Legionella pneumophila is an intracellular pathogen and the etiological agent of Legionnaires’ disease, a severe atypical pneumonia. This bacterium is ubiquitous to freshwater ecosystems where it spreads in the planktonic form but is primarily found associated with protozoa. Protozoa serve as a niche for its replication because the extracellular environment often does not offer sufficient nutrients to support the growth of this bacterium. L. pneumophila is an opportunistic pathogen in humans and utilizes an arsenal of virulence factors to colonize hosts and cause Legionnaires’ disease. The transition between extracellular and intracellular milieus triggers a series of metabolic, morphological and genetic changes that define two developmental stages in this bacterium: replicative and transmissive. Relatively high concentration of nutrients triggers the replicative stage of growth, where the bacterium has the appearance of a thin, elongated rod without the presence of flagella. In addition, is characterized by active metabolism and expression of genes required for productive replication. In contrast, once nutrient levels are relatively low, L. pneumophila switches to its transmissive form. In this form, the bacterium activates a genetic program that includes the expression of many traits associated with the transmissive stage, such as coccoid cell shape, motility, pigmentation and important virulence factors. These multifaceted changes in gene expression leading the differentiation from replicative to the transmissive form, are controlled by two-component regulatory systems. Specifically, the LetAS two-component system plays a key role in the regulation of cell morphology and in the production of the pigment pyomelanin. Here we report the identification of a LetAS-regulated protein, Lpg0586 (designated as Larp1), capable of inducing changes in cell morphology and pigment production. We found that Larp1 expression was accompanied by accumulation of the RecA protein, but evaluation of recA deletion mutants indicated that RecA is not involved in cell morphology changes in L. pneumophila. The specific reason as to why RecA accumulates upon Larp1 expression remains to be elucidated. However, we show that upon synthetic HGA treatment, L. pneumophila cultures display cell elongation and increased RecA levels. Lastly, Larp1 expression restored pyomelanin production in an un-pigmented mutant and increased the transcription of important genes involved in the pyomelanin production pathway. Based on these findings, Larp1 is the first LetAS-regulated protein reported to be involved in pyomelanin production.

Diese Arbeit befasst sich mit der Untersuchung des Metabolismus sowie der Reaktivität verschiedener Wirk- und Arzneistoffe mittels flüssigchromatographischer und massen-spektrometrischer Methoden, sie gliedert sich dabei in vier Projekte. Zur Bestimmung des Metabolitenprofils wurde ein passendes In-vitro-Inkubationssystem mit Cytochrom-P-450-Systemen entwickelt. So wurden der Metabolismus und die Pharmakokinetik der Mip-Inhibitoren SF110, SF235 und SF354 gegen Legionellen, sowie neuer antitrypanosomaler Verbindungen MB209, MB343 und MB444 und von Daptomycin bestimmt. Darüber hinaus wurde die antibakterielle Aktivität des Daptomycins gegenüber einem unbekannten Staphylokokkus-Stammes S. sciuri ermittelt. Außerdem wurden Reaktivitätsuntersuchungen neu synthetisierter Inhibitoren gegen Tuberkulose und S. aureus durchgeführt. Die untersuchten Mip-Inhibitoren lieferten ein Metabolitenprofil, welches durch Ester- und Amidhydrolysen sowie Hydroxylierungen geprägt wurde. Die Verbindung SF110 schien dabei bereits eine gewisse Instabilität der Esterbindung aufzuweisen, da auch im Blindwert entsprechende Spaltprodukte identifiziert werden konnten. Die Hauptmetabolite von SF235 und SF354 bildeten sich durch unterschiedliche Hydrolysen, da die Spaltung des Moleküls von den jeweiligen Substituenten abhängig ist. Innerhalb dieser Substanzklasse dominiert die mikrosomale Enzymkatalyse, da der größte metabolische Umsatz sowie die meisten Metabolite mittels mikrosomaler Fraktion des Menschen bzw. der Maus gefunden wurden. Die Klasse der Mip-Inhibitoren wird somit vor allem durch Cytochrom-P-450-Enzyme umgesetzt, wobei die Hydrophilie durch Einführung polarer OH-Gruppen der Moleküle erhöht wird. Die Hydroxylierung scheint dabei positionsspezifisch, bedingt durch sterische Hinderungen oder dirigierende Einflüsse, abzulaufen. Stabilitätsvergleiche zwischen SF110, SF235 und SF354 zeigten, dass die Einführung einer Amidbindung anstelle der korrespondierenden Esterbindung die Substanzklasse maßgeblich metabolisch stabilisiert. Im Rahmen des murinen In-vivo-Metabolismus wurde beobachtet, dass SF235 einem deutlich stärkeren Metabolismus unterlag als SF354 und sich der Metabolismus vor allem innerhalb der ersten 30 min vollzog. Demgegenüber zeigten die In-vitro-Ergebnisse gegenteilige Ergebnisse, bei denen SF354 die am stärksten metabolisierte Substanz war. Diese widersprüchlichen Ergebnisse deuten darauf hin, dass In-vitro-Modelle nur als Anhaltspunkt verwendet werden sollten, um mögliche Trends abzuleiten. Metabolismusstudien der Chinolonamide, die gegen die afrikanische Schlafkrankheit wirken sollen, veranschaulichten, dass die größte enzymatische Umsetzung aller drei getesteten Verbindungen mittels cytosolischer Fraktion erfolgte. Die Enzymreaktionen werden vermutlich durch ALDH bzw. MAO dominiert und nicht durch CYP bzw. FMO. Die gebildeten Metabolite in den verschiedenen Fraktionen unterlagen (ω-1)-Oxidationen, N-Desalkylierungen, Amidhydrolysen und aromatischen Hydroxylierungen. Auffallend war, dass eine Hydroxylierung am aromatischen Benzylring nur erfolgen konnte, sofern der Benzylaromat keinen Fluorsubstitutenten trug, da dieser desaktivierend wirkte. Die aromatische Hydroxylierung am Chinolonamid erfolgte dagegen bei allen drei Substanzen. Es wurde somit lediglich eine Hydroxylierung am Benzylring von MB343 festgestellt. Die enzymatische Aktivität aller Substanzen folgte einer Reaktionskinetik 1. Ordnung. Die unterschiedlichen Stabilitäten der Substanzen zeigten einen deutlichen Trend: MB209 wurde, da es die instabilste Verbindung darstellt, im größten Maße umgesetzt, gefolgt von den stabileren Derivaten MB343 und MB444. Die Untersuchung der enzymatischen Aktivitäten zeigte, dass die drei Substanzen, verglichen mit der Leitstruktur GHQ168, eine um den Faktor zehn geringere Aktivität aufwiesen [19]. Aufgrund der eingeführten Fluoratome weisen die Substanzen somit eine wesentlich höhere Stabilität auf. Diese Ergebnisse wurden durch die Untersuchung der Halbwertszeit bestätigt, bei der MB444 den höchsten Wert besaß. Weiterhin ist die Position des Fluorsubstituenten am Chinolongerüst ausschlaggebend für die metabolische Stabilität, wobei MB444 aufgrund des para-Fluorsubstituenten am Chinolonamid die stabilste Verbindung darstellt. Durch Inkubation von Daptomycin mit unterschiedlichen S. sciuri-Isolaten wurde ein möglicher Inaktivierungsmechanismus beobachtet, bei dem das Antibiotikum durch Spaltung des cyclischen Aminosäureringes, durch Deacylierung des Fettsäureschwanzes, einer Kombination beider Mechanismen oder durch eine Spaltung des heteroaromatischen Ringsystems von Tryptophan inaktiviert wurde. Die Proteasen des Daptomycin-resistenten S. sciuri-Isolats TS92 führten zu einem Daptomycinabbau von 35 %, unabhängig von der eingesetzten Menge des Arzneistoffes. Das Ausmaß des Abbaus scheint darüber hinaus vom eingesetzten Inkubationsmedium abhängig zu sein, da die Proteasen voraussichtlich auf ein bestimmtes Nährmedium angewiesen sind. Der sensitive S. sciuri-Stamm TS93 lieferte die höchste Abbaurate an Daptomycin mit 55 % und widerlegt damit die Vermutung, dass Daptomycin die geringste antibakterielle Aktivität gegenüber diesem S. sciuri-Stamm aufweist. Im In-vitro-Metabolismus zeigte Daptomycin insgesamt eine sehr geringe Umsetzungsmenge mit maximal 5 % nach 4 h und einer geringen Metabolitenbildung. Hier wurde nur ein Metabolit gefunden, welcher auch mittels S. sciuri-Inkubation identifiziert wurde. Dieser Mechanismus könnte somit auf anderem Wege verlaufen. Die Reaktivitätsstudien der kovalenten Inhibitoren der FadA5-Thiolase gegen Tuberkulose zeigten, dass nur die Verbindungen C1 und C4 eine Reaktivität gegenüber der Aminosäure Cystein93 im aktiven Zentrum besaßen, die somit für den gewünschten Einsatzzweck geeignet sein könnten. Weiterhin wurde bei den kovalenten Inhibitoren der Enoyl-ACP-Reduktase mit dem Enzym FabI, welches im aktiven Zentrum ein Tyrosin besitzt, keine Reaktion festgestellt, da keine Addukte identifiziert wurden. Dies ist vermutlich auf die Unlöslichkeit im verwendeten TRIS-Puffer zurückzuführen. / This work deals with the investigation of the metabolism as well as the reactivity of different drug candidates as well as active pharmaceutical substances by means of liquid chromatographic and mass spectrometric methods. It is divided into four projects. In order to determine the metabolite profile, a suitable in-vitro incubation system using cytochrome P-450-systems was developed. Thus, the metabolism and pharmacokinetics of the Mip inhibitors SF110, SF235, and SF354 against Legionella, as well as of new antitrypanosomal compounds MB209, MB343, and MB444 and of daptomycin were determined. In addition, the antibacterial activity of daptomycin against an unknown Staphylococcus strain S. sciuri was determined. In addition, reactivity studies of newly synthesized inhibitors against tuberculosis and S. aureus were performed. The Mip inhibitors investigated showed a metabolite profile being characterized by ester and amide hydrolysis as well as hydroxylation. The ester moiety of compound SF110 seemed to be unstable, as metabolites could be also identified in the negative control. The major metabolites of SF235 and SF354 were formed by different hydrolyses, whereby the cleavage mechanism of the molecule is dependent on the respective substituents. The substance class is dominated by microsomal enzyme catalysis, as the highest metabolic turnover and, eventually, the most metabolites were found using a microsomal fraction of the human and mouse. The class of Mip inhibitors is thus represented mainly by cleavage due to cytochrome P-450 enzymes, wherein the hydrophilicity of the substrate is increased by introducing polar hydroxyl groups. Hydroxylation seems to be site specific due to steric hindrance or directing influences. Comparing the stability of SF110, SF235, and SF354 revealed that introducing an amide bond instead of an ester bond significantly stabilizes the substance class metabolically. In murine in vivo metabolism results, SF235 was found to be metabolized more significantly than SF354 within the first 30 min of incubation. In contrast, the in vitro results showed the opposite. SF354 was the most metabolized substance. The contradictory results suggest that in vitro models should only be used as an indicator to derive possible trends. Metabolism studies of quinolonamides active against African sleeping sickness, demonstrated that the highest enzymatic conversion of all three tested compounds was caused by the cytosol fraction. The enzyme reactions are probably catalyzed by ALDH or MAO and not by CYP or FMO, respectively. The formed metabolites found in various fractions were subject to (ω-1)-oxidations, N-dealkylations, amide hydrolyses, and hydroxylations. It was observed that hydroxylation could only take place on the aromatic benzyl ring if it did not carry any fluorine substituents having a deactivating effect. The aromatic hydroxylation of the quinolonamide, however, was carried out in all three substances. Thus, only hydroxylation on the benzyl ring of MB343 was observed. The enzymatic activity of all substances followed a first-order kinetic. The different stabilities of the substances had a clear trend: MB209 showed the highest enzymatic activity as it represents the most unstable compound, followed by MB343 and MB444. The enzymatic activities of the three substances were ten times lower compared to the enzymatic activity of lead structure GHQ168 [19], which exhibits a much higher stability due to the fluorine atoms. These results were confirmed by a half-life study in which MB444 was the most stable compound. The position of the fluorine substituent on the quinolone determines the metabolic stability, making MB444 the most stable compound because it carries a p-fluorine substituent on the quinolonamide. When incubating Daptomycin with different S. sciuri isolates, a possible inactivation mechanism of the antibiotic agent was observed in which the cyclic amino acid ring was opened, the fatty acid tail deacylated, or a combination of both mechanisms as well as the heteroaromatic ring system of tryptophan was cleaved. The proteases of the daptomycin-resistant S. sciuri isolate TS92 led to a daptomycin degradation of 35%, regardless of the initial concentration used. The degradation also seems to depend on the incubation medium since the proteases probably rely on a specific nutrient medium. The sensitive S. sciuri strain TS93 showed the highest degradation rate of daptomycin with 55 % and thus refutes the assumption that it has the smallest antibacterial sensitivity against daptomycin. Overall, DAP showed a very low in vitro metabolism with a conversion rate of maximum 5% after 4 h and a low metabolic rate. Here, only one metabolite could be found which was also identified by means of S. sciuri incubation. Thus, this mechanism could proceed in a different way. The reactivity studies of the covalent inhibitors of the thiolase of the FadA5 enzyme against tuberculosis showed that only compounds C1 and C4 targeted cysteine93, thus being suitable for the desired purpose. Furthermore, no reaction was observed for in the covalent inhibitors of the enoyl-ACP reductase with the enzyme FabI, which carries a tyrosine in the active site, since no adducts were identified. This is probably due to the insolubility in the TRIS buffer.

Legionella pneumophila is a pathogen that can proliferate in premise (i.e., building) plumbing and, when aerosolized during water use, infect the lungs of exposed individuals and cause a deadly form of pneumonia known as Legionnaires' disease. Given that it is one of the primary sources of tap-water associated disease throughout much of the world, this organism has been the subject of intense research, ranging from aiming to understand key aspects of its physiology that allow it to proliferate in premise plumbing, to the specific virulence factors that make it so infectious to humans. The work presented here starts with a comprehensive review of published studies related to the L. pneumophila proteome, i.e., the set of expressed proteins associated with a given strain under a given set of environmental conditions, showing how the field has progressed in parallel to improvements in mass spectrometry technologies and how proteomics can be used as a tool to understand this unique and important organism. Copper is a natural antimicrobial that can be present in drinking water due to passive release from copper pipes or intentionally dosed (e.g., copper-silver ionization systems) for microbial control. However, some L. pneumophila strains have recently been found to exhibit copper resistance, an adaptive process that is not fully understood at the physiological level. Chapter Two describes the copper survivability of three outbreak-associated strains of L. pneumophila and examines the copper-induced proteome of QC1, a strain found to display high resistance to copper. Pairwise comparisons of the proteomes of copper-resistant and copper sensitive strains indicated that L. pneumophila QC1 adapts to copper exposure via the induction of redox and metal homeostasis proteins, while concomitantly inducing motility and pathogenesis related proteins, suggestive that copper induces a search for a host protozoan strain for protection. In 2014 and 2015, Flint, Michigan experienced the largest per capita community-wide Legionnaires' Disease outbreak in US history. The outbreak was associated with a change in the source of the municipal drinking water supply from Detroit water, which was sourced from the Great Lakes and subject to appropriate corrosion control, to the Flint River, which was not appropriately controlled for corrosivity. The underlying drivers of this outbreak have been debated and include: elevated iron in the water serving as a nutrient for L. pneumophila, diminished chlorine in the water due to reactions with iron, reduced copper in the water due to shifts in pH influencing release from copper pipes, and shifts in potentially key components of the microbial community. In Chapter Three of this dissertation, we employ controlled microcosm studies to establish a fundamental understanding of interactive effects of pipe material and water of varying iron bioavailability (ferric chloride, ferrous chloride and ferric pyrophosphate) on the microbial community and its relationship with L. pneumophila numbers. The combination of copper pipes and Flint River water decreased the diversity of the microbial community to a larger degree than copper pipes with Detroit water, implying greater copper bioavailability in the former condition. Several Order were found to be significantly associated with high or low numbers of culturable L. pneumophila recovered from the microcosms. Most notably, the Order Pseudomonadales was significantly associated to the reactors with low culturable L. pneumophila. This order contains Pseudomonas species known to inhibit the growth of L. pneumophila. The findings reported in this dissertation can be used to develop more informed management practices for drinking water systems to reduce the risk of Legionnaires' Disease outbreaks associated with premise plumbing. Specifically, 1) copper might be inducing a more pathogenic form of copper resistant L. pneumophila, 2) the use of corrosive control in municipal water systems goes beyond the influence on lead and copper pipes, but also on the microbial community, which in part influences L. pneumophila, and 3) there are organisms, such as Pseudomonadales species, associated with environments with low culturable L. pneumophila which might be introduced to the drinking water systems as probiotics. / Doctor of Philosophy / Legionella pneumophila is a microbe found in drinking water plumbing systems. This organism causes Legionnaires' Disease, a severe form of pneumonia that particularly affects immunocompromised individuals. Due to its health and economic impact, there are worldwide efforts to understand the biology of this organism, from the conditions that allows it to grow in the drinking water plumbing, to the specific components that allows it to infect humans. In this dissertation, we first review the published studies related to the L. pneumophila proteome, a powerful tool used to functionally describe biological organisms. This first chapter showed how proteomics can be used to understand this unique and important organism. In the next chapter we studied how copper metals may influence the proteome of L. pneumophila. Copper pipes have been extensively used to control the growth of microorganisms in drinking water systems, however some studies have reported that copper may promote the growth of L. pneumophila. In this chapter, we showed that a copper resistant strain of L. pneumophila adapts to copper exposure by inducing motility and pathogenesis related proteins, suggesting that it might be more infectious. In the last chapter of this dissertation, we investigated the combined effect of pipe material and water chemistry, on the microbial community and its relationship with L. pneumophila. The combination of copper pipes and a more corrosive water decreased the diversity to a larger degree, in comparison to the other evaluated conditions. Several organisms were also identified to be significantly associated with the high or low culturable L. pneumophila. This is of particular interest because they might be used as potential probiotics to control the growth of L. pneumophila. The findings reported in this dissertation can help to better understand the significance of water chemistry and pipe material, particularly copper pipes, for the purpose of reducing risk of Legionnaires' Disease outbreaks associated with drinking water systems.

La multi-résistance aux drogues des bactéries est un problème majeur en clinique. L’un des mécanismes de résistance consiste à effluer les composés toxiques hors de la cellule grâce à des protéines de la membrane interne nommées pompes d’efflux. Ces protéines appartiennent à cinq familles (MFS, RND, MATE, SMR et ABC) et peuvent fonctionner en association avec deux autres types de protéines (protéine du périplasme et protéine de la membrane externe) pour former un canal. Dans le cadre d’une thématique de recherche basée sur l’étude des mécanismes de résistance auxdrogues de la bactérie pathogène Legionella pneumophila, une approche bioinformatique menée sur lesgénomes de trois souches séquencés (souches Lens, Paris et Philadelphia) a permis d’identifier des protéinespouvant participer à l’efflux. Notre but a été de vérifier l’implication de ces protéines dans la résistance auxdrogues et dans la virulence de Legionella en ciblant un ou plusieurs gènes codant pour des composants desystèmes d’efflux. Pour inactiver les gènes, nous avons choisi une stratégie de recombinaison homologue. Lesrecombinants ont été testés pour leur sensibilité à des composés toxiques afin de voir si les gènes ciblés jouentun rôle dans l’efflux d’E. coli. Un de ces mutants, le mutant MF201, altéré pour le gène codant pour une protéinehomologue à TolC chez E. coli s’est avéré être 2 à 16 fois plus sensible aux drogues testées comparé à lasouche sauvage. De plus, ce mutant présente un défaut important de virulence dans Acanthamoeba castellanii,Dictyostelium discoideum et les macrophages U937. Ce premier résultat implique que la protéine TolC-like deLegionella aurait un rôle clef dans la relation hôte pathogène et sous-tend un lien entre multi-résistance auxdrogues et virulence. Par ailleurs une étude de l’expression des gènes codant pour des pompes à efflux a étéinitiée afin de comprendre leur rôle au cours du cycle infectieux de Legionella. / Bacterial multi-drug resistance is of major concern in the case of clinic. One of the resistance mecanisms used by bacteria is the efflux of noxious compounds out of the cell thanks to inner membran proteins called efflux pumps. This proteins belong to five families (MFS, RND, MATE, SMR and ABC) and can function in close association with two partners (periplasmic protein and outer membrane protein) to form a canal. In our new research axis based on the study of the drug resistance of the bacterium Legionella pneumophila, we conducted a bioinformatical approach to identify efflux pumps proteins coded by the sequenced genome of three strains (strains Lens, Paris and Philadelphia). Our goal was to study the role of this proteins in Legionella drug resistance and in its virulence. The bioinformatic approach data allowed us to choose one or several genes coding for potential efflux pump components for genetic invalidation by an homologousrecombination strategy. The bacterial mutants were exposed to different noxious compounds in order to know ifthe target genes invalidated were implicated in the efflux of drugs. One of this mutants, strain MF201, which isdeleted for the gene encoding a protein homologous to E. coli TolC protein, revealed to be 2 to 16 times moresensitive to the drug tested compared to the wild-type strain. Furthermore, this mutant showed an importantvirulence defect in Acanthamoeba castellanii, Dictyostelium discoideum and U937 macrophages. This first resultsmeans that the TolC-like protein of Legionella could be a key factor in host-pathogen interaction and stronglysuggests a link between multi-drug resistance and virulence. We also initiated a transcriptomic approach to studyefflux pump genes expression in order to understand their role during the infectious cycle of Legionella.

Legionella pneumophila est une bactérie gram/négative de l'environnement qui infecte et se multiplie au sein des protozoaires aquatiques, comme les amibes. Elle peut également infecter les macrophages pulmonaires humains, causant une forme sévère de pneumonie appelée légionellose (ou maladie du légionnaire). L'importance du Système de Sécrétion de Type IV (SST4) Icm/Dot est clairement démontrée, de même que celle du Système de Sécrétion de Type II (SST2) Lsp. Des études bioinformatiques ont suggéré l'existence d'un Système de Sécrétion de Type I (SST1), mais aucune étude n'a à ce jour démontré sa fonctionnalité, ni même un éventuel rôle dans la virulence. Ce travail consiste à étudier la fonctionnalité et le rôle dans la virulence d'un SST1 potentiel de L. pneumophila. La fonctionnalité de pompes d'efflux potentielles, possédant une structure très proche d'un SST1, est également investiguée. Des mutants de L. pneumophila invalidés pour les gènes codant pour ce SST1 potentiel (lssB, lssD et tolC) ont été construits : ils possèdent une virulence fortement atténuée vis-à-vis de plusieurs types de cellules hôtes. L'entrée dans la cellule est affectée chez ces mutants, bien que le reste du cycle intracellulaire ne soit pas altéré. La fonctionnalité de ce SST1 a été démontrée par la sécrétion de protéines hybrides entre un rapporteur et la protéine RtxA, qui fait partie de la famille des protéines RTX (Repeat/in ToXins), classiquement sécrétées par des SST1. Enfin, la fonctionnalité de plusieurs pompes d'efflux potentielles a été démontrée : des composés toxiques expulsés par ces pompes ont été identifiés, ainsi qu'une pompe majeure (HelA/HelB/HelC). D'autres analyses sont en cours pour caractériser plus précisément l'importance de ces pompes d'efflux / Legionella pneumophila is a gram/negative pathogen that infects and survives within protozoans, such as amoebas. It can also infect human lung macrophages, causing a disease called Legionnaire’s disease. The Type IV Secretion System Icm/Dot is known to be involved in the virulence of L. pneumophila, as well as the Type II Secretion System Lsp. Bioinformatics studies suggested the presence of a Type I Secretion System (T1SS), but its functionality and importance have not been demonstrated to date. This work aims to study the functionality and the implication in the virulence of the putative T1SS of L. pneumophila. Investigation efforts also concerned putative efflux pumps, which share high similarity with T1SS. Mutant strains of L. pneumophila were constructed by deletion of genes encoding the T1SS (lssB, lssD and tolC): they are defective for the entry into the host cells. The creation of the Legionella replicative vacuole is not altered though. Then the functionality of the LssB/LssD/TolC T1SS was demonstrated in a heterologous host: the reconstructed T1SS allows the secretion of hybrid proteins created by fusing a reporter with parts of the RTX protein RtxA. Finally, the functionality of several putative efflux pumps was also demonstrated: several substrates were identified for those efflux pumps, as well as a major pump (HelA/HalB/HelC). Investigations are currently made to decipher the importance of such efflux systems

Cheng Yee Wan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 95-112). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / Table of Contents --- p.vi / List of Figures --- p.xi / List of Plates --- p.xiv / List of Tables --- p.xvi / Abbreviations --- p.xviii / Chapter 1. --- Introduction --- p.1 / Chapter 1.1 --- Legionella pneumophila --- p.1 / Chapter 1.1.1 --- Bacterial morphology and ultrastructure --- p.2 / Chapter 1.1.2 --- Microbial ecology and natural habitats --- p.4 / Chapter 1.1.2.1 --- Association with amoeba --- p.5 / Chapter 1.1.2.2 --- Association with biofilm --- p.5 / Chapter 1.2 --- Legionnaires' disease and clinical significance --- p.6 / Chapter 1.2.1 --- Epidemiology --- p.6 / Chapter 1.2.1.1 --- Worldwide distribution --- p.6 / Chapter 1.2.1.2 --- Local situation --- p.7 / Chapter 1.2.2 --- Clinical presentation --- p.7 / Chapter 1.2.3 --- Route of infection and pathogenesis --- p.8 / Chapter 1.2.4 --- Diagnosis --- p.10 / Chapter 1.2.4.1 --- Culture of Legionella --- p.10 / Chapter 1.2.4.2 --- Direct fluorescent antibody (DFA) staining --- p.13 / Chapter 1.2.4.3 --- Serologic tests --- p.13 / Chapter 1.2.4.4 --- Urine antigen testing --- p.14 / Chapter 1.2.4.5 --- Detection of Legionella nucleic acid --- p.15 / Chapter 1.2.5 --- Risk factors --- p.15 / Chapter 1.2.6 --- Treatment for Legionella infection --- p.16 / Chapter 1.3 --- Detection of Legionella in environment --- p.16 / Chapter 1.4 --- Disinfection methods --- p.17 / Chapter 1.4.1 --- Physical methods --- p.19 / Chapter 1.4.1.1 --- Filtration --- p.19 / Chapter 1.4.1.2 --- UV-C irradiation --- p.20 / Chapter 1.4.1.3 --- Thermal eradication (superheat-and-flush) --- p.21 / Chapter 1.4.2 --- Chemical methods --- p.21 / Chapter 1.4.2.1 --- Chlorination --- p.21 / Chapter 1.4.2.2 --- Copper-silver ionization --- p.22 / Chapter 1.4.3 --- Effect of biofilm and other factors on disinfection --- p.23 / Chapter 1.5 --- Photocatalytic oxidation (PCO) --- p.24 / Chapter 1.5.1 --- Generation of strong oxidants --- p.24 / Chapter 1.5.2 --- Disinfection mechanism(s) --- p.27 / Chapter 1.5.3 --- Major factors affecting the process --- p.28 / Chapter 2. --- Objectives --- p.30 / Chapter 3. --- Materials and Methods --- p.31 / Chapter 3.1 --- Chemicals --- p.31 / Chapter 3.2 --- Bacterial strains and culture --- p.31 / Chapter 3.3 --- Photocatalytic reactor --- p.33 / Chapter 3.4 --- PCO efficacy tests --- p.33 / Chapter 3.5 --- PCO sensitivity tests --- p.35 / Chapter 3.6 --- Optimisation of PCO conditions --- p.35 / Chapter 3.6.1 --- Optimization of TiO2 concentration --- p.36 / Chapter 3.6.2 --- Optimization of UV intensity --- p.36 / Chapter 3.6.3 --- Optimization of depth of reaction mixture --- p.36 / Chapter 3.6.4 --- Optimization of stirring rate --- p.37 / Chapter 3.6.5 --- Optimization of initial pH --- p.37 / Chapter 3.6.6 --- Optimization of treatment time and initial cell concentration --- p.37 / Chapter 3.6.7 --- Combinational optimization --- p.37 / Chapter 3.7 --- Transmission electron microscopy (TEM) --- p.38 / Chapter 3.8 --- Fatty acid profile analysis --- p.40 / Chapter 3.9 --- Total organic carbon (TOC) analysis --- p.42 / Chapter 3.10 --- UV-C irradiation --- p.44 / Chapter 3.11 --- Hyperchlorination --- p.44 / Chapter 3.12 --- Statistical analysis and replication --- p.45 / Chapter 3.13 --- Safety precautions --- p.45 / Chapter 4. --- Results --- p.46 / Chapter 4.1 --- Efficacy test --- p.46 / Chapter 4.2 --- PCO sensitivity --- p.47 / Chapter 4.3 --- Optimization of PCO conditions --- p.48 / Chapter 4.3.1 --- TiO2 concentration --- p.48 / Chapter 4.3.2 --- UV intensity --- p.48 / Chapter 4.3.3 --- Depth of reaction mixture --- p.51 / Chapter 4.3.4 --- Stirring rate --- p.56 / Chapter 4.3.5 --- Effect of initial pH --- p.56 / Chapter 4.3.6 --- Effect of treatment time and initial concentrations --- p.56 / Chapter 4.3.7 --- Combinational effects --- p.63 / Chapter 4.4 --- Transmission electron microscopy (TEM) --- p.66 / Chapter 4.4.1 --- Morphological changes induced by PCO --- p.66 / Chapter 4.4.2 --- Comparisons with changes caused by UV-C irradiation and chlorination --- p.67 / Chapter 4.5 --- Fatty acid profile analysis --- p.71 / Chapter 4.6 --- Total organic carbon (TOC) analysis --- p.73 / Chapter 4.7 --- UV-C irradiation --- p.74 / Chapter 4.8 --- Hyperchlorination --- p.74 / Chapter 5. --- Discussion --- p.76 / Chapter 5.1 --- Efficacy test --- p.76 / Chapter 5.2 --- PCO sensitivity --- p.76 / Chapter 5.3 --- Optimization of PCO conditions --- p.77 / Chapter 5.3.1 --- Effect of TiO2 concentration --- p.77 / Chapter 5.3.2 --- Effect of UV intensity --- p.78 / Chapter 5.3.3 --- Effect of depth of reaction mixture --- p.79 / Chapter 5.3.4 --- Effect of stirring rate --- p.79 / Chapter 5.3.5 --- Effect of initial pH --- p.80 / Chapter 5.3.6 --- Effect of treatment time and initial concentrations --- p.81 / Chapter 5.3.7 --- Combinational effect --- p.82 / Chapter 5.4 --- Transmission electron microscopy (TEM) --- p.83 / Chapter 5.4.1 --- Morphological changes induced by PCO --- p.83 / Chapter 5.4.2 --- Comparisons with changes caused by UV-C irradiation and chlorination --- p.85 / Chapter 5.5 --- Fatty acid profile analysis --- p.85 / Chapter 5.6 --- Total organic carbon (TOC) analysis --- p.86 / Chapter 5.7 --- Comparisons of the three disinfection methods --- p.88 / Chapter 6. --- Conclusion --- p.91 / Chapter 7. --- References --- p.95 / Chapter 8. --- Appendix --- p.113

L'implication des tours aéro-réfrigérantes dites « ouvertes », dans les cas de légionellose, demeure à l'heure actuel un problème de santé public malgré la multitude de composés biocides disponibles qui, parfois, sont écotoxiques et appliqués à de forte concentrations. L'efficacité de la majorité de ces biocides est étudiée vis-à-vis des formes planctoniques des microorganismes. Cette étude s'intéresse à la mise au point de deux procédés de traitement du risque Legionella pneumophila : H2O2/UV et ClO2, avec la prise en compte particulière des communautés microbiennes fixées et notamment des protozoaires qui constituent l'hôte naturel de cette bactérie. La démarche expérimentale adoptée pour l'étude de l'efficacité de ces traitements, s'est appuyée sur des biofilms environnementaux naturellement contaminés par des légionelles et issus d'une source thermale. La caractérisation des légionelles isolées des biofilms de cette source montre le maintien du sérogroupe 1 de L. pneumophila et l'apparition de deux autres sérogroupes non reportés dans des études précédentes (sg10 et sg12), avec toutefois une prédominance du sérogroupe 12. Quel que soit le sérogroupe, ces souches environnementales se sont avérées plus virulentes vis-à-vis de l'amibe Acantamoeba castellanii, que les souches cliniques de Lp1 répertoriées. A l'état planctonique elles se sont également avérées très sensibles aux traitements H2O2/UV et UV seul. A l'échelle expérimentale, les deux traitements, H2O2/UV et ClO2, montrent une performance élevée vis-à-vis des biofilms. L'étude a particulièrement mis en évidence le rôle du facteur trophique et de l'adaptation des bactéries au stress oxydatif dans la performance des traitements mais aussi dans l'apparition de la reviviscence. L'application des traitements à des installations en vraie grandeur a permis de conforter les résultats expérimentaux et de mettre l'accent, dans le contexte des sites étudiés, sur les limites de leur efficacité et sur la nécessité d'ajustements des doses appliquées (concentrations des biocides, flux d'irradiation UV, mode d'application) aux particularités des contextes industriels. / Cooling towers are considered as one of the major sources of Legionella pneumophila, the causal agent of Legionnaires' disease. Despite the high number of commercial disinfectants dedicated to it, the Legionella threat is still rising especially in connection with cooling towers. The efficacy of most disinfectants is demonstrated on planktonic bacteria while very few studies have been devoted to their effects on biofilms. The main objective of the study was to optimize two treatments dedicated to the control of biofilms in cooling towers, H2O2/UV and ClO2, so as to reduce the risk associated to Legionella pneumophila while minimizing environmental damages. Their efficacy was studied against environmental biofilms developed in a hot sulphur spring where presence of L. pneumophila is permanent. Their analysis revealed the occurrence of Lp serogroups 1 (Lp1) and of two serogroups not reported in previous studies that were oriented toward water samples, though (Lp10 and Lp12). The environmental strains we isolated display a higher cytotoxicity and virulence towards the amoeba Acantamoeba castellanii than those of known Lp1 epidemic strains and a higher sensitivity to UV and H2O2/UV. In the experimental part of the study, ClO2 and H2O2/UV display a high efficacy against biofilms. Furthermore the study showed the role of trophic parameters and of bacterial adaptation to oxidative stress on the performance of the treatments but also on biofilms regrowth. The experiments performed at the industrial scale corroborate the results gained at the pilot scale and focus on the relationships between the dose and the effectiveness of each treatment. Our results suggest the possibility to apply the process to an industrial scale with necessary adjustments about doses and injection modalities to the context of the considered sites.

Legionella pneumophila, responsable de la maladie du légionnaire, est une bactérie aquatique parasitant les amibes, mais aussi les macrophages alvéolaires humains. Legionella alterne entre une forme infectieuse non réplicative et une forme réplicative intracellulaire, qui n'exprime pas les facteurs de virulence. Ce cycle de vie biphasique est gouverné par un système de régulation complexe permettant son adaptation dans différents hôtes. Le but de mon projet de thèse était d'étudier un des facteurs clés dans la régulation des ARNm, le régulateur post-transcriptionnel global Hfq. L'expression de Hfq est régulée au cours du cycle infectieux chez L. pneumophila: Hfq est peu exprimée en phase réplicative, mais fortement exprimée lors de la phase de transmission, ce qui suggère un rôle dans la transition entre ces deux phases. J'ai identifié un petit ARN (sRNA) que j'ai nommé Anti-hfq puisqu'il est transcrit dans l'orientation antisens à Hfq et chevauche sa région 5' non traduite (UTR). Mes recherches ont mis en évidence un mécanisme sophistiqué par lequel Anti-hfq régule l'expression de Hfq: Anti-hfq interagit avec l'ARNm du gène hfq par sa région complémentaire et ainsi contrôle la stabilité de la protéine. De plus, j'ai montré que la protéine Hfq auto-réprime sa propre traduction en facilitant l'interaction entre Anti-hfq et son propre ARNm. Finalement, Hfq régule son propre renouvellement par le recrutement de la RNase III. De plus, des tests de réplication intracellulaire ont montré que Hfq et Anti-hfq sont nécessaires pour la multiplication intracellulaire de L. pneumophila, ce qui a mis en évidence un rôle important de Hfq et Anti-hfq dans la virulence de cette bactérie. / Legionella pneumophila, the causative agent of the pneumonia-like Legionnaires’ disease, is commonly found in aquatic habitats worldwide where it multiplies within protozoa. To adapt between intra- and extracellular environments, L. pneumophila evolved a biphasic lifecycle wherein it alternates between an infectious and non replicative form and an intracellular form, which does not express the virulent phenotypes. This biphasic life cycle is governed by a complex regulatory network that comprises transcriptional and post-transcriptional regulatory elements, enabling the bacteria to adapt in diverse hosts. During my Ph.D., I focused my attention of the post-transcriptional regulator Hfq, a hexameric, RNA-binding protein and chaperon of small RNAs (sRNA). The expression of this fascinated protein is life cycle regulated: poorly expressed during the replicative phase of growth, whereas significantly upregulated upon entry into the transmissive phase of growth. Moreover, my research research lead to the identification of a sRNA transcribed antisense to the hfq gene overlapping its 5’UTR region. This antisense RNA, named Anti-hfq, was found to regulate hfq expression by base-pairing complementarity, describing a sophisticated mechanism of regulation. In addition, the Hfq protein controls its own translation by facilitating the interaction between Anti-hfq and its own mRNA. Thus, Hfq regulates its turnover, recruiting the endoribonuclease RNaseIII. Furthermore, infection assays revealed that Hfq and Anti-hfq are necessary for efficient replication of L. pneumophila in amoeba revealing an important role of both in bacterial virulence.

Sous des conditions de croissance particulières, certaines bactéries sont capables d'entrer en état de « compétence » pour la transformation naturelle, c'est-à-dire d'exprimer un ensemble de gènes nécessaires à la mise en place d'un système d'import d'ADN exogène dont l'intégration conduit à une transformation génétique et phénotypique. C'est le cas de Legionella pneumophila, bactérie environnementale et agent étiologique de la légionellose. La transformation naturelle a potentiellement participé à l'évolution du génôme de L. pneumophila.Ainsi, l'objectif premier de cette thèse était de décrire les composants principaux du système de transformation naturelle de L. pneumophila, ainsi que son activation et rôle potentiel dans la relation de la bactérie avec ses hôtes. Des méthodes d'analyse transcriptomique et de mutagénèse dirigée ont permis d'identifier les principaux gènes impliqués dans la mise en place du système de transformation naturelle qui, de façon cohérente avec un rôle adaptatif, ne semble pas impliqué dans la virulence bactérienne. Le système inclut un pilus de transformation, structure fréquemment observée chez les espèces naturellement transformables. Le rôle de la protéine structurale MreB dans le mécanisme de transformation naturelle a également été étudié. En proposant un premier modèle du système de transformation naturelle de L. pneumophila, ces travaux ouvrent la voie à une analyse plus détaillée de la dynamique du système et, plus généralement, à une meilleure compréhension des mécanismes de la transformation naturelle chez les bactéries Gram-négatives / Under certain growth conditions, some bacteria are able to develop a « competence » state for natural transformation, that is, to express a panel of genes involved in the assembly of a DNA uptake system that allows bacteria to take up and recombine free exogenous DNA, leading to a genetic and phenotypic transformation. Natural transformation may have played a role in the evolution of the L. pneumophila genome.Thus, the main objective of this work was to describe the main components of the L. pneumophila DNA uptake system and to investigate its role regarding the host-pathogen interaction. Transcriptomic analysis and directed mutagenesis permitted to identify the main components of the system which is not involved in bacterial virulence. The system include a transformation pilus that is a structure frequently found in transformable species. The role of the structural protein MreB has also been investigated.By describing a first model of the natural transformation system of L. pneumophila, this work paves the way to a deeper analysis of the system dynamics and, more generally, to a better understanding of natural transformation in Gram-negative species

Les souches de Legionella pneumophila sérogroupe 1 ST47 Lorraine sont actuellement responsables d'un nombre croissant de cas de légionelloses particulièrement dans le Nord de l'Europe. Cependant, elles ne sont retrouvées que très rarement dans l'environnement quand des investigations sont menées pour rechercher la source de cas de légionellose. Son environnement naturel reste donc méconnu. Notre objectif était donc d'étudier le phénomène de non détectabilité de la souche ST47 dans l'environnement. Nous avons observé que les traitements pré-analytiques (acidification, chauffage) pouvaient interférer avec les paramètres de culture pour certaines souches Lorraine environnementales, et que le milieu GVPC utilisé dans la norme NF T90-431 n'était pas recommandé pour la recherche des légionelles dans les prélèvements respiratoires, et donc potentiellement dans les prélèvements environnementaux. Ainsi, la PCR spécifique ST47, développée en collaboration avec l'équipe de Tim Harrison (Londres, Royaume-Uni), peut constituer un outil de détection intéressant dans les différentes matrices environnementales pour identifier les réservoirs de la souche. Nous avons cherché à cibler ces réservoirs. Nous avons montré, d'une part, que les robinets pouvaient être des réservoirs potentiels de légionelles. D'autre part, les données clinicoépidémiologiques et géographiques des souches Lorraine ST47 ont montré que les cas survenaient essentiellement hors institution (hôpital, maison de retraite) et principalement dans le quart Nord-Est du pays. L'amélioration des connaissances clinico-épidémiologiques et l'utilisation de la PCR spécifique ST47 devraient permettre, en s'affranchissant ou en améliorant les paramètres culturaux, d'identifier les réservoirs environnementaux de cette souche / The recently identified strains of Legionella pneumophila serogroup 1 belonging to Sequence Type (ST) 47 and pulsotype Lorraine are now responsible for an increasing number of Legionnaires’ disease (LD) cases mainly in the North of Europe. The major paradox is that ST47 strains are extremely rarely detected in environmental samples when investigations to identify the source of ST47 associated LD cases are undertaken. Thus its environmental habitat is unknown. The aim of our work was to study the non-detectability of this strain in environmental samples. Firstly, we have observed that pre-treatments (heat, acid) could interfere with recovery of an environmental ST47 Lorraine strain, and secondly, that GVPC medium imposed by the French standard NF T90-431, was not recommended for detection of Legionella spp. In clinical samples and potentially in environmental samples. Thus, to detect and identify ST47 Lorraine strains from clinical and ultimately, environmental samples in order to find the potential source of infection, we developed a strain specific realtime PCR method, in collaboration with Tim Harrison’s team (London, United Kingdom). We have also sought to target these sources. Then, we have shown that L. pneumophila could be detected in aerosols of a tap water. Moreover, epidemiologic French data have demonstrated that most of the LD cases associated with ST 47 strains occurred mainly in North East and were mainly community-acquired. Improved epidemiologic knowledge and the use of the strain specific real-time PCR should enable identification of environmental sources of ST47 Lorraine strain without culturing