Antibiotic resistance is of current concern. Bacteria have become increasingly resistant to commonly used antibiotics and we are facing a growing resistance problem. The present thesis was aimed at studying the impact of antibiotic treatment on pathogenic bacteria as well as on the normal human microbiota, with focus on resistance development. Among the factors that affect the appearance of acquired antibiotic resistance, the mutation frequency and biological cost of resistance are of special importance. Our work shows that the mutation frequency in clinical isolates of Helicobacter pylori was generally higher than for other studied bacteria such as Enterobacteriaceae; ¼ of the isolates displayed a mutation frequency higher than Enterobacteriaceae defective mismatch repair mutants and could be regarded as mutator strains. In H. pylori, clarithromycin resistance confers a biological cost, as measured by decreased competitive ability of the resistant mutants in mice. In clinical isolates, this cost could be reduced, consistent with compensatory evolution stabilizing the presence of the resistant phenotype in the population. Thus, compensation is a clinically relevant phenomenon that can occur in vivo. Furthermore, our results show that clinical use of antibiotics selects for stable resistance in the human microbiota. This is important for several reasons. First, many commensals occasionally can cause severe disease, even though they are part of the normal microbiota. Therefore, stably resistant populations increase the risk of unsuccessful treatment of such infections. Second, resistance in the normal microbiota might contribute to increased resistance development among pathogens by interspecies transfer of resistant determinants.

In recent years molecular biology has become an integral part of the clinical laboratory. With an ever increasing number of methodologies and applications being presented each year it has increased our knowledge of how bacteria cause disease as well as our ability to predict disease outcome. The main focus of this thesis has been to develop methods for identifying biomarkers and prediction methods for bacterial infectious diseases by taking advantage of the ever increasing possibilities of molecular biology. We applied cutting edge techniques in order to establish novel platforms for identifying and characterizing biomarkers of disease. In paper one we describe a novel approach to measure levels of antibiotic resistance and viability of C. trachomatis, a method that is a clear improvement over existing techniques. In the second paper we describe the development of two assays designed to type pertussis toxin subunit 1 in circulating strains, in order to facilitate multi center studies for vaccine escape surveillance. In paper three we develop a novel microarray application designed to identify a large number of bacterial traits of H. pylori simultaneously with human genetic polymorphisms in order to identify a collection of risk factors that could be used as a prediction tool for gastric cancer risk. In the last paper we define the “antigenome” of H. pylori and identified 14 promising, previously unreported antigens as well as a number of potential biomarkers. The platform technologies described in this collection of papers will hopefully help us identifying novel ways of fighting and predicting bacterial disease in future studies.

Bacterial pathogens assemble complex surface structures in an attempt to circumvent host immune detection. A great example is the glycolipid known as lipopolysaccharide or lipooligosaccharide (LPS), the major surface molecule in nearly all gram-negative organisms. LPS is anchored to the bacterial cell surface by a anionic hydrophobic lipid known as lipid A, the major agonist of the mammalian TLR4-MD2 receptor and likely target for cationic antimicrobial peptides (CAMPs) secreted by host cells (i.e. defensins). In this work we investigate LPS modification machinery in related ε-proteobacteria, Helicobacter pylori and Campylobacter jejuni, two important human pathogens, and demonstrate that enzymes involved in LPS modification not only play a role in evasion of host defenses but also an unexpected role in bacterial locomotion. More specifically, we identify the enzyme responsible for 4'-dephosphorylation of H. pylori lipid A, LpxF. Demonstrating that lipid A depohsphorylation at the 1 and 4'-positions by LpxE and LpxF, respectively, are the primary mechanisms used by H. pylori for CAMP resistance, contribute to attenuated TRL4-MD2 activation and are required for colonization of a the gastric mucosa in murine host. Similarly in C. jejuni, we identify an enzyme, EptC, responsible for modification of lipid A at both the 1 and 4'-positions with phosphoethanolamine (pEtN), also required for CAMP resistance in this organism. Suprisingly, EptC was found to serve a dual role in modifying not only lipid A with pEtN but also the flagellar rod protein FlgG at residue Thr75, required for motility and efficient flagella production. This work links membrane biogenesis with flagella assembly, both shown to be required for colonization of a host and adds to a growing list of post-translational modifications found in prokaryotes. Understanding how pathogens evade immune detection, interphase with the surrounding environment and assemble major surface features is key in the development of novel treatments and vaccines. / text

Published information on the structure and regulation of H. pylori promoters is limited. The work presented in this thesis describes the cloning and characterisation of promoter regions from a clinical isolate of H. pylori, and the development of an alternative, non-radioactive method for verifying the location of transcriptional start sites of bacterial promoters. H. pylori 4187E promoters were randomly cloned into the promoter-trap vector pKK232-8 in Escherichia coli DH5α using two sets of restriction enzymes. Vector pKK232-8 contains a promoterless chloramphenicol acetyltransferase (CAT) gene. Seventy-four promoter-containing clones were isolated from selective media based on their resistance to chloramphenicol. The strength of each promoter was analysed qualitatively, using chloramphenicol minimum inhibitory concentrations, and quantitatively, using CAT assays following exposure of the clones to pH 4 and pH 7. Selected promoter fragments were subcloned into the GFP reporter vector pFPV25, containing a promoterless gfp gene. The subclones were exposed to buffered LB broth at pH 4, 5, 6, 7 and 8, for varying lengths of time, to study acid-induced regulation of gene expression. Subclones were examined qualitatively, using visual examination of GFP fluorescence and fluorescence microscopy, and quantitatively, using flow cytometry following acid shock. DNA sequences were determined for 61 of the 74 H. pylori promoters, and sequence alignments with the published H. pylori strains (26695 and J99) were performed. The transcriptional start site of 27 H. pylori promoter fragments was experimentally mapped using a fluorescence-based primer extension protocol developed by our group. Potential -35 and -10 sequences were identified for each promoter, and a new consensus sequence for H. pylori promoters was proposed based upon these results. This study has considerably expanded knowledge of H. pylori promoter sequences and transcriptional start sites based on those which also function in E. coli. It has also revealed several H. pylori promoters which appear to respond to acid stress

Diss. (sammanfattning) Stockholm : Karol inst., 2004. / Härtill 4 uppsatser.

Thesis (M.P.H.)--University of Texas Health Science Center at Houston, School of Public Health, 2007. / Source: Masters Abstracts International, Volume: 45-04, page: 1936. Adviser: Corinne C. Aragaki. Includes bibliographical references.

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No. of bitstreams: 1 poltronierioliveira_ab_me_sjrp.pdf: 1526886 bytes, checksum: b50424a42154b92cbde06c084bf0975d (MD5) Previous issue date: 2016-03-04 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Introdução: A inflamação crônica desencadeada pela bactéria Helicobacter pylori (H. pylori), a qual é considerada o principal fator ambiental relacionado ao câncer gástrico, está associada ao desenvolvimento e progressão de lesões gástricas pré-cancerosas, desencadeando diversas modificações histológicas e moleculares que promovem a transformação maligna do estômago. Para isso, conta com fatores de virulência que promovem alterações superficiais e em vias de sinalização das células epiteliais gástricas. Consequentemente pode levar a alterações no padrão de expressão de genes supressores tumorais e da atividade de enzimas DNA metil transferases (DNMTs), responsáveis pela metilação do DNA e silenciamento gênico. Objetivos: O presente estudo avaliou se a infecção pela bactéria H. pylori, bem como sua erradicação, altera a expressão do RNAm dos genes supressores SOCS1, RPRM, RUNX3 e dos genes de DNMTs (DNMT1, DNMT3A e DNMT3B) em pacientes com gastrite crônica infectados (Hp+) em comparação com indivíduos com gastrite crônica sem infecção (Hp-). Além disso, investigou a ocorrência de correlação negativa entre a expressão do RNAm dos genes supressores tumorais com a dos genes das DNMTs, assim como a associação dos níveis de expressão gênica em relação aos fatores de risco idade, sexo, tabagismo, etilismo e genótipo bacteriano cagA. Material e Métodos: A quantificação relativa (RQ) do RNAm foi realizada por PCR (polymerase chain reaction) quantitativa em tempo real (qPCR) utilizando ensaios TaqMan® em 9 pacientes com gastrite crônica Hp- e 19 Hp+, sendo estes também avaliados três meses depois da terapia de erradicação bacteriana. O diagnóstico molecular e genotipagem do fator de virulência cagA foram realizados por PCR convencional. Resultados: Os resultados mostraram que a infecção pela H. pylori e sua erradicação não alteraram significantemente a expressão dos genes SOCS1, RPRM, RUNX3 e DNMTs, as quais apresentaram, de modo geral, expressão reduzida (RQ< 1,0), enquanto foi observado expressão mais elevada de SOCS1 e RPRM no grupo sem infecção Hp-. Quanto aos fatores de risco, também não foram encontradas associações significantes com os níveis de expressão dos genes avaliados. A análise de correlação não mostrou correlação negativa da expressão gênica entre os supressores tumorais e as DNMTs, mas evidenciou algumas correlações positivas entre a expressão dos genes SOCS1 e DNMT1 e do RPRM com DNMT3A e DNMT3B no grupo Hp+, que podem ter sido casuais. Conclusão: Nossos resultados não indicam que a infecção causada pela bactéria H. pylori e sua erradicação em pacientes com gastrite crônica afetam a expressão dos supressores tumorais SOCS1, RPRM, RUNX3 e das DNMTs, assim como que seja influenciada pelos fatores idade, sexo, tabagismo, etilismo e genótipo bacteriano cagA. Além disso, a expressão reduzida das DNMTs e ausência de correlação negativa com a dos genes supressores tumorais não permite indicar que a baixa expressão dos genes supressores tumorais seja devido a hipermetilação do DNA em consequência da infecção. / Introduction: Chronic inflammation caused by Helicobacter pylori (H. pylori), which is considered the main environmental factor related to gastric cancer, is associated with the development and progression of precancerous gastric lesions, triggering several histological and molecular changes that promote stomach malignant transformation. For this, it has virulence factors promoting superficial and signaling pathways of gastric epithelial cells changes. Consequently, it can lead to alterations in the expression of tumor suppressor genes and DNA enzyme activity methyl transferases (DNMTs), responsible for DNA methylation and gene silencing. Objectives: This study evaluated whether the infection by the bacterium H. pylori and its eradication change the mRNA expression of suppressor genes SOCS1, RPRM, RUNX3 and DNMTs (DNMT1, DNMT3A and DNMT3B) genes in patients with chronic gastritis infected (Hp+) compared to individuals with chronic gastritis without infection (Hp-). In addition, we investigated the occurrence of negative correlation between mRNA expression of tumor suppressor genes with the ones of DNMTs, as well as the association of gene expression levels in relation to the risk factors age, sex, smoking, drinking and bacterial genotype cagA. Methods: The relative quantification (RQ) mRNA was performed by PCR (polymerase chain reaction) quantitative real-time (qPCR) using TaqMan® assays in 9 patients with chronic gastritis Hp- and 19 Hp+, which are also evaluated three months after bacterial eradication therapy. The molecular diagnostics and genotyping of the virulence factors CagA were performed by standard PCR. Results: The results showed that the infection by H. pylori and eradication did not significantly alter the gene expression of SOCS1, RPRM, RUNX3 and DNMTs, which presented, in general, reduced expression (RQ <1.0); on the other hand, higher expression of SOCS1 and RPRM was observed in the group without Hp- infection. As for risk factors, no significant associations with the expression levels of evaluated genes were found. The correlation analysis not showed a negative correlation of gene expression in the tumor suppressor and DNMTs, but showed some positive correlations between the expression of SOCS1 and DNMT1 genes and RPRM with DNMT3A and DNMT3B the Hp + group, which may have been casual. Conclusion: Our findings do not indicate that the infection caused by the bacterium Helicobacter pylori and its eradication in patients with chronic gastritis affect the expression of tumor suppressor SOCS1, RPRM, RUNX3 and DNMTs, as it is influenced by factors such as age, sex, smoking, alcoholism and bacterial genotype cagA. Furthermore, the reduced expression of DNMTs and no negative correlation with the tumor suppressor genes do not indicate that the low expression of tumor suppressor genes is due to DNA hypermethylation in consequence of infection. / CNPq: 474.776/2013-1 / FAPESP: 2012/15036-8

Made available in DSpace on 2014-06-11T19:26:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-02-28Bitstream added on 2014-06-13T18:29:22Z : No. of bitstreams: 1 silva_hm_me_sjrp.pdf: 508031 bytes, checksum: 56b635113c96c5bc5c2ffa3a4cb5324a (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O câncer gástrico é a segunda causa de morte por câncer no mundo e o quinto tipo com maior prevalência no Brasil, sendo previstos 21.800 casos novos em 2008. Esta neoplasia apresenta etiologia bastante complexa, envolvendo fatores genéticos e ambientais. Os fatores etiológicos de maiores destaques incluem a infecção pela bactéria Helicobacter pylori, a ingestão de determinados alimentos, como defumados, enlatados e com elevada quantidade de sal, além do estilo de vida dos indivíduos, associado ao consumo de cigarro e álcool. Uma lesão pré-cancerosa importante no desenvolvimento da neoplasia gástrica é a metaplasia intestinal, podendo aumentar o seu risco em até 10 vezes. Atualmente é reconhecida a participação de alterações epigenéticas como metilação aberrante do DNA, que atua de forma igualmente relevante e complementar no processo de desenvolvimento e progressão do câncer. Vários genes com papel importante no controle do ciclo celular, reparo do DNA, apoptose, angiogênese e adesão celular podem apresentar expressão alterada devido metilação aberrante de sua região promotora, assim a investigação do padrão de metilação de genes envolvidos com o processo neoplásico pode ser uma estratégia interessante para a indicação de marcadores moleculares que possam auxiliar no diagnóstico precoce do câncer. Desta forma, no presente trabalho foi investigado o padrão de metilação dos genes WT1 e RARß em metaplasia intestinal (35 amostras) e suas respectivas mucosas gástricas normais, em comparação com o câncer gástrico (8 amostras) também com suas respectivas mucosas normais, através da técnica MS-PCR (Methylation Specific PCR). Devido à participação da infecção pela H. pylori na carcinogênese gástrica, foi investigada molecularmente a presença dessa bactéria nas amostras... / Worldwide, the gastric cancer is the second cause of death by cancer. In Brazil, it is the fifth type with more abundant, foreseen 21.800 new cases in 2008. This neoplasia presents very complex etiology involving genetic and environmental factors. The main etiologic factors include: infection by H. pylori, intake of specific foods such as curing food, canned food, and high consumption of salt wealthy food, besides people life style associated to alcohol and cigarette consumptions. An important previous-cankered lesion in development of gastric neoplasia is the intestinal metaplasia, what can increase your risk in ten times. At this moment, it is recognized the participation of epigenetic alterations like ADN aberrant methylation, which actuate in a same way considerable and complementary in development process and cancer evolution. Many genes with important role in control of cellular cycle, ADN repair, apoptosis, angiogenesis and cellular adhesion can present changed expression due aberrant metthylation of your promoter region. In this manner, the investigation of metithyation pattern of genes involved with the neoplasic process can be an interesting strategy for the indication of molecular markers that can help in cancer precocious diagnosis. Thus, in this present study were investigated the metthylation pattern of RARß and WT1genes (35 samples) and their respective normal mucous gastrics by technic MSPCR (Methylation Specific PCR). Due to participation of infection by H. pylori in gastric carcinogenesis, it was too molecular investigated the presence of this bacterium in the studied samples and the possible association with the metthylation pattern presented by both genes. The results showed high pattern of methylation in both valued lesions, that is, 97% and 100%, respectively of methylated samples in metaplasia group ...(Complete abstract click electronic access below)

Made available in DSpace on 2014-06-11T19:26:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-12-17Bitstream added on 2014-06-13T20:14:35Z : No. of bitstreams: 1 jorge_yc_me_sjrp.pdf: 4700733 bytes, checksum: 1fa001424eaf0ffba4a8cdeb55c5fce5 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / No presente estudo foram investigados os níveis de expressão gênica e protéica da anexina-1 (ANXA1/AnxA1) e galectina-1 (LGALS1/Gal-1) na carcinogênese do estômago e associações com infecção pela Helicobacter pylori e o genótipo de virulência bacteriano cagA+. A análise foi realizada em 40 biópsias de mucosa gástrica com gastrite crônica (CG), 20 de câncer gástrico (GA) e 10 de mucosa normal (C), pelas técnicas de qPCR para quantificar os níveis de RNAm; imuno-histoquímica para caracterizar a expressão protéica na mucosa gástrica, e PCR para diagnóstico molecular da H. pylori e cepa cagA+. O estudo mostrou resultados inéditos quanto à expressão desses genes em gastrite crônica, ainda sem descrições na literatura. Foi demonstrada expressão relativa elevada do mRNA de ANXA1 em 80% dos casos de GA (média de 4,38 + 4,77) e em 90% dos casos de CG (média de 4,26 + 2,03), sem diferença significante entre os grupos (p = 0,33). O gene LGALS1 apresentou expressão elevada em 60% dos casos GA (média de 2,44 + 3,26) e, expressão constitutiva na CG (média de 0,43 + 3,13), mostrando, portanto, diferença significante entre os grupos (p < 0,01). A imuno-histoquímica revelou que as proteínas AnxA1 e Gal-1 não são expressas na mucosa normal. Ao contrário, durante o processo inflamatório de CG, imunomarcação citoplasmática positiva para a AnxA1 foi observada na porção basal do epitélio e estroma e, para Gal-1 a expressão foi constatada na porção apical e borda estriada do epitélio além do estroma. No adenocarcinoma tipo intestinal foi observada expressão citoplasmática em toda extensão epitelial e estroma tanto para a AnxA1 quanto para a Gal-1. Por outro lado, no tipo difuso imunomarcação positiva também foi observada no núcleo e membrana plasmática... / In this study we investigated the levels of gene and protein expression of annexin-1 (ANXA1/Anxa1) and galectin-1 (LGALS1/Gal-1) in gastric carcinogenesis and associations with Helicobacter pylori infection and bacterial virulence genotype cagA+. The analysis was performed in 40 biopsies of gastric mucosa with chronic gastritis (CG), 20 with gastric cancer (GA) and 10 of normal mucosa (C), by the techniques of qPCR to quantify mRNA levels, immunohistochemistry to characterize the protein expression in gastric mucosa, and PCR for molecular diagnosis of H. pylori cagA+ strains. This is the first study regarding the expression of these genes in chronic gastritis. High ANXA1expression levels were demonstrated in 80% of GA cases (mean 4.38 + 4.77) and in 90% of GC cases (mean 4.26 + 2.03), with no significant difference between groups (p = 0.33). High LGALS1 gene expression was found in 60% of GA cases (average 2.44 + 3.26), and constitutive expression was found in CG (mean 0.43 + 3.13), showing therefore a significant difference between groups (p <0.01). Immunohistochemistry revealed that the proteins AnxA1 and Gal-1 are not expressed in normal mucosa. In contrast, during the inflammatory process of CG, positive cytoplasmic immunostaining for AnxA1 was observed in the basal epithelium and stroma, and Gal-1 expression was detected in the apical portion and striated border of the epithelium and stroma. In intestinal-type adenocarcinoma was observed cytoplasmic expression in all epithelial and stromal extension for both AnxA1 and Gal-1. On the other hand, in diffuse-type adenocarcinoma positive immunostaining was also observed in the nucleus and plasma membrane of both proteins. Infection by H. pylori showed no association with the expression of both genes, but the genotype cagA+ is associated with about 2.5 times... (Complete abstract click electronic access below)

Orientador: Ana Elizabete Silva / Banca: Kátia Ramos Moreira Leite / Banca: Cristiane Damas Gil / Resumo: No presente estudo foram investigados os níveis de expressão gênica e protéica da anexina-1 (ANXA1/AnxA1) e galectina-1 (LGALS1/Gal-1) na carcinogênese do estômago e associações com infecção pela Helicobacter pylori e o genótipo de virulência bacteriano cagA+. A análise foi realizada em 40 biópsias de mucosa gástrica com gastrite crônica (CG), 20 de câncer gástrico (GA) e 10 de mucosa normal (C), pelas técnicas de qPCR para quantificar os níveis de RNAm; imuno-histoquímica para caracterizar a expressão protéica na mucosa gástrica, e PCR para diagnóstico molecular da H. pylori e cepa cagA+. O estudo mostrou resultados inéditos quanto à expressão desses genes em gastrite crônica, ainda sem descrições na literatura. Foi demonstrada expressão relativa elevada do mRNA de ANXA1 em 80% dos casos de GA (média de 4,38 + 4,77) e em 90% dos casos de CG (média de 4,26 + 2,03), sem diferença significante entre os grupos (p = 0,33). O gene LGALS1 apresentou expressão elevada em 60% dos casos GA (média de 2,44 + 3,26) e, expressão constitutiva na CG (média de 0,43 + 3,13), mostrando, portanto, diferença significante entre os grupos (p < 0,01). A imuno-histoquímica revelou que as proteínas AnxA1 e Gal-1 não são expressas na mucosa normal. Ao contrário, durante o processo inflamatório de CG, imunomarcação citoplasmática positiva para a AnxA1 foi observada na porção basal do epitélio e estroma e, para Gal-1 a expressão foi constatada na porção apical e borda estriada do epitélio além do estroma. No adenocarcinoma tipo intestinal foi observada expressão citoplasmática em toda extensão epitelial e estroma tanto para a AnxA1 quanto para a Gal-1. Por outro lado, no tipo difuso imunomarcação positiva também foi observada no núcleo e membrana plasmática... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In this study we investigated the levels of gene and protein expression of annexin-1 (ANXA1/Anxa1) and galectin-1 (LGALS1/Gal-1) in gastric carcinogenesis and associations with Helicobacter pylori infection and bacterial virulence genotype cagA+. The analysis was performed in 40 biopsies of gastric mucosa with chronic gastritis (CG), 20 with gastric cancer (GA) and 10 of normal mucosa (C), by the techniques of qPCR to quantify mRNA levels, immunohistochemistry to characterize the protein expression in gastric mucosa, and PCR for molecular diagnosis of H. pylori cagA+ strains. This is the first study regarding the expression of these genes in chronic gastritis. High ANXA1expression levels were demonstrated in 80% of GA cases (mean 4.38 + 4.77) and in 90% of GC cases (mean 4.26 + 2.03), with no significant difference between groups (p = 0.33). High LGALS1 gene expression was found in 60% of GA cases (average 2.44 + 3.26), and constitutive expression was found in CG (mean 0.43 + 3.13), showing therefore a significant difference between groups (p <0.01). Immunohistochemistry revealed that the proteins AnxA1 and Gal-1 are not expressed in normal mucosa. In contrast, during the inflammatory process of CG, positive cytoplasmic immunostaining for AnxA1 was observed in the basal epithelium and stroma, and Gal-1 expression was detected in the apical portion and striated border of the epithelium and stroma. In intestinal-type adenocarcinoma was observed cytoplasmic expression in all epithelial and stromal extension for both AnxA1 and Gal-1. On the other hand, in diffuse-type adenocarcinoma positive immunostaining was also observed in the nucleus and plasma membrane of both proteins. Infection by H. pylori showed no association with the expression of both genes, but the genotype cagA+ is associated with about 2.5 times... (Complete abstract click electronic access below) / Mestre