O patógeno Escherichia coli pertence ao grupo de cepas que podem causar infecções extraintestinais, designadas como (ExPEC). Existem cepas de E. coli ExPEC, tais como: a E. coli causadora de meningite neonatal (NMEC), a E. coli uropatogênica (UPEC) e a E. coli patogênica para aves (APEC). Na avicultura, esta bactéria é responsável por vários processos patológicos, atuando tanto como agente primário como secundário, sendo responsável por significativas perdas econômicas que ocorrem na produção avícola. Vários trabalhos têm demonstrado que muitos isolados ExPEC de humanos e animais compartilham genes de virulência em comum, sugerindo que ocorra uma troca genética entre essas cepas, e o risco para a saúde humana de tais bactérias ainda é indefinido. Além disto, existe outra preocupação em relação ao fato de estudos sugerirem que a E. coli pode facilmente adquirir resistência a antimicrobianos utilizados por humanos e animais. As aves domésticas são reconhecidas como importante fonte de disseminação de resistência antimicrobiana às amostras de E. coli. O objetivo do presente estudo foi realizar a caracterização de amostras de Escherichia coli patogênica aviária (APEC) e Escherichia coli uropatogênica (UPEC) através da classificação em grupos filogenéticos e da avaliação da resistência antimicrobiana. Neste trabalho foram utilizados os dados disponíveis referentes a 237 cepas de E. coli isoladas de camas de aviários, lesões de celulite e quadros respiratórios de frangos de corte e 211 amostras de E. coli uropatogênica (UPEC) isoladas de pacientes com infecção urinária. Para verificar se existia diferença significativa entre a resistência antimicrobiana a (ampicilina, gentamicina, norfloxacina, amicacina e cefuroxima) e a origem das amostras, e destes mesmos antimicrobianos em relação aos grupos filogenéticos. As amostras APEC diferiram na resistência antimicrobiana das amostras UPEC para ampicilina, gentamicina, norfloxacina e cefuroxima. O mesmo não foi observado para a amicacina. Nas condições do presente trabalho, estes resultados contrariam, parcialmente, os estudos que sugerem que a resistência antimicrobiana é originária das amostras de origem avícola, já que três dos cinco fármacos testados apresentaram maior resistência nas amostras UPEC que nas APEC. Quando analisada a relação entre os grupos filogenéticos observou-se que o perfil de resistência antimicrobiana foi semelhante em todos os grupos, somente para norfloxacina e ampicilina houve diferença, porém a resistência estava bem distribuída entre os quatro grupos, comprovando que a patogenicidade não se relaciona com a resistência antimicrobiana. Este fato já havia sido caracterizado em trabalho anterior da mesma autora. Estes resultados ressaltam a necessidade de realizar monitorizações rotineiras e constantes visando conhecer as flutuações da patogenicidade e da resistência antimicrobiana, separadamente. / The pathogen Escherichia coli, belongs to the group of strains that can cause extraintestinal infections, designated as (ExPEC). There are strains of extraintestinal E. coli ExPEC as: a E. coli that causes neonatal meningitis (NMEC), a uropathogenic E. coli (UPEC) and a avian pathogenic E. coli (APEC). In poultry, this bacterium is responsible for several pathological processes, acting as primary agent and secondary as well, and it is also responsible for significant economic losses that occur in poultry production. Several articles show that many ExPEC isolates from humans and animals share common virulence genes, suggesting a genetic exchange between these strains, and the risk to human health of more bacteria is still undefined. In addition, there is another concern about studies which suggest that E. coli can readily acquire antimicrobial resistance when used by animals and humans. Poultry is recognized as an important source of dissemination of antimicrobial resistance in E. coli samples. The objective of the present study was to characterize samples of avian pathogenic Escherichia coli (APEC) and uropathogenic Escherichia coli (UPEC) using phylogenetic groups and antimicrobial resistance. In this study, we used data available on 237 strains of E. coli isolated from avian litter, cellulitis lesions and respiratory lesions of broilers and 211 uropathogenic E. coli (UPEC) samples isolated from patients with urinary tract infection. To verify if there was a significant difference between the antimicrobial resistance (ampicillin, gentamicin, norfloxacin, amicacin, cefuroxime) and the origin of the samples, and of these same antimicrobials and phylogenetic groups. The APEC samples differed in antimicrobial resistance of the UPEC for ampicillin, gentamicin, norfloxacin and cefuroxime. The same was not observed for amikacin. Under the conditions of the present study, these results partially contradict the studies which suggest that antimicrobial resistance originates from samples of poultry origin, three of the five drugs tested, presented higher resistance in the UPEC samples than in the APEC. When analyzing the relationship between the phylogenetic groups, it was observed that the antimicrobial resistance profile was similar in all groups, only for norfloxacin and ampicillin there was a difference, but the resistance was well distributed among the four groups, proving that the pathogenicity was not related with antimicrobial resistance. This fact had already been characterized in previous paper by the same author. These results highlight the need to perform routine and constant monitoring in order to know the fluctuations in pathogenicity and antimicrobial resistance, separately.

Orientador: Cristiano Gallina Moreira / Resumo: As infecções do trato urinário são frequentes no mundo todo, sendo a Escherichia coli Uropatogênica (UPEC) o patógeno responsável pela maior parte dos casos de cistite e pielonefrite aguda. A patogenicidade das UPECs está relacionada a expressão de diversos fatores de virulência, sendo a regulação da expressão desses fatores mediada por moléculas sinalizadoras químicas que permitem a comunicação célula-célula inter e intra-reinos, o que facilita o processo de colonização e estabelecimento da patogênese. Um dos sistemas responsáveis por essas cascatas de sinalização é composto por uma proteína sensora de membrana (QseC) e outra reguladora de resposta citoplasmática (QseB), constituindo o sistema de dois componentes QseBC, capaz de reconhecer sinais produzidos pelo hospedeiro e por outras bactérias, levando a regulação da expressão de genes de virulência do patógeno. Estudos realizados pelo nosso grupo, evidenciaram atenuação da virulência de patógenos Gram-negativos na ausência do gene qseC, levando ao desenvolvimento de moléculas que atuassem inibindo essa via como o LED209. O objetivo do presente trabalho foi caracterizar cepas multi-droga resistentes (MDR) de UPECs obtidas a partir de isolados clínicos, além de investigar, in vitro e in vivo, a participação da via QseBC na patogênese e na virulência de cepas de UPECs e isolados clínicos MDR, com o uso do composto LED209 na atenuação da virulência frente a esses patógenos. Também constituiu o objetivo, o uso do ácido 3,4-di-... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Urinary tract infections are found commonly worldwide, whereas Uropathogenic Escherichia coli (UPEC) is the most prevalent pathogen, responsible for utmost cases of cystitis and acute pyelonephritis. The pathogenicity of UPECs is related to the expression of several virulence factors, and the regulation of the expression of these factors is mediated by chemical signaling molecules. The communication allow inter-intra-kingdom and cell-to-cell facilitates the process of colonization and establishment of pathogenesis. QseBC two-component system is capable of recognizing signals produced by the host leading to regulation of pathogen virulence gene expression. This system consists of membrane sensing protein (QseC) and a cytoplasmic response regulator (QseB) that mediate the entire cascade of virulence genes. Studies conducted by our group showed attenuation of the virulence of Gram-negative pathogens in the absence of the qseC gene, leading to the development of molecules that act by inhibiting this pathway such as LED209. The aim of the present study was to characterize UPEC multidrug-resistant strains (MDR) from clinical isolates. Investigate, in vitro and in vivo, the involvement of the QseBC pathway in the pathogenesis and virulence of UPEC strains and clinical isolates. The use of LED209 and the 3,4-dihydroximandelic acid (DHMA), norepinephrine intermediate metabolite, as chemoattractant, were employed to attenuate of virulence against these pathogens. The results showed a h... (Complete abstract click electronic access below) / Mestre

The main causative agent of human urinary tract infections is the uropathogenic Escherichia coli (UPEC) pathotype. It may cause disease due to its ability to express a number of bacterial virulence factors. Fimbrial adhesins are particularly important for the initial establishment of infection in the urinary tract. The fimbriae are hair-like structures protruding from the bacterial cell and by attaching to specific receptors in the urinary tract they mediate adherence to different cell types, allowing the bacteria to resist the shear forces from urine flow. The UPEC strains generally carry multiple determinants for fimbrial adhesins. Previous studies have indicated that there is a co-regulation between different fimbrial genes and one factor that has been implicated in this is the PapB protein, acting as a transcriptional regulator of P-fimbrial expression. The PapB protein can be regarded as the prototype of a family of fimbrial regulators that show high homology between different fimbrial operons. One homolog is FocB, regulator of F1C fimbriae. In this study, the role of the FocB protein in the regulation of F1C fimbriae as well as in the co-regulation with other fimbrial genes was investigated. It was observed that FocB binds to DNA, similarly to PapB, in an oligomeric fashion and that PapB and FocB can form hetero-oligomeric complexes, which appear to have a repressive role in the regulation of the F1C fimbriae. In addition, the FocB protein also had a repressive effect on transcription of the fim operon, which encodes theType 1 fimbriae. For further analysis of FocB in vitro, we developed efficient procedures for purification of the protein and established conditions for its crystal formation with the aim to conduct X-ray diffraction studies. By the hanging-drop vapour-diffusion method, we obtained crystals that in the X-ray analysis diffracted sufficiently well to allow modelling of a high resolution structure of FocB. The structural model was considered in relation to the DNA binding properties of the protein. The FocB analysis represents the first structural model of this family of transcriptional factors. This model should aid in further understanding of the roles and functions of these proteins in the regulation of the UPEC fimbrial operons. The complexity of the system, with multiple factors involved in the regulation of fimbrial operons, was revealed in earlier studies of the PapI protein showing that PapI activates transcription of the pap operon as a part of a complex with the global regulator Lrp. However, PapI itself did not appear to bind to DNA and its mode of action has remained unclear. By genetic analyses and in vitro studies we show that PapI may interact also with the α subunit of the RNA polymerase. This finding indicates that PapI might directly interact with the transcriptional apparatus and thus aid in the activation of pap expression. Bacteria are frequently releasing outer membrane vesicles (OMVs) from their surface. We studied the release of the haemolysin toxin from E. coli in connection with formation of OMVs and found that the toxin was tightly associated with the vesicles in an active form. By overproduction of the PapB or PapI regulators in order to maximise the population of bacteria expressing fimbriae, we could detect P fimbriae proteins associated with OMVs that displayed specific adhesion to receptor-coated beads. This suggests a possible scenario in which the vesicles canfunction as directed vehicles of bacterial virulence factors.

A DNA microarray capable of detecting 445 virulence factors (VFs) and antibiotic resistance genes was used to assess human and animal fecal E. coli isolates for pathogenic potential and host specificity. The only enteric pathotype detected was atypical EPEC, which was found in 3.7% of all isolates. 17% of human isolates were extraintestinal pathotypes, with the majority of these being uropathogenic. Isolates from humans and chickens were the most likely to have resistance to at least one class of antibiotic. VFs that were found almost exclusively in human isolates, when compared to one other group, included sat (10% of human isolates and no animal isolates), iucD and iut (24% of human, <1% mammal) and iha (16% human, <1% wild avian). Decision trees utilizing multiple probes to identify the source of an E. coli isolate were able to correctly identify the source of 79% of validation isolates in a human vs. animal comparison. / Environment Canada

The purpose of this study was to investigate the feasibility of using bacteriophages - viruses that can lyse bacteria - to control infections caused by uropathogenic Escherichia coli (UPEC) in dogs and cats. Prior to phage experiments, UPEC were subjected to virulence factor genotyping by multiplex polymerase chain reaction assay and phylogenetic 'fingerprinting' by Pulsed-Field Gel Electrophoresis (PFGE). Twenty-five of 30 assessed virulence factor gene (VFG) markers were detected at least once in 31 UPEC isolated from 20 UK cats and 89 UPEC isolated from dogs (56), cats (22) and people (11) living in New Zealand (NZ). The PFGE banding patterns of UPEC isolates from different individuals were markedly dissimilar unless isolates had been collected at the same hospital within one month of each other. In contrast, ≥2 UPEC strains isolated from each of 3 UK cats diagnosed with multiple UTIs were indistinguishable by PFGE. Antibiograms inaccurtely predicted UPEC clonality and, of clinical importance, underestimated the number of relapsing or persistent infections in these cats. A comparison of VFG profiles and PFGE banding patterns of UPEC isolated from NZ and UK cats demonstrated a geographically uneven distribution of pathotypic and phylogenetic traits and indicated that, among other factors, the source of UPEC must be considered when comparing UPEC from different host species. When comparing UPEC isolates from NZ dogs, cats and people, strains with similar VFG profiles were found among the different host species. Other strains, with VFG profiles that differed according to the host species of origin were also detected. The latter finding, which is in contrast to the results of previous studies, may be of interest to researchers aiming to predict the potential zoonotic risk posed by particular UPEC strains sourced from dogs and cats. Forty bacteriophages (phages for short) were isolated from sewage waters and propagated on UPEC strains. The ability of these phages to cause bacterial lysis was tested on 31 canine UPEC, 22 feline UPEC and 7 faecal E. coli. In contrast to faecal E. coli, UPEC strains were highly susceptible to phages. Ten phages with a particularly broad host range each lysed ≥27/53 (≥51%) UPEC strains. Used in combination, these 10 phages were predicted to be able to lyse 49/53 (92%) of the UPEC strains in the collection. Morphological and genotypic studies on 5 of these 10 phages demonstrated that 4 of them belonged to the lytic T4-like genus, while one phage showed similarity to the temperate phage P2. Overall, results of this project indicate that the majority of canine and feline UPEC - with very diverse PFGE banding patterns and VFG profiles - are susceptible to lysis by naturally occurring phages. Hence, phages show promise as therapeutic agents for treatment of canine and feline UTI and, perhaps, for other infections caused by UPEC.

O patógeno Escherichia coli pertence ao grupo de cepas que podem causar infecções extraintestinais, designadas como (ExPEC). Existem cepas de E. coli ExPEC, tais como: a E. coli causadora de meningite neonatal (NMEC), a E. coli uropatogênica (UPEC) e a E. coli patogênica para aves (APEC). Na avicultura, esta bactéria é responsável por vários processos patológicos, atuando tanto como agente primário como secundário, sendo responsável por significativas perdas econômicas que ocorrem na produção avícola. Vários trabalhos têm demonstrado que muitos isolados ExPEC de humanos e animais compartilham genes de virulência em comum, sugerindo que ocorra uma troca genética entre essas cepas, e o risco para a saúde humana de tais bactérias ainda é indefinido. Além disto, existe outra preocupação em relação ao fato de estudos sugerirem que a E. coli pode facilmente adquirir resistência a antimicrobianos utilizados por humanos e animais. As aves domésticas são reconhecidas como importante fonte de disseminação de resistência antimicrobiana às amostras de E. coli. O objetivo do presente estudo foi realizar a caracterização de amostras de Escherichia coli patogênica aviária (APEC) e Escherichia coli uropatogênica (UPEC) através da classificação em grupos filogenéticos e da avaliação da resistência antimicrobiana. Neste trabalho foram utilizados os dados disponíveis referentes a 237 cepas de E. coli isoladas de camas de aviários, lesões de celulite e quadros respiratórios de frangos de corte e 211 amostras de E. coli uropatogênica (UPEC) isoladas de pacientes com infecção urinária. Para verificar se existia diferença significativa entre a resistência antimicrobiana a (ampicilina, gentamicina, norfloxacina, amicacina e cefuroxima) e a origem das amostras, e destes mesmos antimicrobianos em relação aos grupos filogenéticos. As amostras APEC diferiram na resistência antimicrobiana das amostras UPEC para ampicilina, gentamicina, norfloxacina e cefuroxima. O mesmo não foi observado para a amicacina. Nas condições do presente trabalho, estes resultados contrariam, parcialmente, os estudos que sugerem que a resistência antimicrobiana é originária das amostras de origem avícola, já que três dos cinco fármacos testados apresentaram maior resistência nas amostras UPEC que nas APEC. Quando analisada a relação entre os grupos filogenéticos observou-se que o perfil de resistência antimicrobiana foi semelhante em todos os grupos, somente para norfloxacina e ampicilina houve diferença, porém a resistência estava bem distribuída entre os quatro grupos, comprovando que a patogenicidade não se relaciona com a resistência antimicrobiana. Este fato já havia sido caracterizado em trabalho anterior da mesma autora. Estes resultados ressaltam a necessidade de realizar monitorizações rotineiras e constantes visando conhecer as flutuações da patogenicidade e da resistência antimicrobiana, separadamente. / The pathogen Escherichia coli, belongs to the group of strains that can cause extraintestinal infections, designated as (ExPEC). There are strains of extraintestinal E. coli ExPEC as: a E. coli that causes neonatal meningitis (NMEC), a uropathogenic E. coli (UPEC) and a avian pathogenic E. coli (APEC). In poultry, this bacterium is responsible for several pathological processes, acting as primary agent and secondary as well, and it is also responsible for significant economic losses that occur in poultry production. Several articles show that many ExPEC isolates from humans and animals share common virulence genes, suggesting a genetic exchange between these strains, and the risk to human health of more bacteria is still undefined. In addition, there is another concern about studies which suggest that E. coli can readily acquire antimicrobial resistance when used by animals and humans. Poultry is recognized as an important source of dissemination of antimicrobial resistance in E. coli samples. The objective of the present study was to characterize samples of avian pathogenic Escherichia coli (APEC) and uropathogenic Escherichia coli (UPEC) using phylogenetic groups and antimicrobial resistance. In this study, we used data available on 237 strains of E. coli isolated from avian litter, cellulitis lesions and respiratory lesions of broilers and 211 uropathogenic E. coli (UPEC) samples isolated from patients with urinary tract infection. To verify if there was a significant difference between the antimicrobial resistance (ampicillin, gentamicin, norfloxacin, amicacin, cefuroxime) and the origin of the samples, and of these same antimicrobials and phylogenetic groups. The APEC samples differed in antimicrobial resistance of the UPEC for ampicillin, gentamicin, norfloxacin and cefuroxime. The same was not observed for amikacin. Under the conditions of the present study, these results partially contradict the studies which suggest that antimicrobial resistance originates from samples of poultry origin, three of the five drugs tested, presented higher resistance in the UPEC samples than in the APEC. When analyzing the relationship between the phylogenetic groups, it was observed that the antimicrobial resistance profile was similar in all groups, only for norfloxacin and ampicillin there was a difference, but the resistance was well distributed among the four groups, proving that the pathogenicity was not related with antimicrobial resistance. This fact had already been characterized in previous paper by the same author. These results highlight the need to perform routine and constant monitoring in order to know the fluctuations in pathogenicity and antimicrobial resistance, separately.

O patógeno Escherichia coli pertence ao grupo de cepas que podem causar infecções extraintestinais, designadas como (ExPEC). Existem cepas de E. coli ExPEC, tais como: a E. coli causadora de meningite neonatal (NMEC), a E. coli uropatogênica (UPEC) e a E. coli patogênica para aves (APEC). Na avicultura, esta bactéria é responsável por vários processos patológicos, atuando tanto como agente primário como secundário, sendo responsável por significativas perdas econômicas que ocorrem na produção avícola. Vários trabalhos têm demonstrado que muitos isolados ExPEC de humanos e animais compartilham genes de virulência em comum, sugerindo que ocorra uma troca genética entre essas cepas, e o risco para a saúde humana de tais bactérias ainda é indefinido. Além disto, existe outra preocupação em relação ao fato de estudos sugerirem que a E. coli pode facilmente adquirir resistência a antimicrobianos utilizados por humanos e animais. As aves domésticas são reconhecidas como importante fonte de disseminação de resistência antimicrobiana às amostras de E. coli. O objetivo do presente estudo foi realizar a caracterização de amostras de Escherichia coli patogênica aviária (APEC) e Escherichia coli uropatogênica (UPEC) através da classificação em grupos filogenéticos e da avaliação da resistência antimicrobiana. Neste trabalho foram utilizados os dados disponíveis referentes a 237 cepas de E. coli isoladas de camas de aviários, lesões de celulite e quadros respiratórios de frangos de corte e 211 amostras de E. coli uropatogênica (UPEC) isoladas de pacientes com infecção urinária. Para verificar se existia diferença significativa entre a resistência antimicrobiana a (ampicilina, gentamicina, norfloxacina, amicacina e cefuroxima) e a origem das amostras, e destes mesmos antimicrobianos em relação aos grupos filogenéticos. As amostras APEC diferiram na resistência antimicrobiana das amostras UPEC para ampicilina, gentamicina, norfloxacina e cefuroxima. O mesmo não foi observado para a amicacina. Nas condições do presente trabalho, estes resultados contrariam, parcialmente, os estudos que sugerem que a resistência antimicrobiana é originária das amostras de origem avícola, já que três dos cinco fármacos testados apresentaram maior resistência nas amostras UPEC que nas APEC. Quando analisada a relação entre os grupos filogenéticos observou-se que o perfil de resistência antimicrobiana foi semelhante em todos os grupos, somente para norfloxacina e ampicilina houve diferença, porém a resistência estava bem distribuída entre os quatro grupos, comprovando que a patogenicidade não se relaciona com a resistência antimicrobiana. Este fato já havia sido caracterizado em trabalho anterior da mesma autora. Estes resultados ressaltam a necessidade de realizar monitorizações rotineiras e constantes visando conhecer as flutuações da patogenicidade e da resistência antimicrobiana, separadamente. / The pathogen Escherichia coli, belongs to the group of strains that can cause extraintestinal infections, designated as (ExPEC). There are strains of extraintestinal E. coli ExPEC as: a E. coli that causes neonatal meningitis (NMEC), a uropathogenic E. coli (UPEC) and a avian pathogenic E. coli (APEC). In poultry, this bacterium is responsible for several pathological processes, acting as primary agent and secondary as well, and it is also responsible for significant economic losses that occur in poultry production. Several articles show that many ExPEC isolates from humans and animals share common virulence genes, suggesting a genetic exchange between these strains, and the risk to human health of more bacteria is still undefined. In addition, there is another concern about studies which suggest that E. coli can readily acquire antimicrobial resistance when used by animals and humans. Poultry is recognized as an important source of dissemination of antimicrobial resistance in E. coli samples. The objective of the present study was to characterize samples of avian pathogenic Escherichia coli (APEC) and uropathogenic Escherichia coli (UPEC) using phylogenetic groups and antimicrobial resistance. In this study, we used data available on 237 strains of E. coli isolated from avian litter, cellulitis lesions and respiratory lesions of broilers and 211 uropathogenic E. coli (UPEC) samples isolated from patients with urinary tract infection. To verify if there was a significant difference between the antimicrobial resistance (ampicillin, gentamicin, norfloxacin, amicacin, cefuroxime) and the origin of the samples, and of these same antimicrobials and phylogenetic groups. The APEC samples differed in antimicrobial resistance of the UPEC for ampicillin, gentamicin, norfloxacin and cefuroxime. The same was not observed for amikacin. Under the conditions of the present study, these results partially contradict the studies which suggest that antimicrobial resistance originates from samples of poultry origin, three of the five drugs tested, presented higher resistance in the UPEC samples than in the APEC. When analyzing the relationship between the phylogenetic groups, it was observed that the antimicrobial resistance profile was similar in all groups, only for norfloxacin and ampicillin there was a difference, but the resistance was well distributed among the four groups, proving that the pathogenicity was not related with antimicrobial resistance. This fact had already been characterized in previous paper by the same author. These results highlight the need to perform routine and constant monitoring in order to know the fluctuations in pathogenicity and antimicrobial resistance, separately.

Inflammatory bowel disease (IBD), comprises Crohn’s disease (CD) and ulcerative colitis (UC), and is a chronic relapsing inflammation of gastrointestinal tract without any known cause or cure. Currently, it is accepted that IBD is a result of a dysfunctional immune response to commensal bacteria in a genetically susceptible host, and that environmental factors can trigger the onset or reactivation of the disease. This thesis considers the possibility of a specific pathogenic agent as well as an imbalance in the composition of the normal microflora in the pathogenesis of IBD. Gut biopsy tissues were taken from a population-based case-control tissue bank held at the University of Manitoba. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP) were employed to assess the diversity of gut microbiota. The phylogenetic, virulence and biochemical characteristics of Escherichia coli isolated from IBD biopsies were examined using multi-locus sequence typing (MLST), DNA microarray technology and API 20E system. Utilizing ARISA and T-RFLP, a remarkable increase in the order of unclassified Clostridia was detected in inflamed tissues, particularly in CD patients (P < 0.05). Moreover, species richness and diversity were the highest in non-inflamed IBD biopsies. Culture-based quantification detected a significantly higher number of E. coli in IBD tissues (P < 0.05). Phylogenetic analysis revealed the tendency of E. coli isolated from IBD patients to be grouped into separate clonal clusters based on their allelic profiles (P = 0.02). A link was detected between uropathogenic E. coli (UPEC) CFT073 and strains isolated from IBD, with regards to gene distribution and virulence, using microarray technology. Amino acid substitutions N91S and S99N in FimH, the adhesive subunit of E. coli type I fimbria, were significantly associated to IBD (P < 0.05). This study demonstrated an increase in the microbial diversity of non-inflamed IBD tissues and suggested a recruitment phase of bacterial adherence and colonization, before the inflammation sets in. Furthermore, E. coli isolated from IBD tissues were distinct from commensal strains in both clonal and virulence characteristics and shared remarkable traits with extraintestinal pathogenic E. coli. Features involved in bacterial adhesion to epithelial cells may hold the key to E. coli pathogenesis in IBD.

Inflammatory bowel disease (IBD), comprises Crohn’s disease (CD) and ulcerative colitis (UC), and is a chronic relapsing inflammation of gastrointestinal tract without any known cause or cure. Currently, it is accepted that IBD is a result of a dysfunctional immune response to commensal bacteria in a genetically susceptible host, and that environmental factors can trigger the onset or reactivation of the disease. This thesis considers the possibility of a specific pathogenic agent as well as an imbalance in the composition of the normal microflora in the pathogenesis of IBD. Gut biopsy tissues were taken from a population-based case-control tissue bank held at the University of Manitoba. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP) were employed to assess the diversity of gut microbiota. The phylogenetic, virulence and biochemical characteristics of Escherichia coli isolated from IBD biopsies were examined using multi-locus sequence typing (MLST), DNA microarray technology and API 20E system. Utilizing ARISA and T-RFLP, a remarkable increase in the order of unclassified Clostridia was detected in inflamed tissues, particularly in CD patients (P < 0.05). Moreover, species richness and diversity were the highest in non-inflamed IBD biopsies. Culture-based quantification detected a significantly higher number of E. coli in IBD tissues (P < 0.05). Phylogenetic analysis revealed the tendency of E. coli isolated from IBD patients to be grouped into separate clonal clusters based on their allelic profiles (P = 0.02). A link was detected between uropathogenic E. coli (UPEC) CFT073 and strains isolated from IBD, with regards to gene distribution and virulence, using microarray technology. Amino acid substitutions N91S and S99N in FimH, the adhesive subunit of E. coli type I fimbria, were significantly associated to IBD (P < 0.05). This study demonstrated an increase in the microbial diversity of non-inflamed IBD tissues and suggested a recruitment phase of bacterial adherence and colonization, before the inflammation sets in. Furthermore, E. coli isolated from IBD tissues were distinct from commensal strains in both clonal and virulence characteristics and shared remarkable traits with extraintestinal pathogenic E. coli. Features involved in bacterial adhesion to epithelial cells may hold the key to E. coli pathogenesis in IBD.

Escherichia coli é um bacilo Gram-negativo, anaeróbico facultativo e de distribuição cosmopolita. E. coli coloniza o intestino de humanos e outros animais endotérmicos logo após o nascimento, estabelecendo-se como um importante membro da microbiota intestinal. Algumas cepas de E. coli podem adquirir fatores de virulência, assumindo assim, uma natureza patogênica, como é o caso das E. coli patogênicas extraintestinais (ExPEC). As cepas ExPEC apresentam a capacidade de colonizar e se disseminar em diversos nichos no hospedeiro, e são divididas em UPEC (E. coli uropatogênica), NMEC (E. coli causadora de meningite neonatal) e APEC (E. coli patogênica para aves). UPEC, NMEC e APEC compartilham fatores associados à virulência. Para serem aptas a causar doença, cepas ExPEC devem apresentar pelo menos um fator associado à adesão, um fator para captação de ferro (sideróforo) e um fator de resistência ao soro, podendo, também, apresentar genes que codificam toxinas e invasinas. Embora sejam conhecidos muitos fatores de virulência associados à patogenicidade de cepas ExPEC, a regulação da expressão de tais fatores ainda não foi elucidada. Fumarato-nitrato-redutase (FNR) é uma proteína que atua como regulador global, agindo como um sensor da presença de oxigênio em bactérias gramnegativas. Já foi demonstrado que FNR está relacionada à regulação da virulência de bactérias patogênicas como Shigella flexneri e Salmonella enterica serovar Typhimurium. Este trabalho teve como objetivo a análise epidemiológica e caracterização de cepas APEC, bem como a investigação do controle da expressão de fatores associados à virulência de ExPEC pelo regulador global FNR. Os resultados da análise epidemiológica das cepas APEC mostram o perfil de resistência aos agentes antimicrobianos, a prevalência dos fatores de virulência e dos grupos filogenéticos (de acordo com a classificação EcoR) e a relação filogenética dos isolados, fornecendo um panorama da caracterização de E. coli patogênicas aviárias de lesões severas de celulite e de infecção sistêmica oriundas da região sul do Brasil. Em relação ao FNR, este estudo mostrou a influência deste regulador sobre importantes fatores associados à virulência, estando envolvido no controle de várias etapas do estabelecimento da infecção por cepas ExPEC. A deleção de fnr na cepa UPEC CFT 073 reduziu a motilidade, a expressão das fimbrias tipo I e tipo P, reduziu a expressão da hemolisina e controlou a expressão da ilha de patogenicidade do α- cetoglutarato. Além disso, a deleção de fnr fez tornou as bactérias incapazes de invadir células dos rins e da bexiga e de causar doença in vivo em camundongos de 6 semanas. FNR também foi capaz de controlar as etapas da infecção por NMEC 56. Uma vez deletado, as bactérias perderam a capacidade de causar bacteremia, de crescer no fluido cerebrospinal e de causar doença in vivo em ratos de 5 dias de idade. A deleção de fnr em APEC O1 resultou na diminuição da expressão da proteína OmpT plasmidial, da fímbria do tipo I e do auto-transportador AatA. A principal contribuição deste trabalho foi demonstrar que FNR atua na regulação da expressão de importantes fatores associados à virulência de cepas ExPEC (UPEC, NMEC e APEC), sendo importante para o estabelecimento da infecção por essas cepas. Neste trabalho, verificamos que, além da função já conhecida de regular os genes envolvidos na manutenção de um meio anaeróbico, FNR também atua no controle de genes associados à virulência de cepas ExPEC, refletindo na capacidade de causar doença que tais cepas apresentam. / Escherichia coli is a Gram-negative bacillus, facultative anaerobic and has cosmopolitan distribution. E. coli colonizes the intestine of humans and other endothermic animals immediately after birth, establishing as an important member of the intestinal microbiota. Some strains of E. coli can acquire virulence factors thereby assuming a pathogenic nature, as in the case of extraintestinal pathogenic E. coli (ExPEC). ExPEC strains have the ability to colonize and spread out in different niches of the host, and are divided into UPEC (uropathogenic E. coli), NMEC (newborn meningitis E. coli) and APEC (avian pathogenic E. coli). UPEC, NMEC and APEC share virulence factors. To be able to cause disease, ExPEC strains must produce virulence factors required for adherence, for iron uptake (siderophore) and for resistance to serum and may also contain genes encoding toxins and invasins. Although many virulence factors associated with the pathogenicity of ExPEC strains are known, the regulation of the expression of these factors has not yet been fully elucidated. Fumarate nitrate reductase (FNR) is a global regulatory protein, acting as a sensor of oxygen in Gram- negative bacteria. It has been shown that FNR relates virulence of pathogenic bacteria such as Shigella flexneri and Salmonella enterica serovar Typhimurium. The aim of this study was to do an epidemiological analysis and characterization of APEC strains as well as the investigation of regulation of ExPEC’s virulence factors by the global FNR regulator. The results of epidemiological analysis of APEC strains showed the profile of antimicrobial resistance , the prevalence of virulence factors and phylogenetic groups (according to the EcoR group) and the phylogenetic relationship of the isolates, providing an overview of the characterization of avian pathogenic E. coli causing severe cellulitis lesions and systemic infection originating from southern Brazil. In relation to FNR, this study showed the influence of this important regulator of virulence factors that is involved in controlling various stages of establishment of infection by ExPEC strains. Deletion of fnr in UPEC strain CFT 073 reduced motility and expression of type I and type P fimbriae, reduced the expression of hemolysin and control the expression of the pathogenicity island of α -ketoglutarate. Furthermore, fnr mutant strains were unable to invade cells of kidney and bladder, and to colonize the urinary tract of 6 weeks-old mice. FNR was also able to control the stages of infection of NMEC 56. The fnr mutant lost its ability to cause bacteremia, grow in cerebrospinal fluid, cause disease in 5 days old rats. Deletion of fnr in APEC O1 resulted in decreased expression of genes corresponding to the plasmid encoded OmpT protein, type I fimbriae and autotransporter AatA. The main contribution of this work was to demonstrate that FNR regulates expression of important virulence factors of ExPEC strains (UPEC, NMEC and APEC), which is important for the establishment of infection by these strains. In this work, we found that, besides the already known function in regulating genes involved in maintaining an anaerobic environment, FNR also acts in the control of virulenceassociated genes of ExPEC strains, reflecting the ability of these strains to cause disease.