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Antibiotic resistance is a worldwide threat to human health yet fewer new antibiotics are being approved. New antimicrobial drugs are urgently required. 3 Deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) is a target for antimicrobial drug design. KDO8PS catalyzes the condensation of D-arabinose-5 phosphate (A5P) with phosphoenolpyruvate (PEP) to produce KDO8P. KDO8PS catalyzes the first committed step in the lipopolysaccharides (LPS) biosynthesis pathway in Gram-negative bacteria and is critical for bacterial pathogenicity/virulence. We have characterized KDO8PS from Campylobacter jejuni (cjKDO8PS), a new metal-dependent KDO8P synthase (KDO8PS). cjKDO8PS is a tetramer in solution and optimally active at pH 7.5 and 60 °C. We have kinetically established that cjKDO8PS follows a rapid equilibrium sequential ordered ter ter kinetic mechanism, where Mn2+ binds first, followed by PEP, then A5P. Pi dissociates first, before KDO8P, then Mn2+. cjKDO8PS was inhibited by KDO8P oxime, a novel slow tight-binding inhibitor. KDO8P oxime is a competitive inhibitor with respect to PEP and A5P, but uncompetitive with respect to Mn2+, with Ki = 10 ± 1 μM and an ultimate Ki* = 0.28 ± 0.10 μM. KDO8P oxime has a residence time (tR) of 5 days on the enzyme, a parameter that is highly correlated to in vivo efficacy. Crystallization conditions for the cjKDO8PS‧Mn2+‧KDO8P oxime complex have been found and can be optimized to obtain a crystal structure that shows how KDO8P oxime interacts with the active sites. / Thesis / Doctor of Science (PhD) / The relentless increase in global antibiotic resistance is, regrettably, not matched with an increase in new effective antibiotics. New antimicrobial drug discovery strategies are desperately needed. Enzymes are key targets for drug design because they catalyze the majority of biological processes. In this project we sought to study and inhibit the activity of KDO8P synthase (KDO8PS) from Campylobacter jejuni, a common cause of food poisoning. KDO8P synthase is a critical enzyme involved in the lipopolysaccharide (LPS) biosynthesis in Gram-negative bacteria. The LPS acts as a permeability barrier and is crucial for bacterial pathogenicity/virulence. We found that C. jejuni KDO8PS is potently inhibited by KDO8P oxime, a novel inhibitor of KDO8PS. This inhibitor presents a unique opportunity to study these enzymes and a platform from which antibiotics against Gram-negative bacteria can be developed.

The severity of flood events is predicted to increase as a consequence of climate change and may lead to a higher burden of waterborne infectious diseases in the United States. Contaminated floodwater transports bacterial, protozoal, and viral pathogens that typically cause moderate intestinal or respiratory disease, but can also lead to more serious disseminated infections among immunocompromised, young, and older people. Hydroclimatology and drinking water infrastructure influence the transmission of disease, but their roles are not well-understood and may vary by pathogen-type or geographic region. Specific outbreaks of waterborne disease have been attributed to major floods and cases have been positively associated with some meteorological variables, but the association between infections and flooding has not been systematically examined. In this dissertation, we examine the association between seasonal and extreme floods and parasitic and bacterial infections using multiple flood-indicator variables and exposure definitions. In Chapter 2, we use multimodel inference and generalized linear mixed models to determine the effect of seasonal meteorology on hospitalizations across the US. We found that hospitalization rates were generally higher in rural areas and in places that relied on groundwater for drinking water sources. Soil moisture, precipitation, and runoff were associated with significant increases in hospitalizations for Legionnaires' disease, Cryptosporidiosis, and Campylobacteriosis, respectively. In Chapter 3, we use 23 years of weekly case data to examine the effect of cyclonic storms on six waterborne infections in a conditional quasi-Poisson statistical model. Storm exposure was defined separately for distinct storm hazards, namely wind speed and cumulative rainfall, and effects were examined over 3 weeks post-storm. We found that exposure to storm-related rainfall was associated with immediate and lagged increases in cases. In Chapter 4, we use a nonparametric bootstrap to examine the effect of anomalous meteorological conditions, i.e. extremes unrelated to cyclonic storms, on Legionnaires' disease hospitalizations. We also assess the effect of exposure to specific cyclonic storms in a GLMM framework and compare these approaches. Extreme precipitation and months with cyclonic storms were positively associated with Legionnaires' disease hospitalizations. Determining the effect of flooding on Legionnaires' disease is particularly important as it causes severe illness and has steadily increased in incidence for 20 years. An objective of this dissertation was to develop a framework for examining flood-disease dynamics in the context of hydrometeorological and infrastructure-related factors that may influence transmission. We demonstrated that drinking water source, rurality, and geography may play an important role in these dynamics; the analyses also underscored, however, the urgent need for more extensive epidemiological surveillance and water quality data. Climate change will likely place a considerable strain on aging water infrastructure in the US. A nuanced understanding of flood-disease dynamics is central to mitigating these effects.

Public health costs of foodborne campylobacteriosis are estimated to cost more than a billion dollars in the United States annually. This pathogen has been primarily associated with chicken production and processing which is a ~$33 billion industry. To further identify practices that could reduce Campylobacter presence, concentration, and persistence in chicken prior to consumption a quantitative microbial risk assessment (QMRA) was conducted for boneless, skinless chicken breast meals prepared and consumed domestically in the contiguous United States. This QMRA model was developed with @RISK software (Palisade Corp., Ithaca, NY) and data inputs can be easily modified and updated. QMRA is a powerful analytic method that can be utilized to model the dynamics between the food pathogen, food commodity, and ingestion. It provides insight into the impacts of the process in its interaction and its surrounding environment. The baseline model determined that consumption of this product resulted in annual means of infections: 328,257, illnesses: 108,174, hospitalizations: 27,754, deaths: 37, cases of Campylobacter-associated Guillain-Barré Syndrome (GBS): 1,373, and cases of Campylobacter-associated Irritable Bowel Syndrome (IBS): 9,501. The associated annual economic burdens were ~$192 million for acute campylobacteriosis, ~$77 million for GBS, and ~$96 million for IBS. The effects of targeting and modifying the baseline model's inputs within the farm-to-fork process were studied as follows: Post grow-out (1) prevalence and (2) concentration of Campylobacter on chickens at the farm prior to transport, (3) transport crate cleaning frequency prior to loading, (4) temperature storage conditions at post processing/ pre-retail, (5) the frequency of handwashing in the preparation and handling of a chicken meal, and (6) the combination Campylobacter mitigation models using the inputs from (2) and (4). Mean yearly illnesses are estimated to decrease by approximately half if on-farm Campylobacter prevalence was lowered to 35-50% from the baseline level of 76%. An additional ~50,000 illnesses can be expected if the proportion of home preparers who do not wash their hands increases from 8.3% (baseline) to 20%. The combined effects of reducing on-farm Campylobacter concentrations and increasing the proportion of product frozen in-plant have greater impacts on reducing yearly campylobacteriosis and associated costs than either intervention alone. / Doctor of Philosophy / Campylobacter is a major foodborne bacterial pathogen that is not well known by the general public, although public health costs are estimated to cost more than a billion dollars in the United States annually. Chicken production is a ~$33 billion industry that is affected by the contamination of this pathogen. In this study, a quantitative microbial risk assessment (QMRA) was performed to study the impact of Campylobacter on chicken meals prepared in the home. Societal and economic burdens were evaluated as well. The models developed provide comprehensive simulations that describe the spread, persistence, and the concentration of Campylobacter throughout the farm to fork process in the annual consumption of boneless, skinless chicken breast meals prepared and consumed domestically in the contiguous United States. Additional simulation models were created to compare methods for reducing Campylobacter along the food chain that could lead to fewer cases of campylobacteriosis in the United States, or what could happen if there was a breakdown in a hygiene step in the preparation of the chicken meal.

Enteric infections are widespread throughout the world and continue to pose a serious health threat, especially to younger children. Bacterial pathogens apply a plethora of distinct virulence mechanisms to efficiently infect and establish host colonization, consequently leading to various diseases. Campylobacter jejuni is currently the leading cause of bacterial foodborne diarrheal disease worldwide. However, in comparison to other enteric pathogens, relatively little is known about how this bacterium establishes infections and mediates virulence in humans. Its genome lacks classical virulence factors or toxins known from other enteric pathogens and only encodes three known sigma factors, suggesting additional layers of gene regulation. Recent transcriptome studies in C. jejuni confirmed the existence of several small regulatory RNAs (sRNAs). However, their function remains largely elusive. This thesis aimed to uncover novel regulators of C. jejuni virulence and physiology. Therefore, a dual RNA sequencing (dual RNA-seq) experiment was performed upon infection of Caco-2 cells in a recently advanced human intestinal three-dimensional (3D) infection model, in parallel to standard two-dimensional (2D) infection of monolayers. This deep-sequencing approach allows for the simultaneous quantification of host and pathogen transcriptomes on a global scale and was intended to unravel new bacterial host-adaptation and virulence-associated factors, as well as to assess host measures in response to C. jejuni infection. While only a small number of human genes were differentially regulated upon infection with C. jejuni NCTC11168 wild-type (WT) bacteria, a large proportion of bacterial genes were found to be differentially expressed. A closer look at the bacterial transcriptome post infection revealed little overlap between up- or downregulated genes in the 3D tissue model compared to 2D cell culture. In addition, different functional classes were enriched in adhered and internalized bacteria within these two different infection environments. Strikingly, several sRNAs were found to be upregulated during infection, highlighting their potential importance for host-pathogen interactions. In many bacterial species, sRNAs are involved in post-transcriptional regulation and fine-tuning of diverse fundamental processes including pathogenesis. Since their role in C. jejuni physiology was largely unexplored, candidates from the dual RNA-seq experiment were selected to uncover their putative targets and characterize their function in C. jejuni NCTC11168. Therefore, sRNA mutant strains were generated and tested for distinct phenotypic traits such as growth defects, protein expression, and motility in comparison to WT bacteria. Furthermore, growth-dependent differences in sRNA expression were determined and total RNA sequencing (RNA-seq) experiments with sRNA deletion mutants were performed to unravel their targetome, in combination with in-silico predictions. Since flagellar motility is a crucial virulence factor that allows Campylobacter to navigate through the viscous mucus of the human intestine, sRNA involvement in this process was explored in more detail. In contrast to transcriptional control of the hierarchically expressed flagellar components, little is known about post-transcriptional regulation of the flagellar biosynthesis cascade in C. jejuni. To this end, one sRNA (CJnc230), encoded downstream of the flagellar hook structural gene flgE and strongly upregulated after infection of the 3D tissue model, was selected to investigate a potential functional link to bacterial motility. CJnc230 is dependent on the flagellar sigma-54 factor (RpoN) and was found to be co-transcribed with the upstream gene flgE, requiring three distinct ribonucleases (RNases) for its processing and maturation. Termination site sequencing (term-seq) and differential RNA sequencing (dRNA-seq) techniques were used to further dissect CJnc230 biogenesis, revealing the boundaries of the most abundant CJnc230 fragment and the presence of an alternative transcriptional start site (TSS) originating from an independent promoter. RNA-seq was performed with an overexpression mutant of CJnc230 to decipher its biological function. In-vitro and in-vivo approaches confirmed direct interaction of the CJnc230 single-stranded region with the ribosome binding site (RBS) of Cj1387c (putative transcriptional regulator) and flgM (anti-sigma-28 factor) mRNAs, thereby repressing their translation. Phenotypic characterization further demonstrated that the CJnc230 overexpression mutant exhibits increased motility and flagellar filament length. The latter is most likely due to increased expression of the major flagellin flaA after repression of FlgM and indirect transcriptional activation of late flagellar genes, dependent on the flagellar sigma-28 factor (FliA). In contrast to CJnc230, the FliA-dependent sRNA CJnc170 was shown to decrease filament length and motility when overexpressed with a heterologous promoter. These observations suggest renaming CJnc230 and CJnc170 to FlmE and FlmR (flagellar length and motility enhancer/repressor), respectively, and that sRNA-mediated post-transcriptional regulation fine-tunes C. jejuni flagellar biosynthesis through balancing of the hierarchically expressed components. In summary, this thesis reveals the importance of C. jejuni sRNAs during infection and dissects the molecular targetome of selected candidates. Moreover, validation of target interactions and downstream functions uncovered a previously uncharacterized role for the CJnc230 sRNA in flagellar biogenesis and its effect on motility, a key determinant of C. jejuni virulence. / Infektionen des Gastrointestinaltrakts sind weltweit verbreitet und stellen nach wie vor eine Gesundheitsbedrohung, insbesondere für Kleinkinder, dar. Bakterielle Krankheitserreger nutzen eine Vielzahl unterschiedlicher Virulenzmechanismen, um den Wirt effizient zu infizieren und zu besiedeln, was zu verschiedenen Krankheiten führen kann. Campylobacter jejuni ist momentan die häufigste Ursache für über die Nahrung übertragene, bakterielle Durchfallerkrankungen weltweit. Im Vergleich zu anderen Darmpathogenen ist jedoch relativ wenig darüber bekannt, wie dieses Bakterium eine Infektion auslöst und welche Virulenzmechanismen diese beim Menschen vermitteln. Dem Genom von C. jejuni fehlen klassische Virulenzfaktoren oder Toxine, die von anderen Darmpathogenen bekannt sind, und es enthält nur drei bekannte Sigmafaktoren, was auf zusätzliche Ebenen der Genregulation schließen lässt. Jüngste Transkriptomstudien an C. jejuni bestätigten die Existenz mehrerer kleiner regulatorischer RNAs (sRNAs). Deren Funktion ist jedoch noch weitgehend ungeklärt. Ziel dieser Doktorarbeit war es, neue Regulatoren der Virulenz und Physiologie von C. jejuni aufzudecken. Dazu wurde ein duales RNA-Sequenzierungsverfahren (dual RNA-seq) nach Infektion von Caco-2-Zellen in einem kürzlich entwickelten dreidimensionalen (3D) Infektionsmodell des menschlichen Darms angewendet, parallel zu herkömmlichen Infektionen in zweidimensionaler (2D) Zellkultur. Diese Hochdurchsatz-Sequenziermethode ermöglicht die globale Quantifizierung des Transkriptoms von Wirt und Erreger in derselben Probe und sollte neue bakterielle Anpassungs- und Virulenzfaktoren aufdecken, sowie die Reaktion des Wirts auf die Infektion mit C. jejuni erfassen. Während nach der Infektion mit C. jejuni NCTC11168 Wildtyp (WT)-Bakterien nur wenige menschliche Gene dereguliert waren, wurde bei einem großen Teil des bakteriellen Transkriptoms eine veränderte Genexpression festgestellt. Ein genauerer Blick verriet, dass es nur wenige Überschneidungen zwischen hoch- und herunterregulierten bakteriellen Genen im 3D-Gewebemodell im Vergleich zu 2D-Zellkultur gab. Darüber hinaus waren, je nach Infektionsumgebung, verschiedene funktionelle Klassen von Genen unterschiedlich stark in adhärenten und internalisierten Bakterien repräsentiert. Auffallend war außerdem, dass mehrere sRNAs während der Infektion hochreguliert waren, was deren mögliche Bedeutung für die Interaktion zwischen Wirt und Erreger unterstreicht. In vielen Bakterienarten sind sRNAs an der post-transkriptionellen Regulierung und Feinabstimmung verschiedener grundlegender Prozesse beteiligt, unter anderem auch an der Pathogenese. Da ihre Rolle in der Physiologie von C. jejuni aber weitgehend unerforscht ist, wurden Kandidaten aus dem dualen RNA-seq Experiment ausgewählt, um mögliche Zielgene aufzudecken und ihre Funktion in C. jejuni NCTC11168 zu charakterisieren. Dazu wurden sRNA-Mutantenstämme erzeugt und auf unterschiedliche phänotypische Merkmale, wie Wachstumsdefekte, Proteinexpression und Motilität, im Vergleich zu WT-Bakterien getestet. Darüber hinaus wurden wachstumsabhängige Unterschiede in der sRNA-Expression bestimmt und RNA-Sequenzierungsexperimente (RNA-seq) mit den Deletionsmutanten durchgeführt, um deren Zielgen-Repertoire in Kombination mit in-silico Vorhersagen zu entschlüsseln. Da flagellare Motilität ein wichtiger Virulenzfaktor ist, der es Campylobacter ermöglicht, durch die zähflüssige Mukusschicht des menschlichen Darms zu navigieren, wurde die Beteiligung von sRNAs an diesem Prozess genauer untersucht. Im Gegensatz zur hierarchisch geordneten Transkription der einzelnen Komponenten der bakteriellen Geißel, ist über die post-transkriptionelle Regulation der Flagellen-Biosynthese in C. jejuni nur wenig bekannt. Daher wurde eine sRNA (CJnc230) ausgewählt, die hinter dem Strukturgen flgE (flagellarer Haken) liegt und nach Infektion des 3D-Gewebemodells stark hochreguliert war, um eine mögliche funktionelle Verbindung zur bakteriellen Motilität zu untersuchen. CJnc230 ist abhängig vom alternativen Sigmafaktor RpoN (Sigma 54) und wird zusammen mit dem vorgelagerten Gen flgE transkribiert, wobei drei verschiedene Ribonukleasen (RNasen) für die Prozessierung und Reifung erforderlich sind. Mit Hilfe von termination site sequencing (term-seq) und differential RNA sequencing (dRNA-seq) wurde die Biogenese von CJnc230 weiter aufgeschlüsselt. Dabei wurden die Enden des am häufigsten vorkommenden CJnc230-Fragments und die Existenz einer alternativen Transkriptionsstartstelle (TSS), die von einem unabhängigen Promotor stammt, aufgedeckt. Um die biologische Funktion von CJnc230 zu entschlüsseln, wurde RNA-seq mit einer Überexpressionsmutante der sRNA durchgeführt. In-vitro und in-vivo Ansätze bestätigten die direkte Interaktion der einzelsträngigen Region von CJnc230 mit der Ribosomenbindestelle (RBS) der mRNAs von Cj1387c (potenzieller Transkriptionsfaktor) und flgM (anti-Sigma-28-Faktor), wodurch die Translation unterdrückt wird. Die phänotypische Charakterisierung zeigte außerdem, dass die CJnc230-Überexpressionsmutante eine erhöhte Motilität und Länge des Geißelfilaments aufweist. Letzteres ist höchstwahrscheinlich auf eine verstärkte Expression des Hauptflagellins flaA nach Repression von FlgM und eine indirekte transkriptionelle Aktivierung von späten flagellaren Genen, die vom alternativen Sigmafaktor FliA (Sigma 28) abhängig sind, zurückzuführen. Im Kontrast zu CJnc230 wurde gezeigt, dass die FliA-abhängige sRNA CJnc170 die Filamentlänge und Motilität verringert, wenn sie mit einem heterologen Promotor überexprimiert wird. Diese Beobachtungen legen eine Umbenennung von CJnc230 und CJnc170 in FlmE bzw. FlmR (flagellar length and motility enhancer/repressor) nahe und zeigen, dass die Flagellen-Biosynthese in C. jejuni zusätzlich durch sRNA-vermittelte, post-transkriptionelle Feinabstimmung der hierarchisch exprimierten Komponenten im Gleichgewicht gehalten wird. Zusammenfassend zeigt diese Doktorarbeit die Bedeutung von C. jejuni sRNAs während der Infektion auf und entschlüsselt die Zielgene ausgewählter Kandidaten. Darüber hinaus wurde durch die Validierung von sRNA-mRNA Interaktionen und nachgeschalteten Funktionen eine bisher nicht charakterisierte Rolle für die CJnc230 sRNA in der Flagellen-Biogenese und ihre Auswirkung auf die Motilität, ein Hauptmerkmal der Virulenz von C. jejuni, aufgedeckt.

Having a comprehensive view of the entire gene complement and coding capacity of bacterial pathogens, and how their gene expression is regulated, is crucial for understanding their strategy for survival, stress adaptation as well as host colonization and infection. In pathogens like Campylobacter jejuni, where homologs of key virulence factors used by other enteric pathogens are absent, it is important to gain a complete census of genes to understand how it causes disease. Deep sequencing approaches have expanded our knowledge on global gene expression profiles and aided in a better understanding of the coding complexity in bacteria. For example, they revealed small regulatory RNAs (sRNAs) involved in, e.g., stress response and adaptation or highlighted the concept of genes within genes, including dual-function sRNAs or alternative open reading frames (ORFs) within or antisense to known genes. Techniques like ribosome profiling (Ribo-seq) spotlighted a major gap in bacterial genome annotations, as it revealed that the so-called small proteome/sORFome (census of small proteins and small ORFs) is largely underrepresented. Small proteins, here defined as independently translated proteins ≤ 70 amino acids (aa), were overlooked or even discarded from genome annotations, and challenges in the biochemical detection further hindered their characterisation. Nevertheless, recently characterised examples of small proteins were identified as important players in physiological processes such as virulence and stress response. In C. jejuni, the leading cause of bacterial gastroenteritis, a recent differential RNA-seq (dRNA-seq) analysis revealed several sRNAs, some of which were shown to be relevant for infection. However, the small proteome of C. jejuni has not been systematically explored, leaving it unclear how many small open reading frames (sORFs) are encoded in the C. jejuni genome and expressed in vivo. Consequently, their function in C. jejuni physiology remains largely elusive, which is further hampering the understanding of how this major foodborne pathogen causes disease in humans. The focus of this thesis was to globally catalogue sORFs in C. jejuni, validate their translation status in vivo and functionally characterise infection-relevant candidates. Therefore, classical Ribo-seq, translation initiation site (TIS) profiling and a novel translation termination site (TTS) profiling method were combined to systematically investigate sORFs of C. jejuni. In addition, mass spectrometry and epitope tagging followed by western blotting were used to validate sORF translation. Collectively, these methodologies revealed novel and hidden sORFs encoded in diverse genomic contexts, as well as further annotation refinements. Hence, the C. jejuni small proteome was expanded almost two-fold by adding 42 novel sORFs to the annotation, and translation of 47 out of 54 already annotated sORFs was validated. Among these, the novel small protein CioY (34 aa), previously missed in the C. jejuni strain NCTC11168 genome annotation, was found to be adjacently encoded to the CioAB terminal oxidase. Further analysis showed that CioY is part of this terminal oxidase with potentially similar functions as the 37 aa-long CydX in E. coli. To aid further characterisation of novel sORFs and to allow for broad access to the translatomics data and our updated annotation, the online resource CampyBrowse was established. To gain insights into the potential functions of small proteins, available functional genetics datasets were inspected to identify candidates that might affect C. jejuni virulence. A transposon sequencing (Tn-seq) screen of C. jejuni infections of human Caco-2 cells in our lab identified the small protein Cj0978c (Mot2, 57 aa) required for motility and colonization. This thesis revealed that the small lipoprotein is necessary for flagellar disk and stator assembly, as it is required for stability and localisation of the basal disk protein FlgP. In addition, to allow for identification of potential interaction partners of small proteins, gradient profiling by sequencing (Grad-seq) as well as thermal proteome profiling (TPP) were successfully established for C. jejuni. While TPP is a sensitive method that is able to detect even slight changes in complex compositions, e.g., due to the absence of a small protein-binding partner, Grad-seq will be a valuable resource to study the C. jejuni complexome, the entire set of protein and RNA complexes. Overall, this thesis expands the genome map of C. jejuni NCTC11168 with novel high-confidence sORFs by using diverse Ribo-seq approaches combined with extensive validation. This integrative translatomic approach will promote the general understanding of the coding complexity in bacteria and allow for future characterisation of diverse small protein/sORF candidates in C. jejuni. Moreover, functional characterisation of Mot2 revealed the importance of a small protein for the functionality of the complex flagella machinery – a crucial virulence-determining process of C. jejuni. / Das gesamte Genkomplement bakterieller Pathogene sowie ihre Kodierungskapazität und Regulierung zu kennen, ist für das Verstehen von Überlebensstrategien, Stressanpassung sowie Wirtskolonisierung und Infektionen entscheidend. Dies ist besonders bei Krankheitserregern wie Campylobacter jejuni wichtig, denen homologe Gene von relevanten Virulenzfaktoren anderer Darmpathogenen fehlen, um zu verstehen, wie sie Krankheiten verursachen. Hochdurchsatz-Sequenziermethoden haben unser Wissen über globale Genexpressionsprofile erweitert und zu einem besseren Verständnis der Komplexität von Bakteriengenomen beigetragen. So wurden beispielsweise kleine regulatorische RNAs (sRNAs) entdeckt, die unter anderem an der bakteriellen Stressanpassung beteiligt sind, oder das Konzept von Genen innerhalb beschriebener Gene enthüllt. Beispiele dafür sind sogenannte dual-function sRNAs, oder alternative offene Leserahmen (ORFs) innerhalb von oder antisense zu bereits bekannten Genen. Techniken wie ribosome profiling (Ribo-seq) haben eine große Lücke in bakteriellen Genomannotationen aufgedeckt, und aufgezeigt, dass das sogenannte kleine Proteom/sORFom (Gesamtheit kleiner Proteine und kleiner ORFs) weitgehend unterrepräsentiert ist. Kleine Proteine, hier als unabhängig translatierte Proteine mit einer Länge von bis zu 70 Aminosäuren (aa) definiert, wurden in Genomannotationen übersehen, oder sogar aussortiert, und Schwierigkeiten beim biochemischen Nachweis beeinträchtigten zusätzlich ihre Charakterisierung. Dennoch haben jüngste Studien gezeigt, dass kleine Proteine wichtige Akteure bei physiologischen Prozessen wie der bakteriellen Virulenz und Stressreaktion sind. Bei C. jejuni, dem Hauptverursacher bakterieller Gastroenteritis, bestätigte eine differential RNA-seq-Analyse (dRNA-seq) die Existenz mehrerer sRNAs, von denen sich einige als infektionsrelevant erwiesen. Das kleine Proteom von C. jejuni wurde jedoch nicht systematisch untersucht, so dass unklar ist, wie viele kleine ORFs (sORFs) im Genom von C. jejuni kodiert und in vivo exprimiert werden. Folglich ist ihre Funktion in der Physiologie des Bakteriums nach wie vor weitgehend unbekannt und erschwert dadurch unser Verständnis darüber, wie dieser wichtige Lebensmittelkeim Krankheiten beim Menschen verursacht. Der Fokus dieser Dissertation lag auf der globalen Katalogisierung von sORFs in C. jejuni, der Validierung ihrer Translation in vivo und der funktionellen Charakterisierung von infektionsrelevanten Kandidaten. Daher wurden Ribo-seq, Translationsinitiationsstellen (TIS)-Profiling und das neue Translationsterminationsstellen (TTS)-Profiling kombiniert, um die Gesamtheit der sORFs von C. jejuni zu untersuchen. Darüber hinaus wurden Massenspektrometrie, Epitopmarkierung und Western Blot Analysen zur Validierung der Translation von sORFs eingesetzt. Insgesamt enthüllte eine Kombination dieser Methoden neue sORFs in den verschiedensten genomischen Kontexten, sowie weitere Nachbesserungen der Annotation. So konnten 42 neue kleine Proteine in die Annotation aufgenommen und damit das kleine Proteom von C. jejuni um nahezu das Zweifache vergrößert werden. Außerdem wurde die Translation von 47 der 54 bereits annotierten sORFs validiert. Das neuartige kleine Protein CioY (34 aa), das zuvor in der Genomannotation von C. jejuni NCTC11168 übersehen wurde, ist in unmittelbarer Nähe der terminalen Oxidase CioAB kodiert. Diese Doktorarbeit hat gezeigt, dass CioY eine Untereinheit dieser terminalen Oxidase ist, und möglicherweise ähnliche Funktionen wie das 37 aa-lange CydX in E. coli hat. Um die weitere Charakterisierung neuer sORFs zu unterstützen und einen breiten Zugang zu den Datensätzen und unserer aktualisierten Annotation zu ermöglichen, wurde die Online-Ressource CampyBrowse eingerichtet. Um kleine Proteine zu identifizieren, welche möglicherweise die Virulenz von C. jejuni beeinflussen könnten, wurden verfügbare funktionelle Datensätze untersucht. Ein vorheriger Tn-seq-Screen aus unserem Labor von C. jejuni infizierten menschlichen Caco-2-Zellen, identifizierte das für die Motilität und Kolonisierung erforderliche kleine Protein Cj0978c (Mot2, 57 aa). Diese Dissertation hat gezeigt, dass das kleine Lipoprotein für den Zusammenbau von funktionellen flagellaren Motoren notwendig ist, da es für die Stabilität und Lokalisierung des basalen flagellaren Disk-Proteins FlgP erforderlich ist. Zur Identifizierung potenzieller Interaktionspartner kleiner Proteine wurden gradient profiling by sequencing (Grad-seq) und thermal proteome profiling (TPP) für C. jejuni erfolgreich etabliert. Während TPP eine sensitive Methode ist, mit der selbst geringfügige Veränderungen in der Komplexzusammensetzung, z. B. durch das Fehlen eines kleinen Proteinbindungspartners, erkannt werden können, dient Grad-seq als wertvolle Ressource zur Untersuchung des C. jejuni-Komplexoms, der Gesamtheit an Protein- und RNA-Komplexen. Insgesamt erweitert diese Doktorarbeit die Genomannotierung von C. jejuni NCTC11168 durch die Kombination verschiedener Ribo-seq-Ansätze und einer umfassenden Validierung um neue sORFs. Dieser integrative Ansatz fördert das allgemeine Verständnis über die Komplexität von bakteriellen Genomannotationen und ermöglicht die künftige Charakterisierung verschiedener kleiner Proteine/sORFs in C. jejuni. Darüber hinaus hebt die funktionelle Charakterisierung von Mot2 die Bedeutung eines kleinen Proteins für die Funktionalität der komplexen Flagellenmaschinerie hervor – ein entscheidender Virulenzmechanismus von C. jejuni.

Une exposition aux viandes comporte un risque pour la santé, et les maladies transmises par ces viandes causent un fardeau important mondialement. En Afrique centrale, le gibier est une viande communément consommée en zone urbaine. L’absence d’information sur le niveau de consommation de gibier, ainsi que sur sa contamination, limite l’évaluation des risques sanitaires associés au gibier. Une étude transversale a visé la description du niveau de consommation des viandes parmi 205 ménages de Port-Gentil (Gabon), ainsi que certains déterminants de la consommation de ces viandes. Une seconde étude transversale a quantifié la contamination musculaire de gibier vendu à Port-Gentil par Salmonella, Campylobacter et Shigella. Sur une base de trois jours, 86% des ménages ont consommé de la volaille, 84% du poisson, 44% du bœuf, 25% du porc et 24% du gibier. La consommation de gibier fut plus fréquente le dimanche et parmi les ménages à revenu élevé. Le gibier fut principalement acquis en carcasse entière sans conservation particulière, mais toujours consommé bouilli. Des trois bactéries ciblées, seule Salmonella a été isolée parmi un de 128 échantillons de gibier. Ces études fournissent des informations utiles pour mieux comprendre les facteurs de risque pour la santé associés à la consommation de viandes au Gabon. Des études sur la contamination des viandes, notamment celles des carcasses de gibier, seront nécessaires pour mieux apprécier les risques spécifiques à chaque différente bactérie pathogène. / Meat poses some risks to human health and meat-borne diseases constitute a high burden worldwide. In central Africa, bushmeat is commonly consumed in the urban setting. A lack of information on bushmeat consumption and contamination limits the evaluation of risks to human health linked to bushmeat. A cross-sectional survey was conducted among 205 households of Port-Gentil (Gabon) to quantify relative consumption levels of different meat types and to explore certain determinants of meat consumption. A separate cross-sectional study aimed to determine the prevalence of Campylobacter, Salmonella and Shigella within bushmeat sold in markets of Port-Gentil. Based on a three-day recall period, 86% of household consumed poultry compared to 84% for fish, 44% for beef, 25% for pork and 24% for bushmeat. Bushmeat consumption was more important on Sundays and within high monthly income households. Most bushmeat was acquired as whole carcasses without formal meat conservation methods, but all bushmeat was boiled prior to consumption. One Salmonella was detected among one of 128 bushmeat samples, whereas no Campylobacter or Shigella were detected. This study provides useful information to help better understand risk factors associated with the consumption of bushmeat in Gabon. Further studies on bacterial contamination of meat, including bushmeat carcasses, are required to better understand potential health risks specific to different bacterial pathogens.

Campylobacter spp., principalmente as espécies C. coli e C. jejuni, são a causa mais comum de doença bacteriana veiculada por alimentos na Europa, Estados Unidos e alguns outros locais do mundo. No Brasil, há uma escassez de estudos de C. coli, o que dificulta avaliar a dimensão do envolvimento dessa bactéria como causadora de doença nos seres humanos e em animais, bem como, determinar o impacto de sua presença em alimentos e no meio ambiente. O objetivo desse trabalho foi caracterizar molecularmente linhagens de C. coli isoladas de origens diversas no Brasil pela pesquisa da presença de genes relacionados à virulência por PCR, perfil de sensibilidade a antimicrobianos e pela análise da similaridade genotípica por métodos de tipagem molecular. Adicionalmente, o Índice de Discriminação (D) de tais metodologias foi verificado. Foram estudadas 63 linhagens de C. coli, isoladas de humanos (12), animais (21), alimentos (10) e ambiente (20), entre os anos de 1995 e 2011, nos Estados do Rio de Janeiro, São Paulo e Minas Gerais. Todas as linhagens apresentaram os genes flaA, cadF e sodB. O gene cdtB foi detectado em 20 (31,7%) linhagens, o gene flhA foi detectado em 11 (17,5%) linhagens, o gene dnaJ foi encontrado em 10 (15,9%) linhagens, o gene pldA foi detectado em sete (11,1%) linhagens, o gene iamA foi detectado em três (4,8%) linhagens, os genes cdtC e docA foram encontrados em duas (3,2%) linhagens, os genes cdtA e crsA foram encontrados em uma (1,6%) linhagem e os genes ciaB, wlaN, virB11 e racR não foram detectados. Dentre as 63 linhagens estudadas, 42 foram susceptíveis a todos os antimicrobianos testados. Das 21 linhagens resistentes, 10 (15,9%) foram resistentes a tetraciclina e doxaciclina, seis (9,5%) foram resistentes a ciprofloxacina e uma (1,6 %) foi resistente a eritromicina. Somente quatro (6,3%) linhagens foram resistentes a pelo menos duas diferentes classes de antibióticos testados simultaneamente. O dendrograma de similaridade genética de Pulsed field gel electrophoresis (PFGE) agrupou as 63 linhagens estudadas em dois grupos principais denominados PFGE-A e PFGE-B com similaridade genômica de 44,9% entre eles. Entretanto, algumas linhagens isoladas de humanos, animais, ambiente e alimentos apresentaram uma alta similaridade genotípica acima de 80% entre elas e, foram agrupadas em sete subgrupos denominados PFGE-A1 a PFGE-A7. O dendrograma de similaridade genômica das sequências da SVR do gene flaA agrupou as linhagens ii estudadas em dois grupos principais designados SVR-A e SVR-B, com similaridade acima de 83,1 % entre eles. Ademais, o depósito das sequências da SVR do gene flaA no banco de dados online demonstrou que os alelos 30 e o 1647 foram os mais frequentemente encontrados e permitiu a comparação das linhagens estudadas com os alelos descritos no banco de dados. Sete alelos, dentre os 22 encontrados, não haviam sido previamente descritos. A análise do locus CRISPR por HRMA dividiu as linhagens de C. coli em quatro diferentes perfis de melting. O Multilocus sequence typing (MLST) foi utilizado para tipar 20 linhagens de C. coli e foram obtidos 18 STs diferentes dos quais apenas dois já haviam sido previamente descritos. O D das metodologias de PFGE, sequenciamento da SVR do gene flaA, análise do locus CRISPR por HRMA e MLST foi de 0,986, 0,916, 0,550 e 0,989, respectivamente. Pode- se concluir que o potencial patogênico das linhagens de C. coli não foi evidenciado o que pode estar relacionado ao fato da maioria dos estudos envolvendo patogênese terem sido realizados para a espécie C. jejuni. Algumas linhagens apresentaram-se resistentes aos antimicrobianos testados, o que é preocupante uma vez que tais linhagens podem disseminar genes de resistência a outras isoladas de diversas fontes. Os resultados gerados pelos métodos de tipagem molecular por PFGE e sequenciamento da pequena região variável (SVR) do gene flaA demonstraram uma alta similaridade genotípica entre algumas linhagens de C. coli, sugerindo que uma possível contaminação tenha ocorrido entre linhagens isoladas de fontes clínicas e não clínicas ao longo de 16 anos no Brasil. Ademais, a análise dos alelos da SVR do gene flaA nos permitiu concluir que os alelos prevalentes nas linhagens estudadas diferem daqueles encontrados nos países Europeus. Os dados obtidos por MLST sugerem que as linhagens estudadas possuem uma grande diversidade genética entre si e em comparação com as linhagens isoladas em diferentes locais do mundo. Finalmente, as técnicas de MLST e PFGE foram as mais eficientes e adequadas na genotipagem das linhagens de C. coli estudadas. / Campylobacter spp., mainly the C. coli and C. jejuni species, are the most common cause of bacterial disease conveyed by food in Europe, United States, and other places worldwide. In Brazil, there is a paucity of studies on C. coli, which makes it difficult to evaluate the involvement of this bacterium as a cause of diseases in humans and animals, as well as to determine the impact of its presence in food and the environment. The aim of this study was to molecularly characterize C. coli strains isolated from diverse origins in Brazil by searching for the presence of virulence-related genes by PCR, antimicrobial sensitivity profile, and analysis of the genotypic similarity by molecular typing methods. Addicionaly, the Discriminatory Index (D) of those methodologies was acessed. Sixty-three C. coli strains isolated from humans (12), animals (21), food (10), and the environment (20) between 1995 and 2011, in the States of Rio de Janeiro, São Paulo, and Minas Gerais were studied. All strains presented the flaA, cadF and sodB genes. The cdtB gene was detected in 20 (31.7%) strains; the flhA gene was detected in 11 (17.5%) strains; the dnaJ gene was detected in 10 (15.9%) strains; the pldA gene was detected in 7 (11.1%) strains ; the iamA gene was detected in three (4.8%) strains; the cdtC and docA genes were found in two (3.2%) strains; the cdtA and crsA were found in one (1.6%) strain and the ciaB, wlaN, virB11 and racR genes were not detected. Among the 63 strains studied, 42 were susceptible to all antimicrobials tested. Of the 21 resistant strains, 10 (15.9%) were resistante to tetracycline and doxaciclyne, six (9.5%) showed resistance to ciprofloxacin, and one (1.6%) was resistant to erythromycin. Only four (6.3%) strains were simultaneously resistant to at least two different classes of the antibiotics tested. The dendrogram of genetic similarity of Pulsed field gel electrophoresis (PFGE) grouped the 63 strains studied into two groups namely PFGE-A and PFGE-B with a genomic similarity of 44.9% among them. However, some strains isolated from humans, animals, the environment and food presented a high genotypic similarity above 80% and were subdivided into seven groups designated as PFGE-A1 to PFGE-A7. The dendrogram of genetic similarity of the SRV-flaA gene sequences grouped the strains studied into two groups namely SVR-A and SVR-B, with similarity above 83.1% among them. Besides, the deposit of the SVR sequences of the flaA gene in the online database showed that the alleles 30 and 1647 were the iv most frequently found and allowed the comparison between the strains studied with the alleles described in the database. Seven alleles, among the 22 found have never been described before. The CRISPR locus analysis divided the C. coli strains into four different melting profiles. The Multilocus sequence typing (MLST) was used to type 20 C. coli strains and revealed 18 different STs among which just two had been previously described. The D of PFGE, SVR- flaA sequence, HRMA of CRISPR locus analysis and MLST was 0.986, 0.916, 0.550 and 0.989, respectively. In conclusion, the pathogenic potential of the C. coli strains was not highlighted, which could be related to the fact that the majority of the pathogenicity studies were performed with C. jejuni species. Some strains showed resistance to the antibiotics tested what is a concern once those strains may spread the resistance genes to other strains isolated from different sources. The results obtained by PFGE and SVR-flaA sequence showed a high genomic similarity among some C. coli strains which may suggest that a possible contamination may have occurred among clinical and non-clinical sources during 16 years in Brazil. Furthermore, the analysis of SVR- flaA alleles allowed the conclusion that the prevalent alleles in the strains studied were different from those found in European countries. The data obtained by MLST suggests that the strains studied had a high genomic diversity among them and in comparison with strains isolated from different places worldwide. Finally, the MLST and PFGE technicques were the most efficient and adequate in genotyping the C. coli strains studied.

Campylobacter jejuni é a espécie bacteriana mais comumente relacionada como causa de gastroenterite em humanos em vários países. Porém, o isolamento e o estudo de C. jejuni não são muito frequentes no Brasil, o que dificulta avaliar a dimensão dessa bactéria como causadora de doença em humanos e animais, bem como, determinar o impacto de sua presença em alimentos e no meio-ambiente. O objetivo desse trabalho foi avaliar a diversidade genética por cinco diferentes técnicas de tipagem molecular, o potencial patogênico pela pesquisa de 16 genes de virulência por PCR e o perfil de resistência pela concentração inibitória mínima por Etest® frente a quatro antimicrobianos e pela análise in silico de genes de resistência e pontos de mutação de linhagens de C. jejuni isoladas no Brasil. Foram estudadas 121 linhagens de C. jejuni isoladas de humanos (51), animais (35), alimentos (33) e ambiente (02) nos estados de Minas Gerais, São Paulo, Rio de Janeiro e Rio Grande do Sul, no período de 1996 a 2016. Todas as linhagens apresentaram os genes flaA, flhA, iamA, docA, ciaB, cdtA, cdtB, cdtC, racR, dnaJ, pldA, cadF, sodB e csrA. O gene wlaN foi detectado em 15 linhagens, e uma linhagem apresentou o gene virB11. Dentre as 121 linhagens estudadas, 68 linhagens foram resistentes a pelo menos um dos antimicrobianos testados. A resistência à ciprofloxacina, doxiciclina, tetraciclina e eritromicina foi observada em 43,8%, 34,7%, 34,7% e 4,9% das linhagens, respectivamente. O dendrograma de similaridade genética de Pulsed field gel electrophoresis (PFGE) agrupou as 121 linhagens estudadas em três grupos com similaridade genômica de 46,9% entre eles. Apesar da alta diversidade genômica entre as linhagens estudadas, algumas linhagens isoladas de diferentes fontes, locais e anos, apresentaram uma similaridade genotípica acima de 80% entre elas e, foram agrupadas em 21 subgrupos. Pelas sequências da SVR do gene flaA as linhagens estudadas foram agrupadas em dois grupos com linhagens isoladas de fontes clínicas e não clínicas e de humanos e animais com similaridade acima de 80,9 % entre elas e tipadas em 40 SVR-flaA alelos, sendo os alelos 57, 49 e 45 os mais frequentemente detectados. A análise do locus CRISPR por HRMA tipou as linhagens de C. jejuni em 23 diferentes variantes sendo que algumas variantes continham linhagens de origem clínica e não clínica e de humanos e animais. A árvore de SNPs gerada a partir dos dados do sequenciamento do genoma completo alocou as 116 linhagens sequenciadas em dois principais grupos. O grupo SNP-A agrupou 97 linhagens e o grupo SNP-B agrupou 19 linhagens, com linhagens de fontes clínicas e não clínicas e de humanos e animais, respectivamente. A técnica de Multilocus sequence typing (MLST) tipou as 116 linhagens de C. jejuni em 46 STs, e não foi observada a predominância de um ST. O índice de discriminação das metodologias de análise de SNPs no genoma completo, PFGE, MLST, sequenciamento das SVR do gene flaA e análise do locus CRISPR por HRMA foi 1,0, 0,982, 0,941, 0,939 e 0,874, respectivamente. Na análise in silico de genes de resistência e pontos de mutação, 95 linhagens apresentaram ao menos um gene de resistência ou ponto de mutação conhecido, sendo que a porcentagem de correlação entre os resultados de resistência fenotípicos e genotípicos foi maior que 66,7%; 94,6% e 96,8% para eritromicina, tetraciclina e ciprofloxacina, respectivamente. Conclui-se que a alta frequência da maioria dos genes de virulência pesquisados evidenciou o potencial patogênico das linhagens de C. jejuni estudadas. A resistência a antimicrobianos de primeira escolha utilizados para o tratamento da campylobacteriose encontrada nas linhagens estudadas é preocupante, podendo levar à falha terapêutica quando o tratamento é necessário. Os resultados obtidos pelas metodologias de tipagem molecular realizadas sugerem que uma possível contaminação possa ter ocorrido entre fontes clínicas e não clínicas e entre humanos e animais, ao longo de 20 anos no Brasil. Pelo índice de discriminação, foi observado que as metodologias de análise de SNPs no genoma completo e PFGE, em comparação com as outras técnicas de tipagem, foram as mais eficientes em discriminar as linhagens de C. jejuni do presente estudo. / Campylobacter jejuni is the most commonly bacterial species related as a cause of gastroenteritis in humans in several countries. However, the isolation and the study of C. jejuni have not been very frequently in Brazil, which makes it difficult to evaluate the involvement of this bacterium as a cause of diseases in humans and animals, as well as to determine the impact of its presence in food and the environment. The aim of this study was to evaluate the genetic diversity by five different molecular typing techniques, the pathogenic potential by searching for the presence of 16 virulence genes by PCR and the resistance profile by the minimum inhibitory concentration by Etest® against four antibiotics and by the in silico analyses of resistance genes and mutation points of C. jejuni strains isolated in Brazil. A total of 121 C. jejuni strains isolated from humans (51), animals (35), food (33) and the environment (02) in the States of Minas Gerais, Sao Paulo, Rio de Janeiro and Rio Grande do Sul, between 1996 to 2016 were studied. All strains presented the genes flaA, flhA, iamA, docA, ciaB, cdtA, cdtB, cdtC, racR, dnaJ, pldA, cadF, sodB and csrA. The wlaN gene was detected in 15 strains, and one strain presented the virB11 gene. Among the 121 strains studied, 68 strains were resistant to at least one of the antibiotics tested. Resistance to ciprofloxacin, doxycycline, tetracycline and erythromycin was observed in 43.8%, 34.7%, 34.7% and 4.9% of the strains, respectively. The Pulsed field gel electrophoresis (PFGE) dendrogram of genetic similarity clustered the 121 strains studied in three groups with a genomic similarity of 46.9% among them. Despite the high genomic diversity among the strains studied, some strains isolated from different sources, places and years, presented a genotypic similarity above 80% among them and were grouped into 21 subgroups. By flaA-SVR sequencing the strains studied were clustered into two groups with strains isolated from clinical and non-clinical sources and from humans and animals with a similarity above 80.9% among them and typed in 40 flaA-SVR alleles, being the alleles 57, 49 and 45 the most frequently detected. The analysis of the CRISPR locus by HRMA typed the C. jejuni strains in 23 different variants, with some variants containing strains from clinical and non-clinical origin and from humans and animals. The SNP tree generated from the whole genome sequencing data grouped the 116 strains sequenced into two major groups. SNP-A grouped 97 strains and SNP-B grouped 19 strains, with strains from clinical and non-clinical sources and from humans and animals, respectively. Multilocus sequence typing (MLST) technique typed the 116 C. jejuni strains in 46 STs, and it was not observed a predominant ST. The discrimination index of the analysis of SNPs in the whole genome, PFGE, MLST, flaA-SVR sequencing and analysis of the CRISPR locus by HRMA was 1.0, 0.982, 0.941, 0.939 and 0.874, respectively. In the in silico analyses of resistance genes and mutation points, 95 strains showed at least one resistance gene or known mutation point, and the percentage of correlation between phenotypic and genotypic resistance results was greater than 66.7%; 94.6% and 96.8% for erythromycin, tetracycline and ciprofloxacin, respectively. In conclusion, the high frequency of the majority of the virulence genes studied highlighted the pathogenic potential of the C. jejuni strains studied. Resistance to antimicrobials of first choice used for the treatment of campylobacteriosis found in the strains studied is worrying and may lead to therapeutic failure when treatment is required. The results obtained by the molecular typing methodologies performed suggest that a possible contamination may have occurred between clinical and non-clinical sources and between humans and animals over 20 years in Brazil. By the discrimination index, it was observed that the methodologies of analysis of SNPs in the whole genome and PFGE, in comparison to the other typing techniques, were the most efficients in discriminating the C. jejuni strains of the present study.