Studies on resistance and response to vancomycin in Enterococcus faecalis: a last resort antibiotic

Dissertation presented to obtain a Ph.D. degree in Biochemistry by Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa.

Gold nanoprobes for the detection of mutations associated with antibiotic resistance in Mycobacterium tuberculosis complex

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

Novel antibiotic-loaded orthopaedic bone cements: insights on drug release profiles and biocompatibility

Acrylic bone cement (BC) is widely used as an anchor of artificial joints. Bacterial infection due to biofilm formation and inflammation are common and difficult to treat problems associated with commercial available BC formulations. Research on novel BC compositions is urgently needed. The main objective of this thesis was to develop a new biocompatible antibiotic-loaded BC with improved release profile. To achieve that aim several additives were incorporated, as an antibiotic (levofloxacin) to combat bacterial growth, an anti-inflammatory drug (diclofenac) to decrease the inflammatory process and two well-known and broadly used biopolymers, alginate and chitosan in order to increase matrix porosity, and in this way to intensify the amount of released drug. Novel BC formulations were tested in order to find the most suitable one that had potential to proceed to clinical application. Numerous tests were conducted as: a) evaluation of drug release profiles in different biomimetic media, b) mechanical and surface studies, c) microbiological activity testing against Staphylococcus aureus and d) in vitro biocompatibility assays (fibroblasts and osteoblasts). In general, the addition of biopolymers increased drug release, didn’t compromised BC mechanical properties and increased BC hydrophilicity. Microbiological testing revealed that Lev[BC]Chi was the only matrix that reduced significantly biofilm formation. On the contrary, alginate and diclofenac loading into BC seemed to increase biofilm growth. Biocompatibility studies showed some decrease in cell viability, in particularly on osteoblasts, mainly due to the high amounts of released drugs. In conclusion, the present work has shown that the matrix with more potential to proceed in further investigations was Lev[BC]Chi. Other conditions (namely additives and drugs concentrations) should be evaluated with the other tested BC matrices before being discharged.

Development of biocompatible and “smart” porous structures using CO2-assisted processes

Dissertação apresentada para a obtenção do grau de Doutor em Engenharia Química, especialidade Engenharia da Reacção Química, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

Positive Epistasis Drives the Acquisition of Multidrug Resistance

The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact-epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.

Functional studies on BolA and related genes: increasing the understanding of a protein with pleiotropic effects

Dissertation presented to obtain a Doctoral degree in Biology by Instituto de Tecnologia Química e Biológica

A contribuição das bombas de efluxo QacA e Smr para a multirresistência em Staphylococcus aureus

RESUMO: O efluxo de compostos antimicrobianos é um mecanismo importante na multirresistência em bactérias. Bombas de efluxo codificadas em plasmídeos, como a QacA e a Smr, estão implicadas na susceptibilidade reduzida a biocidas, geralmente utilizados na prevenção e controlo de infecções nosocomiais, incluindo as causadas por estirpes de Staphylococcus aureus resistentes à meticilina (MRSA). Neste trabalho pretendeu-se avaliar a relevância de QacA e Smr no perfil de susceptibilidade dos isolados clínicos MRSA SM39 e SM52, que transportam os plasmídeos pSM39 e pSM52 com os determinantes qacA e smr, respectivamente. A actividade de efluxo das estirpes SM39 e SM39 curada (sem pSM39) e das estirpes SM52 e RN4220:pSM52 (estirpe susceptível RN4220 transformada com pSM52) foi caracterizada por: (1) determinação da concentração mínima inibitória (CMI) de biocidas, corantes e antibióticos, na ausência e presença dos inibidores de efluxo tioridazina, clorpromazina, verapamil e reserpina; e (2) fluorometria em tempo-real. A determinação de CMIs demonstrou que a actividade de efluxo mediada por QacA e Smr está envolvida na susceptibilidade reduzida aos biocidas e corantes testados, que incluíram o brometo de hexadeciltrimetilamónio, a cetrimida, o cloreto de benzalcónio, a berberina, o cloreto de dequalínio, a pentamidina e o brometo de etídeo. Os ensaios fluorométricos confirmaram a elevada actividade de efluxo presente nas estirpes com os genes qacA ou smr. A determinação de CMIs para antibióticos β-lactâmicos em conjunto com o teste da nitrocefina revelou a presença simultânea do gene qacA e de uma β-lactamase no plasmídeo pSM39. Este trabalho evidencia a importância das bombas de efluxo QacA e Smr na resistência a biocidas em estirpes MRSA e na sobrevivência destas estirpes em ambiente hospitalar e na comunidade, para além de destacar a questão da potencial co-resistência entre biocidas e antibióticos.--------------- ABSTRACT: Drug efflux has become an important cause of multidrug resistance (MDR) in bacteria. Plasmid-encoded MDR efflux pumps, such as QacA and Smr, are implicated in reduced susceptibility to biocides, generally used in the prevention and control of nosocomial infections, including the ones caused by methicillin-resistant Staphylococcus aureus (MRSA). In this work, we aimed to evaluate the relevance of QacA and Smr to the susceptibility profile of the clinical MRSA isolates SM39 and SM52, which harbor the plasmids pSM39 and pSM52 that carry the determinants qacA and smr, respectively. Efflux activity of strain SM39 and its plasmid-free counterpart, SM39 cured, SM52 and RN4220:pSM52 (susceptible strain RN4220 transformed with pSM52) was characterized by: (1) determination of minimum inhibitory concentration (MIC) of biocides, dyes and antibiotics, in the absence and presence of the efflux inhibitors thioridazine, chlorpromazine, verapamil and reserpine; and (2) real-time fluorometry. MIC determination showed that QacA and Smr mediated efflux was involved in the reduced susceptibility profile to the biocides and dyes tested, which included hexadecyltrymethylammonium bromide, cetrimide, benzalkonium chloride, berberine, dequalinium chloride, pentamidine and ethidium bromide. Fluorometric assays confirmed the higher efflux activity present in strains harboring qacA or smr genes. Moreover, MIC determination for β-lactam antibiotics together with the nitrocefin test confirmed the presence of a β-lactamase in the plasmid carried by SM39 strain, pSM39. This work highlights the relevance of QacA and Smr to the biocide resistance in MRSA strains, and consequently to their survival and maintenance in the hospital environment and in the community. Furthermore, the presence of a β-lactamase and qacA determinants in the the same plasmid reinforces the question of the potencial biocide/antibiotic co-resistance in MRSA strains.

Understanding the relationship between central metabolism and virulence in the human pathogen Streptococcus pneumoniae

Dissertation presented to obtain the Ph.D. degree in Biochemistry

Novel insights into the action of antimicrobial agents against human pathogens

Dissertation presented to obtain the Ph.D degree in Biochemistry

Spore differentiation in relation to the infectious cycle of the enteric pathogen Clostridium difficile

Clostridium difficile is a gram positive, spore former, anaerobic bacterium that is able to cause infection and disease, with symptoms ranging from mild diarrhea to pseudomembranous colitis, toxic megacolon, sepsis and death. In the last decade new strains have emerged that caused outbreaks of increased disease severity and higher recurrence, morbidity and mortality rates, and C. difficile is now considered both a main nosocomial pathogen associated with antibiotic therapy as well as a major concern in the community.(...)

Amidation of peptidoglycan in Staphylococcus aureus

Staphylococcus aureus is one of the most important contemporary human pathogens. The evolutionary “success” of this species is closely related to its remarkably capacity to acquire antibiotic resistance traits. In this perspective, it is important to extend our knowledge concerning the mechanisms of antibiotic resistance in S. aureus and to identify new antimicrobials targets.(...)

Estimativa dos custos das infeções nosocomiais da corrente sanguínea relacionadas com o cateter venoso central no Centro Hospitalar de Lisboa Ocidental

RESUMO - Introdução: As Infeções nosocomiais da corrente sanguínea associada a cateter venoso central (INCS-CVC) provocam um aumento das despesas hospitalares, traduzindo num aumento dos dias de internamento, consumo de antibióticos e de meios complementares de diagnóstico e terapêutica (MCDT). O presente estudo pretende avaliar os custos das INCS-CVC nos serviços de internamento do CHLO, no ano de 2012. Metodologia: Realizou-se um estudo retrospetivo de caso-controlo para determinar os custos adicionais inerentes às INCS-CVC. Foram identificados, em 2012, 32 doentes com infeção e 31 sem infeção. Os controlos foram extraídos da população tendo igual grupo diagnóstico Homogéneo (GDH), idade, sexo, serviço e duração de internamento e presença de CVC. As principais fontes de informação foram os registos da Comissão Controlo de Infeção (CCI) e do processo clinico eletrónico (PCE). A estimativa dos custos teve em consideração a duração de internamento, consumo de antibióticos e de MCDT. Resultados: A idade média dos casos e controlos foi de 66 e 69, respetivamente (p=0,432), 50% dos casos e 51,6% dos controlos eram do sexo masculino. Um total de 22 casos foi comparado com 22 controlos. A duração média de internamento dos casos e controlos foi de 70,8 e 36,6 dias, respetivamente (p=0,000). Em média o custo adicional por doente com antibióticos foi de 256€ (p=0,001). Nos casos o consumo de análises clinica foi 2,5 vezes superior e de exames imagiológicos 2 vezes superior aos controlos. O custo total médio adicional por doente foi de 20.737,6€. Conclusão: A ocorrência de INCS-CVC resultou num aumento significativo de utilização de recursos hospitalares e consequentemente num aumento dos custos hospitalares.

The role of pneumococcal carbon metabolism in colonisation and invasive disease

Streptococcus pneumoniae is a common asymptomatic commensal of the human nasopharynx. However, it is better known as a threatening pathogen that causes serious diseases such as pneumonia, meningitis and sepsis, as well as other less severe but more prevalent infections (e.g. otitis media). With the increase of antibiotic resistance and the limited efficacy of vaccines, pneumococcal infections remain a major problem. Therefore, the discovery of new therapeutic targets and preventive drugs are in high demand.(...)

Avaliação da monitorização diária da proteína C-Reativa no doente crítico

RESUMO: O objectivo desta Tese de Doutoramento foi estudar o valor da Proteína CReactiva(PCR) como marcador de infecção e sepsis. Por definição, um marcador da infecção não está presente se o doente não está infectado, deve aparecer concomitantemente ou idealmente preceder a instalação da infecção, deve desaparecer com a instituição de terapêutica antimicrobiana adequada e permanecer elevado se a infecção for refractária ao tratamento. Do ponto de vista biológico, a PCR é o protótipo das proteínas de fase aguda, com uma marcada elevação da sua concentração sérica em resposta a diversos estímulos inflamatórios em particular infecções bacterianas. A sua concentração sérica depende apenas da intensidade do estímulo e da velocidade de síntese hepática, não sendo influenciada por nenhum factor ou tratamento a não ser que este tenha influência directa sobre o estímulo desencadeante, o que a torna um marcador de infecção com grande potencial. Nesta Tese comparou-se a PCR com marcadores clássicos de infecção, temperatura e contagem leucocitária, em diversas situações clínicas analisando doentes com infecções documentadas e doentes controlos, sem infecção. Globalmente os resultados dos trabalhos desta Tese mostram que a PCR é um bom marcador de infecção de acordo com a definição previamente apresentada. Em conjunto com a restante avaliação clínica e laboratorial, a monitorização diária da PCR nos doentes sem infecção mostrou ser útil como sentinela da infecção, isto é, apresenta valores baixos nos doentes sem infecção e sobe precocemente nos doentes que desenvolvem uma infecção. Nos doentes com infecção documentada revelou um ser bom marcador de resposta à terapêutica e evolução clínica, diminuindo naqueles que melhoravam e persistindo elevada nos que tinham mau prognóstico, bem assim como identificar diferentes perfis evolutivos. Em suma, a monitorização diária da PCR mostrou utilidade ao longo de todo o internamento na Unidade de Cuidados Intensivos, quer na presença quer na ausência de infecção. Deste todo, a monitorização diária da PCR pode a possibilitar uma utilização mais racional e judiciosa da terapêutica antimicrobiana, contribuindo dessa forma para uma diminuição da toxicidade e da pressão antibiótica, menor risco de emergência de resistências e finalmente diminuição dos custos. Uma vez que, os doentes internados nas Unidades de Cuidados Intensivos apresentam as mesmas doenças que os restantes doentes admitidos no hospital apenas se distinguindo pela sua maior gravidade, poder-se-á extrapolar que a PCR também é potencialmente um bom marcador de infecção nestes doentes. ----------------ABSTRACT: The aim of this PhD Thesis was to assess the value of C-Reactive Protein (CRP) as a marker of infection and sepsis. A marker of infection should be absent in a non-infected patient, should increase alongside or ideally precede the development of an infection, and finally should assess the therapeutic response, that is to say decrease or even disappear with adequate antimicrobial therapy or on the opposite remain elevated if the infection is refractory to the prescribed treatment. The biology of CRP makes it the prototype of acute phase proteins, with marked and sharp elevations of its serum concentration in response to several inflammatory stimulus in particular bacterial infections. Besides, CRP level depends only of the intensity of the stimulus and the rate of hepatic synthesis. Its concentration is not modified by any therapy or intervention. Only those interventions affecting the inflammatory process responsible for the acute phase reaction can change the CRP level. These properties make CRP a potentially good marker of infection. In this Thesis the value of CRP was studied in comparison to traditional markers of infection, like temperature and white cell count, in different clinical situations analysing patients with documented infections and a control group without infection. The aggregated results of the analysis presented in this Thesis illustrate that CRP could be used as a marker of infection. In conjunction with other clinical and laboratory manifestations of sepsis, daily CRP measurement in patients without infection was useful in prediction of infection as its concentration remains low in patients without infection whereas if an infection appears its levels raise markedly. In addition, in patients with documented infections CRP was useful as a marker of therapeutic response and follow-up, with marked decreases in patients with good outcome and remaining elevated in those with poor prognosis, as well as the recognition of different patterns of evolution. In summary, daily CRP measurement was helpful in critical ill patients along the entire Intensive Care Unit stay, both in the presence and in the absence of infection. As a result, daily CRP measurement can assure a better and more rational use of antibiotics and consequently contribute to a decrease in the antibiotic toxicity and demand, reducing the risks of emergence of resistant strains aas well as costs. Provided that patients admitted to an Intensive Care Unit presented the same clinical diagnosis as those admitted to the wards but with higher severity, one can speculate that CRP is also a potentially good marker of infection in these of patients.