Resistance to artemisinin combination therapies (ACTs) has emerged in southeast Asia threatening the most widely used treatment against antimalarial-resistant Plasmodium falciparum worldwide. Artemisinin resistance has been associated with a reduced rate of parasite clearance following treatment with an ACT and is attributed to increased survival of ring-stage parasites. Single nucleotide polymorphisms (SNPs) in kelch gene (K13) has been associated with delayed in vivo clearance half-life of artemisinin-resistant P. falciparum and is the only known molecular marker of resistance. The absence of reliable in vitro phenotypes for artemisinin resistance has limited our understanding of the resistance mechanism(s) and fitness costs, therefore we have culture adapted and cloned patient isolates from Thailand and Cambodia that had clinical resistant phenotypes. Stable reduced susceptibility to artemisinin derivatives and mefloquine was observed using a modified [3H]hypoxanthine drug susceptibility assay. In addition we devised an in vitro phenotype assay of artemisinin resistance, known as the delayed clearance assay (DCA), that was positively correlated with the in vivo delayed clearance and presence of K13 SNPs of artemisinin resistance. Remarkably we discovered for the first time altered patterns of intraerythrocytic development in artemisinin-resistant P. falciparum. In the absence of drug pressure most artemisinin-resistant clones have a prolonged ring phenotype with temporally compressed trophozoite stage, yet with the normal overall asexual life cycle period. Parasites remain in ring-stage up to 14 hours longer than wild-type, whereas time spent in trophozoite-stage is dramatically reduced. One parasite, PL08-09 (5C), exhibited an accelerated 36-hour life cycle in the absence of drug pressure and progressed through asexual development in equal time spent at each intraerythrocytic stage. These data support our hypothesis that parasite resistance to artemisinin results from reduced exposure to drug at the most susceptible stage of development (trophozoite). Interestingly, the most prevalent K13 mutation C580Y is associated with both cell cycle phenotypes. Another cell cycle phenotype, ring-stage dormancy, has been associated with artemisinin resistance in vitro reducing the dormant period of artemisinin-resistant parasites following dihydroartemisinin exposure allowing resistant parasite cultures recrudesce before wild-type. However, sensitive parasites have the ability to enter ring-stage dormancy causing recrudescence in vitro. It is possible that multiple cell cycle phenotypes enhance the survival and fitness of the resistant parasite population as a whole in the face of antimalarial exposure. We have demonstrated that there is a fitness cost associated with artemisinin resistance and remains an important component in the spread of genetic mutations associated with artemisinin resistance. Resistant parasites outcompeted sensitive in vitro only when exposed to dihydroartemisinin. Two mutations associated with artemisinin resistance, including a mutation in K13, were lost in artemisinin resistant parasite by the end of the study. Conversely, parasite cultures maintained artemisinin resistance phenotypes in vitro only if exposed to artemisinin drug pressure every 21-42 days. The mechanism of artemisinin resistance remains elusive and how the parasites alter their intraerythrocytic development is unknown. Therefore. we transfected green fluorescent protein (GFP) or luciferase into artemisinin-resistant P. falciparum clones from Thailand and Cambodia to aid the study the cell cycle phenotypes associated with artemisinin resistance. Artemisinin resistance phenotypes were maintained in stably transfected clones. Increased growth of artemisinin-resistant clones was observed following exposure to ACT partner drug. Low concentrations of antimalarials synchronized the luciferase expression of artemisinin-resistant parasites having different cell cycle phenotypes in the absence of drug pressure. Ring-stage dormancy was observed with many antimalarial drugs and contributes to recrudescence observed by antimalarials other than artemisinin. Our results show evidence that current ACT treatments are selecting multidrug resistant parasites in the field that are better able to tolerate all antimalarials through regulatory cell cycle mechanisms. These cell cycle phenotypes associated with artemisinin resistance contribute to reducing the fitness cost associated with genetic mutations causing artemisinin resistance. This leads to the survival of the most fit population of parasites that survive combination drug treatments, thus demonstrating the importance of discovering novel drugs to target ACT-resistant P. falciparum.

Influenza A viruses are important pathogens of humans, other mammals and birds. Swine are considered to be the ‘mixing vessel’ for influenza viruses because of their susceptibility to infection with not only swine influenza viruses but also human and avian influenza viruses. After infection of pigs with different influenza viruses, reassortment events between genomic RNA segments and point mutations can take place which can result in novel influenza virus strains capable of causing human pandemics. To combat infections, vaccination is available in many countries for humans, but not typically used in pigs. However, anti-influenza drugs have been used to treat livestock, and mutations conferring drug resistance occur in circulating strains. The mechanisms responsible for the emergence and spread of drug resistant mutations against amantadine and oseltamivir have been studied previously but often gave conflicting results. Therefore, this PhD thesis focused on resolving the mechanisms responsible for this rapid drug resistance spread. In chapter one I examine the extent of reassortment events in swine influenza A viruses by analysing within subtype reassortment and extrapolating the results for the between subtype reassortment. Reassortment is one of the mechanisms that can be responsible for mutations, conferring resistance to drugs, to spread between strains, and thus spread in the host population. The findings of this chapter show that the genomic segments most prone to reassortment code for a polymerase (PB1) and both glycoproteins, within all three subtypes studied. Since particular mutations in the matrix protein (MP) segment cause resistance to amantadine, my study focused on MP compared to other segments and revealed moderate level of reassortment. MP reassorts well with polymerases, both within and between subtype, while nonstructural (NS) is least likely to reassort. Chapter two of this thesis aimed at resolving the origin and spread of the most common drug resistance conferring mutation in swine influenza viruses which causes amantadine resistance. I show first that this mutation occurred in swine influenza viruses and was therefore not transmitted from the recently ancestral avian influenza strains, and second that the prevalence of resistance in swine influenza viruses is due to functional linkage of mutations at other sites and not by direct drug pressure. In chapter three I examine the mechanisms responsible for the rapid rise and spread of oseltamivir resistance in human influenza H1N1 viruses which arose in the absence of drug use. The primary mutation lies in the neuraminidase glycoprotein but because of the close functional interaction I focus on changes in haemagglutinin that occurred in association with resistance. The results showed several mutations in haemagglutinin were associated with resistance suggesting selection acting on haemagglutinin in order to balance the activity of both glycoproteins. Overall these results show the importance of functional linkage between segments as a mechanism for the occurrence of drug resistance conferring mutations, and reassortment as a means of spreading these mutations into newly emerging strains.

Combating drug resistant malaria has been historically challenging, and remains so today. Recent reports from Southeast Asia show that Plasmodium falciparum is developing resistance to even our best defenses; artemisinin-based therapies. This development threatens to become a significant challenge in controlling malaria infections worldwide, making research into developing and characterizing new antimalarial drugs increasingly important. The purpose of this study was to characterize the resistance potential of novel antimalarial compound JPC-3210 in vitro using P. falciparum clones. JPC-3210 is a new long acting drug with potential to be used in combination with fast-acting drugs like artemisinins to cure drug resistant malaria. In this study several methods were used to characterize the efficacy and resistance potential of JPC-3210. To determine the frequency of resistance generation in P. falciparum clones, parasites were kept under continuous drug pressure for thirty days, at which point drug pressure was removed and cultures were observed for signs of recrudescence. P. falciparum clones also were exposed to increasing levels of intermittent drug pressure that involved 3-4 days of drug exposure followed by a recovery period. The step-wise experiment was conducted over three months with drug pressure being increased step-wise until a maximal concentration of 700 ng/ml of JPC-3210; resistance was measured phenotypically in drug susceptibility assays at multiple time points. Additionally, the ability of JPC-3210 to induce dormant stage parasites, and its effect on dihydroartemisinin (DHA)-induced dormant stages was assessed in both a chloroquine resistant parasite (W2) and in an artemisinin resistant clone (4G). Results showed that the frequency of resistance against JPC-3210 in W2 clones was less when compared to that of atovaquone. The step-wise pulse exposure of JPC-3210 induced resistance in W2 clones, however, resistance proved unstable. Dormant stage parasites were not induced by JPC-3210, even at high concentrations in W2 or 4G clones, furthermore, the effect of JPC-3210 on dormant-induced parasites was found to be dose dependent, yet the drug did not kill DHA-induced dormant rings. JPC-3210 appears to be a good drug to use in combination with other antimalarial compounds for treatment of P. falciparum, but further research is needed. Future studies to assess the field performance of new antimalarial compounds by investigating resistance and dormancy profiles in vitro, and thereby maximizing out understanding of such drugs and their optimal implementation, are of the utmost importance.

Les antibiotiques sont actuellement parmi les médicaments les plus utilisés, mais les schémas thérapeutiques optimaux ne sont pas toujours bien définis. Le but de cette thèse était de développer des modèles pharmacocinétiques (PK) et pharmacodynamiques (PK/PD) décrivant les profils de concentrations des antibiotiques ainsi que leurs effets et le développement de résistances bactériennes afin d’optimiser les schémas thérapeutiques.<br/>Un modèle PK de population sur la colistine et sa prodrogue, le colistine methanesulfonate (CMS), a été développé chez les patients recevant la colistine par voie aérosol et/ou sous hémodialyse (HD). Les résultats ont montré un net avantage de la voie aérosol pour le traitement des infections pulmonaires avec une dose de 2 MUI de CMS. Pour les patients sous HD une dose de 1.5 MUI de CMS 2 fois par jour est recommandée avec une dose supplémentaire de 1.5 MUI de CMS après chaque séance de HD.<br/>L’évaluation des performances de différents modèles PK/PD via à une approche par simulation a montré l’importance d’effectuer des études suffisamment longues ainsi que d’obtenir des données microbiologiques complémentaires afin de décrire le développement de la résistance bactérienne.<br/>Un modèle PK/PD incluant taux de mutation et résistance adaptative à la colistine d’une souche bioluminescente de Pseudomonas aeruginosa a été développé à partir de données in-vitro. Une résistance rapide, importante et partiellement réversible a été décrite. Ces résultats confirment l’importance des 24 premières heures dans le traitement des infections, que la colistine seule ne peut pas complétement éliminer les mutants de Pseudomonas aeruginosa et que des associations semblent nécessaires. / Antibiotics are among the most commonly prescribed drugs, however optimal dosages are not yet well defined. The aim of this thesis was to develop pharmacokinetic (PK) and pharmacokinetic-pharmacodynamics (PK/PD) models that characterize the course of antimicrobial drug concentrations and effects over time, with an emphasis on the development of resistance. These models were applied to optimize dosing regimens of antimicrobial therapies.<br/>A population PK model for colistin and its prodrug, colistin methanesulfonate (CMS) was developed in critically ill patients receiving colistin by nebulization and/or undergoing an intermittent hemodialysis (HD). Results predicted clear benefits of using aerosol delivery of 2MIU CMS dose for the treatment of pulmonary infections. For patients with HD session dosing regimen of CMS should be 1.5 MIU twice daily with an additional dose of 1.5 MIU after each HD session.<br/>An assessment of the performances of different PK-PD models by using a simulation approach have shown the importance of longer study designs and of complementary microbiological data to predict accurately bacterial resistance development.<br/> A semi-mechanistic PK/PD model that incorporates mutation rate and adaptive resistance development of a bioluminescent strain of Pseudomonas aeruginosa against colistin was developed based on in-vitro data. A high, quick and partially reversible resistance was described. These results confirm that the first 24 h of treatment are critical in the management of infections, that colistin alone cannot eradicate completely the mutants of Pseudomonas aeruginosa that were selected during the experiments and that combination therapies seem necessary.

Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Abstract Cancer is a major global killer and a challenge for the healthcare worldwide. Earlier cancer has been treated with surgery, radiation, chemotherapy and hormonal therapy. Unfortunately the efficiency of these therapies has shown to be limited and this has raised an enthusiasm for development of new, targeted cancer therapies that are based on activated oncogenes. The challenge of the targeted therapies is therapy resistance, de novo, adaptive and acquired. This work investigated targeted therapy sensitivity and resistance in lung cancer, breast cancer, colorectal cancer, and melanoma cell lines. The results of this study indicate that in some non-small cell lung cancer cell lines, dual PI3K and MEK inhibition is a more efficacious treatment than inhibition of either solely. It was also showed that the maximal effect of the dual inhibition can be achieved with alternative dosing schedules that are potentially more tolerable in clinical use. Furthermore, by combining ABT-263, entinostat or dasatinib to the dual PI3K and MEK inhibition, the efficiency of the therapy can be increased. Bcl-xl downregulation is a major determinant of the apoptotic response to the triple inhibitor treatment. The current work showed that cancer stem cells can mediate resistance to targeted therapies. Since these cells follow the stochastic model, concurrent therapy with a targeted agent and a stem cell targeting drug might be needed for maximal therapeutic efficiency. This study also showed that Gö6976 acts as a potent inhibitor of mutant EGFR despite the presence of T790M, the most important mechanism of acquired resistance for EGFR tyrosine kinase inhibitors in lung cancer, both in vitro and in vivo. / Tiivistelmä Syöpä on yksi johtavia kuolemanaiheuttajia ja tauti on maailmanlaajuinen haaste terveydenhuollolle. Perinteiset syöpähoidot käsittävät kirurgian, sädehoidon, kemoterapian ja hormonaalisen hoidon, mutta näiden rinnalle on noussut uusia, aktivoituneiden onkogeenien signaalien estoon perustuvia hoitoja. Tämä työ tutki kohdennettuja syöpähoitoja ja näihin hoitoihin liittyvää resistenssiä keuhko-, rinta- ja paksusuolen syövän sekä melanooman solulinjoissa. Tulokset osoittavat, että joissakin ei-pienisoluisen keuhkosyövän solulinjoissa yhdistetty PI3K- ja MEK-esto aiheuttaa tehokkaamman vasteen kuin kummankaan signaalireitin esto yksistään. Tässä työssä näytettiin myös, että maksimaalinen vaste yhdistetylle PI3K- ja MEK-estolle voidaan saavuttaa vaihtoehtoisilla annostelutavoilla, jotka ovat voisivat olla paremmin siedettyjä kliinisessä käytössä kuin kahden lääkkeen jatkuva annostelu. Tämä tutkimus osoitti lisäksi, että kaksoiseston tehokkuutta voidaan lisätä yhdistämällä hoitoon kolmas lääkeaine, ABT-263, entinostaatti tai dasatinibi. Bcl-xl proteiinilla on keskeinen rooli apoptoottisen vasteen määrittäjänä näille kolmen lääkkeen käsittelyille. Tämä työ osoitti, että syövän kantasolut voivat välittää resistenssiä kohdennetuille syöpähoidoille. Nämä solut noudattavat niin kutsuttua stokastista mallia, joten parhaan vasteen saaminen saattaa edellyttää että hoito kohdentuu sekä erilaistuneisiin että kantasolutyyppisiin syöpäsoluihin. Tässä tutkimuksessa osoitettin lisäksi, että Gö6976 toimii mutatoituneen EGFR:n estäjänä, huolimatta kehittyvää keuhkosyövissä resistenssiä välittävästä T90M mutaatiosta, sekä in vitro -että in vivo -malleissa.

No description available.

Philosophiae Doctor - PhD / One of the most common HIV-associated opportunistic infections is candidiasis, caused by Candida albicans or other Candida species. In immune suppressed subjects, this commensal organism can cause an increase in patient morbidity and mortality due to oropharyngeal or systemic dissemination. Limited information exists on the prevalence and antifungal susceptibility of Candida species in the African continent, the most HIV-affected region globally and home to new and emerging drug resistant Candida species. The mechanisms of Candida drug resistance in the African continent have also not been described. In this study, 255 Candida species isolated from the oral mucosa of HIV-positive South African and Cameroonian patients were identified using differential and chromogenic media and their drug susceptibility profiles tested using the disk diffusion method and the TREK Sensititre system, an automated broth microdilution method. Candida cell wall fractions were run on SDSPAGE and HPLC-MS with the aim of identifying peptides specifically expressed by antifungal drug resistant isolates. Comparisons between the two groups of isolates revealed differences in Candida species prevalence and drug susceptibility with interesting associations observed between specific drug resistance and duration of ARV therapy. This study showed that fluconazole, the drug of choice for the treatment of candidiasis in the African continent, is not an effective therapy for most cases of Candida infection, and suggests that regional surveillance be implemented in the continent. A multiple-drug resistant Candida strain was identified in this study, a finding that has not previously been documented. The use of proteomics tools allowed for the identification of peptides involved in drug resistance and the elucidation of Candida colonization mechanisms in HIV-infected African patients.

Magister Scientiae - MSc / Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). TB mainly affects lungs of patients but other parts of the body can also be affected. It kills approximately 2 million people annually. HIV/AIDS and drug resistance make TB difficult to control. Mtb CarD protein forms a physiological complex with Ribonucleic Acid Polymerase (RNAP). This complex causes Mtb to undergo dormancy rendering it difficult to control using current antibiotics. CarD and a size-reduced subunit β1 (denoted β1m for “minimized”) of Thermus thermophilus RNAP, in which the central domain has been replaced by a Gly-Gly linker, were produced and purified using affinity nickel nitrilotriaceticacid and glutathione-Stransferase (GST) affinity chromatography techniques respectively. CarD N terminal domain (CarDN) was generated from CarD by inserting a stop codon by site directed mutagenesis. CarD was stabilised by adding 5 % (v/v) glycerol to PBS pH 7.4 ensuring protein stability of up to 67 days rather than 2 days without glycerol. CarDN was stable in PBS pH 7.4 without addition of glycerol. This suggests that the CarD C terminal domain may be responsible for CarD instability. To further purify the proteins both anion exchange and gel permeation chromatography techniques were used. CarD and CarDN degrade immediately after anion exchange potentially because of the high ion concentration which partially unfolds the protein making it prone to proteolytic cleavage. GST-pull down assays were used to demonstrate complex formation between RNAP β1m and both CarD and CarDN confirming that complex formation is dependent on the N-terminal domain of CarD.

Magister Public Health - MPH / Tuberculosis (TB) is a major health problem worldwide, with an estimated 9 million new cases accounting for an estimated 1.5 million deaths in 2012. Non-compliance with TB treatment has become a major barrier to achieving global TB control targets. Namibia is one of the worst affected countries in Africa with a high case notification rate (CNR) of all forms of TB and relatively low treatment success rate compared to the WHO targets. The study aimed at investigating TB treatment compliance and measuring its association to patient characteristics and treatment outcomes, in determining the effects of compliance on treatment outcomes in Windhoek District. This information is crucial for TB programme management and development of targeted strategies. A quantitative observational analytic study using a retrospective cohort design was adopted. New adult Pulmonary Tuberculosis (PTB) patients treated under DOTS in Windhoek District between 1st January 2013 and 31st December 2013 were included in the study based on specified criteria. Data was collected from the patients TB treatment cards using an extraction tool. Selection and information bias was eliminated by using clearly defined inclusion and exclusion criteria using a pre-tested standardised tool. Statistical analysis using descriptive and analytic statistics was done using Epi Info 7 to determine compliance, treatment outcomes and to measure the associations. Overall treatment compliance (89%), initial phase compliance (97.2%) and continuation phase compliance (88.1%) were reported in the study. Age (OR=4.3 95% CI (1.72 – 9.90), p-value=<0.01) and type of area (OR=0.02 95% CI (1.00 – 1.13), p-value=0.05) were associated with compliance in the continuation phase. Overall, type of area (OR=0.03 95% CI (0.00 – 0.91), p-value=0.04) remains associated with treatment compliance. Treatment success is reported among 86.1% of patients. Poor treatment outcomes are associated with non-compliance in the initial phase ( =49.98, p-value=<0.01), continuation phase ( =98.81, p-value=<0.01) and overall ( =110.02, p-value=<0.01). Overall treatment compliance (89%) although higher than expected was lower than the WHO recommended 90% compliance. Very high compliance (97.2%) were reported in the initial phase of treatment whilst compliance was also lower than desired (88.1%) in the continuation phase. Non-compliance recorded in the continuation phase is in agreement with the literature. Age and type of area are associated with compliance as reported in the continuation phase and overall in this study is new contribution of knowledge. The findings suggest that treatment compliance is associated with treatment success in both phases of treatment and overall. Low compliance especially in the continuation phase could lead to poor treatment outcomes such as prolonged infections, relapse, high TB mortality and drug resistance leading to increased programme costs. The study concludes that non-compliance results in poor treatment outcomes highlighting the need for interventions that address compliance in all phases but specifically within the continuation phase and amongst those at risk of having reduced compliance such as those in rural areas and young adult patients aged (15 – 34 years). Recommendations to the District Management Team and TB Programme Managers include: identification of measures that promote treatment compliance; support and monitoring of TB patients’ compliance continuously; strengthening CB-DOT by increasing CB-DOT points and enhancing CB-DOT supporters’ capacity as well as strengthening record keeping as a monitoring tool to increase compliance and improve treatment outcomes.