C. jejuni, a pathogenic gram-negative bacterium infecting the human gastrointestinal tract has lately been shown to cause bacteraemia to a wider extent than previously known. In some genotypes, this is thought to be related to GDP-Mannose 4,6 dehydratase encoded by the gene wcbK in the capsule polysaccharide operon and its potential phase variated regulated nature mediated by a homopolymeric guanine tract. This potential regulatory tract has been reported to be controlling the survival in serum by switching expression of wcbK “ON” or “OFF”. This master thesis report evaluates C. jejuni’s ability to survive human serum and low pH, as proxies for the conditions that bacteria meet in human blood or the stomach, respectively. By next generation sequencing, I evaluated the correlation between survival in human serum and the wcbK gene’s “ON” or “OFF” state. Furthermore, the temporal stability of the serum resistant phenotype was assessed over multiple generations. I found that a serum resistant fraction of the C. jejuni population could be enriched by selection in normal human serum. The serum resistant part of the population did not decrease during repeated subculture for 10 generations in bacterial culture medium. However, there was no correlation between the extent of serum resistance in the population and the “ON” or “OFF” state of the wcbK gene.

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.

This study was conducted to determine the extent in which Campylobacter jejuni colonized live birds would survive evisceration and contaminate the processed carcasses. Birds were infected with a marker strain of Campylobacter jejuni and allowed to grow to market age. Cloacal and fecal samples were analyzed to determine the level of Campylobacter jejuni present in the live bird. Prior to slaughter, birds were selectively subjected to two different temperatures (21 and 32°C) and three different times of feed withdrawal for chickens (3, 6,and 9 hours and turkeys 0, 4, and 8 hours). Birds were then slaughtered and the carcasses were sampled to determine the level of Campylobacter jejuni that survived. Results indicated a difference between chickens and turkeys, especially regarding the infective dose and bacterial survival rates. No significant differences in carcass contamination due to feed withdrawal times at either temperature were noted. The correlation of fecal samples with cloacal samples was significant for year 2 with r = .53 (p .04). For turkeys, the correlations were not significant. A longitudinal study of turkeys showed that the percentage of birds infected with Campylobacter jejuni peaked when the birds were 5-7 weeks old. The amount of Campylobacter contamination in each turkey peaked when the birds were 5 weeks old and then dropped off quickly. / Master of Science

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.

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.

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.

D. Tech. (Department of Biotechnology, Faculty of Applied and Computer Sciences), Vaal University of Technology. / Salmonella enterica serovar Typhimurium and Campylobacter jejuni are the leading causes of Salmonellosis and Campylobacteriosis that is characterised by gastroenteritis. These waterborne diseases can be easily prevented by home water treatment methods such as solar disinfection (SODIS). The SODIS process involves placing microbiologically unsafe water in clear plastic or glass bottles and exposing them to direct sunlight for approximately six to eight hours. SODIS kills microbes through a combination of DNA-damaging effects of ultraviolet (UV) radiation and thermal inactivation from solar heating. The result is microbiologically safe water. Continuous drinking of SODIS treated water may confer some immunological effects on the consumer. These immunological effects have not been thoroughly explored. Therefore, the objectives of this study were to firstly, characterise the effects of solar irradiation on the viability of S. Typhimurium and C. jejuni; secondly, to determine the cytotoxicity and modulation of cell death of solar irradiated S. Typhimurium and C. jejuni on macrophages. Thirdly, to analyse the chemokine and cytokine profiles of macrophages infected with solar irradiated S. Typhimurium and C. jejuni. Lastly, to analyse the host-cell interactions of macrophages infected with solar-irradiated and non-solar irradiated S. Typhimurium and C. jejuni using a proteomic approach. In all the experiments, S. Typhimurium and C. jejuni were (i) heat/chemically treated, (ii) solar and non-solar irradiated for 4 and 8 hours. A murine macrophage cell line RAW264.7 was co-cultured with the differentially treated bacteria species for 3 and 24 hours. Appropriate controls were included. The impact of solar irradiated S. Typhimurium and C. jejuni on intracellular growth, proliferation, cytotoxicity, and apoptosis on macrophages was assessed. Intracellular growth of the both bacterial species was assessed with the gentamicin protection assay, and cytotoxicity was determined by Lactate Dehydrogenase Assay (LDH). The macrophages treated with solar irradiated S. Typhimurium and C. jejuni showed no intracellular growth after 48 hours post-infection. However, the non-irradiated S. Typhimurium survived within the macrophages and were highly toxic to the macrophages (average cytotoxicity of 91%±32). The non-solar irradiated C. jejuni were metabolically active but non-culturable, whereas the solar-irradiated C. jejuni was metabolically inactive. Thus, solar irradiated C. jejuni showed a lower percentage cytotoxicity (2.57% ± 0.32%) in comparison to non-solar irradiated C. jejuni at 24 hours post-infection (p.i.) (30.28% ± 0.05%). Flow cytometric analysis showed that the non-irradiated S. Typhimurium brought about a statistically significant increase in the percentage of necrotic cells (48% ± 2.99%), whereas bacteria irradiated for 8 hours produced a lower percentage of necrotic cells (25% ± 5.87%). The heat/chemical attenuated samples had the lowest percentage of necrotic cells (21.15% ± 5.36%) at 24 h p.i. Macrophages treated with solar irradiated and non-solar irradiated C. jejuni did not induce necrosis, but apoptotic cell death. At 24 h p.i., the highest proportion of apoptotic cell death was observed in macrophages treated with non-solar irradiated C. jejuni whereas the solar irradiated C. jejuni showed a lower percentage of apoptotic cell death. Therefore, there is great possibility that S. Typhimurium and C. jejuni could become avirulent after SODIS treatment and this could prevent gastroenteritis in consumers of SODIS-treated water. The activation of macrophages infected with solar irradiated S. Typhimurium and C. jejuni was also assessed in this study. The production of nitric oxide (NO) was determined using the Greiss Reagent Assay, whereas the production of chemokines, cytokines, and growth stimulating factors by the RAW264.7 cells in vitro was measured using the Luminex 200. The results showed that both solar and non-solar irradiated S. Typhimurium inhibited the production of nitric oxide in the RAW264.7 cells. The heat/chemically attenuated S. Typhimurium induced a significant increase (p<0.0.5) in the production of NO2− in the macrophages when compared to the unstimulated RAW264.7. The chemokine and cytokine levels produced by the macrophages were similar in the solar inactivated S. Typhimurium and the live untreated S. Typhimurium. However, macrophages treated with heat/chemically attenuated S. Typhimurium showed an anti-inflammatory response by inhibiting the production of pro-inflammatory cytokines such as IL-1, IL-1, IL-2, IL-6, and IL-17 in macrophages. The macrophages treated with solar and non-solar irradiated C. jejuni possibly produced an anti-inflammatory effect since the amount of pro-inflammatory cytokines in the samples was significantly reduced during the late infection period (24 h p.i.). This study also analysed the proteomic profiles of macrophages treated with LPS, non-solar irradiated, solar irradiated, heat/ chemical inactivated S. Typhimurium, and C. jejuni. This was carried out using SWATH-mass spectrophotometry-based proteomics. Proteins were extracted from infected macrophages after 24 hours p.i. HILIC-based sample clean-up and digestion, DDA LCMS-MS (spectral library), SWATH LCMS-MS, and data processing were carried out. A total of 15,077 peptides matching to 2,778 proteins were identified at 1% FDR with numerous differentially expressed proteins (DEPs) detected in macrophages treated with lipopolysaccharide (LPS), non-solar irradiated C. jejuni (NS), heat-attenuated C. jejuni (HA) and 4h-solar irradiated (SI4) and 8h-solar irradiated (SI8) C. jejuni, respectively. Pathway analysis revealed that most of the upregulated proteins in macrophages treated with solar irradiated C. jejuni were involved in oxidation-reduction processes, endoplasmic reticulum stress, transport, antigen processing and presentation of exogenous peptide antigens via MHC class I (TAP-dependant) and ATP-biosynthetic processes. The KEGG-pathways also revealed the roles of some upregulated proteins in lysosomal and phagosome pathways. In conclusion, our results revealed that there is coordinated up-regulation of MHC-I processing pathways occurred at 24 h p.i. It is likely that proteins from solar irradiated C. jejuni may undergo proteasomal degradation, and the peptides are transported to the endoplasmic reticulum (ER) and loaded onto MHC-I molecules. Peptide loading results in class I complexes consolidation and transit to the cell surface where antigens can be presented to circulating CD8 + T cells. Additionally, solar irradiated C. jejuni also undergoes degradation in the phagosome. The phagosome has the potential to create antigens that can be expressed on the cell surface of macrophages to stimulate different lymphocytes and induce appropriate immune responses, thus, connecting the innate to adaptive immunity, and this could also have health benefits via the consumption of SODIS treated water. However, proteomic analysis of S. Typhimurium showed no significant differentially expressed proteins in macrophages treated with LPS, non-solar irradiated, and solar irradiated S. Typhimurium. This may be due to an overestimation of the extracted protein. However, DEPs in macrophages treated with heat-attenuated S. Typhimurium showed that macrophages may have adapted an anti-inflammatory M2 phenotype because the IFN-γ signalling pathway was downregulated. This may have contributed to non-expression of the chemokine IFN-γ in RAW264.7 cells. Moreover, proteins such as Hmox1 and Sqstm1 were upregulated, and this is also characteristic of M2 macrophages. This study provided new insights on the effect of solar irradiated Salmonella Typhimurium and Campylobacter jejuni on the proliferation and activation of macrophages in vitro.

It is now widely accepted that surface contamination plays an important role in the transmission of both respiratory and gastrointestinal infections in the domestic environment and community setting. The efficiency of transfer of a pathogen to the hand from a fomite is important in modeling transmission in microbial risk assessment models. The objective of this study was to use published literature to assess the role of fomites and hands in disease transmission, and to conduct fomite-to-finger transfer studies from various porous and nonporous fomites under different relative humidity condition using non-pathogenic strains of Escherichia coli, Staphylococcus aureus, MS2 coliphage, Bacillus thuringiensis spores, and poliovirus 1; to evaluate the persistence of bacteria and viruses on surfaces; to examine bacteria and virus transfer from treated surfaces; and to conduct a foodborne quantitative microbial risk assessment using Campylobacter jejuni from the data obtained in these studies. It was found that numerous factors influence the transfer efficiency of microorganisms, with moisture being the most important, with greater transfer under humid conditions. Other factors influencing transfer include drying time, contact time, pressure, friction, type of material, and porosity of the fomite. Percent transfer was greater under high relative humidity for both porous and nonporous surfaces. Most organisms on average had greater transfer under high relative humidity (40 - 65%) compared to low relative humidity (15 - 32%). Relative humidity and fomite type influenced the survival of all studied organisms; survival was greater on nonporous surfaces than those for porous surfaces. Test organisms were reduced up to 99.997% on the fomites after the surfaces were wiped with a disinfectant wipe. Microbial fomite-to-finger transfer from disinfectant wipe-treated surfaces were, lower than from non-treated surfaces. The disinfectant-wipe intervention reduced the risk of Campylobacter infection, illness, and death by 2 to 3 orders on all fomites. The disinfectant-wipe intervention reduced the annual risk of illness below the reported national average of diagnosed Campylobacteriosis cases 1.3E-04. This risk assessment demonstrates that the use of disinfectant wipes to decontaminate surface areas after chicken preparation reduces the risk of C. jejuni infections up to 99.2%.

Chez les bactéries à chromosome circulaire, la réplication peut engendrer des dimères que le système de recombinaison site-spécifique dif/Xer résout en monomères afin que la ségrégation des chromosomes fils et la division cellulaire se fassent normalement. Ses composants sont une ou deux tyrosines recombinases de type Xer qui agissent à un site de recombinaison spécifique, dif, avec l’aide de la translocase FtsK qui mobilise l’ADN au septum avant la recombinaison. Ce système a été d’abord identifié et largement caractérisé chez Escherichia coli mais il a également été caractérisé chez de nombreuses bactéries à Gram négatif et positif avec des variantes telles que les systèmes à une seule recombinase comme difSL/XerS chez Streptococcus sp et Lactococcus sp. Des études bio-informatiques ont suggéré l’existence d’autres systèmes à une seule recombinase chez un sous-groupe d’ε-protéobactéries pathogènes, dont Campylobacter jejuni et Helicobacter pylori. Les acteurs de ce nouveau système sont XerH et difH. Dans ce mémoire, les premières recherches in vitro sur ce système sont présentées. La caractérisation de la recombinase XerH de C. jejuni a été entamée à l’aide du séquençage de son gène et de tests de liaison et de clivage de l’ADN. Ces études ont montré que XerH pouvait se lier au site difSL de S. suis de manière non-coopérative : que XerH peut se lier à des demi-sites de difSL mais qu’elle ne pouvait, dans les conditions de l’étude effectuer de clivage sur difSL. Des recherches in silico ont aussi permis de faire des prédictions sur FtsK de C. jejuni. / DNA replication can form dimers in bacteria harboring a circular chromosome. The dif/Xer recombination system resolves monomers them so that chromosome segregation and cell division take place normally. This system is composed of one or two tyrosine recombinases that act at a specific recombination site, dif, with the help of the FtsK translocase that mobilises DNA to the septum before recombination. The Xer system has been first identified and widely characterized in Escherichia coli where XerC and XerD are the recombinases. The system has been found and studied in many other Gram negative and positive bacteria. A different form, carrying a single recombinase acting on an atypical site, has been identified in Streptococci and Lactococci, difSL/XerS. In silico studies suggested the existence of other single recombinase systems in a sub-group of pathogenic ε-proteobacteriasuch as Campylobacter jejuni and Helicobacter pylori. The components of this system were identified as XerH and difH. In this thesis, the first in vitro studies made on this system are presented. The characterization of the XerH recombinase of C. jejuni started with the sequencing of its gene and with the DNA binding and cleavage assays. These studies showed that XerH could bind difSL of S. suis non-cooperatively, that it could bind difSL half-sites and that it was unable to perform cleavage on difSL. Also, in silico comparisons permitted predictions on FtsK of C. jejuni.

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No. of bitstreams: 2 Dissertação Tassiana Ramires.pdf: 1728606 bytes, checksum: a63d0903f11cb3f858c5a7fd4e32ad97 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-20 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Campylobacter termofílicos são, atualmente, as principais bactérias causadoras de doenças gastrointestinais em todo o mundo. Esse grupo é assim denominado devido a sua temperatura ótima de multiplicação oscilar entre 42 °C e 43 °C, sendo Campylobacter jejuni, C. coli, C. lari e C. upsaliensis, as principais espécies envolvidas nos casos de campilobacteriose em humanos. Dentre essas espécies, a mais relacionada à essa doença é C. jejuni, seguida por C. coli. O principal reservatório desses micro-organismos são as aves, principalmente os frangos, possivelmente pela temperatura corporal desses animais ser similar à temperatura ótima para Campylobacter termofílicos. Com isso, o objetivo desse estudo foi avaliar a ocorrência, a diversidade genética, o perfil de resistência a antimicrobianos e a presença de genes associados à virulência em isolados de Campylobacter termofílicos provenientes de frangos de corte e na cama de aviário em granjas aviárias da região sul do Rio Grande do Sul, Brasil. Um total de 48 amostras foram coletadas em três diferentes granjas (A, B e C), incluindo uma amostra de swab de arrasto da cama do aviário e 15 pools de amostras de swab de cloaca em cada granja. Das três granjas amostradas, apenas a granja C apresentou contaminação por Campylobacter termofílicos, sendo todos os isolados identificados por técnicas fenotípicas e moleculares como C. jejuni. Dessas 16 amostras positivas, obtiveram-se 28 isolados, sendo 16 pelo isolamento em ágar Preston e 12 do ágar mCCD. A diversidade genética entre os isolados foi avaliada por PFGE, verificando-se que todos os isolados apresentaram um único padrão de macrorestrição, sugerindo clonalidade entre os isolados e a presença de apenas uma fonte de infecção por Campylobacter nessa granja. O perfil de resistência a antimicrobianos foi avaliado pelo teste de disco difusão em ágar, utilizando-se oito antimicrobianos distintos, de três classes diferentes: tetraciclina, quinolonas e macrolídeos. Os isolados apresentaram perfil similar de resistência a antimicrobianos, sendo resistentes às quinolonas e tetraciclinas e sensíveis aos macrolídeos. Devido a relação clonal e ao perfil de resistência similar, um isolado representativo foi selecionado para detecção dos genes de virulência. A técnica de PCR foi utilizada para detectar a presença dos genes ciaB, cadF, cdtA, cdtB e cdtC, sendo o isolado selecionado positivo todos os genes pesquisados. Dessa forma, a presença de C. jejuni resistente a antimicrobianos e com potencial de virulência em frangos de corte prontos para o abate e na cama de aviário durante o período de produção é um risco à saúde pública, pois esses micro-organismos podem ser introduzidos no ambiente do abatedouro e contaminar as carcaças durante o abate. / Thermophilic Campylobacter are currently the leading bacteria causing of gastrointestinal diseases worldwide. This group is so named because its optimal multiplication temperature oscillates between 42 °C and 43 °C, being Campylobacter jejuni, C. coli, C. lari and C. upsaliensis, the main species involved in cases of human campylobacteriosis. Among these species, the most related to this disease is C. jejuni, followed by C. coli. The main reservoir of these microorganisms are birds, especially chickens, possibly because the body temperature of these animals coincides with the optimal temperature for thermophilic Campylobacter. Therefore, the aim of this study was to verify the occurrence, genetic relationship, antimicrobial susceptibility, and the presence of virulence genes in thermophilic Campylobacter from broilers and broiler bedding from the southern region of Rio Grande do Sul, Brazil. A total of 48 samples were collected in three different farms (A, B and C), which comprising one sample of drag swab and 15 pools of cloacal swabs in each farm. From the three farms sampled, only the farm C showed thermophilic Campylobacter contamination. All isolates were identified by phenotypic and molecular techniques such as C. jejuni. Of these 16 positive samples, 28 isolates were obtained, 16 being isolated by Preston agar and 12 by mCCD agar. The genetic diversity among the isolates was evaluated by PFGE, and it was observed that all the isolates belonged to the same macrorestriction pattern, suggesting clonality among the isolates and the presence of only one source of Campylobacter infection in this farm. The antimicrobial resistance profile was evaluated by the agar disc diffusion test using eight distinct antimicrobial agents from three different classes: tetracyclines, quinolones and macrolides. The isolates presented a similar antimicrobial resistance profile, being resistant to quinolones and tetracyclines and susceptible to macrolides. As the isolates shared the same PFGE pattern and similar resistance profile, a representative isolate was chosed for investigation of virulence genes. A PCR assay was carried out aiming to identify the presence of ciaB, cadF, cdtA, cdtB and cdtC virulence genes and all the genes evaluated were found. Thus, the presence of C. jejuni resistant to antimicrobial agents and harboring virulence genes in broilers and broiler farm during the broiler production period may represents a potential risk to public health, because these microorganisms can be introduced into the abattoir environment and may contaminate the carcasses during slaughter.