Sleep is very important for health and academic performance. The amount of sleep is variable and depends among other things, on the age of the individual. Today there are many varieties of motion sensors that can be used in healthcare and clinical research for sleep registration, such as Actigraph GT9X Link and Actiwatch 2. The purpose of this study was to compare these two sensors, Actigraph and Actiwatch, for sleep registration by analyzing different sleep variables. The more precise sensor of the two will be used in the Energymetabolic laboratory in the case of survey or research. The method involved participants wearing both sensors for two nights and one day and trying to live as normal as possible. A sleep diary was used to complete the registrations, with related questions about sleep. There were 17 healthy participants between the ages 21 and 31. The results showed that the registrations from both sensors have varying spread and deviations. Overall the results were similar between the sensors and the sleep diary, and it was shown that there is no significant difference between the sensors. However, Actigraph deviated on most occasions from the diary. The Energymetabolic laboratory have access to many Actigraph GT9X Link sensors. This means that an evaluation has to be made to decide whether the cost of replacing the Actigraph GT9X Link sensors with Actiwatch 2 is worth it for the small improvement in precision.

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No. of bitstreams: 1 cruz_bc_dr_jabo.pdf.pdf: 3422888 bytes, checksum: a396717b2b2074de76c0871a37c4eebb (MD5) Previous issue date: 2017-10-27 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Rhipicephalus (Boophilus) microplus (Canestrini, 1888) é o mais importante ectoparasito da pecuária brasileira, cujo controle exige conhecimentos comportamentais de seu ciclo biológico para melhor sucesso na atuação sobre e fora do hospedeiro, combatendo-o em épocas do ano desfavoráveis ao mesmo. A maioria das informações sobre sua biologia e ecologia foi originada em outros países ou então há muito tempo. Baseado nas mudanças climáticas recentes e ausência de informações sobre ecologia e biologia deste ixodídeo na região, este estudo, conduzido em bioma de Cerrado e clima tropical com estação seca (Aw), obteve tais dados pela observação, ao longo de dois anos, dos fatores envolvidos nas suas fases de vida parasitária e não parasitária, além de avaliar o comportamento desta cepa quanto à evolução do perfil de resistência/susceptibilidade aos acaricidas. Observando a fase de vida parasitária deste carrapato, foi possível perceber sua adaptação às mudanças climáticas, com cinco gerações anuais registradas em dois anos consecutivos pela primeira vez na literatura. Constatou-se que não houve correlações significativas entre seu ciclo parasitando bovinos e os níveis de chuva, temperaturas ambiental e ao nível do solo e umidade relativa do ar. Já a fase de vida livre foi influenciada pelos fatores climáticos, com correlação positiva entre pluviosidade/pré-postura, correlações negativas entre temperatura/pré-postura, incubação e pré-eclosão, entre umidade relativa do ar/incubação e pré-eclosão. Os dados obtidos indicaram que o período de seca (outono e inverno) é mais favorável à manutenção do carrapato bovino no ambiente, além de albergar as maiores cargas parasitárias nos hospedeiros. A dinâmica populacional calculada reforça a adaptação deste ixodídeo às mudanças climáticas, culminando na existência de 5,212 gerações anuais mesmo em condições climáticas e ambientais distintas, oscilando entre 2,6 e 8,3 gerações/ano. Considerando estes dados, foi proposta uma metodologia de controle estratégico específica, tratando os animais entre a segunda metade da primavera e a primeira metade do verão (outubro a fevereiro). Estes tratamentos na estação chuvosa levariam a populações menores na estação seca, reduzindo também o “spring rise”. A análise da eficácia de diferentes compostos químicos por meio do Teste de Pacote de Larvas gerou resultados contraditórios, com alta eficácia registrada para piretróides e organofosforados, e oscilações na eficácia do amitraz. Estes valores levantaram questionamentos sobre a aplicabilidade desta técnica no monitoramento da resistência. Futuros estudos devem ser propostos, analisando a real eficácia dos Testes de Pacote de Larvas, confrontando diferentes metodologias in vivo e in vitro; comparando a dinâmica populacional deste ixodídeo em diferentes pastagens, formas de manejo, taxas de lotação, altitudes e biomas; atestando a eficácia da metodologia de controle estratégico proposta e, principalmente, confirmando a possibilidade de observarem-se mais de oito gerações de R. microplus por ano em condições climáticas ideais. / Rhipicephalus (Boophilus) microplus (Canestrini, 1888) is the main ectoparasite in Brazilian cattle industry, and its control demands behavioral knowledge of its biologic cycle, for increased success in actions over and out of the hosts, with treatments in periods of the year less favorable to this tick. Most of the information about its biology and ecology was originated in other countries or a long time ago. Based in recent climate changes and absence of ecologic and biologic data on this region, the present study, conducted in the Brazilian “Cerrado” biome and tropical savanna climate (Aw), obtained such data through the observation, during two consecutive years, of factors involved on parasitic and free living phases of its cycle, also evaluating the behavior of this strain regarding evolution of its resistance/susceptibility profile against acaricides. Observing the parasitic phase of the Southern Cattle Tick, it was possible to detect adaptations of this ixodid to climate changes, with five annual generations in two consecutive years being registered for the first time in literature, without significant correlations between its period parasitizing bovines and rain levels, environmental and soil level temperatures and relative air humidity. The free living period of its cycle was affected by climatic variables, with positive correlation between rainfall and the period before oviposition, and negative correlations between temperatures and the period before oviposition, egg incubation and period before hatching, and between relative air humidity and egg incubation and the period before larval hatching. Obtained data indicate that the dry season (autumn and winter) is more favorable for maintenance of the Southern Cattle Tick on the environment, as well as presenting highest parasitic burdens in hosts. Population dynamics calculated reinforces the adaptations of such ixodid to climate changes, leading to the existence of 5.212 yearly generations even in distinct climatic and environmental conditions, varying between 2.6 and 8.3 generations per year. Considering such data, a specific strategic control methodology was proposed, treating animals between the second half of spring and the first half of summer (October to February). Such treatments in rainy seasons would lead to smaller populations on the dry season, also reducing the “spring rise”. Analysis of efficacy of different chemical compounds using the Larval Packet Test generated contrasting results, with high efficacy indexes registered for pyrethroids and organophosphates, with variations in amitraz efficiency. Such values lead to a questioning of the applicability of such technique in monitoring resistance. Future studies must be proposed, analyzing the real efficacy of Larval Packet Tests, confronting different in vivo and in vitro methodologies; comparing population dynamics of such ixodid in different pastures, husbandry methods, stocking rates, altitudes and biomes; confirming the efficacy of the proposed strategic control method and, above all, confirming the possibility of observing more than eight R. microplus yearly generations in ideal climatic conditions. / 2014/14820-2

Les amibes sont des organismes unicellulaires eucaryotes, de 10 à 300 µm, pouvant vivre sous forme parasite ou évoluer librement dans les sols et les milieux aquatiques ou encore adopter l’une ou l’autre forme en fonction de l’environnement. Certaines amibes libres sont hautement pathogènes pour les animaux et l’homme, en particulier Naegleria fowleri qui se développe dans les eaux naturellement chaudes à des températures comprises entre 27 et 45°C. Cette espèce est responsable d'une encéphalite généralement mortelle, la méningo-encéphalite amibienne primitive (MEAP), dont un cas a été recensé en Guadeloupe en 2008. Un enfant de 9 ans ayant contracté la maladie est décédé quelques jours après un bain dans les eaux chaudes de Dolé, sur la commune de Gourbeyre. Notre travail de Thèse à l’Institut Pasteur, en collaboration avec l’ARS, a permis d’initier un programme de recherche sur ces amibes pathogènes très peu connues sur notre territoire, afin de mieux évaluer le risque lié aux baignades dans les sources géothermales de la Guadeloupe. Nous avons développé et mis au point une méthode de détection et de dénombrement des amibes faisant appel à la biologie moléculaire qui est aujourd’hui appliquée en routine au sein de notre laboratoire. Depuis Janvier 2011, un suivi mensuel a révélé la présence des amibes thermophiles et de l’amibe pathogène dans presque tous les sites analysés (Ravine Chaude, Bains de La Lise et Bain du Curé à Pigeon, Bains Jaunes, Bain de Dolé, Bain de Capes, Bain des Amours, Bain de la rivière Grosse-Corde, Chute du Carbet, Bain de Morphy et Bain chaud de Matouba), à l’exception des eaux chaudes soufrées et/ou salées de Sofaïa et de l’Anse Thomas à Bouillante. Le séquençage des produits de PCR obtenus et déposés dans Genbank nous a permis de confirmer l’appartenance de cette souche de N. fowleri, au type 3 Euro-américain, identique à celui détecté lors de l’accident de 2008 (Moussa et al. 2013). Le nombre d’amibes pathogènes retrouvées varie de 2 à 30 amibes/litre selon les bains, sans dépasser la limite de 100 amibes/litre recommandée par les autorités sanitaires. En dépit de ces faibles concentrations, une surveillance régulière des bassins est nécessaire. Sur l’ensemble de l’année 2011-2012, l’espèce pathogène N. fowleri a été la plus fréquemment rencontrée par rapport aux espèces non pathogènes N. lovaniensis et Hartmanella sp. Ces données de surveillance ont amené l’ARS et les communes concernées à organiser une campagne de sensibilisation à destination des populations locales et touristiques, reposant sur l’installation de panneaux de prévention à proximité des principaux sites où N. fowleri a été retrouvée.La présence régulière de N. fowleri tout au long de l’année dans la plupart des bains chauds et notamment dans les bains les plus fréquentés, a orienté notre travail sur la recherche de l’origine de leur contamination. Nous avons découvert que les sources géothermales ne sont pas contaminées à leur émergence, mais que les amibes proviennent de la terre en amont des bassins. Ce résultat qui montre que le sol est le réservoir naturel des amibes, nous a permis de proposer aux collectivités un moyen de lutte efficace en canalisant l’eau depuis l’émergence jusqu’au bassin, sans passer par le sol. / Amoebas are eukaryotic unicellular organisms, measuring from 10 to 300 µm, being able to live under a parasite form or to evolve freely in soils and aquatic media. They can even adopt either form depending of the environment. Some free living amoebas are highly pathogenic for animals and humans, especially Naegleria fowleri which develops in naturally hot waters at temperatures between 27 and 45°C. This species is responsible for an encephalitis generally lethal, the primary amoebic meningoencephalitis (PAM), a case of which occured in Guadeloupe in 2008. A 9-year-old child having contracted the disease, died a few days after a bath in the hot waters of Dolé, in Gourbeyre. Our Thesis at the Institut Pasteur of Guadeloupe, in association with the ARS, initiated a research program on these pathogenic amoebas poorly known in our territory, to better estimate the risk to contract the disease while bathing in geothermal recreational waters of Guadeloupe. We developed and worked out a method of detection and enumeration of amoebas using the molecular biology, which is currently applied in routine in our laboratory. Since January, 2011, a monthly monitoring of the baths revealed the presence of thermophilic free living amoebas and pathogenic amoeba in almost all the analyzed sites (Ravine Chaude, La Lise, Bain du Curé à Pigeon, Bains Jaunes, Bain de Dolé, Bain de Capès, Bain des Amours, Bain de la rivière Grosse-Corde, Chutes du Carbet, Morphy and the hot bath of Matouba), with the exception of sulphurated and/or salty hot waters of Sofaïa and the Anse-Thomas in Bouillante. The sequencing of the PCR products obtained were deposited in Genbank and confirmed that the Guadeloupean N. fowleri belonged to the Type-3 Euro-American, identical to that detected in the patient in 2008 (Moussa et al. 2013). The number of pathogenic amoebas varied from 2 to 30 amoebas / liter according to the baths, without exceeding the limit of 100 amoebas / liter recommended by the health authorities. In spite of this rather low concentration the baths require a regular surveillance. On the full year 2011-2012, the pathogenic species N. fowleri was the most frequently encountered species followed by N. lovaniensis and Hartmanella sp. These data of the surveillance led the ARS and the municipalities concerned to organize an awareness campaign destinated to the local and tourist population, based on the installation of prevention panels near the main sites where N. fowleri was found. The regular presence of N. fowleri during the year in most of the hot baths, especially the most frequented ones, leads us to look for the origin of their contamination. We discovered that geothermal springs are not contaminated at their emergence, but that amoebas come from the soil upstream the baths. This result which shows that soil is the natural reservoir of amoebas, allowed us to propose to the authorities effective means of prevention by installing pipes to carry the water from the emergence to the bath, without touching the soil.

La contamination microbienne des units de soins dentaires (USD) est connue depuis les années 60. L'eau circule à l'intérieur des USD dans des conditions favorables au développement d'un biofilm (faible débit, nature des surfaces, stagnation). Ce biofilm, réservoir de micro-organismes potentiellement pathogènes, peut représenter un risque infectieux pour les patients et le personnel dentaire exposés à l'eau et aux aérosols générés lors des soins dentaires, en particulier s'ils sont immunodéprimés.Des micro-organismes provenant de l'eau, tels que les amibes libres, peuvent être retrouvés dans ce biofilm. Des protozoaires ubiquitaires de l'environnement du genre Acanthamoeba ou Hartmannella, connus comme pathogènes opportunistes chez l'Homme (kératites, méningo-encéphalites) et ayant la capacité de servir d'hôte pour le développement intracellulaire de certains microorganismes pathogènes (ex : Legionella pneumophila), ont en effet été isolés dans l'eau des USD.D'autre part, des micro-organismes provenant de la cavité buccale d'un patient peuvent également se retrouver dans le système d'eau des USD, en même temps que des traces de salive et/ou de sang, suite à un dysfonctionnement ou un mauvais entretien des valves anti-reflux des porte-instruments rotatifs. Les levures du genre Candida sont des commensaux du tube digestif humain, pathogènes opportunistes notamment responsables d'infections oro-pharyngées, et parfois retrouvées dans les USD.Ce travail a consisté d'une part en l'étude de la capacité de deux amibes libres : A. castellanii et H. vermiformis, ainsi que de trois espèces de Candida : C. albicans, C. glabrata et C. parapsilosis, à survivre dans l'eau, en présence ou non de salive. Les résultats montrent une influence dose-dépendante et espèce-dépendante de la salive sur la survie des trois levures, et aucun effet sur la viabilité des amibes. Des interactions ont pu être mises en évidence entre amibes libres et levures : A. castellanii est capable d'internaliser puis de digérer les trois espèces de levures, induisant leur élimination rapide, indépendamment de la présence de salive. En revanche, H. vermiformis permet la survie et la prolifération de Candida spp. dans l'eau, même en l'absence de salive.Enfin, dans une démarche de prévention et de lutte contre le risque infectieux lié à l'eau des USD, l'efficacité de différents traitements chimiques communément utilisés : le chlore (NaOCl), le peroxyde d'hydrogène (H2O2) et l'Oxygenal 6©, a été étudiée sur les différentes espèces de Candida et d'amibes libres. Ces traitements montrent une efficacité variable : le chlore requiert l'utilisation de concentrations élevées (>26 ppm) et peu compatibles avec l'usage courant des USD. Le H2O2 ne présente pas d'activité significative dans les conditions testées (de 0.07% à 0.9% v/v). En revanche, l'Oxygenal 6© apparaît le plus efficace pour l'éradication des levures du genre Candida et des amibes libres dans l'eau (dès 0.05%). / Microbial contamination of dental unit waterlines (DUW) is known since the 60's. Water circulates throughout DUW with environmental conditions encouraging biofilm development (low flow, surface material, stagnation). This biofilm, which is a reservoir of potentially pathogenic micro-organisms, may represent an infectious risk for patients and dental staff exposed to water and aerosols generated during dental cares, in particular for immunocompromised persons. Micro-organisms coming from water, such as free-living amoebae (FLA), may be isolated in this biofilm. Protozoa belonging to Acanthamoeba or Hartmannella genera are ubiquitous in the environment; they are known to be opportunistic pathogens for Human (keratitis, meningo-encephalitis), to encourage intracellular development of some pathogenic micro-organisms (for example: Legionella pneumophila), and they have already been isolated in DUW.On the other hand, micro-organisms coming from the oral cavity of an infected patient may also be isolated in DUW water, mixed with saliva traces and/or blood, mainly because of the dysfunction or the poor maintenance of anti-retraction valves. Candida yeasts colonize human's oral cavity and digestive tract as commensals or opportunistic pathogens, thus implicated in oro-pharyngeal infections; they are sometimes isolated in DUW.This work focused first on the study of the survival capacity of two species of FLA: A. castellanii and H. vermiformis, and three species of yeasts: C. albicans, C. glabrata and C. parapsilosis, in water, with or without saliva. Results showed that the addition of saliva permitted both survival and proliferation of all three tested Candida species whereas no effect was observed on FLA growth. Then, interactions have been demonstrated between FLA and yeasts: A. castellanii were able to internalize and then digest the three tested yeasts species, inducing their rapid degradation, independently of saliva presence. Conversely, H. vermiformis were able to promote Candida survival and proliferation in water, with or without saliva.Finally, in order to prevent and fight against infectious risk associated with DUW water, the efficacy of commonly used chemical treatments: chlorine (NaOCl), hydrogen peroxide (H2O2) and Oxygenal 6©, was studied against the three species of Candida and the two species of FLA. These treatments showed a variable efficacy: chlorine was effective only using the highest tested concentrations (> 14 ppm), which are not compatibles with DUW use. H2O2 displayed no significant activity in the experimental conditions (0.07% to 0.9% v/v). Oxygenal 6© seemed to be the more effective for eradication of Candida yeasts and FLA, in water (even with 0.05% v/v).

Les amibes libres sont des protozoaires retrouvés dans de nombreux environnements où ils ingèrent par phagocytose des bactéries, des champignons, des virus ou d'autres protozoaires. Le modèle d'étude principal de cette thèse, divisée en deux grandes parties, a été Acanthamoeba castellanii. La première partie de la thèse a concerné l'étude de la préférence trophique des amibes, en présence de différents micro-organismes. Parmi ceux-ci, deux bactéries, Klebsiella pneumoniae et Staphylococcus aureus, se sont montrées les plus attractives pour les protozoaires étudiés. Des extraits bactériens ont été fractionnés et leur étude a permis de mettre en évidence la nature protéique des composés chimioattractifs impliqués dans ce dialogue intergenre. Certaines données de la littérature ont rapporté les similitudes entre A. castellanii et d'autres cellules phagocytaires que sont les macrophages. La seconde partie de la thèse a permis de comparer les activités de phagocytose d'A. castellanii et de la lignée macrophagique Thp-1 vis-à-vis de quatre micro-organismes : le champignon filamenteux Aspergillus fumigatus, les bactéries Klebsiella pneumoniae et Staphylococcus aureus, et un Adénovirus sérotype B3. L'influence des deux types de cellules phagocytaires sur la croissance des micro-organismes a également été étudiée. Ces travaux ont permis de mettre en évidence des différences de comportements des amibes libres par rapport aux macrophages vis-à-vis de micro-organismes pathogènes, montrant qu'il n'est pas toujours possible d'extrapoler les résultats d'études amibes libres/micro-organismes aux relations macrophages/micro-organismes. / Free living amoebae (FLA) are protoza found in various environments where they can feed by phagocytosis on bacteria, fungi, viruses or other protozoa. Acanthamoebae castellanii was used as the main model in this thesis, divided in two parts. The first part of the thesis relied on the trophic preference of amoebae, in presence of different microorganisms. Amongst them, two bacteria, Klebsiella pneumoniae and Staphylococcus aureus, appeared as the most attractive for the studied protozoa. Bacterial extracts have been fractionned and their study has shown the protein nature of the chemoattractants involved in this interspecies crosstalk.Literature data have reported similarities between A. castellanii and other phagocytic cells such as macrophages. The second part of the thesis allowed us to compare phagocytic activities of A. castellanii and Thp-1 macrophagic cells towards four microorganisms: the filamentous fungus Aspergillus fumigatus, the bacteria Klebsiella pneumoniae and Staphylococcus aureus and an Adenovirus B3 serotype. The influence of the two phagocytic cells on the microorganisms' growth has also been investigated. This has evidenced the behavior differences between FLA and macrophages towards pathogenic microorganisms, showing that results obtained by studying amoebae and microorganisms relationships could not be extrapolated in all cases to the relationships between macrophages and microorganisms.

Topic of this master thesis is classification of free living data sensed with Faros. Faros is small compatible device which measure ECG and 3-axes accelerometric data. The first part of master thesis is find out how automatically measure free living activities by accelerometer and ECG. In next part was measured data of 8 activities from 10 probands. Automatic algorithms are made for this data in Matlab. This algorithms were used for this datasets and compare with manually recorded references. In the end of master thesis data were statistically evaluated.

Dans l'objectif d'anticiper et de réduire la prolifération de l'amibe pathogène Naegleria fowleri dans les circuits de refroidissement de certaines centrales électriques, notre travail vise à mieux comprendre l'écologie de cette amibe dans des environnements complexes tels que les biofilms d'eau douce récemment reconnus comme niche écologique préférentielle des amibes libres. Des essais de laboratoire ont été réalisés pour déterminer l'impact des facteurs environnementaux naturels et anthropiques: température, nature du matériau support de la formation du biofilm, charge nutritionnelle et monochloramination sur le comportement et le devenir de Naegleria fowleri dans le biofilm. Ces travaux ont permis de démontrer que la survie, l'implantation, la croissance, le maintien et le déclin de Naegleria fowleri dans les biofilms sont principalement gouvernés par la concomitance des facteurs température et ressource nutritive. Les autres facteurs: nature du matériau, désinfection à la monochloramine et compétition amibienne, se présentent plutôt comme des paramètres de perturbation ou d'inhibition de cette dynamique. Par ailleurs, les résultats obtenus sur la colonisation du biofilm par les amibes confortent le rôle prépondérant de cet habitat comme réservoir naturel des amibes libres et Naegleria fowleri / This study is aiming at preventing and reducing the proliferation of the pathogenic free-living amoeba Naegleria fowleri in several power plant cooling circuits. This work contributes to provide a better understanding of the ecology of this amoeba in complex environments such as freshwater biofilms, which recently has been recognized as privileged ecological niche for free-living amoebae. Laboratory tests were conducted to determine the impact of environmental factors such as temperature, type of support material for the biofilm formation, nutritional resources and monochloramination treatment on the behavior and the fate of Naegleria fowleri in the biofilm. This work has demonstrated that the survival, implantation, maintain, growth and decline of Naegleria fowleri in biofilms are mainly governed by a combination of the temperature and nutritional resource factors. The other factors: type of support material, monochloramination treatment, and amoebic competition, appeared rather as disruptive or inhibitory parameters of this dynamic. Moreover, the obtained results for the amoebic colonization of the biofilm matrix confirm the crucial role of this habitat as natural reservoir for free-living amoebae and Naegleria fowleri

The Incomati River Estuary is prone to pollutants from anthropogenic activities such as agricultural and industrial activities in the upper catchments. The main aim of the study was to use free-living nematodes as pollution indicators in the Incomati River Estuary. The main objectives were to determine the relationship between nematodes assemblage and environmental variables, and to identify environmental factors that play a role in nematodes community structuring. Lastly, it was to identify free-living nematode genera that can be used as pollution indicators in the Incomati River Estuary. Four sites were selected following the salinity gradient of the Incomati River Estuary. Site E1 with a salinity range of 0-3NST (Oligohaline Zone), E2 with a salinity 3-5NST (Euhaline Zone), E3 with a salinity 6-18NST (Mesohaline Zone), and E4 with 20-27 NST (Polyhaline Zone) were selected and monitored bi-monthly from June 2017 to April 2018. Two sediments samples were collected per site during neap tide using a handheld perplex corer which was 1m long with a 3.6 diameter and 10cm penetration height. Plastic bottles with a height of 13cm and a diameter of 7cm were used to store the sediment samples. One of the two sediment samples was used for free-living nematodes, and the other bottle was used for the analysis of environmental factors. All environmental factors were analysed at Labserve Laboratory, Mbombela Town, Mpumalanga Province. Sediment particle size and organic matter analyses were done following the procedure set by Parker (1983) and Buchanan (1971) respectively. Metal analysis was done following the procedure used by Gyedu-Ababio et al.1999. Nutrients were done using different methods. For nitrates (NO3) analysis, a copper cadmium method by Bate and Heelas, 1975 was used, while a method designed by Strickland and Parson, 1972 was used to analyse orthophosphate. A mixed acid digestion procedure of Oles and Dean 1965 was followed for total phosphate. A method by Lorenzen and Jeffrey, 1980 was used for the analysis of chlorophyll-a. Heterotrophic bacteria analysis were done following a procedure by (Atlas, 1997). Nematodes were extracted using a method by Furstenberg et al.1978, with sucrose as a separating agent. Nematodes were counted following a procedure by Giere, 1993. Nematodes feeding types were investigated using Wieser, 1953 procedure. Different statistical packages including PRIMER version 6 were used to analyse the data. A Bray-Curtis Cluster analysis indicated a similarity between sites E1 (Oligohaline Zone) and E2 (Euhaline Zone), and between site E3 (Mesohaline Zone) and E4 (Polyhaline Zone) which was attributed to similar sediment particle sizes distribution within the sites. There was no significant difference (p>0.05) of sediments particle size between the sites. The highest concentration of metals was found at site E2 which was situated in the Euhaline Zone, whilst the second highest concentration was found at site E1 which was situated in the Oligohaline Zone. A PERMANOVA analysis indicated that there was a significant difference (p<0.05) of Metal concentration between sites sampled. The PCA analyses indicated that there was a positive correlation between Metals and Sediment Particle Size such as Granules. It was observed that sediment particle size and organic matter influenced the distribution of metals in the Estuary. The highest concentration of chlorophyll-a and nitrates (NO3) were found at site E3 which was situated in the Mesohaline Zone, and the second highest was found at site E4 which was situated in the Polyhaline Zone. There was a positive correlation between Heterotrophic bacteria and environmental factors such as zinc, fine sand, very fine sand and mud. This indicated that certain metals and sediment particles size played a role in structuring food source for meiofauna, especially nematodes. The number of free-living nematodes were found to decrease towards site E1. This indicated that salinity influenced the diversity and density of free-living nematodes in the estuary. Site E2 had the lowest diversity and richness followed by site E1. The lower diversity, richness and Maturity Index at site E2 and E1 indicated that these sites were under stress. A Bray-Curtis Cluster analysis indicated that there was a spatio-temporal variation of diversity and density of free-living nematodes in the estuary. All four nematodes feeding types were found in the Estuary and feeding type 1B was the dominant feeding type at the sites, followed by feeding type 2A. The highest number of feeding type 1B (non-selective deposit feeders) was identified at site E2. The life strategy characterisation (colonizer- persisters) indicated that site E2 was dominated by colonizer and intermediate genera (c-p 2 and 3), which indicated that the site was under stress. The study found that genera such as Terschellingia and Theristus were pollution indicators because they were found in higher abundance at a site that was mostly polluted by metals, organic matter, and total phosphate. Further studies in other River Estuaries in South Africa and SADC should be undertaken to add to the findings of the current study. / Environmental Studies / Ph. D. (Environmental Sciences)

Les espèces bactériennes opportunistes responsables d'infections nosocomiales chez l'Homme se rencontrent dans les environnements terrestres et aquatiques. Elles sont très souvent caractérisées par une résistance naturelle aux antibiotiques leur conférant un phénotype appelé Multi-Drug Resistant (MDR). L'efflux d'antibiotiques via des pompes, est un des mécanismes à l'origine de cette multi-résistance. Alors que le rôle de ces pompes chez des bactéries isolées en milieu clinique est connu, aucune donnée n'est disponible concernant leur rôle chez les bactéries associées avec d'autres organismes eucaryotes du sol tels que les amibes. Pourtant des données de la littérature indiquent que les amibes, jusqu'alors principalement connues pour leur rôle prédateur de bactéries sont susceptibles d'héberger des bactéries " résistantes " aux amibes (ARB). Parmi ces ARB, des pathogènes opportunistes ont été identifiés dont certains sont connus pour être porteurs de pompes à efflux. Les pompes à efflux de ces bactéries pourraient donc intervenir dans l'adaptation aux amibes du sol. Afin de vérifier cette hypothèse, nous avons, dans un premier temps, isolé et identifié la flore amibienne et les ARB de différents sols. Parmi les ARB identifiées, Stenotrophomonas maltophilia, Pseudomonas aeruginosa et Burkholderia cepacia sont caractérisées par des propriétés d'antibiorésistance contrastées et de virulence élevées. Des études d'interaction ont montré que S. maltophilia se multipliait dans des amibes axéniques et que des pompes à efflux Sme étaient surexprimées. Par ailleurs des molécules sécrétées par l'amibe stimulent la croissance bactérienne et des études préliminaires de profilage métabolique ont montré la présence de différents métabolites secondaires produits par l'amibe au cours de l'interaction avec S. maltophilia pouvant jouer un rôle dans l'expression des pompes à efflux / The opportunistic bacterial species, responsible for nosocomial infections in humans, occurs in terrestrial and aquatic environments. They are often characterized by natural resistance to antibiotics giving them a phenotype called Multi-Drug Resistant (MDR). The efflux of antibiotics via pumps, is one of the mechanisms behind this multi-resistance. While the role of these pumps in bacteria isolated from hospital is known, no data are available regarding their role in bacteria associated with other soil eukaryotic organisms such as amoebae. Nevertheless, data from the literature indicate that amoebae, mainly known to be predators of bacteria, are likely to harbour "amoeba resistant bacteria” (ARB). Among these ARB, opportunistic pathogens have been identified, some of which are known to be carriers of efflux pumps. The efflux pumps of these bacteria could thus interfere in the adaptation to soil amoebae. In order to verify this hypothesis, we first isolated and identified the amoebal population and the ARB of different soils. Among the identified ARB, Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Burkholderia cepacia are characterized by high contrast antibiotic resistance and high virulence. Interaction studies showed that S. maltophilia could multiplied in axenic amoebae and Sme efflux pumps were overexpressed. Furthermore, molecules secreted by the amoeba stimulate bacterial growth and preliminary studies of metabolic profile have shown that production of various secondary metabolites by the amoeba during the interaction with S. maltophilia could play a role in the efflux pumps expression

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