Salmonella enterica sérovar Typhi est une bactérie pathogène humain-spécifique et l’agent étiologique de la fièvre typhoïde. Parmi ses facteurs de virulence, il y a 14 systèmes d’adhésion putatifs nommés fimbriae qui ont été identifiés dans le génome de S. Typhi. Les fimbriae sont regroupés en opérons qui codent pour des structures protéiques extracellulaires, pour une machinerie de sécrétion et d’assemblage et parfois pour des régulateurs. Ceux-ci sont peu exprimés en conditions de laboratoire et peu étudiés chez S. Typhi. Parmi les 14 fimbriae de S. Typhi, 12 appartiennent à la classe des chaperon-placier, c’est-à-dire qu’ils possèdent un chaperon et un placier qui leur sont dédiés pour la formation de la structure fimbriaire. Je crois que ces fimbriae sont importants pour la pathogenèse de S. Typhi. Le but de ce projet est l’analyse fonctionnelle des fimbriae de type chaperon-placier chez S. Typhi. Pour ce faire, j’ai voulu établir une caractérisation générale des 12 fimbriae de type chaperon-placier, puis j’ai concentré l’étude sur la régulation de 2 de ces fimbriae, c’est-à-dire Fim et Std. La caractérisation générale des fimbriae de type chaperon-placier consistait à déterminer l’expression des promoteurs fimbriaires lors de la croissance en différentes conditions de culture mimant l’infection, à déterminer la présence et la morphologie des fimbriae à la surface de la bactérie et à évaluer l’effet des fimbriae sur la pathogenèse de S. Typhi (formation de biofilm, interactions avec les cellules de l’hôte et motilité bactérienne). L’expression maximale des fimbriae a été obtenue principalement en milieu minimal. J’ai observé pour la première fois 6 des 12 fimbriae par microscopie électronique à transmission. Chaque fimbria présentait des effets sur au moins une étape testée sur la pathogénèse. La régulation de std et fim a été étudiée en déterminant le rôle de régulateurs globaux et par criblage d’une banque de mutants par insertion de transposon. Principalement, j’ai découvert que le promoteur std était activé par Crp, responsable de la répression catabolique, tandis que fim voit son expression modulée par la chaîne de transport d’électrons (Ndh) et des perturbations de l’enveloppe (OmpR). Finalement, nos résultats démontrent que les fimbriae de type chaperon-placier sont importants pour la 6 pathogenèse de S. Typhi et que deux de ceux-ci sont régulés par des signaux environnementaux importants rencontrés par la bactérie lors de l’infection. / Salmonella enterica serovar Typhi is a human-specific pathogenic bacteria and the etiologic agent of typhoid fever. Among its virulence factors, there are 14 putative adhesion systems named fimbriae identified in the S. Typhi genome. Each fimbria is clustered in an operon that encodes for extracellular proteinaceous structures, for the secretion and assembly machinery and sometime for regulators. Fimbrial genes are poorly expressed under laboratory conditions, with few studied in S. Typhi. Among the 14 fimbriae, 12 belong to the chaperone-usher class, where each one encodes a dedicated chaperone and usher that form the fimbrial structure. I propose that fimbriae are important for S. Typhi pathogenesis. The aim of this project is the functional analysis of all the chaperone-usher fimbriae of S. Typhi. My goals were to establish a general characterization of the 12 chaperone-usher fimbriae, and to study specifically the regulation of 2 fimbriae, Fim and Std. The general characterization of chaperone-usher fimbriae includes the determination of the expression of fimbrial promoters in different growth conditions mimicking infection, the observation of the presence and morphology of fimbriae at the bacterial surface, and the evaluation of the role of fimbriae on S. Typhi pathogenesis (biofilm formation, host-cells interactions and motility). Fimbrial expression was generally higher when cells were grown in minimal medium. I was able to observe for the first time the presence of 6 out of 12 fimbriae by transmission electron microscopy. Regarding the role of fimbriae in pathogenesis, each fimbria was involved in at least one step. Regulation of std and fim was studied by evaluating the implication of several general regulators and by screening a transposon-based library. Overall, I discovered that the std promoter was activated by Crp, responsible of catabolic repression, and that fim was modulated by the activity of the electron transport chain and by envelope perturbations. Finally, my results demonstrated that the chaperone-usher fimbriae are important for S. Typhi pathogenesis and two of them are regulated by important environmental signals encountered during bacterial infection.

Chapter Introduction Salmonellae are gram negative bacteria that cause gastroenteritis and entericfever. S. enterica is divided into seven phylogenetic groups, subspecies 1, 2,3a, 3b, and 4, 6, 7. Subspecies1 includes 1,367 serovars, some of which are commonly isolated from infected birds and mammals. The other subspecies mainly colonize cold blooded animals. Salmonella typhimurium, Salmonella typhiandSalmonella enteritidis are some of the serovars, which belong to s.enterica species. S. typhimurium is one of the important causes for food poisoning in humans. It causes typhoid like fever in mice. In immuno compromised patients the infection is often fatal if it is not treated with antibiotics. Clinical features of food poisoning include abdominal pain, vomiting, nausea, abdominal cramps, dehydration etc. S. typhi causes typhoid fever in humans. No other host has been identified for this serovar. Main source of infection is contaminated food and water. No age is exempted but it is less common before2 years. Incubation period is 360 days. Clinical features include stepladder type fever, malaise, headache, hepato splenomegaly, coated tongue, Neutrogena etc. It may be fatal if untreated. Among the serovars of Salmonella infecting humans S. typhimurium and S. typhi are the most important. While S. typhimurium infects many host species including birds and mammals, S. typhi is single host adapted and infects only human. The single host adaptation of S. typhi presents it with the need for establishing are servoir of infection in the community which can serve as a source of fresh infection. Also the single host adaptation of S. typhi has made it a highly specialized pathogen which has evolved certain unique genes needed for human colonization at the same time has lost a set of genes which are needed for survival in other hosts and in the highly variable external environment. This has led to the accumulation of a vast number of pseudo genesin S. Typhi. A comparative study of the two serovars is useful in many ways. Due to varied host defense systems encountered by the two serovars owing to different niche of infection the bacterial counter defense mechanisms are also different. By focusing on the differences between genes involved in the bacterial defense of host immune response we can decipher the role played by various genes in combating the antibacterial host response. Chapter 2 The role of TolA and peptidoglycan modification in detergent resistance of pathogenic Salmonella The major Salmonella serovars that infect human are Salmonella enterica serovar Typhi (S.typhi) which cause systemic typhoid and Salmonella enterica serovar Typhimurium (S. typhimurium) which cause gastro enteritis. S. typhi resides in the gall bladder during chronic infection and S .typhimurium infects intestine .Thus both pathogens encounter high concentrations of bile and have developed mechanisms to counter it. The Tol Pal complex spanning the outermembrane and the inner cytoplasmic membrane plays an important role in maintaining the stability of the outer membrane and providing detergent resistance. The tolA gene of S. Typhi Is shorter by 27 aminoacid than S. typhimurium. The tolA gene knockout of S. typhimurium and S. typhi differed in their tritonX resistance behavoiur, morphology and low osmolality tolerance. S. typhi tolA was unable to complement the tolA defect in S. typhimurium which could probably due to the difference in the peptidoglycan layer. An analys is of the peptidoglycan modifying genes of both the serovars revealed that dacD, pbgP, ynhG are different. dacD, pbgP genes are pseudogenes in S. typhi and ynhG has a major deletion in S. typhi. Further studies reveal that a double knockout of dacD and pbpG in S. typhimurium makes it sensitive to low osmolality similar to S. typhi. Based on these results we propose a mechanism, where shortening of TolA increases detergent resistance by bringing the outer membrane into closer contact with the peptidoglycan layer, but this is achieved at the cost of reduced Lpp (Bruan’slipoprotein) peptidoglycan linkage which plays a major role in low osmolality tolerance. The pathogen S. typhi is highly adapted to the human host and cannot infect any other host. The single host adaptation and the need to survive in high concentrations of bile have made S. typhi to acquire higher bile resistance at the cost of lowered osmotic tolerance through shortening TolA and reduced Lpp and peptidoglycan binding. Chapter 3 Development of a DNA vaccine against Salmonella The immune response against Salmonella is multifaceted involving both the innate and the adaptive immune system. The characterization of specific Salmonella antigens inducing immune response could critically contribute to the development of epitope based vaccines for Salmonella. We have tried to identify aprotective Tcellepitope (s) of Salmonella, as cell mediated immunity conferred by CD8+T cells is the most crucial subset conferring protective immunity against Salmonella. It being a proven fact that secreted proteins are better in inducing cell mediated immunity than cell surface and cytosolic antigens, we have analyzed all the GenBank annotated Salmonella pathogenicity island 1 and 2 secreted proteins of S. typhimurium and S. typhi. They were subjected to BIMAS and SYFPEITHI analysis to map MHCI and MHC II binding epitopes. The huge profile of possible T cell epitopes obtained from the two classes of secreted proteins were tabulated and using a scoring system that considers the binding affinity and promiscuity of binding to more than one allele, SopB and SifB were chosen for experimental confirmation in murine immunization model. The entire Sop Band SifB genes were cloned into DNA vaccine vectors and were administered along with live attenuated Salmonella and it was found that SopB vaccination reduced the bacterial burden of organs by about 5fold on day4 and day8 after challenge with virulent Salmonella and proved to be a more efficient vaccination strategy than live attenuated bacteria alone. Chapter 4 PCR based diagnosis and Serovar Determination of Blood Borne Salmonella Typhoid fever is becoming an ever increasing threat in the developing countries. We have improved considerably upon the existing PCR based diagnosis method by designing primers against a region which is unique to S. typhiand S. paratyphiA, corresponding to the gene STY0312 in S. typhi and its homolog SPA2476 in S. paratyphiA. An additional set of primers amplify another region in S. typhi CT18 and S. typhiTy2 corresponding to the region between the genes STY0313 toSTY0316 but which is absent in S.paratyphi A. The threat of false negative result arising due to mutation in hypervariable genes has been reduced by targeting a gene unique to typhoidal Salmonella as a diagnostic marker. The amplified region has been tested for genomic stability by amplifying them from clinical is olates of patients from various geographical locations in India, there by showing that this region is potentially stable. These set of primers can also differentiate between S. typhiCT18, S. typhiTy2 and S. paratyphi A which have stable deletions in this specific locus. The PCR assay designed in this study has a sensitivityof95%ascompared to the Widal test which had only 63%. As observed, in certain cases the PCR assay was more sensitive than the blood culture test as the PCR based detection could also detect dead bacteria.