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Salmonella enterica is a facultative intracellular pathogen capable of eliciting severe, systemic disease necessitating antibiotic intervention. Systemic infection is facilitated by intracellular replication within host immune cells, which is enabled by complex regulatory networks governed by two-component systems (TCSs). Intracellular-active TCSs sense antimicrobial chemical cues in the microenvironment and respond adaptively through transcriptional regulation to support intracellular survival. SsrA/SsrB and PhoQ/PhoP are two essential TCSs that elicit a robust defense against host immunity by regulating clusters of virulence genes and integrating novel targets to support regulon expansion and enhance pathogenicity. Metabolic adaptation is critical to bacterial survival and can initiate host-pathogen interactions that influence infection outcome. Further, mitigation of host immunity by manipulation of arginine metabolism has been documented in intracellular pathogens. Herein, I investigated TCS-mediated regulatory evolution pertaining to arginine metabolism, hypothesizing that adaptations to metabolic regulation might confer a fitness advantage to Salmonella replicating intracellularly. I explored intracellular regulation of de novo biosynthesis and extracellular import of arginine, establishing PhoP-mediated regulation of arginine transport. I determined that arginine transport contributes to bacterial fitness in macrophages and began to investigate the mechanism by which arginine importation enriches for intracellular replication. This work informs on evolutionary mechanisms that serve to enhance virulence in Salmonella and provides further insight into our understanding of the intracellular lifestyle of infection. / Thesis / Master of Science (MSc) / Salmonella enterica is an intestinal pathogen that survives within host immune cells and causes systemic disease. These bacteria replicate within antimicrobial cells by using sensory networks to detect harmful immune factors and respond adaptively by eliciting change in gene expression to defend against immune-based killing. The amino acid arginine is an important component of host immunity, as well as bacterial antimicrobial defenses; therefore, I hypothesized that bacterial metabolism might be adapted to the host immune cell environment in order to mitigate arginine-dependent antimicrobial activity. Here, I establish that arginine metabolism is controlled by intracellular-specific sensory networks, and demonstrate that this regulation is important for bacterial survival. This work provides evidence for the importance of this amino acid in Salmonella infection, which informs on our overall understanding of systemic disease.

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To revitalize the antibiotic pipeline, it is critical to identify and validate new antimicrobial targets. An uncharted area of antibiotic discovery can be explored by inhibiting nutrient biosynthesis. Herein, we investigate the potential of inhibiting biotin biosynthesis in monotherapy and combination therapy approaches to treat multidrug-resistant Gram-negative pathogens. In chapter 2, we validate biotin biosynthesis as a viable target for Gram-negative pathogens. Historically, biotin biosynthesis was overlooked as a target in Gram-negative pathogens as there was no observed fitness cost associated with its inhibition in standard mouse infection models. We discovered traditional mouse models do not accurately represent the biotin levels in humans. We developed an innovative mouse model to account for this discrepancy, validating biotin biosynthesis as an antimicrobial target in the presence of human-mimicking levels of biotin. Exploiting this sensitivity, we show that an inhibitor of biotin biosynthesis, MAC13772, is efficacious against Acinetobacter baumannii in a systemic murine infection model. In chapter 3, we continue to investigate the potential of targeting biotin biosynthesis in a combination therapy approach. In this work, we identify the ability of MAC13772 to synergize with colistin exclusively against colistin-resistant pathogens. The first committed step of fatty acid biosynthesis requires biotin as a cofactor; therefore, it is indirectly inhibited through the action of MAC13772. We propose that the inhibition of fatty acid biosynthesis leads to changes in membrane fluidity and phospholipid composition, restoring colistin sensitivity. The combination of a fatty acid biosynthesis inhibitor and colistin proved superior to either treatment alone against mcr-1 expressing Klebsiella pneumoniae and colistin-resistant Escherichia coli murine infection models. Together, these data suggest that biotin biosynthesis is a robust antibiotic target for further development in monotherapy and combination therapy approaches. / Thesis / Doctor of Philosophy (PhD)

Salmonella is a Gram-negative intracellular pathogen that causes gastroenteritis and typhoid fever in humans. Salmonella can survive and replicate within host cells and has adapted several mechanisms to evade host immune defenses. The innate immune system plays an important role as a first-line of defense against pathogens such as Salmonella, and is mediated in part by toll-like receptors (TLRs). TLRs recognize fundamental components of pathogenic microorganisms and activation of TLRs leads to downstream signaling cascades eventually resulting in the expression of pro-inflammatory cytokines (4) and also has a role in activating adaptive immunity through presentation of antigens to lymphocytes (86). There are several lines of evidence that suggest that TLR activation may have therapeutic potential in therapies against infectious disease and several TLR agonists have been shown to protect against both bacterial and viral infection in mice (7; 8; 38; 66; 75; 84; 89; 121). To understand how TLR-agonist treatment of host cells affects Salmonella pathogenesis, RAW 264.7 murine macrophages were treated with the TLR agonists liposaccharide (LPS), poly(I:C), peptidoglycan, and CpG-ODN. Treatment of macrophages with all TLR-agonists results in increased phagocytosis of Salmonella compared to control-treated macrophages. These increases in phagocytic activity, however, do not enhance macrophage anti-microbial activity, since Salmonella infection of TLR-treated macrophages results in increased intracellular replication compared to control-treated cells. Infection with Salmonella mutants indicates that increased intracellular replication of Salmonella in TLR-treated macrophages is dependent on a functional SPI-2 type III secretion system. This also indicates that there was not a generalized defect in macrophage anti-bacterial function. These data exemplify how interactions between macrophage defense mechanisms and bacterial virulence factors can result in evasion of the innate immune response. Studying how TLR-agonist treatment affects Salmonella pathogenesis will give us a better understanding of the host-pathogen relationship and may provide insight into novel strategies to fight intracellular microorganisms. / Thesis / Master of Science (MSc)

<p>Disease caused by the Gram-negative <italic>Haemophilus</italic> cryptic genospecies begins with colonization of the maternal genital or neonatal respiratory tract. The primary goal of this work was to identify and characterize the molecular determinant(s) of <italic>Haemophilus<i/talic> cryptic genospecies adherence as a means to better understand the specific adaptation of this species to the urogenital tract and neonatal respiratory tract. Using transposon mutagenesis of prototype strain 1595, we identified a locus that is essential for <italic>Haemophilus</italic> cryptic genospecies adherence to a variety of epithelial cell lines of both genital and respiratory origin. This locus encodes a protein called Cha that shares homology with trimeric autotransporters. Trimeric autotransporters are composed of an N-terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a short C-terminal membrane anchor domain and are classically characterized by head-stalk-anchor domain architecture. By generating chimeric proteins, we demonstrated that the C-terminus of Cha trimerizes in the bacterial outer membrane and is capable presenting a heterologous passenger domain (Hia) in a functional form, thus confirming that Cha is a trimeric autotransporter. Southern analysis revealed that <italic>cha</italic> is unique to the <italic>Haemophilus</italic> cryptic genospecies and is ubiquitous among these strains. </p><p>Similar to a number of trimeric autotransporters, the passenger domain of Cha contains scattered clusters of YadA-like head domains associated with head-to-stalk neck adaptor motifs, predicted coiled-coil stalks and a series of identical tandem coding repeats which are not required for adherence. By evaluating the adherence capacity of <italic>H. influenzae</italic> expressing Cha deletion derivatives, we established that the N-terminal 473 residues of Cha harbor the binding domains responsible for Cha-mediated adherence to epithelial cells. In additional studies, we demonstrated that this same N-terminal region mediates bacterial aggregation through inter-bacterial Cha-Cha binding. </p><p>Further analysis revealed that variable Cha-mediated adherence is linked to spontaneous changes in the number of identical tandem repeats predicted to comprise a coiled-coil stalk domain. Variation in repeat copy number has a direct effect on Cha adhesive and aggregative activity, independent of an impact on transcription of the <italic>cha</italic> locus or surface localization of Cha protein. Moreover, length of Cha surface fibers correlates with repeat copy number expansion. We propose two hypotheses to explain how repeat expansion inhibits bacterial aggregation and host cell binding: 1) Variation in the number of 28-amino acid repeats may influence the conformation of Cha, thus changing the surface accessibility of the Cha binding pocket. 2) Repeat expansion results in the formation of long, flexible Cha fibers on the bacterial cell surface that may have a greater propensity to interact with neighboring Cha trimers at the N-terminus, thereby precluding adherence to other bacteria or host epithelial cells. </p><p>In additional studies screening adherent cryptic genospecies isolates for expression of Cha protein, we identified an additional, antigenically-divergent Cha variant that we refer to as Cha2. Amino acid sequence and domain comparison of Cha2 with Cha (now Cha1) revealed that the structurally undefined N-terminal sequences (encompassing the Cha1 adhesive and aggregative domain) are strikingly divergent. Inspite of this, Cha2 mediates efficient adherence to human epithelial cells, similar to Cha1.</p><p>Identification of Cha offers insight into the apparent tissue tropism associated with the <italic>Haemophilus</italic> cryptic genospecies. We speculate that the unique regulation of Cha adhesive activity enhances the adaptive capability of this pathogenic organism in the human host.</p> / Dissertation

Infections with the bacterial pathogen Chlamydia trachomatis are a critical public health problem. Chlamydia remains the number one cause of preventable blindness worldwide and the leading cause of bacterial sexually transmitted infections in the United States. In humans, repeat and persistent infections with Chlamydia result in severe inflammation. Inflammation in the conjunctiva can result in blindness, while inflammation in the genital tract can result in pelvic inflammatory disease, ectopic pregnancy or infertility. In order to curb the increasing incidence of Chlamydia infections worldwide it will be necessary to develop a protective vaccine that affords long-term protection and prevents pathologies. To better inform vaccine development we must understand the mechanisms that drive long-term immunity in the genital tract and elucidate critical interactions between Chlamydia and host cells to uncover potential mechanisms of immune evasion.

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

abstract: Teleosts have the most primitive adaptive immune system. However, in terms of functionality the teleost immune system is similar to birds and mammals. On the other hand, enteric bacterial pathogens of mammals and birds present conserved regulatory mechanisms that control virulence factors. In this context, deletion of conserved genes that control virulence factors have been successfully used as measure to construct live attenuated bacterial vaccines for mammals and birds. Here, I hypothesize that evolutionary conserved genes, which control virulence factors or are essential for bacterial physiology in Enterobacteriaceae, could be used as universal tools to design live attenuated recombinant bacterial vaccines from fish to mammals. The evolutionary conserved genes that control virulence factors, crp and fur, and the essential gene for the synthesis of the cell wall, asd, were studied in Edwardsiella ictaluri to develop a live recombinant vaccine for fish host. The genus Edwardsiella is one of the most ancient represent of the Enterobacteriaceae family. E. ictaluri, a host restricted pathogen of catfish (Ictalurus punctatus), is the causative agent of the enteric septicemia and one of the most important pathogens of this fish aquaculture. Although, crp and fur control different virulence factors in Edwardsiella, in comparison to other enterics, individual deletion of these genes triggered protective immune response at the systemic and mucosal level of the fish. Deletion of asdA gene allowed the creation of a balanced-lethal system to syntheses heterologous antigens. I concluded that crp, fur and asd could be universally used to develop live attenuate recombinant Enterobacteriaceae base vaccines for different hosts. / Dissertation/Thesis / Ph.D. Microbiology 2012

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