Frente ao iodofor, quatro amostras mostraram-se resistentes na concentração indicada e 59 na sub-concentração. A combinação da fagotipificação e do perfil de PFGE permitiu alcançar uma melhor discriminação das amostras, sendo essas técnicas consideradas as mais adequadas. Por outro lado, a presença de linhagens clonais parecem estar presentes na região, indicando possíveis pontos comuns de infecção.