Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Individuals latently infected with Mycobacterium tuberculosis (M.tb) contain the infection without showing signs of illness. Steroid hormones such as glucocorticoids (GCs) however can lead to reactivation of TB. Currently two different injectable contraceptives are available in South Africa, medroxyprogesterone acetate (MPA) and norethisterone enanthate (NET). MPA is able to bind to and activate the glucocorticoid receptor (GR) and possesses selective GC activity, a pharmacological characteristic absent in NET. The aim of this study was to investigate the immune modulatory effects of the two contraceptives MPA and NET on immune responses to mycobacteria in vitro and in vivo. Human peripheral blood mononuclear cells (PBMCs) were infected with BCG (M. bovis Bacille Calmette-Guérin) and treated with MPA, NET, progesterone or cortisol and cytokine expression was measured in order to determine whether the synthetic progestins mimic endogenous progesterone or the GC cortisol. MPA, but not NET suppressed the expression of IFN-γ, IL-1α, IL-1β, IL-2, IL-12p40 and IL-13 similarly to cortisol. Furthermore expression of miRNAs, small double stranded RNA molecules that bind to complementary sequences in mRNAs of target genes and cause their degradation, was determined under the different experimental conditions. The expression of several miRNAs including miR-30c, miR-222, miR-454 and miR-331-3p were differentially influenced by MPA, cortisol and/or NET in PBMCs stimulated with BCG. For example, BCG induced the expression of miR-454 (p=0.003) which was then inhibited to basal levels by cortisol (p=0.008), MPA (p=0.002) and NET (p=0.002). These results demonstrate that steroid hormones including the contraceptives MPA and NET can modulate immune responses to mycobacteria at the miRNA level. To determine the effect of MPA and NET on BCG-induced expression of miRNAs in vivo a mouse model was used. C57BL/6 mice were injected weekly with either MPA or NET using a dose equivalent to humans and then infected with BCG. Mice treated with MPA had a higher spleen bacterial load 21 days after infection compared to both NET treated and control mice (p=0.023). In whole blood, MPA and NET treatment suppressed the BCG-induced production of miR-100 and miR-509-3p to basal levels. In contrast to NET, MPA induced expression of miR-99a expression independent of BCG infection. In the lung, the site of disease, a total number of 22 out of 377 miRNAs tested were differentially expressed 21 days after infection. The results of this study indicate that both synthetic progestins altered the immune response to BCG at the level of cytokine expression as well as the miRNA level. MPA was found to mimic cortisol by inhibiting secretion of inflammatory cytokines whereas NET appeared to have more progestogenic properties. Each of the steroid hormones was observed to induce a characteristic miRNA expression profile, both in vitro as well as in vivo, although not identical. These results highlight that the two contraceptives – although used interchangeably by women in developing countries - are pharmacologically unique and differentially modulate immune responses to mycobacteria. These data support the urgent need for further research into the link between hormonal contraceptives and susceptibility to infectious diseases. / AFRIKAANSE OPSOMMING: Individue wat latent met Mycobacterium tuberculosis ( M.tb ) geïnfekteer is, onderdruk die infeksie en wys geen simptome van die siekte nie. Steroïed hormone soos glukokortikoïede (GKe) kan egter tot die heraktivering van TB lei. Daar is tans twee verskillende inspuitbare voorbehoedmiddels beskikbaar in Suid-Afrika, medroksiprogesteroon-asetaat (MPA) en noretisteroon enantaat (NET). MPA is staat om aan die glukokortikoïed reseptor (GR) te bind en dit te aktiveer. MPA beskik ook selektiewe GK aktiwiteit, 'n farmakologiese eienskap wat afwesig is in NET. Die doel van hierdie studie was om die immuun-regulerende effekte van die twee voorbehoedmiddels, MPA en NET, op immuunresponse teen mikobakterieë in vitro en in vivo te ondersoek. Menslike perifêre bloed mononukleêre selle (PBMSe) is met BCG geïnfekteer en met MPA, NET, progesteroon of kortisol behandel. Sitokien uitdrukking was gemeet om vas te stel of die sintetiese progestiene, endogene progesteroon of die GK kortisol naboots. MPA, maar nie NET, onderdruk die produksie van IFN-γ, IL- 1α, IL- 1β, IL- 2, IL- 12p40 en IL- 13 soortgelyk aan kortisol. Verder is uitdrukking van miRNAs, klein dubbelstring RNS molekules wat aan komplimentêre volgorde in mRNAs van teiken gene bind en wat hul degradering veroorsaak, bepaal in elk van die verskillende eksperimentele toestande. Die uitdrukking van verskeie miRNAs insluitende miR-30c, miR-222, miR-454 en miR-331-3p is differensieël beïnvloed deur MPA, kortisol en/of NET in PBMSe wat met BCG gestimuleer is. Byvoorbeeld, BCG veroorsaak die uitdrukking van miR-454 wat dan geïnhibeer word tot agtergrondvlakke deur kortisol, MPA en NET. Hierdie resultate toon dat steroïed hormone, insluitend die voorbehoedmiddels MPA en NET, die immuunrespons teen mikobakterieë op miRNA-vlak affekteer. Om die effek van MPA en NET op BCG-geïnduseerde uitdrukking van miRNAs in vivo te bepaal, is ʼn muismodel gebruik. C57BL/6 muise is weekliks met 'n dosis van MPA of NET, ekwivalent aan dosisse gebruik in die mens, ingespuit en met BCG geïnfekteer. Muise wat met MPA behandel is, het 'n hoër bakteriële lading in die milt 21 dae na infeksie in vergelyking met NET-behandelde muise en kontrole muise. In hul bloed, onderdruk MPA en NET behandeling die BCG-geïnduseerde produksie van miR-100 en miR-509-3p tot basale vlakke. In teenstelling met NET, induseer MPA die uitdrukking van miR-99a onafhanklik van BCG infeksie. In die long is 'n totaal van 23 miRNAs differensieël uitgedruk 21 dae na die infeksie. Die resultate van hierdie studie dui daarop dat beide sintetiese progestien die immuunrespons teen BCG verander op sitokien sowel as miRNA vlak. MPA boots hoofsaaklik kortisol na deur inhibering van sitokien-produksie terwyl NET meer progesterone eienskappe het. Op miRNA vlak veroorsaak elk van die steroïed hormone 'n kenmerkende miRNA uitdrukkingsprofiel, beide in vitro asook in vivo. Hierdie resultate beklemtoon dat die twee voorbehoedmiddels - alhoewel hulle afwisselend gebruik word deur vroue in ontwikkelende lande - farmakologies uniek is en differensieël die immuunrespons reguleer teen Mycobacterium. Hierdie data ondersteun die dringende behoefte aan verdere navorsing in verband met hormonale voorbehoedmiddels en vatbaarheid vir aansteeklike siektes.

Thesis (MSc)--Stellenbosch University, 2016. / ENGLISH ABSTRACT: Tuberculosis (TB) is one of the world’s deadliest diseases, with one third of the population being infected by it. The diagnosis of active tuberculosis entails finding and identifying Mycobacterium tuberculosis (Mtb), the causative pathogen in a specimen of bodily fluid from the patient. Multiple samples will improve the diagnostic yield and specimen volumes should therefore be as large as possible, which is often challenging for patients and especially younger children. Alternatively, a smaller volume could be required if there was a manner in which to concentrate the bacteria within a specimen, through use of a substrate which has an affinity for the pathogenic species. Polymers having intrinsic cellular activity are of interest as such substrates, one such being the natural polysaccharide, chitosan. In this thesis, a variety of modified chitosan derivatives were prepared as potential Mtb-capturing substrates. This was achieved by modifying chitosan with a variety of moieties, selected based on possible interactions with the Mtb cell wall, to render various quaternary ammonium salts of the polymer chitosan. The quaternized chitosan derivatives were then used to synthesize nano-substrates having an affinity for Mtb. Polymer coated superparamagnetic magnetite nanoparticles (SPMNs) were synthesized via an in situ co-precipitation technique, in which modified chitosan is able to chelate with the metal core. Polymer nanofibers were also electrospun via the electrospinning technique. The prepared derivative, N-trimethylammonium chitosan chloride (TMC), was electrospun into nanofibers by blending with suitable non-ionogenic polymers, namely polyvinyl alcohol (PVA), polyethylene oxide (PEO), polyvinyl pyrrolidone (PVP) and polyacrylamide (PAM), required to facilitate nanofiber formation. Affinity studies were conducted between the modified chitosan nano-substrates and the bacillus Calmette-Guérin (BCG) strain of Mycobacterium bovis, the attenuated Mtb-mimic bacteria, for evaluation as mycobacterium capturing substrates. The successful capture of BCG onto the surfaces of the various modified chitosan nanofibers and modified chitosan coated superparamagnetic nanoparticles was confirmed by fluorescence microscopy (FM), light microscopy (LM), transmission electron microscopy (TEM) and field emission scanning electron microscopy (FE-SEM). Analysis of the FM, TEM and FE-SEM images indicated that the chitosan coated nanoparticles functionalized with a C12 aliphatic quaternary ammonium moiety (CS-qC12), captured the most BCG through a combination of ionic and hydrophobic interaction. TMC blended with PVA, to produce nanofibers crosslinked with genipin, were found to have the strongest interaction with BCG of the nanofibrous mats tested. These findings were corroborated by water contact angle measurements, which established that PVA was the least hydrophilic of the non-ionogenic polymers and had hydrogen bond donating groups only, factors influencing the cellular adhesive properties of affinity substrates. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is een van die wêreld se mees dodelikste siektes, met ‘n derde van die bevolking wat geïnfekteer is daarmee. Ten einde aktiewe TB te diagnoseer moet Mycobacterium tuberculosis (Mtb), die voorsakende patogeen in ʼn monster van die pasiënt se liggaamlike vloeistof, gevind en ïdentifiseer word. Veelvuldige monsters sal die diagnotiese opbrengs verhoog en monster volumes moet dus so groot as moontlik wees wat dikwels ʼn uitdaging vir pasiënte en veral jonger kinders kan bied. Alternatiewelik kan ʼn kleiner monster van die pasiënt vereis word indien daar ʼn manier was om die bakterieë in ʼn monster te konsentreer deur die gebruik van ʼn substraat wat ʼn affiniteit toon vir die patogeniese spesie. Polimere met ʼn intrinsieke sellulêre aktiwiteit, wek belangstelling as sodanige substraat, een synde die natuurlike polisakkaried, chitosan. In hierdie tesis is ʼn verskeidenheid gemodifiseerde chitosan afgeleides voorberei as potensiële Mtb-vaslegging substrate. Dit is gedoen deur chitosan te modifiseer met ʼn verskeidenheid funksionele groepe, gekies op grond van moontlike interaksies met die Mtb selwand, ten einde ʼn verskeidenheid kwaternêre ammonium soute van die chitosan polimeer te bekom. Die kwaternêre chitosan afgeleides is gevolglik gebruik om nano-substrate te sintetiseer wat ʼn affiniteit toon vir Mtb. Polimeer bedekte superparamagnetiese magnetiet nanopartikels (SPMNs) is gesintetiseer via ʼn in situ mede-neerslag metode, waarvolgens die gemodifiseerde chitosan polimere in staat is om met die metaal kern te chelaat. Polimeer nanovesels is ook geëlektrospin deur die elektrospin tegniek te gebruik. Die voorbereide afgeleide N-trimetielammonium chitosan chloried (TMC) is tot nanovesels geëlektrospin deur vermenging met geskikte nie-ionogeniese polimere, naamlik poliviniel-alkohol (PVA), polietilene-oksied (PEO), poliviniel-pirrolidoon (PVP) en poliakrielamied (PAM), wat vereis word ten einde nanovesels te produseer. Affiniteit studies is uitgevoer tussen die gemodifiseerde chitosan nano-substrate en die bacillus Calmette-Guérin (BCG) stam van Mycobacterium bovis, die verswakte Mtb-mimiek bakterieë vir evaluering as mycobakterium-vaslegging substrate. Die suksesvolle vasvang van BCG op die oppervlaktes van die verskillende gemodifiseerde chitosan nanovesels en gemodifiseerde chitosan bedekte SPMNs is bevestig deur fluoressensie mikroskopie (FM), lig mikroskopie (LM), transmissie elektron mikroskopie (TEM) en veld-emissie-skandering elektron mikroskopie (FE-SEM). Analise van die FM, TEM en FE-SEM beelde het getoon dat die chitosan bedekte nanopartikels met byvoeging van ʼn C12 alifatiese kwaternêre ammonium groep, die meeste BCG vasgevang het deur ʼn kombinasie van ioniese en hidrofobiese interaksie. TMC vermeng met PVA om nanovesels te vorm, gekruisbind met genipin, is gevind om die sterkste interaksie met BCG te toon. Hierdie bevindings is bevestig deur water-kontak-hoek-metings, wat getoon het dat PVA die minste hidrofilies van die nie-ionogeniese polimere was en slegs waterstof-binding skenkings groepe het, alles faktore wat die sellulêre bindingskwaliteite van affiniteit-substrate sal beïnvloed.

Cell surface carbohydrates play an important role in a wide variety of biological processes such as inflammation, tumor metastasis, and viral and bacterial infection. The goal of our research has been two-fold. The first objective was the synthesis of antimycobacterial compounds. A mannose containing tetrasaccharide from the mannan core of lipoarabinomannan (LAM) of Mycobacterium tuberculosis has been synthesized using α-D-methylmannopyranoside as starting material and Koeings-Knorr reactions to couple saccharides. The synthesis was completed in nine steps and in 14% total yield. This compound should be useful in competitive inhibition studies with macrophages or as an immunological marker. We have successfully synthesized nonsulfated mimics of the aminosterol antibiotic from 5α-cholestan-3-one in two steps in 40-70% total yield. The critical step in this synthesis is the addition of the boronic acid functional group using 2-o-formylphenylboronic acid. It is hypothesized that the addition of boronic acids will improve the antibacterial and anti-angiogenic activity of these compounds. The second objective was the synthesis of a simple fluorescent receptor for simple carbohydrates. A receptor using anthracene as the fluorophore has been completed demonstrating an improved yield over previous methods. This receptor is the first to show selectivity for myo-inositol over other saccharides.

L'eau et le sol sont considérés comme des sources potentielles de mycobactéries non-tuberculeuses (MNT). Parmi les infections humaines causées par les MNT d'origine environnementale, les infections pulmonaires et cutanées sont souvent décrites. Le manque de connaissances sur leur cycle de vie dans l'environnement requiert des outils analytiques, qui ne sont actuellement pas adaptés à ce type d'échantillons. Cette thèse vise donc premièrement à proposer des méthodes de quantification en bactériologie et en biologie moléculaire dans le but de déterminer les sources des MNT dans les bassins versants. Ainsi, la comparaison des méthodes d'isolement de MNT a montré que le traitement au chlorure de cetylpyridininium de l'eau suivi d'une culture en milieu riche supplémenté par un mélange d'antibiotiques (polymyxine B, amphotéricine, acide nalidixique, triméthoprime, carboxy-pénicilline) limitait la croissance des microorganismes interférents et éliminait moins de MNT que les autres méthodes comparées (Radomski et al. 2010, doi: 10.1128/AEM.00942-10). Bien que des espèces de MNT potentiellement pathogènes aient été isolées de l'eau de surface de la Seine en utilisant ces outils bactériologiques, la quantification des MNT ne s'est pas avérée reproductible. En conséquence, une méthode de quantification par polymérisation en chaîne en temps réel (qPCR) a été développée pour énumérer le genre Mycobacterium dans l'eau (Radomski et al. 2010, doi: 10.1128/AEM.02659-09). La nouvelle méthode développée, ciblant l'ARNr 16S, était plus spécifique que les autres méthodes qPCR publiées, ciblant un autre locus de l'ARNr 16S et le gène hsp65 (respectivement 100 % versus 44 % et 91 %). La comparaison des méthodes d'extraction d'ADN mycobactérien a montré que la lyse enzymatique combinée au bromure d'hexadécyltriméthylammonium était la procédure la plus efficace pour énumérer par qPCR les MNT dans des échantillons environnementaux. Ainsi, ces méthodes d'extraction d'ADN et de qPCR ont été utilisées pour étudier des sources de MNT dans des bassins versants. Dans un second temps, nous avons étudié trois sources potentielles de MNT : une ponctuelle et deux diffuses. Plus précisément, une station d'épuration (STEP) a été choisie comme source ponctuelle de MNT et a été étudiée en temps sec en fonction d'indicateurs de contamination fécale et des paramètres globaux habituellement contrôlés. Les MNT ont atteint 5,52×105±3,97×105 copies/L dans l'eau en entrée de STEP (84 % d'échantillons positifs), n'ont pas été détectées dans l'eau en sortie de STEP après décantation physico-chimique et biofiltration et ont été estimées à 1,04×106 ±1,75×106 copies/g dans les boues de STEP (50 % d'échantillons positifs). La plupart des MNT (98±2 %, correspondant à 2,45±0,78 log10) ont été éliminées par décantation physico-chimique et les MNT restantes (0,74×104 ±1,40×104 copies/L) ont été éliminées par biofiltration (53 % d'échantillons positifs). Ces résultats ont montré également que Mycobacterium, Escherichia coli et les entérocoques intestinaux possèdent des comportements significativement différents conduisant respectivement à trois modèles : hydrophobe, hydrophile et intermédiaire. Concernant les sources diffuses, la densité de MNT a été mesurée dans divers sols ruraux et urbains qui ont été caractérisés par différents paramètres physico-chimiques. Les densités de MNT les plus importantes ont été mesurées dans des sols de forêts tourbeuses (9,27×104±5,00×104 copies/g sec) et dans des sols faiblement urbanisés proches de marécages côtiers (1,71×106±2,85×106 copies/g sec) alors qu'aucune MNT n'a été détectée dans les autres types de sols étudiés. De plus, la densité de MNT a été significativement associée à des sols proches de zones acides et des teneurs fortes des sols en eau, matière organique et fer. Ces résultats suggéreraient que les MNT sont dépendantes de leur production intra et extracellulaire de chélateurs de fer et indiqueraient que les zones faiblement urbanisées pourraient être impactées par la proximité de marais acides. Afin d'étudier une autre source diffuse, les MNT et d'autres paramètres ont été mesurés lors d'événements pluvieux dans l'eau de surface de la Marne et de ses principaux affluents. Les densités de MNT ont été estimées à 2,16×105±2,36×105 copies/L dans environ 20 % des échantillons d'eau collectés, et elles ne différaient pas entre les zones péri-urbaines et rurales échantillonnées. Nos résultats ont montré que la pluviométrie et la durée de l'évènement expliquaient la diminution du nombre de MNT détectées dans l'eau de surface au cours de l'événement pluvieux de faible intensité (6,6 mm/h de pluviométrie cumulées en 5,5 h). Ces résultats ont souligné que certains affluents de la Marne pouvaient apporter des MNT en temps sec, mais qu'au cours de l'évènement pluvieux suivi les densités de MNT diminuaient.En guise d'amélioration à ces études appliquées, des réflexions sur les défis relatifs à la surveillance des microorganismes pathogènes dans l'environnement ont été explorées. En nous focalisant sur la MNT la plus pathogène, M. avium, nous avons discuté des défis de la détection et de l'énumération et proposé un guide d'adaptation des méthodes médicales aux échantillons environnementaux (Radomski et al. 2011, ed. A. Méndez-Vilas, Vol. 2). Ce guide se présente sous la forme d'un arbre de décision permettant de choisir les outils analytiques les plus appropriés pour surveiller les microorganismes pathogènes dans l'environnement. De plus, une stratégie in silico de comparaison de génomes bactériens totalement séquencés a été développée dans le but de décrire des nouvelles cibles de détection. L'analyse in silico des génomes totalement séquencés a permis de détecter 11 protéines présentant entre 80 % et 100 % de similarité dans les génomes mycobactériens et moins de 50 % de similarité dans les génomes non-mycobactériens des genres Corynebacterium, Nocardia et Rhodococcus. Sur la base d'alignements des séquences d'ADN de ces cibles potentielles, il a été possible de dessiner des amorces PCR et une sonde pour détecter le gène codant la sous-unité C de la synthase de l'adénosine triphosphate qui semble exclusivement conservée dans le génome mycobactérien. Le développement d'outils analytiques, en particulier la qPCR, a permis de montrer qu'une STEP éliminait efficacement les MNT et que le traitement des eaux usées est nécessaire pour préserver l'eau de surface de cette source ponctuelle de MNT. Il a été mis en évidence que les événements pluvieux diminuent la densité de MNT dans l'eau de surface et que les sols acides sont des sources naturelles majeures de MNT qui pourraient impacter des zones faiblement urbanisées en temps de pluie via le ruissellement. Concernant les réflexions sur la surveillance des microorganismes pathogènes dans l'environnement, l'arbre de décision des outils analytiques appropriés et la nouvelle stratégie in silico de détection de cibles moléculaires pourraient être appliqués pour l'étude d'autres microorganismes de l'environnement / Water and soil are considered as potential sources of nontuberculous mycobacteria (NTM) infections. Among human infections caused by environmental NTM, pulmonary infections and cutaneous infections are often described. However, lack of knowledge about their life cycle in the environment requires analytical tools, which are not currently adapted to these kinds of samples. The aim of this thesis is to propose bacteriological and molecular quantitative methods, in order to determine the sources of NTM in watersheds. Comparison of NTM isolation methods showed that treatment with cetylpyridinium chloride of water, followed by culture on a rich medium supplemented with antibiotic cocktail (polymyxin B, amphotericin, nalidixic acid, de trimethoprim, azlocillin) decreased the growth of nontarget microorganisms, while inhibiting less NTM than the other compared methods (Radomski et al. 2010 doi: 10.1128/AEM.00942-10). Although potentially pathogenic NTM species were isolated from surface water of the Seine River using these bacteriological tools, enumeration of NTM was not reproducible. Consequently, a quantitative real-time polymerase chain reaction (qPCR) method was developed in order to enumerate Mycobacterium spp. in water (Radomski et al. 2010 doi: 10.1128/AEM.02659-09). This newly developed method, targeting 16S rRNA, was more specific than the two previously published qPCR methods targeting another 16S rRNA locus and the hsp65 gene (100% versus 44% and 91%, respectively). Comparison of DNA extraction methods showed that the enzymatic lysis and hexadecyltrimethylammonium bromide procedure was the most effective combination for mycobacterial DNA extraction with the aim to enumerate NTM in environmental samples by qPCR. Thus, these extraction and qPCR methods were used in order to study NTM sources in watersheds.Secondly, we studied three potential sources of NTM : one point source and two nonpoint sources. More precisely, a wastewater treatment plant (WWTP) was chosen as a potential point source of NTM and was studied according to indicators of fecal contamination and usually monitored parameters. NTM reached 5.52×105±3.97×105 copies/L in the influent of WWTP (84% of positive samples). They were not detected in the effluent after physico-chemical decantation and biofiltration, and were estimated at 1.04×106 ±1.75×106 copies/g in sludge (50% of positive samples). Most NTM (98±2%, i.e. 2.45±0.78 log10) were removed by the physical-chemical decantation, and the remaining NTM (0.74×104 ±1.40×104 copies/L) were removed by biofiltration (53% of positive samples). These results showed also that Mycobacterium, Escherichia coli and intestinal enterococci follow significantly different behaviors as hydrophobic, hydrophilic and intermediate models, respectively. Concerning the nonpoint sources, NTM were enumerated in a variety of rural and urban soils which were characterized by different physico-chemical parameters. The highest NTM densities were measured in peat forest soils (9.27×104±5.00×104 copies/g dw) and in lightly urbanized soils near a costal swamp (1.71×106±2.85×106 copies/g dw), whereas they were not detected in the other monitored soils. NTM density was significantly associated with soils near acidic areas and high moisture, organic matter, and iron content in soils. These results emphasized that NTM are dependent upon the production of surface and extracellular iron-binding compounds, and may mean that lightly urbanized area could be impacted by the proximity of the acidic swamp. In order to study another nonpoint source, NTM and other parameters were measured during wet events in surface water of Marne River and their main effluents. NTM density was estimated at 2.16×105±2.36×105 copies/L in about 20% of surface water samples, and NTM densites did not differ among rural and peri-urban sampling areas. Our results showed that the pluviometry and rain duration explained the decrease of detected NTM abundances in surface water during a slightly intense wet event (6.6 mm/h of cumulated rain during 5.5 h). These results emphasized that some tributaries of the Marne River may constitute a source of NTM, however their influence on NTM density in surface water of the Marne River decreased during the slightly intense wet event.In order to improve these applied studies, challenges dealing with pathogenic microorganism monitoring in environment were explored. Focusing on the most pathogenic NTM, M. avium, we discussed the challenges for detection and enumeration and proposed a guidance for the adaptation of clinical methods to environmental samples (Radomski et al. 2010 ed. A. Méndez-Vilas, Vol. 2). This guidance was proposed as a decision tree allowing to choose the most suitable analytical tools in order to monitor pathogenic microorganisms in environment. Moreover, an in silico strategy of whole sequenced bacterial genome comparison was developed in order to describe new targets for NTM detection. In silico analysis of whole sequenced genomes allowed to detect 11 proteins showing between 80% and 100% of similarity with mycobacterial genomes, and less than 50% of similarity with closely related genomes of Corynebacterium, Nocardia and Rhodococcus genera. Based on the DNA sequence alignments of these potential targets, it was possible to design a primer pair and a probe in order to detect by PCR the gene coding for adenosine-5'-triphosphate synthase subunits C which seems exclusively conserved in mycobacterial genome.Using the developed analytical tools, especially the qPCR, we showed that a WWTP removed efficiently NTM from the influent, and that waste water treatment is necessary in order to preserve surface water against this NTM point source. It was shown that storm events decrease NTM densities in surface water and in contrast that acidic soils are major NTM natural sources which may impact lightly urbanized areas during wet weather when runoff water suspends soil matter. Concerning challenges dealing with pathogenic microorganism monitoring in environment, the decision tree of suitable analytical tools and the new in silico strategy of molecular target detection might be also useful for the study of other environmental microorganisms

Master of Science - Molecular Medicine and Haematology / The completion of the genome sequence of Mycobacterium tuberculosis strain H37Rv revealed that 10% of the coding capacity is devoted to two, large multigene families that are characterised by repeat sequences. These are the PE and PPE families that code for acidic, glycine rich proteins. A subgroup of the PE family is the polymorphic GC rich sequence (PGRS) gene subfamily. Genome comparisons of clinical isolates of M. tuberculosis have confirmed the polymorphic character of some of these genes suggesting they may be analogous to the contingency loci found in other pathogenic bacteria. Certain PE-PGRS proteins play a direct role in virulence in M. marinum, other PE-PGRS genes are cell surface associated, and some PE-PGRS proteins are variable surface antigens, supporting a potential role in host pathogen interactions. A reporter assay designed to investigate mutations in a PE-PGRS repeat-containing sequence was used to assess mutation rates in various M. smegmatis host strains by fluctuation analysis. A wide spectrum of mutations was observed and the evidence suggests that slipped-strand mispairing between proximal and distal PGRS sequences located in cis is the predominant type of mutational event at such loci. Moreover, slipped-strand mispairing at such loci occurs at a moderately higher rate than base substitution mutagenesis and is mediated by the normal replicative polymerase.

L’émergence de formes multirésistantes de tuberculose et la résistance intrinsèque de Mycobacterium abscessus à de nombreux anti-infectieux imposent l’identification de nouveaux antibiotiques et de nouvelles stratégies thérapeutiques. Les mycobactéries sont naturellement peu sensibles aux β-lactamines par production d’une β-lactamase et de cibles atypiques de faible affinité, les L,D-transpeptidases, qui sont efficacement inactivées par une seule classe de β-lactamines, les carbapénèmes. L’objectif de la thèse est d’étudier le mode d’action des β-lactamines afin de proposer des stratégies permettant d’optimiser ces antibiotiques. Pour comprendre la spécificité des L,D-transpeptidases vis-à-vis des carbapénèmes, nous avons étudié la cinétique et le mécanisme de la réaction d’inactivation de ces enzymes par différentes méthodes de spectroscopie en flux arrêté. Nos résultats indiquent que l’efficacité des carbapénèmes est due à leur capacité à former rapidement un intermédiaire tétrahédrique et à la stabilité de l’acylenzyme. La spécificité des L,D-transpeptidases pour les carbapénèmes ne dépend pas de leurs chaînes latérales, qui pourraient être modifiées pour améliorer les propriétés pharmacologiques de ces antibiotiques. Chez M. abscessus, nous avons identifié un inhibiteur de la β-lactamase, l’avibactam, qui augmente l’activité de certaines β-lactamines in vitro, en intracellulaire et dans un modèle d’infection du poisson zèbre. Nos résultats montrent que les β-lactamines peuvent être optimisées pour le traitement des infections dues aux mycobactéries multirésistantes par l’amélioration de l’inactivation des cibles ou l’inhibition des β-lactamases. / The emergence of multidrug-resistant tuberculosis and the intrinsic resistance of Mycobacterium abscessus to most antibiotics require the identification of new drugs and new therapeutic strategies. Mycobacteria are naturally poorly susceptible to β-lactam antibiotics due to production of a β-lactamase and of atypical low-affinity targets, the L,D-transpeptidases, which are effectively inactivated by a single class of β-lactams, the carbapenems. The aim of the thesis is to study the mode of action of β-lactams to propose strategies for the optimization of these antibiotics. To understand the specificity of L,D-transpeptidase for carbapenems, we have studied the kinetics and mechanism of inactivation of these enzymes using various stopped-flow spectroscopic methods. Our results indicate that the efficacy of carbapenems is due to their ability to rapidly form a tetrahedral intermediate and to the stability of the acylenzyme. The specificity of the L,D-transpeptidases for carbapenems does not depend upon the side chains of the drugs, which may be modified to improve their pharmacological properties. In M. abscessus, we have shown that the β-lactamase inhibitor avibactam increases the activity of various β-lactams in vitro, intracellularly, and in zebrafish model. Our results show that β-lactams can be optimized for the treatment of infections due to multidrug-resistant mycobacteria by improving inactivation of the targets and by inhibiting the β-lactamases.

O ferro (Fe) é um dos metais mais importantes para a homeostase. Está envolvido em vários processos fisiológicos como, por exemplo, processo redox, síntese de DNA, metabolismo energético e transporte de biomoléculas. A regulação da concentração deste metal é bem controlada já que o seu excesso pode culminar na produção de espécies reativas de oxigênio que causam dano celular e sua escassez inibe o sistema imunológico. Um dos elementos chaves para o sucesso da cura de doenças infecciosas está na capacidade do hospedeiro em conter a proliferação do microrganismo e na ativação controlada da imunidade celular. Assim como os organismos eucariotos, grande parte dos organismos procariotos necessita de Fe para proliferação e manutenção das atividades biológicas. Deste modo, a interação entre esses dois organismos promove uma batalha para a captura deste metal que pode influenciar no curso de uma doença infecciosa tanto para o beneficio do hospedeiro quanto para o patógeno invasor. A Tuberculose (TB) é a maior causa de morte por doença infecciosa em adultos no mundo sendo responsável pela morte de 1 milhão de pessoas anualmente. Embora a doença tenha grande possibilidade de cura e tratamento disponível para a população, a reincidência de TB é alta e o surgimento de cepas resistentes à antibioticoterapia cresce gradativamente. Diante disso, é necessário compreender cada vez mais o processo fisiopatológico envolvido na TB para buscar novos alvos terapêuticos para cura e redução dos índices de mortalidade. O presente estudo tem como objetivo avaliar a expressão de genes envolvidos na homeostase do ferro em macrófagos humanos após a infecção com Mycobacterium tuberculosis H37Rv e o isolado clinico hipervirulento Mycobacterium tuberculosis Beijing 1471 com e sem suplementação de ferro. Para isso, macrófagos infectados foram lisados para obtenção e purificação de RNA total e o estudo de expressão gênica foi realizado utilizando a tecnologia de PCR em tempo real (RT-qPCR). Além disso, foi determinada a concentração de ferro no sobrenadante dessas culturas bem como o crescimento desses microrganismos no interior dos macrófagos. Genes envolvidos no controle da internalização do Fe em macrófagos foram diferentemente expressos nas culturas infectadas em relação ao controle não infectado. Também foi possível observar que a expressão desses genes varia com o tempo de infecção e com o tratamento com ferro, demostrando que existe um esforço da célula hospedeira em conter a infecção. Não foi observado variação significativa com relação à dosagem de ferro no sobrenadante das culturas infectadas em relação ao controle e o crescimento das micobactérias dentro dos macrófagos não variou de maneira significativa com relação aos tratamentos empregados. Dessa forma, este estudo contribuiu para o esclarecimento da resposta do macrófago frente à infecção com micobactérias que apresentam perfil de virulência distinto entre si e a interação do ferro neste processo patológico. / Iron (Fe) is one of the most important metals to homeostasis. It is involved in various physiological processes such as redox process, DNA synthesis, energy metabolism and transport of biomolecules. The concentration regulation of this metal is well-controlled since its excess can lead to the production of reactive oxygen species that cause cell damage and its scarcity inhibits the immune system. One of the key elements for the cure of infectious diseases is the host\'s ability to contain the spread of the organism and control activation of cellular immunity. Just as eukaryotes, most prokaryotes organisms require Fe for its proliferation and maintenance of biological activities. Thus, the interaction between these two organisms promotes a battle to capture this metal that can influence the course of an infectious disease either to the benefit of the host or to the invading pathogen. Tuberculosis (TB) is the leading cause of death from infectious disease among adults worldwide and is responsible for the death of 1 million people annually. Although the disease has high possibility of cure and treatment available to the population, the recurrence of TB is high and the emergence of resistant strains to antibiotics grows gradually. Therefore, it is necessary to understand more the pathophysiological process involved in TB to seek new therapeutic targets for healing and reduction in mortality. The present study aims to evaluate the expression of genes involved in iron homeostasis in human macrophages after infection with Mycobacterium tuberculosis H37Rv and the hypervirulent clinical isolate Mycobacterium tuberculosis Beijing in 1471 with and without iron supplementation. For this, macrophages were lysed and purificated to obtain total RNA, and the study of gene expression was performed using the technology of Real-time PCR (RT-qPCR). Furthermore, the iron concentration in the supernatant of these cultures was determined as well as growth of these microorganisms in macrophages. Genes involved in controlling internalization of Fe in macrophages were differently expressed in infected compared to uninfected control cultures. It was also observed that the expression of these genes varies with the time of infection and treatment with iron, showing that there is an effort of host cell to contain the infection. No significant variation was observed onto the iron dosage in the supernatant of infected compared to control cultures and the growth of mycobacteria inside macrophages did not vary significantly between treatments. Thus, this study contributed to the clarification of the macrophage response to infection with mycobacteria that have distinct virulence profile among themselves and the interaction of the iron in this disease process.

BCG é uma das vacinas mais usadas no mundo. Avanços na manipulação genética têm permitido o seu uso como carreador de antígenos heterólogos, porém o aprimoramento dos sistemas de expressão se faz necessário, sendo o promotor um importante elemento, uma vez que regula o nível de produção do antígeno, induzindo uma resposta imunológica adequada. Avaliamos a atividade de diferentes promotores de micobactérias, como o PAg, PAN, PBlaF*, Phsp60 e um promotor ainda não caracterizado do micobacteriófago L5, usando o gene gfp como repórter da expressão, todos clonados no vetor extracromossomal, pLA71. Foi possível avaliar as cepas de M. smegmatis e BCG fluorescentes para quase todas as construções e alguns plasmídeos pLA71-p mostraram características diferentes dependentes da micobactéria transformada. Numa escala de força de expressão, os diferentes promotores se apresentaram como fraco (pLA71-PAN-gfp), médio (pLA71-PBlaf*-gfp) e forte (pLA71-Phsp60-gfp). Os rBCG foram usados para infecção de macrófagos e a atividade dos promotores não foi afetada após a internalização. Para ensaio de localização, camundongos foram inoculados com BCG e foi possível confirmar a presença de colônias (recombinantes ou não) nos pulmões após 1 e 3 dias de inoculação, por plaqueamento em meio sólido e por microscopia confocal. / BCG is one of the most widely used vaccines in the world. Advances in genetic manipulation have allowed their use as a carrier for heterologous antigens, however the improvement of systems of expression is necessary, the promoter being an important element, since it regulates the expression level of the antigen, inducing an adequate immune response. We evaluated the activity of different promoters of mycobacteria, such as PAg, PAN, PBlaF* and Phsp60, and the not yet characterized promoter of the micobacteriophage L5, using GFP as a reporter gene expression activity, all cloned in the extrachromosomal vector, pLA71. It was possible to evaluate promoters in the M. smegmatis and BCG strains, fluorescent for almost all constructions and some pLA71-p plasmids showed different characteristics dependent on the transformed mycobacterium. The different promoters showed expression levels as weak (pLA71-PAN-gfp), medium (pLA71-PBlaf*-gfp) and strong (pLA71-Phsp60-gfp). The rBCG were used for infection of macrophages and the activity of the promoters wasnt affected after internalization. For BCG location test, mice were inoculated and it was possible to confirm the presence of colonies (recombinant or not) in the lungs after 1 and 3 days after inoculation by plating on solid medium and by confocal microscopy.

A Tuberculose vem acometendo animais selvagens desde o surgimento das primeiras coleções organizadas. Particularmente, macacos são altamente suscetíveis as micobactérias, gerando grandes perdas econômicas para as instituições, além do risco de transmissão para o homem e animais. As principais micobatérias, que causam a doença em primatas em cativeiro, são o Mycobacterium tuberculosis e Mycobacterium bovis. Acredita-se que primatas do "novo mundo" são menos suscetíveis do que os do "velho mundo", entretanto observa-se que tuberculose tem sido documentada em várias espécies. A principal forma de transmissão é através de aerossóis contendo os bacilos. A doença pode evoluir para a forma ativa ou latente, dependendo do estado imunológico do animal. Os sinais clínicos podem ser insidiosos, com somente uma alteração comportamental, seguido por anorexia e letargia, alterações respiratórias ou simplesmente o animal pode aparecer morto no recinto. O diagnóstico clínico é difícil e problemático, sendo que muitas vezes as lesões consistentes com a doença só são observadas na necropsia. Por isso o uso de outras ferramentas de diagnóstico é importante, como o teste de tuberculinização, cultivo e isolamento bacteriano, que são os mais usados na rotina das instituições, e os exames radiográficos do tórax e abdômen, testes moleculares e sorológicos. Toda instituição que mantém primatas em cativeiro deveriam possuir programas de prevenção para evitar a entrada da micobactéria dentro da coleção, principalmente ao se adquirir novos animais. Por isso, o emprego de medidas de biossegurança é essencial para diminuir o risco de doenças para o homem e para os animais dentro das instituições. Essas medidas consistem na implantação de uma série de procedimentos e normas operacionais rígidas, como programas de quarentena, programas de saúde para os funcionários e formação de equipe capacitada e treinada. / Tuberculosis has been affecting wild animals since the arising of the first organized collections. Specially, monkeys are highly susceptible to mycobacteria, which cause great economic losses in the institutions, beyond the risk of transmission to man and animals. The main species of mycobacteria, that cause disease in nonhuman primates in captivity, are Mycobacerium tuberculosis and Mycobacterium bovis. It is believed that nonhuman primates from the "new world" are less susceptible than the "old world" ones, however it is noted that tuberculosis has been continually documented in several species. Aerosols that contain infectious bacilli are the main transmission mode. The disease can progress to active or latent form, which depends on the animal's immune status. The clinical signs can be insidious, with only a behavior change, followed by anorexia and lethargy, respiratory alteration or the animal can appear dead in the room. The clinical diagnostic is difficult and problematic, and often lesions are only observed at necropsy. Therefore, the use of other diagnostic tools is important, as the tuberculin skin test, bacterial culture and isolation, that are most used during the routine of institutions, and radiography of the chest and abdomen, molecular and serological tests. Every institution that maintains nonhuman primates in captivity should have prevention programs to avoid the entry of mycobacteria inside of collection, mainly when new animals are acquired. Thus, the use of biosecurity measures is essential to reduce the risk of disease in humans and animals within institutions. These measures consist in implanting series of rigid procedures and operational standards, like quarantine programs, health programs for employees and formation of the qualified team.

Introdução: A revisão da literatura disponível no PubMed evidencia que há relatos de surtos de infecções por micobactérias de crescimento rápido ocorridos no Brasil, mas não há dados nacionais que permitam orientar o tratamento empírico até que o perfil de sensibilidade e a identificação da espécie estejam disponíveis. Não há estudo nacional com amostragem significativa de M. fortuitum nem tampouco análise da relação clonal entre isolados de vários pontos do território nacional. Este trabalho pretende trazer contribuições quanto ao entendimento da disseminação de clones de M. fortuitum no Brasil, assim como o perfil de sensibilidade dessa espécie no Brasil. Material e métodos: Foram utilizadas no estudo 121 isolados pertencentes ao banco de micobactérias do Fleury Medicina e Saúde, referentes ao período de janeiro de 2001 a dezembro de 2010. A identificação da espécie for determinada por sequenciamento parcial do gene rpoB, a clonalidade foi avaliada por eletroforese em campos alternados e a susceptibilidade antimicrobiana foi avaliada utilizando-se placas de microdiluição RAPMYCOI. Resultados e conclusões: Foram detectados três grupos clonais, sendo dois presentes na cidade de Campinas e o terceiro na cidade de Florianópolis. Foi observada a persistência do grupo clonal MFBRA2 na cidade de Campinas por seis anos. A maioria dos casos isolados em diferentes estados brasileiros pertence a grupos clonais distintos. O índice de similaridade de Dice mínimo para a identificação de um grupo clonal de M. fortuitum ao analisar fragmentos de restrição gerados por XbaI deve ser de 98%. Todos os isolados testados foram sensíveis à amicacina, tigeciclina, imipenem, ciprofloxacina, moxifloxacina, sulfametoxazol-trimetoprim e linezolida, o que permite seu uso no tratamento empírico das infecções por M. fortuitum. Houve uma baixa taxa de sensibilidade à doxiciclina o que não subsidia seu uso em tratamento empírico. A taxa de sensibilidade de 89% para claritromicina não permite seu uso empírico no tratamento das infecções por M. fortuitum. / Introduction: The literature available on PubMed shows that there are reports of outbreaks of infections caused by rapidly growing mycobacteria occurred in Brazil, but there is no national data to guide empiric treatment until the susceptibility profile and identification of the species are available. No national study of significant sample of M. fortuitum nor analysis of the clonal relationship between isolates from various parts of the country. This work aims to bring contributions to the understanding of the spread of clones of M. fortuitum in Brazil, as well as the susceptibility pattern of this species in Brazil. Material and methods: We studied 121 isolates belonging to the mycobacteria collection from Fleury Medicina e Saúde, collected during the period from January 2001 to December 2010. Species identification was determined by partial sequencing of the rpoB gene, clonality was assessed by pulsed field gel electrophoresis and antimicrobial susceptibility was assessed using microdilution plates RAPMYCOI. Results and conclusions: There were three clonal groups, with two present in the city of Campinas and the third in Florianopolis. We observed the persistence of the clonal group MFBRA2 in Campinas for six years. Most cases isolated in different Brazilian states belong to different clonal groups. Our data indicate that Dice\'s similarity index for identification of a M. fortuitum clonal group should be at least 98% when analyzing restriction fragments generated by XbaI. All isolates tested were susceptible to amikacin, tigecycline, imipenem, ciprofloxacin, moxifloxacin, linezolid, and trimethoprim-sulfamethoxazole, which allows its use in the empirical treatment of infections caused by M. fortuitum. There was a low sensitivity to doxicycline which does not subsidize its use in empiric treatment. The rate of 89% sensitivity does not allow the empirical use of clarithromycin in the treatment of infections caused by M. fortuitum.