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Yes / Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.

Les mycobactéries sont classées parmi les bactéries contenant des acides mycoliques dans leur paroi et un haut GC% dans leur génome. Elles peuvent être isolées à partir du sol ou d'environnement d'eau douce où vivent aussi les protozoaires libres. Plusieurs études ont montré une possibilité de co-isolement des mycobactéries et des amibes à partir de ces sources environnementales. Il a été montré également que la plupart des mycobactéries de l'environnement ont la capacité à survivre dans les trophozoites et les kystes d'amibes et dans certaines cellules eucaryotes, y compris les macrophages. Les manipulations génétiques des mycobactéries en général et des mycobactéries du complexe Mycobacterium tuberculosis en particulier sont compliquées et aucune étude de modification génétique des mycobactéries (pathogènes ou non pathogènes) n'avait été réalisée dans notre laboratoire avant notre travail de thèse. Dans notre travail de thèse, nous avons montré que les amibes ou d'autres organismes phagocytaires peuvent servir comme sources et lieu de transfert des gènes chez les mycobactéries. Ce transfert des gènes peut avoir contribué à l'adaptation des mycobactéries à un mode de vie intracellulaire. Nous avons développé ensuite deux systèmes de coculture: Mycobacterium smegmatis-Acanthamoeba polyphaga et Mycobacterium gilvum-A. polyphaga et nous avons clarifié le spectre des interactions des mycobactéries à croissance rapide avec les amibes. Ce modèle d'interaction mycobactéries-amibes a été utilisé pour tester l'hypothèse contraire au paradigme dominant que l'addition des gènes réduit la virulence des bactéries. / Mycobacteria are mycolic-acid containing, high GC% bacterial organisms which can be recovered from soil and fresh water environments where free-living protozoa also live. Co-isolation of mycobacteria and amoeba collected from such environmental sources has been reported. Several experiments further demonstrated the ability of most environmental mycobacteria to survive in the amoebal trophozoites and cysts and in some eukaryotic cells including macrophages. Genetic modification of mycobacteria in general and mycobacteria belonging to Mycobacterium tuberculosis complex in particular are complicated and no studies using genetic modification of mycobacteria (pathogenic or non-pathogenic) had been performed in our laboratory prior to our work. In our thesis work, we showed that amoebae or other phagocytic organisms can serve as sources and places for gene transfers in mycobacteria. Gene transfers may have contributed to the adaptation of mycobacteria to an intracellular lifestyle. In addition, we developed two co-culture systems: Mycobacterium smegmatis-Acanthamoeba polyphaga and Mycobacterium gilvum-A. polyphaga and we clarified the spectrum of rapid-growing mycobacteria and amoeba interactions. This model of mycobacteria-amoeba interactions was then used to test another hypothesis according to which unlike the prevailing paradigm, the addition of genes does not reduce the virulence of bacteria. For the first time in our laboratory we modified two species of the M. tuberculosis complex, M. tuberculosis H37Rv and Mycobacterium bovis BCG to observe the effect of these changes on their pathogenicity and survival.

Die Familie der Mykobakterien setzt sich aus pathogenen und apathogenen Vertretern zusammen. In dieser Arbeit wurden 3 Mitglieder dieser Familie für Untersuchungen herangezogen: ihr prominentester pathogener Vertreter Mycobacterium tuberculosis, der Erreger der Tuberkulose, das als Impfstoff eingesetzte Mycobacterium bovis BCG, das durch Attenuierung aus dem Rindertuberkulose-Erreger Mycobacterium bovis hervorging und das apathogene Bodenbakterium Mycobacterium smegmatis. Ein Schlüssel zum Verständnis der Mykobakterien und speziell ihrer Widerstandsfähigkeit ist die Kenntnis ihrer komplexen Zellwand. Peptidoglycan als deren Bestandteil und insbesondere der mittels Undecaprenyl-Monophosphat bewerkstelligte Transport von Peptidoglycan-Vorläufern aus dem Cytoplasma an die Zelloberfläche steht dabei im Zentrum der Zellwandbildung. In M. tuberculosis, M. bovis BCG und M. smegmatis wurden Deletionsmutanten für die Undecaprenyl-Phosphokinase (Upk) hergestellt. Für M. smegmatis wurde gezeigt, daß die delta upk Deletionsmutante, in Übereinstimmung mit Deletionsmutanten homologer Gene in anderen Bakterien, eine erhöhte Sensitivität gegenüber dem die Zellwandsynthese hemmenden Antibiotikum Bacitracin aufwies. Überraschenderweise zeigte M. tuberculosis delta upk diesen Phänotyp nicht. Weiterhin ließ sich für M. smegmatis delta upk im Vergleich zum M. smegmatis Wildtyp Peptidoglycan an der Zelloberfläche in geringerem Maße nachweisen. Eindrucksvoll zeigte sich die Bedeutung der Undecaprenyl Phosphokinase in der gestörten Entwicklung von Biofilmen im Falle der M. smegmatis delta upk Mutante. Dies galt sowohl für in vitro Bedingungen als auch für ein, im Rahmen dieser Arbeit, neu entwickeltes in vivo Modell. Vergleiche von M. tuberculosis Wildtyp und M. tuberculosis Mutante auf der Ebene von Proteom- und Transkriptom-Analysen führten zur Identifikation eines zum mykobakteriellen Fettsäure-Synthese II (FASII) System gehörenden Operons, das im Falle der upk-Deletion verstärkt exprimiert wurde und damit möglicherweise einen Kompensationsmechanismus für die fehlende Phosphokinase darstellt. Eine reduzierte Persistenz von M. smegmatis delta upk in infizierten Makrophagen legte nahe, daß Upk bei mykobakteriellen Infektionen eine entscheidende Rolle für das Überleben der Bakterien und ihre Virulenz spielt. Dies konnte erstmals für M. tuberculosis im Rahmen von Maus-Infektionsversuchen gezeigt werden. M. tuberculosis delta upk ließ sich als neues Mitglied in eine Reihe von als growth in vivo (giv) klassifizierten Mutanten einreihen. Die Herstellung von Deletionsmutanten wird als Möglichkeit betrachtet, verbesserte Impfstoffe herzustellen. Die physiologische Konsequenz der Deletion sollte bestenfalls neben einer Attenuierung des Ausgangsbakteriums (gilt besonders für M. tuberculosis) eine Überexpression protektionsrelevanter Antigene zur Folge haben. Im Vergleich zum bestehenden Impfstoff M. bovis BCG führte die Impfung von Mäusen mit M. bovis BCG delta upk sowohl zu geringerer bakterieller im Anschluß an die Vakzinierung als auch zu einer verbesserten Langzeit-Protektion gegen Tuberkulose. / The family of mycobacteria is composed of pathogenic and apathogenic bacteria. This study was performed with 3 members of this family, the most prominent pathogenic member, Mycobacterium tuberculosis, the causative agent of tuberculosis, the vaccine strain Mycobacterium bovis BCG which was developed by attenuation of the bovine tuberculosis agent Mycobacterium bovis, and Mycobacterium smegmatis which is apathogenic and widely distributed in soil. A key to understanding mycobacteria and, especially, their resistance is to understand the complexity of their cell wall. Peptidoglycan is a major component of the cell wall and the transport of peptidoglycan precursors out of the cytoplasm to the bacterial surface by undecaprenyl monophosphate is central to cell wall synthesis. Therefore, deletion mutants of the undecaprenyl phosphokinase gene (upk) were generated in M. tuberculosis, M. bovis BCG, and M. smegmatis. In the case of M. smegmatis it was shown that a delta upk deletion mutant, as with deletion mutants of homologous genes in other bacteria, exhibited an increased sensitivity to the antibiotic bacitracin, indicating that cell wall synthesis was hampered. Surprisingly, M. tuberculosis delta upk did not exhibit this phenotype. Furthermore, a lower level of peptidoglycan was detected on the cell surface of an M. smegmatis delta upk mutant compared to M. smegmatis wildtype. Relevance of the undecaprenyl phosphokinase was demonstrated by impaired biofilm development in the case of the M. smegmatis delta upk mutant. This was observed in vitro as well as in vivo using an animal model which was newly developed in this thesis. A fatty acid synthase II (FASII) system related operon revealed by comparative proteome- and transcriptome-analyses comparing M. tuberculosis wildtype and M. tuberculosis delta upk mutant, and may reflect a compensatory mechanism for the loss of upk. Reduced persistence of M. smegmatis in infected macrophages suggested a decisive role of Upk in mycobacterial infection concerning survival and virulence of bacteria. This was later demonstrated to be true for M. tuberculosis in a mouse model. M. tuberculosis delta upk was, therefore, classified as a new member of the group of growth in vivo (giv) mutants. Construction of deletion mutants is a strategy to identify improved vaccines. Ideally, the physiologic consequences of a gene deletion would result in attenuation of the modified bacterium (especially in the case of M. tuberculosis) and overexpression of antigens relevant for protection. Compared to the existing vaccine M. bovis BCG, vaccination of mice with M. bovis BCG delta upk exhibited a lower bacterial load upon vaccination as well as an improved long-lasting protection against M. tuberculosis infection.

Tuberculosis (TB) is a potentially fatal contagious disease that can affect almost any part of the body but is mainly an infection of the lungs. It is caused by micro-organisms of the Mycobacterium tuberculosis complex. It is the second greatest killer worldwide due to a single infectious agent, after the Human Immunodeficiency Virus (HIV). Without treatment, fatality is 50% in immune competent persons. TB remains the leading cause of death among HIV positive persons, causing one fifth of the deaths. The World Health Organization estimates that one third of the world population is infected by this micro-organism but only 5 to 10% develop TB disease. Nevertheless, this enormous reservoir leads to around 1.4 millions deaths annually. Standard curative treatment lasts at least 6 months and includes 4 different drugs. Toxicity of the drugs leading to (severe) adverse events and the long duration of the daily administration challenges patient’s compliance. Subinhibitory concentration of the drugs (due to poor adherence) can induce resistance of the mycobacteria to the provided drugs. Unlike most bacteria where resistance is acquired by plasmids, drug resistance of mycobacteria is obtained by genomic mutations. “Multi drug-resistant tuberculosis (MDR-TB)” is strictly defined as TB resistant to specifically isoniazid and rifampicin, the two main first line drugs. “Extensively drug resistance (XDR)” is defined as MDR-TB with additional resistance to any of the fluoroquinolones (such as ofloxacin or moxifloxacin) and to at least one of three injectable second-line drugs (amikacin, capreomycin or kanamycin). The increase of MDR-TB represents an enormous challenge to Public Health globally. This research examined different aspects of tuberculosis resistance performed in the Belgian National Reference Center, a clinical laboratory setting. <p><p>First of all, a profound analysis of the MDR-TB situation in Belgium was conducted. It is the first retrospective population-based survey of MDR-TB in Belgium, covering a 15-year period (1994-2008). It comprises 174 patients representing more than 80% of the culture positive MDR-TB patients reported to the Belgian register, thus this study is considered of national relevance. It includes bacteriological and molecular data on the isolates as well as clinical aspects of the patients and treatment results. Considering only the patient’s first MDR-TB isolate, an increase over time was observed in the number of isolates resistant to a second-line drug as well as the total number of drugs each isolate was resistant to. XDR-TB was detected since 2002 and panresistant TB (resistant to every available antituberculosis drug) since 2009. Overall, a successful treatment outcome was obtained for 67.8% of the MDR-TB cases. Drug susceptibility testing (DST) of Mycobacterium tuberculosis to first line drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) in liquid culture medium has a turn around time of at least two weeks, after identification of the positive culture (obtained after 2 to 4 weeks) from the patient’s clinical isolate. In order to provide the clinician with valuable information about the isolated mycobacteria leading to patient adapted therapy before bacteriological DST results are available, resistance is predicted by detection of mutations in certain genes of the mycobacteria. It is common practice for rifampicin (rpoB gene) and isoniazid (katG gene and/or inhA promoter region). In this MDR-TB collection, rifampicin resistant related mutations were found in 97.1% (168/173) of the clinical isolates and isoniazid resistant related mutations in 94.1% (160/170). The pncA, embB and gyrA genes have been sequenced to identify possible mutations because of their possible involvement with resistance to pyrazinamide, ethambutol and the fluoroquinolones respectively. However, little is known about the resistance prediction value of the mutations in these genes.<p>The study is also the first study on the molecular epidemiology of MDR-TB in the country. DNA fingerprinting showed a large diversity of strains (67% of the patients were infected by a strain with a unique pattern) and further epidemiological examination revealed limited local transmission of MDR-TB in Belgium.<p><p>The second part investigated the pncA gene and its association with pyrazinamide resistance in MDR-TB isolates from Belgium and in vitro cultured spontaneous mutants. The genetic analysis showed that 98.3% (59/60) of the Belgian clinical MDR pyrazinamide resistant (PZAR) isolates present a mutation in the pncA gene. We found 1.7% (1/60) of the PZAR MDR-isolates encoding wild type pncA and flank. A total (PZAR and PZAS) of 41 different amino acid changes, 3 protein truncations and 5 frameshifts were observed including eight novel mutations: 8Asp>Ala, 13Phe>Leu, 64Tyr>Ser, 107Glu>stop, 143Ala>Pro, 172Leu>Arg and frameshifts starting in codon 55 and 82. Analysis of all observed mutations (i.e. in clinical isolates as well as spontaneous mutants) revealed that they are not always associated with drug resistance and that they are not scattered randomly throughout the gene, but occur rather at preferential sites such as in codons with amino acids associated with either iron or substrate binding and catalytic active sites. The frequency of in vitro mutagenesis to pyrazinamide at pH 6.0 was determined and found to be relatively high at 10-5 CFU/ml.<p><p>Finally, the in vitro activity of tobramycin and clarithromycin (with unclear efficacy against M. tuberculosis) was evaluated on 25 M. tuberculosis clinical isolates with various resistance profiles. The effect of the drugs administered together was examined for possible synergistic effect. The median minimum inhibitory concentration (MIC) of 8 µg/ml obtained for both drugs in this study is rather high but are beyond the concentrations obtained in lung tissues. This suggests that both drugs should be investigated further as potential adjuncts to the treatment of resistant TB when other alternatives have failed; in particularly through new drug delivery systems such as the Dry Power Inhaler which allows local drug deposition with high drug concentrations in the lungs but low toxicity due to limited systemic absorption. In addition, for 36% of the tested isolates a decrease of the MIC of clarithromycin by a single or twofold dilution was observed in the presence of a subinhibitory concentration of tobramycin and no antagonistic effect was seen for the remaining isolates.<p><p>This research illustrates different (laboratory) aspects in the fight against drug resistant TB, all using the Belgian TB collection: characterisation of the Belgian MDR-TB situation on bacteriological, molecular and epidemiological level; profound analysis of genomic mutations and their possible association with drug resistance; and investigation of synergistic activity of drugs with low efficacy against M. tuberculosis.<p> / Doctorat en Sciences biomédicales et pharmaceutiques / info:eu-repo/semantics/nonPublished

Tuberculosis (TB) claims the lives of millions of individuals each year, and is consequently the world’s second-most deadly infectious disease after acquired immune deficiency syndrome (AIDS), responsible for 1.4 million deaths in 2010 alone. Developing countries carry the heaviest burden, with the occurrence of multidrug-resistant (MDR) TB becoming more frequent, making more efficient vaccination and treatment strategies a necessity to combat this epidemic. The ESX-1 gene cluster (encoding the virulence-associated proteins ESAT-6 and CFP-10) and the Type Vll secretion system are thought to be responsible for the transport of extracellular proteins across the hydrophobic, and highly impermeable, cell wall of Mycobacterium, and consequently are thought to play a role in the virulence of this organism. To date, our understanding of tuberculosis pathophysiology and virulence has been described primarily using proteomic and genomic approaches. Subsequently, using the relatively new research approach called metabolomics, and interpreting the data using systems biology, we aimed to identify new metabolite markers that better characterise virulence and the proteins involved, more specifically related to the ESX-1 gene cluster. Using a GCxGC-TOFMS metabolomics research approach, we compared the varying metabolomes of M. smegmatis ESX-1 knock-out (ESX-1ms) to that of the wild-type parent strain and subsequently identified those metabolite markers differing between these strains. Multivariate and univariate statistical analyses of the analysed metabolome were used to identify those metabolites contributing most to the differences seen between the two sample groups. A general increase in various carbohydrates, amino acids and lipids, associated with cell wall structure and function, were detected in the ESX-1ms strain relative to the wild-type parent strain. Additionally, metabolites associated with the antioxidant system, virulence protein formation and energy production in these mycobacteria, were also seen to differ between the two groups. This metabolomics investigation is the first to identify the metabolite markers confirming the role of the ESX-1 gene cluster with virulence and the underlying metabolic pathways, as well as its associated role with increased metabolic activity, growth/replication rates, increased cell wall synthesis and an altered antioxidant mechanism, all of which are believed to contribute to this organism’s increased pathogenicity and survival ability. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2015

Tuberculosis (TB) claims the lives of millions of individuals each year, and is consequently the world’s second-most deadly infectious disease after acquired immune deficiency syndrome (AIDS), responsible for 1.4 million deaths in 2010 alone. Developing countries carry the heaviest burden, with the occurrence of multidrug-resistant (MDR) TB becoming more frequent, making more efficient vaccination and treatment strategies a necessity to combat this epidemic. The ESX-1 gene cluster (encoding the virulence-associated proteins ESAT-6 and CFP-10) and the Type Vll secretion system are thought to be responsible for the transport of extracellular proteins across the hydrophobic, and highly impermeable, cell wall of Mycobacterium, and consequently are thought to play a role in the virulence of this organism. To date, our understanding of tuberculosis pathophysiology and virulence has been described primarily using proteomic and genomic approaches. Subsequently, using the relatively new research approach called metabolomics, and interpreting the data using systems biology, we aimed to identify new metabolite markers that better characterise virulence and the proteins involved, more specifically related to the ESX-1 gene cluster. Using a GCxGC-TOFMS metabolomics research approach, we compared the varying metabolomes of M. smegmatis ESX-1 knock-out (ESX-1ms) to that of the wild-type parent strain and subsequently identified those metabolite markers differing between these strains. Multivariate and univariate statistical analyses of the analysed metabolome were used to identify those metabolites contributing most to the differences seen between the two sample groups. A general increase in various carbohydrates, amino acids and lipids, associated with cell wall structure and function, were detected in the ESX-1ms strain relative to the wild-type parent strain. Additionally, metabolites associated with the antioxidant system, virulence protein formation and energy production in these mycobacteria, were also seen to differ between the two groups. This metabolomics investigation is the first to identify the metabolite markers confirming the role of the ESX-1 gene cluster with virulence and the underlying metabolic pathways, as well as its associated role with increased metabolic activity, growth/replication rates, increased cell wall synthesis and an altered antioxidant mechanism, all of which are believed to contribute to this organism’s increased pathogenicity and survival ability. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2015

Thesis (MScMedSc (Biomedical Sciences. Human Biology and Human Genetics))--University of Stellenbosch, 2010. / Thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Medical Biochemistry at the Faculty of Health Sciences, University of Stellenbosch. / ENGLISH ABSTRACT: Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease which causes approximately 2 million deaths each year. Despite extensive research on tuberculosis and M. tuberculosis, little is understood of the mechanisms of pathogenicity of the organism. The genome of M. tuberculosis contains five ESAT-6 gene cluster regions, each of which contains genes encoding proteins involved in the formation of a dedicated protein secretion system. Included in these regions are genes encoding exported T-cell antigens, serine proteases, ATP-binding proteins and other membrane-associated proteins. Although it is known that some of these secretion systems are involved in virulence and phagosomal escape of M. tuberculosis, and that deletion thereof causes attenuation of the organism, the structure, substrates and functions of the systems are largely unknown. Understanding the structure of the ESX secretion systems will advance our understanding of the mechanisms of mycobacterial pathogenicity and provide clues to ways in which to interfere with these virulence mechanisms. The ESAT-6 gene cluster region 3, encoding the ESX-3 secretion machinery, is the only ESAT-6 gene cluster region which is essential for the in vitro growth of M. tuberculosis. It is however not required for the growth of the saprophytic mycobacterium M. smegmatis. In this study we have identified proteinprotein interactions within the ESX-3 secretion system, using the Mycobacterial – Protein Fragment Complementation (M-PFC) mycobacterial two-hybrid system, and created a model of the M. tuberculosis ESX-3 secretion system. According to this model, the EsxG-EsxH and PE5-PPE4 substrate protein complexes bind to the same components of the ESX-3 secretion machinery and are secreted via the same mechanism. A knock-out of the ESX-3 secretion system in M. smegmatis was generated by homologous recombination to allow further research into the functions and properties of this secretion system. This knock-out was used, together with wild-type M. smegmatis, to investigate the secretion of the M. tuberculosis EsxH protein by the M. smegmatis ESX-3 secretion system. The ESX-3 secretion system interactome may serve as a model for the ESX secretion systems and assist in our understanding of this secretion machinery which is key to the virulence and survival of M. tuberculosis and other pathogenic mycobacteria. Improved understanding of these mechanisms and their role in pathogenicity and survival may provide means of interfering with the secretion machinery, potentially leading to developments in the prevention and treatment of tuberculosis disease. / AFRIKAANSE OPSOMMING: Tuberkulose, wat veroorsaak word deur Mycobacterium tuberculosis, eis jaarliks ongeveer 2 miljoen lewens. Ten spyte van uitgebreide navorsing oor tuberkulose en M. tuberculosis is min bekend oor die meganismes van patogenisiteit van díe organisme. Die genoom van M. tuberculosis bevat vyf ESAT-6 geen groep gebiede wat elk proteïene kodeer wat ‘n toegewyde sekresie sisteem vorm. Ingesluit in elk van díe geen groep gebiede is gene wat T-sel antigene, serien proteases, ATP-bindingsproteïene en ander membraan-geassosieërde proteïene kodeer. Alhoewel dit bekend is dat sekere van hierdie sekresie sisteme betrokke is by virulensie en fagosoom-ontsnapping, en dat delesie daarvan die organisme attenueer, is die struktuur, substrate en funksies van die sisteme grootliks onbekend. Kennis van die struktuur van die ESX sekresie sisteme sal ons verstaan van die meganismes van mikobakteriele patogenisiteit verbeter en leidrade verskaf na maniere om in te meng by díe meganismes van virulensie. Die ESAT-6 geen groep gebied 3, wat die ESX-3 sekresie sisteem kodeer, is die enigste ESAT-6 geen groep gebied wat noodsaaklik is vir die in vitro groei van M. tuberculosis. Dit is egter nie nodig vir die groei van die saprofitiese mikobakterium M. smegmatis nie. In hierdie studie het ons proteïenproteïen interaksies van die ESX-3 sekresie sisteem geïdentifiseer, deur middel van die Mikobakteriële - Proteïen Fragment Komplementasie (M-PFC) mikobacteriële twee-hibriede stelsel. Die interaksies is gebruik om ‘n model van die M. tuberculosis ESX-3 sekresie sisteem te skep. Volgens díe model bind die EsxG-EsxH en PE5-PPE4 substraat proteïen komplekse aan dieselfde komponente van die ESX-3 sekresie apparaat en word deur dieselfde meganisme uitgevoer. ‘n uitklopmutant van die ESX-3 sekresie sisteem word deur homoloë rekombinasie in M. smegmatis gegenereer om verdere ondersoeke na die funksies en eienskappe van hierdie sekresie sisteem in staat te stel. Hierdie uitklopmutant is tesame met die wilde-tipe M. smegmatis gebruik om die sekresie van die M. tuberculosis EsxH proteïen deur die M. smegmatis ESX-3 sekresie sisteem te ondersoek. Die ESX-3 sekresie sisteem interaktoom kan dien as ‘n model vir die ESX sekresie sisteme om te help om ons kennis van hierdie sekresie apparaat, wat belangrik is vir die virulensie en oorlewing van M. tuberculosis en ander patogeniese mikobakterieë, te verbeter. Kennis van hierdie meganismes en hul rol in patogenisiteit en oorlewing mag maniere verskaf om by díe sekresie sisteme in te meng, wat moontlik kan lei tot ontwikkelings in die voorkoming en behandeling van tuberkulose.

Thesis (MSc)--Stellenbosch University, 2005. / ENGLISH ABSTRACT: Please see fulltext for abstract. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) affekteer die hele wêreld, maar dit is veral in ontwikkelende lande 'n groot probleem. In Suid-Afrika, soos in baie ander lande, veroorsaak die immuun-paraliserende uitwerking van HIV -koïnfeksie dat die TB-epidemie voortwoeker. Daar is bewyse dat genetiese faktore in die gasheer die uitkoms van die siekte bepaal, aangesien slegs 10% van die individue wat deur Mycobacterium tuberculosis (M tuberculosis) geïnfekteer word, uiteindelik die aktiewe siekte ontwikkel. Die aangebore immuunsisteem is die liggaam se eerste verdedigingslinie, waarna die verworwe immuunreaksie geïnisieer word. Die bakterium se lotgevalle word moontlik bepaal in hierdie vroeë stadium pas nadat dit ingeasem is. Die kollektien-molekule is veral in die long 'n belangrike deel van die aangebore immuunrespons en sluit die mannose-bindende lektien en die surfaktantproteïene A (SP-A) en D (SP-D) in. Dit is al aangetoon dat hierdie drie kollektien-molekule in die gasheer 'n rol speel in die verdediging teen M tuberculosis. In hierdie ondersoek is veral klem gelê op die surfaktantproteïene, wat voorkom asof dit belangrike en kenmerkende rolle speel in die reaksie teen die ingeasemde bakterieë. SP-A versterk die aanhegting van M tuberculosis aan die alveolêre makrofage en verhoog fagositose, terwyl SP-D die bakterieë agglutineer en so verhoed dat dit deur die makrofage gefagositeer word. Gekontroleerde assosiasiestudies in pasiënte is gedoen deur polimorfismes in hierdie gene, wat geassosieer is met TB in ander bevolkings as ons eie, te bestudeer. 'n Polimorfisme in die amino-terminaal area van die SP-D-geen is positief geassosieer met vatbaarheid vir TB. 'n Familie-gebaseerde studie is ook gedoen om die resultate van die gekontroleerde assosiasiestudie te repliseer. Verskillende resultate is verkry en word moontlik bepaal deur die familiestruktuur wat gebruik is. Die aantal families wat bestudeer is, was relatief min en daarom kan daar nie afgelei word dat die assosiasie wat voorheen waargeneem is vals is nie. 'n Groter studie sal gedoen moet word. Die impak van hierdie polimorfisme is verder ondersoek om te bepaal of dit die totale struktuur van die proteïen beïnvloed. Die effekte van hierdie polimorfisme op die konsentrasie van SP-D in die serum van aktiewe TB-pasiënte is ondersoek en vergelyk met die van kontroles. Ons kon nie vasstel watter rol, indien enige, die polimorfisme in die totale struktuur van die SP-D-molekule speel nie, maar ons het bewys dat die serumkonsentrasie van SP-D beduidend verhoog was in aktiewe TB-pasiënte in vergelyking met kontroles (p < 0.0001). Verder het ons ook gedemonstreer dat die konsentrasie van SP-D beduidend verhoog was in die IT-genotipe van die aktiewe TB pasiënte vergeleke met die kontroles (p < 0.0001). Die IT-genotipe is al voorheen positief geassosieer met vatbaarheid vir TB (T. Roos, ongepubliseerde inligting). Verskeie alleliese variante is geïdentifiseer in die SP-A-gene (SP-A1 en SP-A2) wat saam die volle funksionele SP-A-proteïen vorm. Polimorfismes wat onlangs in die kollageen-agtige area van SP-A 1 en SP-A2 gevind is (Madan et al., 2002) en een nuwe polimorfisme wat in hierdie studie geïdentifiseer is, is ondersoek in 'n Suid-Afrikaanse bevolking. Ons het beduidende positiewe assosiasie tussen 'n polimorfisme in die kollageen-agtige area van die SP-A2 geen en vatbaarheid vir TB (p = 0.007) aangetoon. Ons bevindinge bewys die belangrikheid van die bestudering van mensgenetika, wat die immuunkompetensie rig, om vatbaarheid vir infektiewe siektes te verstaan.

Thesis (MCur)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Mycobacterium Tuberculosis (TB) continues to rank among the world’s most serious problems despite biomedical achievement of effective prophylaxis and chemotherapy. In South Africa, TB is directly linked to the country’s high HIV prevalence rate and other related factors. The required knowledge, as well as people’s attitude towards a better understanding of TB are prerequisites for motivating them to seek early treatment. This study aims to explore the knowledge about and attitude towards TB among non- TB infected clinic attendees. More specifically, this study used a qualitative descriptive design to explore and describe clinic attendees’ knowledge of the cause, symptoms and treatment of TB and to explore their attitude towards the disease. A semi-structured interview technique was used to gather data. Ten clinic attendees between 20-40 years old, able to communicate in English and who had no past history of TB were conveniently sampled. Manual data analysis was done using an inductive approach. Thereafter, a deductive approach using the Health Belief Model was used to guide the discussion of the findings. Nine major themes were identified. The results confirm a gap in participants’ knowledge of the cause, symptoms and treatment of TB. Despite these gaps participants perceived that they were susceptible to TB, the dangers TB could cause and the benefits of completing the treatment. Participants indicated that they would seek medical help if they experienced TB symptoms. However, their fear was their ignorance of TB symptoms on the one hand and the fear of being stigmatized, discriminated against, as well as the quality of health service deliveries on the other hand. The findings highlight the need for on-going education about the cause of TB, transmission, symptoms and treatment at clinics and within the community. Media including radio, television, as well as schools and family should be included in TB education programmes. Immigrants should also be targeted to be included in TB education campaigns. Keys terms: Tuberculosis, Non-TB infected patients, Knowledge and attitude, Health Belief Model. / AFRIKAANSE OPSOMMING: Mycobacterium Tuberkulose (TB) word steeds gekenmerk as een van die ernstigste gesondheidsprobleme ter wệreld, ten spyte van deurbrake met betrekking tot meer doeltreffende profilakse en chemoterapie. In Suid-Afrika, word TB direk gekoppel aan die land se hoë voorkoms van MIV en ander verwante faktore. Die nodige kennis, sowel as ‘n beter begrip van mense se gesindhede teenoor TB, is voorvereistes vir die motivering wat hulle gedrag sal beïnvloed om vir vroeë behandeling te gaan. Hierdie studie het ten doel om die kennis en gesindhede teenoor tuberkulose van ongeïnfekteerde TB-pasiënte in ‘n Kaapstadse kliniek te ondersoek. In die besonder ondersoek die studie, deur ‘n kwalitatiewe beskrywende benadering, die kennis van ‘n spesifieke groep individue wat die kliniek besoek, met betrekking tot die oorsake, simptome en behandeling van TB, asook hulle houding ten opsigte van die siekte. Die studie beklemtoon ook enige vooroordele oor die siekte en identifiseer moontlike redes vir pasiënte se laat-aanmelding van TB by ‘n kliniek. ‘n Semi-gestruktureerde tegniek vir onderhoudvoering is gebruik. Tien pasiënte wat die kliniek besoek tussen die ouderdomme 20-40 jaar oud, wat in staat is om in Engels te kommunikeer, en wat geen vroeëre geskiedenis van TB het nie, is gerieflikheidshalwe per steekproef gebruik. Data is per hand versamel deur gebruik te maak van ‘n induktiewe benadering. Hierna is ‘n deduktiewe benadering gevolg, en die “Health Belief Model” is gebruik om die gesprekke te lei in die bevindinge. Nege hooftemas is geïdentifiseer. Die resultate bevestig ‘n gaping in die kennis van deelnemers oor die oorsake, simptome en behandeling van TB. Ten spyte van die gapings, was deelnemers wel bewus van die feit dat hulle blootgestel is om TB op te doen en oor wat die gevare is wat deur TB veroorsaak kan word, sowel as wat die voordele is om TB-behandeling te voltooi. Deelnemers het aangedui dat hulle mediese hulp sal vra, sou hulle die simptome van TB bespeur. Desnieteenstaande was hulle vrees enersyds oor die onkundigheid van die simptome van TB, en om gestigmatiseer teen gediskrimineer te word, asook die standaard van mediese dienste beskikbaar andersyds. Die bevindinge beklemtoon die behoefte aan voortgesette opvoeding oor die oorsake, oordrag, simptome en behandeling van TB in klinieke en binne gemeenskappe. Media soos radio en televisie, asook skole en families behoort ingesluit te word in sodanige opvoedingsprogramme. Immigrante behoort ook ingesluit te word by massa opvoedingsprojekte. Sleutelterme: Tuberkulose, ongeïnfekteerde TB-pasiënte, Kennis en gesindhede, “Health Belief Model”.