Le système de sécrétion de type VI (SST6) est un complexe multi-protéique permettant l’export d’effecteurs. Ce mécanisme est impliqué à la fois dans la virulence envers les cellules eucaryotes, dans l’activité antibactérienne mais également dans l’acquisition d’ions présents dans ’environnement. Ainsi, le SST6 joue un rôle important dans l’adaptation et la compétition, éléments essentiels dans la colonisation et la persistance au sein d’une niche écologique. Actuellement, très peu d’études portent sur l’importance du SST6 chez des souches environnementales, contrairement aux nombreuses études portant sur des pathogènes tels que Pseudomonas aeruginosa, Burkholderia thailandensis, Vibrio cholerae ou Escherichia coli. Mon sujet de recherche avait pour objectif de caractériser le ou les rôles du SST6 de la souche environnementale Pseudomonas fluorescens MFE01. Ces travaux ont permis d’appréhender certaines fonctions du SST6 de cette souche. Le génome de MFE01 ne comporte qu’un seul cluster de gènes du SST6 où sont regroupés les gènes codant pour la machinerie du SST6 (le « core-component ») à l’exception des gènes hcp. Les protéines Hcp sont des éléments structuraux du SST6 dont elles forment le tube interne qui permet le transfert des effecteurs. Différents gènes hcp sont disséminés sur le chromosome et parmi ces « hcp » orphelins, hcp2 et hcp3 codent respectivement pour les protéines Hcp2 et Hcp3. Ces deux Hcp sécrétées par le SST6, sont associées à l’activité antibactérienne de MFE01 sur différentes souches pathogènes et environnementales, tels que P. aeruginosa, P. fluorescens MFN1032 et Pectobacterium atrosepticum. La protéine Hcp1, codée par le gène orphelin hcp1, est impliquée dans l’inhibition de mobilité de souche compétitrice. Hcp1 permettrait la sécrétion d’au moins deux toxines qui perturberaient l’assemblage du flagelle. Chez MFE01Δhcp1 et MFE01ΔtssC (TssC est un élément de la gaine contractile du SST6), ces toxines seraient accumulées dans le cytoplasme, inhibant ainsi ’assemblage de leur propre flagelle. La surproduction du régulateur FliA, qui contrôle notamment l’assemblage du filament flagellaire, restaure la mobilité chez ces deux mutants. En parallèle, le SST6 de la souche MFE01 est essentiel à la formation et la maturation de biofilm mais également à la compétition bactérienne en biofilm mixte. Ce système interviendrait dans la communication bactérienne indispensable au comportement social, requis lors de l’élaboration des biofilms. / Type VI secretion system (T6SS) is a multiproteic apparatus that secreted proteinaceous effectors. T6SS participate in a variety of functions, whose eukaryote virulence, antibacterial activity or metal ion uptake. These capacities conferring an advantage in adaptation and competition, crucial to colonization or persistence within ecological niche. As well, only a few studies have focused on the T6SS functions of environmental strains, contrary to numerous studies dealing with pathogens as Pseudomonas aeruginosa, Burkholderia thailandensis, Vibrio cholerae or Escherichia coli. The purpose of my research project was to characterize the T6SS function(s) of the environmental strain Pseudomonas fluorescens MFE01. This work had led to understand the various functions of T6SS of MFE01 strain. This strain has a single T6SS cluster where all the core component proteins were gathered, except hcp genes. Three orphan hcp genes where found and are scattered in genome. Hcp proteins form the inner tube allowing effectors secretion. Both Hcp2 and Hcp3 proteins were involved in antibacterial activity on pathogens or environmental strains like P. aeruginosa, P. fluorescens or Pectobacterium atrosepticum. Characterization of Hcp1 proteins role constituted a major focus of this project. Hcp1 proteins participate to motility inhibition of competitive strains through T6SS. Hcp1 may be associated with secretion of at least two toxins perturbing the flagellar filament assembly. In MFE01Δhcp1 and MFE01ΔtssC mutants (Tss is a contractile sheath constituent), these toxins may be accumulated into cytoplasm and perturb assembly of their own flagella. Interestingly, overproduction of FliA flagellar regulator, which controls assembly of flagellar filament, restores motility of both mutants. Simultaneously, T6SS of MFE01 strain contributes to maturation and biofilm formation but also in bacterial competition within mixed biofilm. T6SS may be a mean of bacterial communication and thus coordinate a social behavior, primordial for biofilm formation.

Submitted by Alexandre Sousa (alexandre.sousa@incqs.fiocruz.br) on 2015-06-29T12:53:56Z No. of bitstreams: 1 Tese_Renato_Silva.pdf: 1149696 bytes, checksum: 90cca601f940d32033deeaeb17255312 (MD5) / Approved for entry into archive by Alexandre Sousa (alexandre.sousa@incqs.fiocruz.br) on 2015-06-29T12:54:09Z (GMT) No. of bitstreams: 1 Tese_Renato_Silva.pdf: 1149696 bytes, checksum: 90cca601f940d32033deeaeb17255312 (MD5) / Approved for entry into archive by Alexandre Sousa (alexandre.sousa@incqs.fiocruz.br) on 2015-06-29T12:54:23Z (GMT) No. of bitstreams: 1 Tese_Renato_Silva.pdf: 1149696 bytes, checksum: 90cca601f940d32033deeaeb17255312 (MD5) / Made available in DSpace on 2015-06-29T12:54:23Z (GMT). No. of bitstreams: 1 Tese_Renato_Silva.pdf: 1149696 bytes, checksum: 90cca601f940d32033deeaeb17255312 (MD5) Previous issue date: 2014 / Fundação Oswaldo Cruz. Instituto Nacional de Controle de Qualidade em Saúde / S. epidermidis é o principal agente de infecções associadas a dispositivos médicos implantados, sendo sua habilidade para formar biofilme em superfícies inertes o fator determinante para a persistência desse micro-organismo. Neste estudo avaliamos 52 isolados clínicos desta espécie quanto à susceptibilidade a antimicrobianos, produção de biofilme/natureza química, presença de genes relacionados à virulência (atlE, capB,aap, embp, bhp, IS256 e IS257), e o efeito de concentrações subinibitórias (sub-CIMs) de etanol e clorexidina na produção de biofilme. Além disso, algumas das amostras biofilme-positivas foram estudadas quanto ao efeito de sub-CIMs destes antissépticos na expressão de icaA, icaR, sigB e sarA. Mais de 60% das amostras apresentaram resistência para ≥ 10 drogas e as amostras produtoras de biofilme mostraram, no geral, maior percentual de resistência a antimicrobianos. No teste em placa de microtitulação (MTP), 23 amostras foram produtoras de biofilme, sendo 14 de natureza polissacarídica, 8 proteica e 3 indeterminada. No teste em Ágar Vermelho Congo, somente amostras produtoras de biofilme polissacarídico apresentaram reação positiva. Genes do operon ica foram detectados em 23 isolados, sendo 17 destes classificados como produtores e 6 como não produtores de biofilme no MTP. A frequência dos outros genes relacionados à produção de biofilme foi: embp (69%), aap (29%) e bhp (12%), não sendo detectada correlação entre estes e a produção de biofilme do tipo PIA-independente. Os genes aap (29%) e IS256 (23%) mostraram correlações significativas com: produção de biofilme, presença de ica, perfil biofilme+/ica+, e produção de nível forte de biofilme. O gene IS256 foi ainda correlacionado significativamente com resistência a alguns antimicrobianos. Sub-CIMs de etanol (2 e/ou 4%) determinaram aumento na produção de biofilme em 15 das 17 amostras PIA-dependentes e nas 8 PIA-independentes, mas não induziram produção de biofilme em amostras originalmente não produtoras. Ao contrário do etanol, sub-CIMs de clorexidina não somente não induziram produção, como determinaram redução da produção de biofilme nas amostras biofilme-positivas. Nas amostras PIA-dependentes, o etanol (1%) acarretou aumento da expressão relativa de icaA e redução da expressão de icaR, além de aumento da expressão dos reguladores globais (sarA e sigB), enquanto a amostra PIA-independente mostrou redução na expressão destes reguladores globais. Ao contrário do etanol, a clorexidina (0,5 μg/mL) determinou aumento da expressão de icaR e redução de icaAnas amostras PIA-dependentes, além de redução na expressão de sarA e sigB na amostra PIA-independente. Os resultados indicaram que a produção de biofilme mostrou-se associada com alguns dos potenciais marcadores de virulência, sendo também evidenciada associação de alguns desses marcadores com resistência a certos antimicrobianos. As amostras PIA-dependentes foram prevalentes, destacando-se, porém, o encontro de número expressivo de amostras PIA-independentes. Os genes aap,embp e bhp não se mostraram correlacionados com a produção de biofilme proteico, indicando existência de outros mecanismos envolvidos na formação desse tipo de biofilme. Nas amostras PIA-dependentes, etanol e clorexidina mostraram efeitos opostos na expressão de icaA e icaR, corroborando dados fenotípicos previamente obtidos, e enfatizando a necessidade de ampliação do estudo da clorexidina, tendo em vista o potencial de aplicação prática deste achado. / S. epidermidis is the main agent of infections associated with implanted medical devices, being its ability to form biofilms on inert surfaces the determinant factor for the persistence of this microorganism. Fifth two clinical isolates of this species were evaluated for susceptibility to antimicrobials, biofilm production/chemical nature, presence of genes related to virulence (atlE, capB, aap, embp, bhp, IS256 andIS257), and the effect of subinibitory concentrations (sub-MICs) of ethanol and chlorhexidine in biofilm production. Moreover, some of biofilm-positive samples were studied for the effect of sub-MICs of these antiseptics in the expression of icaA, icaR, sigB and sarA. Over 60% of the samples showed resistance to ≥ 10 drugs and biofilm producers showed, in general, a higher percentage of antimicrobial resistance. In microtiter plate test (MTP), 23 strains were biofilm producers, being 4 of polysaccharide nature, 8 proteinaceous and 3 undetermined. In Congo Red Agar test, only biofilm polysaccharide producer strains showed a positive reaction. ica operon genes were detected in 23 isolates, being 17 of these classified as producers and 6 as non-biofilm producers in MTP. The frequency of other production-related biofilm genes was: embp (69%), aap (29%) and bhp (12%), no being detect a correlation between them and the production of PIA-independent biofilm. The aap (29%) and IS256 (23%) genes showed significant correlations with: biofilm production, presence of ica biofilm, biofilm+/ica+ profile, and strong level of production of biofilm. The IS256 gene was also significantly correlated with resistance to some antibiotics. Sub-MIC of ethanol (2 and / or 4%) led to an increase in biofilm production in 15 of 17 samples PIA-dependent and in the 8 PIA-independent, but did not induce biofilm production in not originally producing samples. Unlike ethanol, sub-MICs of chlorhexidine not only did not induce production as determined reduction of biofilm production in biofilm-positive samples. In PIA-dependent strains, ethanol (1%) caused an increase in the relative expression of icaAand reduced expression of icaR, in addition to increased expression of global regulators (sarA and sigB), while the PIA-independent strain showed reduction in the expression of these global regulators. Unlike ethanol, chlorhexidine (0.5 mg/mL) determined increased expression of icaR and reduction of icaA in PIA-dependent strains, besides a reduction in the expression of sarA and sigB in the PIA-independent strain. The results indicated that biofilm production was associated with some of potential virulence markers, and also evidenced some combination of these markers and resistance to certain antibiotics. The PIA-dependent strains were prevalent, highlighting, however, the encounter of significant number of PIA-independent strains. The aap, embp and bhp genes were not correlated with the production of proteinaceous biofilm, indicating the existence of other mechanisms involved in the formation of such biofilms. In PIA-dependent strains, ethanol and chlorhexidine showed opposite effects on the expression of icaA and icaR, corroborating phenotypic data previously obtained, and emphasizing the need to expand the study of chlorhexidine, in view of the potential of practical application of this finding.

Dans le cadre de la conservation du patrimoine, les micro-organismes se développant sous forme de biofilm sont souvent considérés comme des agents entraînant des problèmes esthétiques et de détérioration du support colonisé. L’objectif général de cette thèse est l’utilisation de la lumière UV-C comme méthode de traitement des biofilms. Dans le but de comprendre la diversité des biofilms, les communautés bactériennes, fongiques et des protistes autotrophes ont été étudiées à l’aide d’une technique de séquençage haut débit. Puis, afin de comprendre les effets des UV-C sur les micro-algales (Chlorella sp.), des essais en laboratoire ont permis de caractériser les réponses physiologiques algales (mort cellulaire, dégradation de la chlorophylle, état de photosystème II, etc.) suite à différents traitements aux UV-C. Tous les dommages observés au niveau cellulaire et moléculaire (dont la mort cellulaire et le « bleaching » de la chlorophylle) ont permis d’optimiser la méthode de traitement. Dans le but de s’assurer de l’innocuité du traitement aux UV-C sur le support des biofilms (peintures pariétales), des pigments et des liants, utilisés à la préhistoire, ont été fortement irradiés. Les résultats ont montré que les composés inorganiques sont insensibles aux UV-C au contraire des molécules organiques. Enfin, le traitement UV-C a démontré son efficacité dans une grotte touristique en permettant d’éradiquer tous les biofilms. De plus, aucune recolonisation n’a été observée deux ans après le traitement, démontrant que la lumière UV-C est le traitement le plus écologique à ce jour. / Development of biofilm on monument heritage are often considered as agents leading to aesthetic issues and biodeterioration of their support. The aim of this study is the use of UV-C light as alternative treatment against Lampenflora. Bacterial, algal and fungal communities were studied using new generation sequencing approach. Following UV-C treatments, physiological responses of Chlorella sp. were studied in laboratory (cell death, chlorophyll degradation, photosystem II status, etc.). Damages at cellular and molecular levels (cell death, bleaching of the chlorophyll) were taken into consideration to optimize the UV-C treatment. Then, to ensure the safety of UV-C for biofilms support (parietal paintings), several pigments and binders, used by prehistoric human, were highly irradiated. The results showed that UV-C radiations were not deleterious for inorganic compounds, while a color change was observed on organic binders. Finally, UV-C treatment has proven its effectiveness in La Glacière show cave by eradicating all biofilms. In addition, no recolonization was observed two years after treatment, showing that this treatment, which is the most environmental friendly to date, is effective over time.

The objective of this study was to evaluate the antimicrobial and anti-caries effects of two plant extracts. The first chapter dealt with a review of the literature whose objective was to discuss the antimicrobial potential of Brazilian natural agents on the biofilm related to dental caries and gingivitis/periodontal disease. The research of the articles was carried out using PubMed. We found a total of 23 papers. Most of the studies were performed using planktonic microorganisms or under clinical trials. Nineteen articles were focused on cariogenic bacteria. From these nineteen articles, eleven were also about periodontopathogenic bacteria. Four studies addressed only periodontopathogenic bacteria. The most tested Brazilian natural agents were green propolis, essential oils of Lippia sidoides and Copaifera sp. Most of the tested agents showed similar results when compared to positive control (essential oils and extracts) or better effect than negative control (green propolis). More studies involving protocols closer to the clinical condition and the use of response variables that allows understanding the mechanism of action of natural agents are necessary before the incorporation of these natural agents into dental products. The second chapter aimed to test the effect of the hydroalcoholic extracts of Myracrodruon urundeuva All. and Qualea grandiflora Mart. leaves on the viability of the microcosm biofilm and on the prevention of enamel demineralization. The microcosm biofilm was produced on bovine enamel, using human saliva pool mixed with McBain saliva (0.2% sucrose) for 14 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva at 100, 10 and 0.1 g/ml and Q. grandiflora at 100 and 0.1 g/ml reduced cell viability similarly to the positive control and significantly more than negative control. M. urundeuva at 1000, 100 and 0.1 g/ml were able to reduce the counting formation unit-CFU counting of lactobacilli sp. and Streptococcus mutans, while Q. grandiflora at 1000 and 1.0 g/ml significantly reduced the S. mutans CFU counting. On the other hand, the natural extracts did not reduce the production of extracellular polyssacharides, lactic acid and the development of enamel caries lesions. The third chapter aimed to evaluate the effect of hydroalcoholic extracts of M. urundeuva and Q. grandiflora (alone or combined) on the viability of S. mutans biofilm and the prevention of enamel demineralization. S. mutans strain (ATCC 21175) was reactivated in BHI broth. Minimum inhibitory concentration, minimum bactericidal concentration, minimum biofilm inhibitory concentration and minimum biofilm eradication concentration were determined to choose the concentrations to be tested under the biofilm model. S. mutans biofilm (5x105 CFU/ml) was produced on bovine enamel using McBain saliva with 0.2% sucrose for 3 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva (isolated or combined) at concentrations equal or higher than 0.625 mg/ml was able to reduce the bacteria viability, whereas Q. grandiflora extract alone showed antimicrobial effect at 5 mg/ml only (p<0.05). On the other hand, none of the extracts was able to reduce the development of enamel caries lesions. Despite the tested natural extracts have antimicrobial effect; they are unable to prevent caries in enamel. / O objetivo foi avaliar os efeitos antimicrobiano e anti-cárie de dois extratos de plantas. O primeiro capítulo se referiu a uma revisão da literatura cujo objetivo foi discutir o potencial antimicrobiano dos agentes naturais brasileiros sobre o biofilme relacionado à cárie dentária e à gengivite/doença periodontal. A pesquisa dos artigos foi realizada usando o PubMed. Foram encontrados 23 trabalhos. A maioria dos estudos foi realizada utilizando microorganismos na fase planctônica ou ensaios clínicos. Dezenove artigos foram focados em bactérias cariogênicas. Dos dezenove artigos, onze também eram sobre bactérias periodontopatogênicas. Quatro estudos abordaram apenas bactérias periodontopatogênicas. Os agentes naturais brasileiros mais testados foram própolis verde, óleos essenciais de Lippia sidoides e Copaifera sp. Os agentes testados apresentaram resultados similares quando comparados ao controle positivo (óleos essenciais e extratos) ou melhor efeito que o controle negativo (própolis verde). Mais estudos próximos da condição clínica e o uso de variáveis de resposta que permitam entender o mecanismo de ação são necessários, para permitir a incorporação desses agentes naturais em produtos odontológicos. O segundo capítulo teve como objetivo testar o efeito dos extratos hidroalcoólicos de Myracrodruon urundeuva All. e Qualea grandiflora Mart. sobre a viabilidade do biofilme microcosmo e na prevenção da desmineralização do esmalte. O biofilme microcosmo foi produzido em esmalte bovino, utilizando pool de saliva humana misturada à saliva de McBain (0,2% de sacarose) durante 14 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva a 100, 10 e 0,1 g/ml e Q. grandiflora a 100 e 0,1 g/ml reduziram a viabilidade dos microrganismos de forma semelhante ao controle positivo e significativamente maior do que o controle negativo. M. urundeuva a 1000, 100 e 0,1 g/ml foi capaz de reduzir a contagem de Unidade formadora de colônia-UFC para Lactobacilos totais e Streptococcus mutans, enquanto a Q. grandiflora a 1000 e 1,0 g/ml reduziu significativamente a contagem de UFC para S. mutans. Os extratos naturais não conseguiram reduzir a produção de polissacarídeos extracelulares-PEC, ácido lático e o desenvolvimento da lesão cariosa em esmalte. O terceiro capítulo teve como objetivo avaliar o efeito dos extratos hidroalcoólicos de M. urundeuva. e Q. grandiflora (sozinhos ou combinados) sobre a viabilidade do biofilme de S. mutans e na prevenção da desmineralização do esmalte. Cepa de S. mutans (ATCC 21175) foi reativada em caldo BHI. Concentração inibitória mínima, concentração bactericida mínima, concentração inibitória mínima de biofilme e concentração de erradicação mínima de biofilme foram determinadas para escolher as concentrações a serem testadas sob o modelo de biofilme. O biofilme de S. mutans (5x105 CFU/ml) foi produzido em esmalte bovino, utilizando saliva de McBain com 0,2% de sacarose durante 3 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva (isolada ou combinada) nas concentrações iguais ou superiores a 0,625 mg/ml foi capaz de reduzir a viabilidade das bactérias, enquanto que o extrato da Q. grandflora apresentou efeito antimicrobiano somente a 5 mg/ml (p<0,05). Nenhum dos extratos reduziu o desenvolvimento da lesão da cárie. Apesar dos extratos naturais terem efeito antimicrobiano, são incapazes de prevenir o desenvolvimento da lesão cariosa em esmalte.

Submitted by Gabriela Lopes (gmachadolopesufpel@gmail.com) on 2018-08-13T19:38:54Z No. of bitstreams: 1 Dissertação Letícia-Final.pdf: 1670426 bytes, checksum: ab2b251db5406cfbebb79dcc3b6f9add (MD5) / Approved for entry into archive by Aline Batista (alinehb.ufpel@gmail.com) on 2018-08-16T19:59:51Z (GMT) No. of bitstreams: 1 Dissertação Letícia-Final.pdf: 1670426 bytes, checksum: ab2b251db5406cfbebb79dcc3b6f9add (MD5) / Made available in DSpace on 2018-08-16T19:59:51Z (GMT). No. of bitstreams: 1 Dissertação Letícia-Final.pdf: 1670426 bytes, checksum: ab2b251db5406cfbebb79dcc3b6f9add (MD5) Previous issue date: 2018-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / O emprego das Boas Práticas de Fabricação na indústria de alimentos, como a higienização de superfícies, é importante para evitar a formação de biofilmes. Campylobacter jejuni, que é o principal agente etiológico da campilobacteriose, pode sobreviver em condições adversas no ambiente pela capacidade de formação de biofilme. As bactérias formadoras de biofilme podem adquirir resistência à compostos utilizados como sanitizantes na etapa de sanitização, como o cloreto de benzalcônio (CB). Assim, faz-se necessário a busca por novos compostos com ação antibacteriana que possam ser utilizados em alternativa aos sanitizantes sintéticos. Os extratos de plantas vêm sendo amplamente estudados devido às suas características antimicrobianas e por serem compostos naturais. O extrato metanólico de Butia odorata Barb. Rodr. (EMB) teve sua ação antibacteriana comprovada em estudos anteriores. Portanto, os objetivos deste estudo foram avaliar a influência da superfície, temperatura, atmosfera e co-cultura com Pseudomonas aeruginosa sobre a formação de biofilme de Campylobacter jejuni isolados de abatedouro de frangos da região sul do Rio Grande do Sul, bem como identificar a presença de alguns genes relacionados à formação de biofilme nesses isolados. Também objetivou-se avaliar a suscetibilidade desses isolados ao EMB e ao CB, através do teste qualitativo de disco difusão em ágar para o EMB, e da concentração inibitória mínima (CIM) e da concentração bactericida mínima (CBM) para o EMB e para o CB. A atmosfera não afetou a formação de biofilme monoespécie de C. jejuni tanto em poliestireno como em aço inoxidável. Houve maior formação de biofilme em temperaturas que não são as ótimas para a multiplicação d e C. jejuni. A forma como P. aeruginosa foi inoculada para formar biofilmes duoespécie com C. jejuni (concomitante ou pré-formado por P . aeruginosa), não influenciou a formação de biofilme pelos isolados. Nos biofilmes duo-espécie com P. aeruginosa, as maiores contagens de biofilme por C. jejuni em aço inoxidável ocorreram a 25 oC. Os sete isolados de C. jejuni avaliados possuem 10 genes envolvidos no processo de formação de biofilme, porém o gene katA não foi encontrado em três isolados, e o gene kpsM não foi encontrado em um isolado, o que não afetou a formação de biofilme por esses isolados. O EMB apresentou atividade antibacteriana contra os sete isolados no teste qualitativo de disco difusão em ágar, com halos de inibição acima de 23 mm. A CIM do EMB ficou entre 83,3 e 166,6 μL.mL-1, e a CBM foi o mesmo valor de CIM em todos os isolados. Já para o CB, o valor de CIM ficou entre 1 e 2 μg.mL-1, e a CBM variou entre 1 e 4 μg.mL-1 entre os isolados. Dessa forma, o EMB pode tornar-se uma boa alternativa ao CB empregado na etapa de sanitização em indústrias de alimentos. / The employment of good manufacturing practice in the food industry, as surfaces sanitization, is important to avoid the biofilm formation. Campylobacter jejuni, which is the main etiological agent of campilobacteriosis, can survives in adverse environmental conditions by capacity of biofilm formation. Biofilm forming bacteria can acquire resistance to compounds used as sanitizers in sanitization step, such as benzalkonium chloride (BC). Thereby, it is necessary the search for new compounds with antibacterial activity which can be used in alternative to syntetic sanitizers. The plants extracts have been widely studied due to it’s antimicrobial characteristics and for being natural compounds. The Butia odorata Barb. Rodr. methanolic extract (BME) had it’s antibacterial activity proven in studies performed previously. Therefore, the aims of this study were evaluate the factors that influence of surface, temperature, atmosphere and co-culture with Pseudomonas aeruginosa on biofilm formation in Campylobacter jejuni isolated from poultry slaughterhouse of Southern Rio Grande do Sul, Brazil, as well identify the presence of some genes related to biofilm formation in these isolates. Moreover, was aimed to evaluate the susceptibility of these isolates to the BME and to the BC, through the agar disc diffusion qualitative test for BME, and minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for BME and BC. The atmosphere did not affected the monospecies biofilm formation both in polystyrene and stainless steel. There was greater biofilm formation in temperatures that are not the optimals for C. jejuni growth. The way how P. aeruginosa was inoculated to form dual-species biofilms with C. jejuni (concomitant or preformed by P. aeruginosa) did not influenced the biofilm formation by the isolates. In duo-species biofilms with P. aeruginosa, the higher biofilm counts of C. jejuni in stainless steel occurred at 25 oC. The seven isolates had 10 genes that are involved in biofilm formation process, but the katA gene was not found in three isolates, and the kpsM gene was not observed in one isolate, which did not affected the biofilm formation by these isolates. The BME presented antibacterial activity against the seven C. jejuni isolates tested in the qualitative test of agar disc diffusion, resulting in inhibition halos above of 23 mm. The MIC of BME ranged between 83,3 and 166,6 μL.mL-1, and the MBC was the same value that MIC in all isolates. Already for BC, the MIC value stay between 1 and 2 μg.mL-1, and the MBC value ranged between 1 and 4 μg.mL- 1 among isolates. In this way, the BME can become a good alternative to the BC employed in sanitization step in food industries.

Pseudomonas aeruginosa (Pa) est une bactérie multi-résistante responsable de plus de 10% des infections nosocomiales en Europe. Pa réagit aux signaux environnementaux en activant un système de régulation complexe qui permet à la bactérie d’adopter une mode de vie planctonique (infection aigue) ou sessile (infection chronique caractérisée par la formation des biofilms). Le système à deux composants GacS/GacA joue un rôle central dans la permutation entre ces deux modes. Pendant une infection chronique, GacS HK forme des homodimeres permettant l’activation de la formation du biofilm. Nos travaux ont confirmé le rôle du domaine périplasmique de GacS HK (GacSp) dans la détection du signal et l’activation de la voie GacS/GacA. Malgré l’instabilité de GacSp, J’ai résolu la structure 3D de ce domaine par la spectroscopie RMN. GacSp adopte un repliement PDC qui caractérise un grand nombre de domaines senseurs connus pour fixer une large gamme de ligands. L’étude de la structure m’a permis de proposer un site de fixation du ligand. Les résultats présentés dans cette thèse montrent l’importance de GacSp et propose une nouvelle piste pour les études thérapeutiques visant à éradiquer le biofilm.La deuxième partie de ma thèse présente la structure cristalline du glycoside hydrolase 39 du B. cellulosilyticus WH2 présente dans le côlon (GH39wh2). GH39wh2 partage la même architecture avec les autres membres de la famille 39, cependant, elle possède un site actif plus large et plus exposé. Les analyses structurales et bioinformatiques ont permis d’attribuer GH39wh2 à un nouveau sous-groupe caractérisé par une fonction endoglycosidase inconnue. / Pseudomonas aeruginosa (Pa) is a Multidrug-Resistant bacterium responsible for more than 10% of nosocomial infections in Europe. Interestingly, Pa can switch its lifestyle between planktonic (acute infection) and sessile lifestyle (biofilm-type chronic infection) through different regulatory pathways, in which GacS/GacA Two Component System (TCS) plays a central decisive role. An active homodimer form of GacS Histidine Kinase (HK) leads to biofilm formation, while the inhibition of GacS by the hybrid HK RetS via cytoplasmic hetero-dimerization promotes acute infection. During my thesis, we unveiled for the first time the sensing role of the periplasmic detection domain of GacS HK (GacSp). I further solved the 3D structure of GacSp using NMR spectroscopy revealing its PDC-like fold, which characterizes a large number of detection domains known to bind a wide range of ligands. The structural analyses of the new GacSp structure suggest a conserved ligand-binding pocket. All together, my results present structural and functional understanding of GacSp role, which form the basis to consider this domain as a new target for anti-biofilm therapy.In the second part of my thesis, I report a 2.5Å resolution crystal structure of a family 39 glycoside hydrolase member (GH39wh2) from the human gut bacteria B. cellulosilyticus WH2. GH39wh2 shares a similar architecture as found in other related GH39 members but unveils an atypical shallow solvent-exposed groove. Complementary biochemical and bioinformatics analyses assign GH39wh2 to a new GH39 subgroup harboring a yet unknown endoglycosidase activity.

Les systèmes bactériens sont complexes et adaptatifs. Soumis à des perturbations, telles qu’un traitement antibiotique, ils survivent, se régénèrent et évoluent. Ceci est d’autant plus vrai pour les biofilms, capables de surmonter des traitements létaux à des bactéries planctoniques. La capacité des systèmes à retrouver leur équilibre initial, certaines fonctions ou compositions après un choc est appelée résilience. La résilience est souvent considérée comme complémentaire à la résistance en écologie. Pourtant, la résilience aux antibiotiques reçoit peu de considération en comparaison de la résistance aux antibiotiques en bactériologie. L’une des raisons de ce désintérêt est que ce concept est souvent mal défini et ambigu. Dans cette thèse, nous proposons tout d’abord une base conceptuelle de la résilience aux antibiotiques. A partir de l’analyse de différentes définitions existantes de la résilience, nous fournissons une démarche pour formaliser le concept de résilience dans le contexte d’une population bactérienne soumise à des traitements antibiotiques. De cette première analyse, le mécanisme biologique de persistance bactérienne est ressorti comme important dans la résilience aux antibiotiques. Ce phénomène repose sur la formation de cellules tolérantes aux antibiotiques, les persisters, dont la formation est influencée par les conditions environnementales. Afin de relier la formation des persisters aux conditions environnementales, nous avons développé des modèles mathématiques de transition phénotypique entre cellules sensibles et persisters que nous avons calibrés et testés à l’aide de données expérimentales. Enfin, nous avons étudié l’effet de la persistance bactérienne sur la résilience aux antibiotiques des biofilms. Pour cela, nous avons développé un modèle individu-centré de biofilm intégrant des transitions entre cellules sensibles et persisters. Différentes stratégies de transition ont été reliées à la capacité des biofilms à croître, survivre et se régénérer après un choc antibiotique. La mise en place d’expériences capables de fournir des données à comparer aux simulations est proposée dans la discussion de cette thèse. Cette thèse contribue à la clarification du concept de résilience aux antibiotiques et à la compréhension du phénomène de persistance bactérienne dans les biofilms. Elle ouvre des perspectives sur l’utilisation du concept de résilience en bactériologie clinique et souligne l’importance de l’hétérogénéité des populations bactériennes dans leur capacité à confronter les perturbations et évoluer. / Bacterial systems are complex and adaptive. When faced with disturbances, such as antibiotic treatments, they survive, recover and evolve. This is particularly true for biofilms, which survive treatments that planktonic cells cannot overcome. The capacity of systems to recover their initial state, some of their functions or composition after a disturbance is called resilience. The resilience concept is often considered complementary to resistance in ecology. However, antibiotic resilience has received little attention compared to antibiotic resistance. One reason of this lack of interest comes from the fact that the resilience concept is often poorly defined and ambiguous. In this thesis, we firstly developed a conceptual framework of antibiotic resilience and applied this framework to the case of a bacterial population faced with antibiotics. This analysis highlighted the importance of the biological mechanism of bacterial persistence. This phenomenon is based on the formation of sub-populations of antibiotic tolerant cells, the persisters, which is influenced by environmental conditions. To relate persister formation to environmental conditions, we developed mathematical models of phenotypic switches between susceptible and persister cells and calibrated and tested them with experimental data. Lastly, we studied the influence of bacterial persistence on biofilm antibiotic resilience. For this purpose, we developed an individual-based model of biofilm with phenotypic switches between susceptible and persister cells. Different strategies of phenotypic switches were related to the dynamics of growth, survival and recovery of bacterial biofilms faced with antibiotic shocks. The setting up of experimentations to obtain data to compare to simulations is presented in the discussion of this thesis. Globally, this thesis contributes to the clarification of the concept of antibiotic resilience and to the understanding of bacterial persistence in biofilms. It gives new perspectives on the use of the resilience concept in clinical bacteriology and emphasizes the importance of the heterogeneity of bacterial populations in their capacity to face disturbances and evolve.

La fermentation malolactique permet une désacidification et une amélioration de la qualité du vin. Elle est réalisée par des bactéries lactiques principalement de l’espèce Oenococcus oeni : cette espèce est privilégiée pour son efficacité et ses intérêts organoleptiques. La capacité de O. oeni à résister au stress du vin et à garder son activité fermentaire est un sujet d’intérêt majeur. Les prélèvements des fûts de chêne ont montré que O. oeni adhère au bois et est capable de persister plusieurs mois dans le vin. Or, dans la majorité des habitats naturels, les microorganismes se développent attachés à un support, au sein d’un écosystème structuré appelé biofilm. Sous cette forme de vie, les cellules bénéficient d’une résistance accrue au stress. Ces deux propriétés que sont l’adhésion à une surface ainsi que la résistance au stress ont donc été étudiées pour O. oeni. Des observations par microscopie électronique à balayage ont ainsi permis de mettre en évidence la formation de biofilms par O. oeni. Puis, nous avons évalué la capacité de résistance au stress du vin de O. oeni sous forme de biofilm. L’intérêt pour le biofilm est croissant dans les industries agroalimentaires et biotechnologiques, en raison de la conservation de son activité métabolique en milieu stressant. C’est pourquoi la fermentation malolactique avec un biofilm de O. oeni a été suivie dans le vin. Enfin, l’influence du biofilm de O. oeni sur les transferts de composés aromatiques entre le bois et le vin a été étudiée. Cette étude est la première caractérisation du biofilm de O. oeni, de sa résistance au stress du vin et de son potentiel fermentaire / Malolactic fermentation improves wine quality, mainly by decreasing acidity. It is carried out by lactic acid bacteria, mainly Oenococcus oeni. This species is favored for its efficiency and its organoleptic outcome. O. oeni ability to withstand wine stress and to keep its fermentation activity is a subject of major interest.Samples of oak showed that O. oeni adheres to wood and is able to persist for several months in wine. However, in the majority of natural habitats, microorganisms grow attached to a surface, within a structured ecosystem called biofilm. In this form of life, cells benefit from an increased stress resistance.These two properties, adherence to a surface and stress resistance, were studied for O. oeni. Observations by scanning electron microscopy have highlighted biofilm formation by O. oeni. Then, we evaluated the wine stress resilience of O. oeni biofilm. Biofilm is a growing interest in food and biotechnology industries, due to the conservation of its metabolic activity in stressful environment. Therefore, malolactic fermentation with an O. oeni biofilm was monitored in wine. Finally, the influence of O. oeni biofilm on transfers of aromatic compounds between wood and wine was studied.This study is the first characterization of O. oeni biofilm, its wine stress resistance and its fermentation potential.

No description available.

Les infections de prothèses vasculaires (IPV) sont des maladies particulièrement graves. Malgré une fréquence finalement assez importante, elles demeurent mal connues. Staphylococcus aureus en est l’agent responsable principal. Les données concernant le traitement antibiotique à administrer pour ces infections sont excessivement pauvres. L’objectif de notre travail était donc de comparer l’efficacité de différents protocoles d’antibiothérapie à l’aide de divers modèles expérimentaux d’IPV. Six souches différentes de S. aureus ont été évaluées : 3 sensibles (SAMS) et 3 résistants à la méticilline (SARM). Nous avons comparé les concentrations minimales inhibitrices et éradicatrices (CMIB et CMEB) au sein du biofilm obtenues avec des techniques classiques sur polystyrène à ceux obtenus à l’aide d’un modèle original in vitro sur Dacron® (dCMIB et dCMEB) ®. Nous avons ensuite utilisé un modèle original d’infection de Dacron chez la souris pour comparer l’efficacité de différents protocoles thérapeutiques. Enfin nous avons visualisé l’effet de ces antibiotiques in vivo par microscopie confocale. Nous avons montré que les mesures classiques de CMIB et CMEB obtenues sur polystyrène pouvaient surestimer la baisse d’efficacité des antibiotiques dans le biofilm et que des mesures sur le matériel d’intérêt pouvaient être plus pertinentes. Dans notre modèle in vivo, la daptomycine pouvait être supérieure que les comparateurs pour certaines souches de SARM et de SAMS mais pas pour toutes. Par contre, si l’ajout de rifampicine était bénéfique pour la cloxacilline et la vancomycine, cela n’était pas le cas pour la daptomycine. Enfin, nous avons visualisés des effets totalement différents sur le biofilm selon les antibiotiques utilisés mais également selon les souches testées. Nos modèles ont permis d’obtenir des informations nouvelles concernant l’antibiothérapie des IPV qui, nous l’espérons, permettront d’aider à la prise en charge des patients. / Prosthetic vascular graft infection (PVGI) is an emerging disease, mostly due to staphylococci, with limited data regarding efficacy of current antistaphylococcal agents. We aimed to assess the efficacy of different antibiotic regimens. Six different strains of methicillin-susceptible (MSSA) and methicillin-resistant S. aureus (MRSA) were used. We compared results of minimal biofilm inhibitory and eradicating concentrations (MBICs and MBECs) obtained with a Calgary Biofilm Pin lid Device (CBPD) to those yielded by an original Dacron®-related minimal inhibitory and eradicating concentrations measure model. We then used an original murine model of Staphylococcus aureus vascular material infection to evaluate efficacy of different antibiotic regimens. We finally visualized the effect of antibiotics on biofilm by confocal microscopy. We demonstrated that classical measures of MBICs and MBECs with CPBD could overestimate the decrease of antibiotic susceptibility in material related infections and that the nature of the support used to measure biofilm susceptibility might be influent since results yielded by our Dacron®-related minimal eradicating assay were lower than those found on a plastic device. In our in vivo model, we shown that daptomycin was significantly more bactericidal than comparators for some strains of MRSA or MSSA but not for all. For the majority of strains, it was as efficient as comparators. The addition of rifampicin to daptomycin did not enhance daptomycin efficacy in our model. Finally, we highlighted an in vivo differential effect on biofilm depending on the antibiotic used but also on the bacterial strain evaluated. Our models represent an option to better define the best antibiotic options for PVGIs.