Massive shift in the pneumococcal nasopharyngeal flora after the 7-valent conjugate vaccine: epidemiological studies and testing pathogenic potential in animal models

Dissertation presented to obtain the PhD degree in Biology/Molecular Biology by Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica

Evaluation of a new vaccine based on pDNA and recombinant protein against Helicobacter pylori

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Transport mechanism in ionic liquid membranes and the study of thiomersal biodegradation

The initial goal of this work was the development of a supported liquid membrane (SLM) bioreactor for the remediation of vaccine production effluents contaminated with a highly toxic organomercurial – thiomersal. Therefore, two main aspects were focused on: 1) the development of a stable supported liquid membrane – using room temperature ionic liquids (RTILs) – for the selective transport of thiomersal from the wastewater to a biological compartment, 2) study of the biodegradation kinetics of thiomersal to metallic mercury by a Pseudomonas putida strain. The first part of the work focused on the evaluation of the physicochemical properties of ionic liquids and on the SLMs’ operational stability. The results obtained showed that, although it is possible to obtain a SLM with a high stability, water possesses nonnegligible solubility in the RTILs studied. The formation of water clusters inside the hydrophobic ionic liquid was identified and found to regulate the transport of water and small ions. In practical terms, this meant that, although it was possible to transport thiomersal from the vaccine effluent to the biological compartment, complete isolation of the microbial culture could not be guaranteed and the membrane might ultimately be permeable to other species present in the aqueous vaccine wastewater. It was therefore decided not to operate the initially targeted integrated system but, instead, the biological system by itself. Additionally, attention was given to the development of a thorough understanding of the transport mechanisms involved in the solubilisation and transport of water through supported liquid membranes with RTILs as well as to the evaluation of the effect of water uptake by the SLM in the transport mechanisms of water-soluble solutes and its effect on SLM performance. The results obtained highlighted the determinant role played by water – solubilised inside the ionic liquids – on the transport mechanism. It became clear that the transport mechanism of water and water-soluble solutes through SLMs with [CnMIM][PF6] RTILs was regulated by the dynamics of water clusters inside the RTIL, rather than by molecular diffusion through the bulk of the ionic liquid. Although the stability tests vi performed showed that there were no significant losses of organic phase from the membrane pores, the formation of water clusters inside the ionic liquid, which constitute new, non-selective environments for solute transport, leads to a clear deterioration of SLM performance and selectivity. Nevertheless, electrical impedance spectroscopy characterisation of the SLMs showed that the formation of water clusters did not seem to have a detrimental effect on the SLMs’ electrical characteristics and highlighted the potential of using this type of membranes in electrochemical applications with low resistance requirements. The second part of the work studied the kinetics of thiomersal degradation by a pure culture of P. putida spi3 strain, in batch culture and using a synthe tic wastewater. A continuous ly stirred tank reactor fed with the synthetic wastewater was also operated and the bioreactor’s performance and robustness, when exposed to thiomersal shock loads, were evaluated. Finally, a bioreactor for the biological treatment of a real va ccine production effluent was set up and operated at different dilution rates. Thus it was possible to treat a real thiomersal-contaminated effluent, lowering the outlet mercury concentration to values below the European limit for mercury effluent discharges.

Genetic diversity and epidemiology of antimicrobial resistant Streptococcus pneumoniae isolates

Dissertation presented to obtain a Ph.D. degree in Biology, speciality in Microbiology, by Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Contributo para o estudo da influência do stress na resposta imunitária à vacina contra a gripe em profissionais de saúde

Resumo: Os profissionais de saúde podem estar expostos a vários factores indutores de stress crónico nomeadamente de natureza profissional destacando-se, entre os seus possíveis efeitos, a diminuição da resposta de anticorpos após administração de vacinas, entre as quais, a vacina contra a gripe. Uma vez que os trabalhadores da saúde estão expostos a factores indutores de stress e, simultaneamente, a agentes biológicos cujos efeitos poderão ser prevenidos pela vacinação, é pertinente estudar a influência do stress na resposta imunitária à vacina contra a gripe em enfermeiros. Constituíram objectivos deste trabalho: (1) estudar a associação entre a presença de stress crónico em enfermeiros hospitalares e a “insuficiente” resposta imunitária à vacina contra a gripe, avaliada um mês após a vacinação (T1); (2) estudar a associação entre a presença de stress crónico em enfermeiros hospitalares e a redução dos títulos de anticorpos dirigidos às hemaglutininas seis meses após a vacinação (T6) e (3) identificar algumas características das unidades de internamento e do trabalho dos participantes que possam estar associadas à presença de stress crónico e estudar a sua possível associação com a resposta imunitária à vacina contra a gripe. Realizou-se um estudo caso-controlo incorporado num estudo de coortes e a amostra em estudo foi constituída por 136 enfermeiros saudáveis (83,8% sexo feminino; média de idades de 33anos) de um hospital universitário. Realizaram-se entrevistas individuais e aplicaram-se as versões portuguesas dos questionários The General Health Questionnaire (GHQ12) e Maslach Burnout Inventory – Human Services Survey (MBI-HSS) para determinação da presença de stress crónico pelo método da triangulação, no início do estudo (T0) e realizou-se a recolha de dados relativos à caracterização de elementos de trabalho nas unidades de internamento. Foi administrada a vacina contra a gripe e determinou-se os títulos de anticorpos dirigidos às hemaglutininas de cada estirpe componentes da vacina contra a gripe utilizada em 2007, antes da vacinação, um mês e seis meses após a vacinação. Não se encontrou associação, ao nível de significância de 5%, entre a presença de stress e a “insuficiente” resposta à vacina contra a gripe, avaliada pela taxa de indivíduos que apresentaram um aumento, ao fim de um mês, inferior a quatro vezes os títulos de anticorpos antes da vacinação. No entanto, encontrou-se uma maior proporção de indivíduos com stress no grupo de participantes em que ocorreu uma diminuição do título de anticorpos dirigidos à hemaglutinina AH1 (ac AH1) em T6, quando comparado com o respectivo grupo controlo. A diferença entre grupos foi estatisticamente significativa, quando se avaliou a presença de stress pelo método da triangulação usando a entrevista (p=0,006), pelo método da triangulação usando o GHQ12 (p=0,045) e ainda usando a combinação dos três critérios (p=0,001). Após análise multivariada, verificou-se que a associação entre a presença de XXVI stress e a redução dos ac AH1 em T6 manteve significado estatístico (respectivamente, p= 0,010, p= 0,042 e p=0,002) e apresentou odds ratio ajustados, em função de cada um dos métodos de avaliação da presença de stress, de 3,643, de 2,733 e de 5,223. A quantidade de trabalho percepcionada como sobrecarga constituiu o factor indutor de stress mais vezes referido (58,8% da amostra e 61,8% dos enfermeiros de unidades de internamento), seguida dos conflitos entre profissionais. O contacto com o sofrimento e a morte de doentes foram identificados em quarto lugar pela amostra, mas em segundo pelos enfermeiros de unidades de internamento. Nesses, verificou-se uma associação positiva entre trabalhar em Serviços onde o número de doentes falecidos foi muito elevado e a presença de stress, medido pelo método da triangulação usando a entrevista (p=0,039), usando o GHQ12 (p=0,019), usando a escala de exaustão emocional do MBI-HSS (p=0,012) e pela combinação dos três métodos (p=0,014). Verificou-se também uma associação positiva entre a presença de stress, identificada pelo método da triangulação usando a escala de exaustão emocional do MBI-HSS, e o trabalho em serviços de internamento onde a percentagem de doentes idosos (p=0,025) e a taxa de letalidade (p=0,036) foram elevadas. Contudo, não se encontrou associação entre a exposição muito frequente ao sofrimento e à morte de doentes e a redução do título de ac AH1 em T6. Possivelmente, a exposição a esse factor indutor de stress, apesar de estar relacionada com a presença de stress nos enfermeiros de serviços de internamento, não foi suficientemente intenso para, por si só, estar associada à redução do título de ac AH1 em T6. A associação encontrada entre a presença de stress crónico e a redução do título de anticorpos AH1 em T6 vem apoiar a resposta à questão de investigação inicialmente colocada de que o stress poderá influenciar negativamente a manutenção dos títulos de anticorpos, mesmo em indivíduos adultos não idosos. Assim, o risco de um enfermeiro com stress apresentar redução do título de anticorpos dirigidos à hemaglutinina da estirpe AH1N1 – A/Solomon Islands/3/2006 ao fim dos seis meses do estudo, foi 3,6, 2,7 ou 5,2 vezes superior ao de um enfermeiro sem stress, consoante o critério de stress ter sido determinado, respectivamente, pelo método da triangulação usando a entrevista, pelo método da triangulação utilizando o GHQ12 ou pela combinação dos três critérios. Summary: Health workers may be exposed to various factors causing chronic stress namely those related directly to their activity, in particular the decrease in the capacity of the response of antibodies after the administration of the vaccines, amongst others the Influenza vaccine. Since health workers are exposed to factors causing stress and at the same time biological agents, whose effects may be prevented through vaccination, it is important to study the influence of stress in the immunity response to the Influenza vaccine on nurses. The aims of this study are: (1) to examine the relation between chronic stress in hospital nurses and the “insufficient” immunity response to the Influenza vaccine, assessed at one month after vaccination (T1); (2) to examine the relation between chronic stress in hospital nurses and the decrease of the hemagglutinin titles of antibodies six months after vaccination (T6); (3) to identify some characteristics of internment units and the work of the participants that may be related to the presence of chronic stress and to study its possible relation with the immunity response to the Influenza vaccine. A control-case study, integrated in a coortes study, was carried out and the sample under analysis consisted of 136 healthy nurses (83,8% female; average age 33 years old) from a university hospital. Several individual interviews were conducted and the portuguese versions of General Health Questionnaire (GHQ12) and Maslach Burnout Inventory – Human Services Survey (MBI-HSS) was applied in order to determine the presence of chronic stress, using the triangulation method at the beginning of the study (T0). Data concerning the particular features of the internment units was collected. The Influenza vaccine was administered and the titles of hemagglutinin antibodies of each strain composing the Influenza vaccine used in 2007, before vaccination, and a month and six months after vaccination, were determined. There was no statistically relevant (5%) relation between stress and the “insufficient” immune response to the Influenza vaccine, according to the rate of individuals that showed, after a month, a level of antibodies concentration lower than four times the level prior to the vaccination. Nevertheless, there was a greater number of individuals with stress in the group of participants in which there was a decrease of the hemagglutinin titles of antibodies AH1 (ac AH1) in T6, when compared to the control group under study. The difference between groups was statistically relevant when assessing the presence of stress by triangulation method using the interview (p=0,006), by triangulation method using the GHQ12 (p=0,045) and by the combination of the three criteria (p=0,001). After multivariate analysis, it was verified that the XXVIII relation between the presence of stress and the reduction of the ac AH1 in T6 was statistically relevant (respectively, p= 0,010, p= 0,042 and p=0,002) and the odds ratio were, according to each of the methods used to assess the presence of stress, 3,643, 2,733 and 5,223. Overwork was the most emphasised stress-causing factor (58,8% of the sample and 61,8% of the nurses working in the Internment Units), followed by conflicts arousing among co-workers. Witnessing the suffering and death of patients was ranked as the fourth cause of stress, but the second by the nurses of the internment units. The former revealed a positive connection between working in the services, where there was a high rate of deaths, and the presence of stress, when assessing the presence of stress by triangulation method using the interview (p=0,039), the GHQ12 (p=0,019), the MBI-HSS emotional exhaustion scale (p=0,012) and by the combination of the three criteria (p=0,014).There was also a connection between the presence of stress, identified by the method of triangulation using the MBI-HSS emotional exhaustion scale, and working in the internment units, where the percentage of elderly people (p=0,025) and the mortality rate (p=0,036) were high. However, there was no connection between frequent exposure to suffering and death in patients and the reduction of ac AH1 titles, in T6. Although one can establish a connection between stress in nurses working in the internment units and the aforementioned stress-causing factor, the exposure to that factor was not, per se, intense enough to reduce the ac AH1 title in T6. The relation found between the presence of chronic stress and the reduction of AH1 antibodies titles in T6, corroborates the hypothesis that stress can negatively influence the title of antibodies, even in non-elderly adults. Thus, and according to the criteria used to define stress, by the triangulation method using the interview, by the triangulation method using the GHQ12 or the combination of the three criteria respectively, the risk of a nurse suffering from stress showing a reduction in the title of hemagglutinin antibodies for the strain AH1N1 – A/Solomon Islands/3/2006 six-month after Influenza vaccine was 3,6, 2,7 or 5,2 times greater than on a nurse suffering from no stress at all. Résumé: Les professionnels de la santé peuvent être exposés à différents facteurs inducteurs de stress chronique de nature professionnelle. On remarque, parmi les effets possibles, une baisse de la réponse des anticorps après l´administration de vaccins, comme en particulier, le vaccin de la grippe. Lorsque les professionnels de la santé ont été exposés à des facteurs inducteurs de stress, et de manière simultanée, à des agents biologiques dont les effets pourront être prévenus par la vaccination, il est pertinent d´étudier l´influence du stress dans la réponse immunitaire au vaccin de la grippe chez les infirmiers. Ils ont constitué des objectifs d´études et de discussion : (1) étudier l´association entre la présence de stress chronique chez les infirmiers, en milieu hospitalier, et la “insuffisant” réponse immunitaire au vaccin de la grippe, vérifiée à un mois après la vaccination (T1); (2) étudier l´association entre la présence de stress chronique chez les infirmiers, en milieu hospitalier, et la réduction de la teneur des anticorps dirigé à la hémaglutinina six mois après la vaccination (T6) (3) identifier certaines caractéristiques des unités d´internement, et étudier les aspects du travail des participants, qui puissent être associée à la présence de stress chronique et étudier sa possible association avec la réponse immunitaire au vaccin de la grippe. Une étude cas-contrôle incorporée dans une étude de groupe a été réalisée et un échantillon, pour étude, a été constitué par 136 infirmiers sains (83,8% de sexe féminin, âge moyen 33 ans) travaillant dans un hôpital universitaire. Des entretiens individuels ont été réalisés et les versions portugaises des questionnaires de General Health Questionnaire (GHQ12) et Maslach Burnout Inventory- Human Service Survey (MBI-HSS) ont été utilisés pour déterminer la présence de stress chronique grâce à la méthode de triangulation, au début de l´étude (T0) et un relevé de données relatives à la caractérisation d´éléments de travail dans les unités d´internement a été fait. Le vaccin de la grippe a été administré et les teneurs en anticorps dirigés aux hémaglutininas de chaque composant du vaccin de la grippe pour 2007 ont été déterminés, avant la vaccination et un mois et six mois après. On n´a pas trouvé d´association, à un niveau significatif de au moins 5%, entre la présence de stress et la “insuffisant” réponse au vaccin de la grippe, évaluée par le taux d´individus qui ont présenté une augmentation, à la fin du mois, inférieur à quatre fois la teneur des anticorps par rapport à avant la vaccination. Cependant , on a trouvé une plus grande proportion d´individus victimes de stress dans le groupe des participants où il y a eu une baisse de la teneur des anticorps dirigé à la hémaglutinina AH1 (ac AH1) en T6, après comparaison avec le respectif groupe de contrôle. La différence entre les groupes a été statistiquement significative lorsqu´on a vérifié la présence de stress grâce à la méthode de triangulation, en utilisant l´entretien (p=0,006), par la méthode de triangulation en utilisant le GHQ12 (p=0,045) et en utilisant aussi la combinaison des trois critères (p=0,001). Après une analyse XXX multivariée, on a vérifié que l´association entre la présence de stress et la réduction des ac AH1 en T6 a conservé un signifié statistique (respectivement, p=0,010, p=0,042 et p=0,002) et a présenté des odds ratio ajustés, en fonction de chacune des méthodes de vérification de la présence de stress de 3,643, de 2,733 et de 5,223. La quantité de travail perçue comme une surcharge constitue le facteur inducteur de stress le plus souvent cité (58,8% de l´échantillon et 61,8% des infirmiers des unités d´internement), suivi par les conflits entre professionnels. Le contact avec la souffrance et la mort des patients a été placé en quatrième position par l´échantillon, mais en deuxième position par les infirmiers des unités d´internement. Dans ces cas, on a vérifié une association évidente entre le fait de travailler dans des services où le nombre de patients décédés a été très élevé et la présence de stress, identifiée par la méthode de triangulation, en utilisant l´entretien (p=0,039), le GHQ12 (p=0,019), l´échelle de fatigue émotionnelle du MBI-HSS (p=0,012) et en utilisant aussi la combinaison des trois critères (p=0,014). On a aussi vérifié une association positive entre la présence de stress, identifiée par la méthode de triangulation, en utilisant l´échelle de fatigue émotionnelle du MBI-HSS et le travail dans des services d´internement où le pourcentage de malade âgés (p=0,025) et le taux de mortalité ont été élevés (p=0,036). Malgré tout, on n´a pas trouvé d´association entre l´exposition très fréquente à la souffrance et à la mort des patients et la réduction de la teneur de ac AH1 en T6. Probablement l´exposition à ce facteur inducteur de stress, bien qu´elle soit liée à la présence de stress chez les infirmiers des services d´internement, n´a pas été suffisamment intense pour, en elle-même, être associée à la réduction de la teneur ac AH1 enT6. L´association trouvée entre la présence de stress chronique et la réduction de la teneur des anticorps AH1 en T6 vient renforcer l´hypothèse que le stress pourra influencer négativement la manutention des teneurs en anticorps même chez les individus adultes jeunes. Donc le risque qu´un infirmier stressé présente une réduction de la teneur en anticorps dirigés à la hémaglutinina de le composant AH1N1-A/Solomon Island/3/2006 à la fin des six mois d´études a été 3,6, 2,7 ou 5,2 fois supérieure à celui d´un infirmier sans stress, après avoir déterminé le critère de stress, respectivement par la méthode de triangulation utilisant l´entretien, par la méthode de triangulation utilisant le GHQ12 ou par la combinaison des trois critères.

Vigilância activa de eventos após vacinação

A vigilância de efeitos indesejáveis após a vacinação é complexa. Existem vários actores de confundimento que podem dar origem a associações espúrias, meramente temporais mas que podem provocar uma percepção do risco alterada e uma consequente desconfiança generalizada acerca do uso das vacinas. Com efeito as vacinas são medicamentos complexos com características únicas cuja vigilância necessita de abordagens metodológicas desenvolvidas para esse propósito. Do exposto se entende que, desde o desenvolvimento da farmacovigilância se tem procurado desenvolver novas metodologias que sejam concomitantes aos Sistemas de Notificação Espontânea que já existem. Neste trabalho propusemo-nos a desenvolver e testar um modelo de vigilância de reacções adversas a vacinas, baseado na auto-declaração pelo utente de eventos ocorridos após a vacinação e testar a capacidade de gerar sinais aplicando cálculos de desproporção a datamining. Para esse efeito foi constituída uma coorte não controlada de utentes vacinados em Centros de Saúde que foram seguidos durante quinze dias. A recolha de eventos adversos a vacinas foi efectuada pelos próprios utentes através de um diário de registo. Os dados recolhidos foram objecto de análise descritiva e análise de data-mining utilizando os cálculos Proportional Reporting Ratio e o Information Component. A metodologia utilizada permitiu gerar um corpo de evidência suficiente para a geração de sinais. Tendo sido gerados quatro sinais. No âmbito do data-mining a utilização do Information Component como método de geração de sinais parece aumentar a eficiência científica ao permitir reduzir o número de ocorrências até detecção de sinal. A informação reportada pelos utentes parece válida como indicador de sinais de reacções adversas não graves, o que permitiu o registo de eventos sem incluir o viés da avaliação da relação causal pelo notificador. Os principais eventos reportados foram eventos adversos locais (62,7%) e febre (31,4%).------------------------------------------ABSTRACT: The monitoring of undesirable effects following vaccination is complex. There are several confounding factors that can lead to merely temporal but spurious associations that can cause a change in the risk perception and a consequent generalized distrust about the safe use of vaccines. Indeed, vaccines are complex drugs with unique characteristics so that its monitoring requires specifically designed methodological approaches. From the above-cited it is understandable that since the development of Pharmacovigilance there has been a drive for the development of new methodologies that are concomitant with Spontaneous Reporting Systems already in place. We proposed to develop and test a new model for vaccine adverse reaction monitoring, based on self-report by users of events following vaccination and to test its capability to generate disproportionality signals applying quantitative methods of signal generation to data-mining. For that effect we set up an uncontrolled cohort of users vaccinated in Healthcare Centers,with a follow-up period of fifteen days. Adverse vaccine events we registered by the users themselves in a paper diary The data was analyzed using descriptive statistics and two quantitative methods of signal generation: Proportional Reporting Ratio and Information Component. themselves in a paper diary The data was analyzed using descriptive statistics and two quantitative methods of signal generation: Proportional Reporting Ratio and Information Component. The methodology we used allowed for the generation of a sufficient body of evidence for signal generation. Four signals were generated. Regarding the data-mining, the use of Information Component as a method for generating disproportionality signals seems to increase scientific efficiency by reducing the number of events needed to signal detection. The information reported by users seems valid as an indicator of non serious adverse vaccine reactions, allowing for the registry of events without the bias of the evaluation of the casual relation by the reporter. The main adverse events reported were injection site reactions (62,7%) and fever (31,4%).