Mycobacterium abscessus is an emerging pathogen with infections increasing worldwide, especially among Cystic Fibrosis (CF) patients. During my PhD, I studied key aspects of the biology of M. abscessus spp.; particularly, I studied host-pathogen interactions, antimicrobial resistance mechanisms, and genetic determinants of virulence. First, I performed phenotypic characterization of M. abscessus spp. clinical isolates obtained from CF patients classified according to subspecies and clustering. I found clustered isolates, representing probable transmission events, were phenotypically distinct from sporadic isolates and showed adaptation phenotypes associated with chronic lung infection, such as enhanced intracellular survival, increased antibiotic resistance, and metabolic adaptations to the host environment. Second, I assessed the role of an inserted element containing an active methyltransferase in M. a. massiliense. Infection experiments with an isolate containing the inserted element (BIR1049wt) and a knockout strain (BIR1049Δ1809078_1815649) showed decreased survival of BIR1049Δ1809078_1815649 within macrophages. RNAseq analysis showed a distinct gene expression pattern between both isolates, with a number of mycobacterial virulence factors upregulated in BIR1049wt. Third, I studied heritable non-mutational antibiotic resistance mechanisms in M. abscessus to linezolid and clofazimine. For both antibiotics, I found clonal isolates of M. abscessus spp. with varying susceptibilities and different gene expression patterns, suggesting transcriptional regulation of antibiotic resistance. Mutation- mediated resistance to clofazimine was also found due to mutations in two transcriptional regulators predicted to regulate efflux pumps. Last, I evaluated the potential of repurposing a kinase inhibitor (compound H) in clinical trials for the treatment of cancer and CF, to treat M. abscessus infection. I found compound H enhanced killing of intracellular M. abscessus in macrophages through stimulation of autophagy and lysosomal function. I further studied over 60 chemical analogues of compound H in order to find a more active and specific compound for M. abscessus infection.

A tuberculose (TB) é uma doença infectocontagiosa causada pelo bacilo 288 Mycobacterium tuberculosis, a qual ocupa a segunda posição mundial entre 289 causas de mortes por um único agente infeccioso. O desenvolvimento da 290 imunidade protetora e o controle da infecção por M. tuberculosis são amplamente 291 atribuídos a função desempenhada por citocinas pró e anti-inflamatórias. No 292 entanto, 90-95% dos indivíduos infectados com o bacilo conseguem conter ou 293 eliminar a infecção enquanto o restante desenvolve a TB ativa. As razões pelas 294 quais 5-10% dos indivíduos com competência imunológica completa são 295 suscetíveis `a TB ainda permanecem desconhecidas. Porém, nas últimas 296 décadas, estudos epidemiológicos têm trazido fortes evidências de que 297 componentes genéticos humanos contribuem significativamente para essa 298 interindividual variabilidade na suscetibilidade `a TB. Assim, o objetivo deste 299 trabalho foi avaliar a influência dos polimorfismos IL2 -330 T>G (rs2069762); IL4 -300 590 C>T (rs2243250); IL6 -174 G>C (rs1800795); IL10 -592 A>C (rs1800872); 301 IL10 -1082 G>G (rs1800896); IL17A -692 C>T (rs8193036); IL17A -197 G>A 302 (rs2275913); TNF -238 G>A (rs361525); TNF -308 G>A (rs1800629) e IFNG +874 303 T>A (rs2430561) localizados em genes de citocinas na suscetibilidade ao 304 desenvolvimento da tuberculose pulmonar (TBP) em uma população de adultos 305 do sul do Brasil.Os resultados obtidos sugerem fortemente um papel protetor para 306 os polimorfismo IL17A -197G>A (rs2275913) e IL6-174 G>C (rs1800795) no 307 desenvolvimento da TBP nessa população. O efeito protetor foi atribuído ao alelo 308 IL17A-197A (OR=0.29; p=0.04), genótipo AA (OR=0.12; p=0.04) e portadores do 309 alelo A (AG/AA) (OR=0.29; p=0.004). Da mesma forma, o polimorfismo IL6-310 174G>C mostrou ter um efeito protetor no desenvolvimento da TBP em 311 portadores do alelo C (CC/CG) (OR= 0.46; p=0.04). Ambos os polimorfismos 312 mantiveram a significância estatística após a correção usando o teste FDR. Os 313 demais polimorfismos avaliados não mostraram evidências que suportem 314 associação ao desenvolvimento da TBP em adultos nesta população. Os 315 polimorfismos IL17A -692 C>T (rs8193036) e IFNG +874 T>A (rs2430561) foram excluídos das análises porque não estavam em equilíbrio de Hardy-Weinberg. Em 317 conclusão, este trabalho identificou pela primeira vez na população do sul do 318 Brasil um efeito protetor dos polimorfismo IL17A -197 G>A e IL6 -174 G>C no 319 desenvolvimento da TBP em adultos. Esses resultados indicam o papel 320 importante para as citocinas pro-inflamatórias IL17A e IL6 na imunofisiologia da 321 TB. / Tuberculosis is an infectious disease caused by Mycobacterium 340 tuberculosis bacillus, which ranks second worldwide position among causes of 341 deaths from a single infectious agent. The development of protective immunity and 342 control of infection by M. tuberculosis are largely attributed to the role of pro and 343 anti-inflammatory cytokines. However, 90-95% of individuals infected with bacillus 344 can contain or eliminate the infection while the remainders develop active TB. The 345 reasons why 5-10% of individuals with full immune competence are susceptible to 346 TB remain unknown. However, in recent decades, epidemiological studies have 347 brought strong evidence that human genetic components contribute significantly to 348 this interindividual variability in susceptibility to TB.Thus the aim of this work was 349 to evaluate the influence of polymorphisms IL2 -330 T>G (rs2069762); IL4 -590 350 C>T (rs2243250); IL6 -174 G>C (rs1800795); IL10 -592 A>C (rs1800872); IL10 -351 1082 A>G (rs1800896); IL17A -692 C>T (rs8193036); IL17A -197 G>A 352 (rs2275913); TNF -238 G>A (rs361525); TNF -308 G>A (rs1800629) and IFNG 353 +874 T>A (rs2430561) located in cytokine candidates genes in the susceptibility to 354 development of pulmonary tuberculosis in south Brazil population.The results 355 strongly suggest a protective role for the IL17A -197G > A (rs2275913) and IL6-356 174 G>C polymorphism (rs1800795) in the development of pulmonary 357 tuberculosis in this population. The protective effect was attributed to IL17A -197 358 allele A (OR = 0.29; p = 0:04), AA genotype (OR = 0:12; p = 0:04) and carriers of 359 the A allele (AG / AA) (OR = 0.29; p = 0.004 ). Likewise, the IL6 -174G>C shows 360 an association for C carriers (CC/CG) (OR= 0.46; p=0.04). Both polymorphisms 361 maintained the statistical significance after correction using FDR test. However, no 362 evidence of association was identified for any other polymorphism studied in this 363 population.IL17A polymorphisms -692 C>T (rs8193036) and IFNG +874 T>A 364 (rs2430561) polymorphisms were excluded from the analysis because they were 365 not in Hardy-Weinberg equilibrium. In conclusion, our results identified for the first 366 time in Southern Brazil population a protective role for IL17A -197 G>A and IL6 -367 174 G>C polymorphisms in adult pulmonary tuberculosis development. These results indicate an important role for IL-17A and IL-6 pro-inflammatory cytokines in 369 immunophysiology of tuberculosis.

Mycobacterium tuberculosis, la bactérie causant la tuberculose, est un pathogène d'importance majeure à l'échelle mondiale. Depuis sa découverte en 1882 par Robert Koch, de nombreuses études se sont penchées sur les caractéristiques de cette bactérie et des souches proches, connues sous le nom de complexe Mycobacterium tuberculosis (MTBC). Dans le cadre de ce travail nous avons commencé par nous intéresser à l'espèce proche "Mycobacterium canettii", qui avait été identifiée au milieu du XXème siècle comme étant également capable de causer des cas de tuberculose chez l'Homme, tout en possédant des caractéristiques phénotypiques propres. Par le biais de l'étude de certains marqueurs phylogénétiques, nous avons pu établir que cette bactérie n'appartenait pas au MTBC au sens strict et pouvait donc être utilisée comme point d'ancrage dans le cadre de l'étude de la phylogénie et de l'émergence de ce dernier. C'est pourquoi nous avons choisi d'étudier la diversité de la collection de souches de "Mycobacterium canettii", qui proviennent toutes d'une même région du globe, la Corne de l'Afrique. L'étude de cette collection, construite au fil des ans par le Service de Santé des Armées (SSA), a permis de mettre en évidence l'émergence d'un groupe particulier de souches au sein de cette espèce, ainsi que d'obtenir des éléments permettant de préciser le positionnement du dernier ancêtre commun (MRCA) du MTBC. Du fait de l'origine géographique exclusive de ce taxon, nous avons ensuite décidé d'évaluer la diversité génétique des souches de Mycobacterium tuberculosis provenant de cette même région du globe. Cette seconde partie de l'étude, menée sur une collection à nouveau constituée par le SSA, a conduit à l'identification d'une nouvelle lignée au sein du MTBC, jusqu'alors inconnue. Cette découverte a un impact important sur la compréhension de l'émergence de Mycobacterium tuberculosis, car elle permet d'envisager un nouveau modèle d'apparition en interprétant cette lignée comme le descendant contemporain de l'écotype fondateur du MTBC. L'évolution de Mycobacterium tuberculosis peut ainsi être comprise suivant une progression liant "Mycobacterium canettii", pathogène occasionnel supposé environnemental, et cette nouvelle lignée. Une fois ce nouveau modèle proposé, nous avons tenté de le dater en extrapolant le taux de mutations observé lors d'évènements épidémiques contemporains, ce qui nous a permis de dater le MRCA du MTBC à environ 10 000 ans. Enfin nous avons mis en parallèle ces éléments concrets avec les connaissances paléo-ethnographiques actuelles concernant la Corne de l'Afrique pour proposer un modèle historiquement argumenté permettant d'expliquer la structuration phylogénétique actuelle du MTBC. / Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogen of world-wide impact. Since its discovery in 1882 by Robert Koch many studies have been focusing on the characteristics of this bacterium and of the most closely related strains known as the Mycobacterium tuberculosis complex (MTBC). In this work we started by studying the closest neighbor to the MTBC, the "Mycobacterium canettii" taxon, which is only found in one particular region of the world, the Horn of Africa. It t has been first identified in the middle of the XXth century as being able to cause tuberculosis in humans, but having at the same time peculiar phenotypic characteristics. Through the study of some phylogenetic markers we have been able to establish that this bacterium does not belong to the MTBC sensu stricto and can therefore be used as an outgroup in order to root the phylogeny to study the emergence of the MTBC. The next step was to study the genetic diversity of a collection of strains of "M. canettii",using the “next generation sequencing” (NGS) approach.. The analysis of this collection, built along the years by the French Army Health Service (SSA), has permitted to show the rapid emergence of a particular clone, as well as to get information enabling to precise the position of the most recent common ancestor (MRCA) of the MTBC. Because of the restricted geographic location of this species, it was also decided to assess the genetic diversity of strains of M. tuberculosis coming from the same part of the globe. This second part of the study, performed on a collection of strains also gathered by the SSA, has lead to the identification of a new, previously unknown, lineage of the MTBC. This discovery has a profound impact on the comprehension of the emergence of M. tuberculosis, as it permits to develop a new model of appearance by interpreting this lineage as the founder ecotype of the MTBC. The evolution of M. tuberculosis can therefore by understood along a path linking "M. canettii", opportunistic pathogen supposedly environmental, and this new lineage. After this proposal of a new model, we tried to date it by extrapolating

Made available in DSpace on 2014-06-11T19:31:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-05-29Bitstream added on 2014-06-13T19:40:42Z : No. of bitstreams: 1 pandolfi_jrc_dr_araiq.pdf: 716701 bytes, checksum: 707d1bc6d263e145f12c4e53feeae657 (MD5) / O presente trabalho evidencia os esforços realizados na tentativa de se aperfeiçoar a técnica de MIRU (Mycobacterial Interspersed Repetitive Units). Esta utiliza como marcadores, diferenças em fragmentos de DNA não codificadores específicos do Mycobacterium tuberculosis e vem sendo empregada para o estudo epidemiológico da tuberculose, pela facilidade de execução. A técnica de MIRU possibilita uma comparação entre linhagens de diferentes áreas geográficas e permite o rastreamento da movimentação de linhagens individuais. Na otimização os seguintes parâmetros foram determinados: 1. protocolos de purificação de DNA; 2. estratégias de amplificação pela PCR; 3. comparações entre um kit de PCR (PCR Master Mix - PROMEGA) e a utilização da PCR da maneira convencional; 4. testes de variadas condições de amplificação utilizando o kit e os reagentes convencionais de PCR; 5. determinação de protocolos de ciclagem para a amplificação dos fragmentos desejados; 6. teste de amplificação sem a prévia extração de DNA das amostras utilizadas. Após a padronização a metodologia foi utilizada na tipagem de 82 amostras de M. tuberculosis que se encontravam divididas em dois grupos, sendo o primeiro com 49 amostras, provenientes de pacientes do Serviço Especial de Saúde de Araraquara (SESA - USP, Araraquara) e o segundo, composto de 33 amostras de bactérias com perfil de resistência a pirazinamida e a outras drogas, provenientes de Maringá. Nesta etapa foram realizados: 7. PCR para a confirmação de gênero e espécie para M. tuberculosis nas 82 amostras analisadas. 8. Aplicação da técnica de MIRU e análise manual de todas as amostras provenientes de pacientes; 9. Emprego de ferramentas de bioinformática (programa PAST Paleontological Statistics Software Package for Education and Data Analysis) para a análise das amostras... / The present work shows efforts to improve the MIRU (Mycobacterial Interspersed Repetitive Units) assay. This methodology, that has been exploited for fingerprinting the Mycobacterium tuberculosis in molecular epidemiological studies, allows for direct and reliable comparison of results between laboratories and the development of large-scale epidemiological studies. In the optimization of MIRU assay, some parameters were defined: DNA purification protocols and PCR strategies were compared, to select the most practical and economical among them. After the standartization, 82 M. tuberculosis strains, from two different groups were analised. The 49 bacteria strains from the first group were sensible and the 33 from the second one were resistant to pyrazinamide and another drugs as isoniazide and/or rifampicin. To stablish the allelic studies the samples were first confirmed as M. tuberculosis by PCR. Then the MIRU assay was applied and the genetic profile was determined. These results generated dendrograms, obtained by bioinformatic tools. This study showed that any kind of DNA purification and even the use of fresh bacterial culture directly into the PCR tube can be used. When the PCR strategies were compared the utilization of the PCR kit seemed to be more practical and to avoid some mistakes that can happens during the home-made PCR mixture preparation. Furthermore, it allows some dilutions higher than those recommended by the manufacturer. In the same way, the home-made mixture in amounts smaller than those suggested can be used. These experiments indicated that only two annealing temperatures can be used to the PCR with the twelve primer pairs, always in the same MgCl2 concentration, allowing the amplification of more samples at the same time. To generate dendrograms with the allelic data from clinical samples... (Complete abstract click electronic access below)

Resumo: O objetivo principal deste trabalho consistiu na síntese, caracterização e investigação da atividade biológica de complexos de cobre(II) contendo ligantes pirazólicos {pirazol (HPz), 3,5- dimetilpirazol (HdmPz), 4-iodopirazol (HIPz) e 1-tiocarbamoil-3,5-dimetilpirazol (HtdmPz)} e moléculas biologicamente ativas {pirazinamida (PZA), rifampicina (RMP) e isoniazida (INH)}. Foram preparadas três séries de compostos, a primeira contendo os ligantes pirazólicos e o pseudo-haleto tiocianato: [Cu(NCS)2(HPz)2] (1), Cu(NCS)2(HdmPz)4].5H2O (2), [Cu(NCS)2(HIPz)2] (3); a segunda contendo o ligante 1-tiocarbamoil-3,5-dimetilpirazol: [Cu2(NCS)2(tdmPz)2] (4), [Cu2Cl2(HtdmPz)2] (5), [Cu2Br2(HtdmPz)2] (6); e a terceira série, contendo como ligantes compostos atualmente usados no tratamento da tuberculose: [CuCl2(PZA)2] (7), [Cu(RMP)] (8), [CuCl2(INH)2]n.H2O (9) e [Cu(SO4)(INH)]n (10). Os compostos foram caracterizados por análise elementar, espectroscopia vibracional na região no IV, espectroscopia de absorção eletrônica no UV/Visível e ressonância paramagnética eletrônica. O composto [Cu(NCS)2(HPz)2] (1) teve sua estrutura determinada através da análise cristalográfica via difratometria de raio-X de monocristal. Os complexos de cobre(II) foram submetidos a ensaios de inibição do crescimento do Mycobacterium tuberculosis, agente etiológico da tuberculose humana, linhagem H37Rv ATCC - 27194. Os compostos [Cu2Cl2(HtdmPz)2] (5), [Cu2Br2(HtdmPz)2] (6), [CuCl2(PZA)2] (7), [Cu(RMP)] (8), [CuCl2(INH)2]n.H2O (9) e [Cu(SO4)(INH)]n (10) mostraram ser bastante eficientes na inibição do crescimento dessa micobactéria, uma vez que apresentaram valores de concentração inibitória mínima (CIM) iguais a 3,25; 14; 10; 0,31; 10 e 0,62 μg/mL, respectivamente. Os complexos 7 - 10 mostraram ser muito promissores no tocante a potencialidade de aplicação como drogas antituberculose, uma vez que ...(Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The main objective of this work consisted in the synthesis, spectroscopic characterization and investigation of the biological activity of copper(II) complexes containing pyrazolyl ligands {pyrazole (HPz), 3,5-dimethylpyrazole (HdmPz), 4-iodopyrazole (HIPz) and 3,5-dimethyl-1- thiocarboxamidepyrazole (HtdmPz)} and biological active molecules {pyrazinamide (PZA), rifampicin (RMP) and isoniazid (INH)}. Three series of compounds were prepared, the first one containing pyrazolyl ligands and the pseudohalide thiocyanate: [Cu(NCS)2(HPz)2] (1), Cu(NCS)2(HdmPz)4].5H2O (2), [Cu(NCS)2(HIPz)2] (3); the second series presents the 3,5-dimethyl-1-thiocarboxamidepyrazole ligand: [Cu2(NCS)2(tdmPz)2] (4), [Cu2Cl2(HtdmPz)2] (5), [Cu2Br2(HtdmPz)2] (6); and the third serie, involves compounds currently used in the treatment of the tuberculosis as ligands: [CuCl2(PZA)2] (7), [Cu(RMP)] (8), [CuCl2(INH)2]n.H2O (9) e [Cu(SO4)(INH)]n (10). The compounds were characterized by elemental analysis, infrared spectroscopy, UV-Vis spectroscopy and electron paramagnetic resonance. The compound [Cu(NCS)2(HPz)2] (1) had its structure determined by single crystal X-ray diffraction. The copper(II) complexes were submitted to the assays of inhibition of the growth of the Mycobacterium tuberculosis H37Rv ATCC - 27194. The compounds [Cu2Cl2(HtdmPz)2] (5), [Cu2Br2(HtdmPz)2] (6), [CuCl2(PZA)2] (7), [Cu(RMP)] (8), [CuCl2(INH)2]n.H2O (9) e [Cu(SO4)(INH)]n (10) had shown to be efficient in the inhibition of the growth of this mycobacteria, because showed minimal inhibitory concentration (MIC) values equals to 3,25; 14; 10; 0,31; 10 e 0,62 μg/mL, respectively. The complexes 7 - 10 are promise compounds in relation to the potential application as antituberculosis drugs, because they showed SI (selectivity index) values greater...(Complete abstract click electronic access below) / Orientador: Regina Célia Galvão Frem di Nardo / Coorientador: Antonio Eduardo Mauro / Colaborador: Adelino Vieira de Godoy Neto / Banca: Sérgio Roberto de Andrade Leite / Banca: Roberto Santana da Silva / Mestre

A tuberculose é uma doença infectocontagiosa causada por bactérias do complexo Mycobacterium tuberculosis (MTBC) que afeta humanos e/ou animais. Membros desse complexo evoluíram clonalmente e possuem grande similaridade genômica, diferenciando-se por polimorfismos de nucleotídeo único (SNPs) e regiões de diferença (RDs). Dentre os patógenos da tuberculose em animais, Mycobacterium bovis, causador da tuberculose bovina, é o membro do MTBC de maior importância global. Desta maneira, o presente estudo tem por objetivo o sequenciamento, a anotação e a análise da estirpe brasileira SP38 de M. bovis, seguido da genômica comparativa desse com outros genomas de M. bovis depositados no GenBank. Mycobacterium bovis SP38 apresenta um genoma tradicional de micobactéria tuberculosa, sendo esse único, circular com 4.347.646 pb, alto conteúdo de GC (65,6%) e 4.216 genes, incluindo 154 pseudogenes, 3 genes de rRNA (RNA ribossomal), 45 de tRNA (RNA transportador), 2 de ncRNA (RNA não codificante), 1 tmRNA (RNA transferência-mensageiro) e 4.011 sequências de DNA codificante (CDSs) (NZ_CP015773.1). Dentre as CDSs, a maioria (2.805 - 69,93%) foi anotado com função e 1.206 (30,07%) como hipotéticos. Para a genômica comparativa, os 31 genomas completos ou em drafts de M. bovis depositados no GenBank, 32 genomas de Mycobacterium bovis BCG e 23 genomas de Mycobacterium tuberculosis foram selecionados. Análises in silico dos padrões de RD resultaram na exclusão de três genomas anotados equivocadamente como M. bovis virulentos. A análise de genes ortólogos sugere que M. bovis está sob processo de decay genômico. A quantificação de sítios polimórficos indica uma maior variabilidade genética em números totais (8.335 em M. tuberculosis, 3.448 em M. bovis virulentos, e 1.088 em M. bovis BCGs) e comparações par-a-par (p ≤0,05) de M. tuberculosis em relação a M. bovis virulentos e BCGs, indicando uma maior pressão evolutiva sob M. tuberculosis, contrastando com o fato de que M. bovis é capaz de infectar um maior número de espécies hospedeiras que M. tuberculosis. A maioria desses sítios polimórficos estão localizados em CDSs hipotéticos (31,7% - 51,3%), sendo associados a família gênica PE/PPE, e apresentam uma proporção de mutações não sinônimas crescentes pela ordem M. bovis BCG, M. bovis virulentos e M. tuberculosis (48,90%, 51,92% e 59,52%, respectivamente). Essa menor proporção de mutações não sinônimas e a categorização funcional dissimilar entre CDSs contendo sítios polimórficos, indica que M. bovis BCG está sujeito a diferentes pressões seletivas quando comparado a M. bovis virulentos e M. tuberculosis. Por fim, a análise filogenética baseada em sítios polimórficos indica agrupamentos filogenéticos de M. bovis suportados pela classificação dos Complexos Clonais (CCs) e não por hospedeiros de origem dos isolados, confirmando que sítios polimórficos podem ser utilizados para classificação filogenética de linhagens genéticas desta espécie bacteriana. Além do mais, 2/28 (7,14%) genomas de M. bovis não puderam ser classificados nos CCs atualmente descritos, sugerindo a existência de complexos ainda não determinados. Este estudo representa o primeiro genoma de uma estirpe nacional de M. bovis a ser completamente sequenciado e a primeira análise de genômica comparativa de genomas desta espécie bacteriana. / Tuberculosis is an infectious disease caused by bacteria of the Mycobacterium tuberculosisComplex (MTBC) that affects human beings and/or animals. Members of this complex clonally evolved and have high genomic similarity, differentiated by single nucleotide polymorphisms (SNPs) and regions of difference (RDs). Among the animal tuberculosis pathogens, Mycobacterium bovis, the causative agent of bovine tuberculosis, is the MTBC member of greatest global importance. Therefore, the aim of the present study is to sequence, assemble and annotate the genome of the Brazilian strain SP38 of M. bovis, followed by the comparative genomics with other M. bovis genomes available in GenBank. Mycobacterium bovis SP38 has a traditional mycobacteria genome. It has a single and circular chromosome with 4,347,646 bp, high GC content (65.6%), and 4,216 genes, including 154 pseudogenes, 3 rRNA genes (ribosomal RNA), 45 tRNA (transfer RNA), 2 ncRNA (non-coding RNA), 1 tmRNA (transfer-messenger RNA), and 4,011 coding DNA sequences (CDSs) (NZ_CP015773.1). The majority of CDSs (2,805 - 69,93%) was annotated with function and 1,206 (30,07%) are hypothetical. For the comparative genomics analyses, the 31 genomes (complete and drafts) of M. bovis available in GenBank, 32 Mycobacterium bovis BCG and, 23 of Mycobacterium tuberculosis were chosen. In silico analysis of the RDs patterns resulted in the exclusion of three genomes, mistakenly annotated as virulent M. bovis. Orthologous gene analysis suggests that strains of M. bovis are under genomic decay. The quantification of polymorphic sites indicates the greater variability in absolute numbers (8,335 in M. tuberculosis, 3,448 in virulent M. bovis, and 1,088 in M. bovis BCG) and in pairwise comparisons (p≤0,05) of M. tuberculosis compared to virulent M. bovis and M. bovis BCG, suggesting that M. tuberculosis is under high evolutionary pressure. This is in contrast to the fact that M. bovis is capable of infecting a higher number of host species than M. tuberculosis. Most of these polymorphic sites are located in hypothetical CDSs (31.7% - 52.3%), being associated with PE/PPE family, and demonstrating a nonsynonymous mutations proportion of the following increasing order: M. bovis BCG, virulent M. bovis and M. tuberculosis (48.90%, 51.92% and 59.52%, respectively). This lower proportion of nonsynonymous mutations and the dissimilar functional categorization of CDSs with polymorphic sites indicates that M. bovis BCG is subjected to different selective pressure when compared to virulent M. bovis and M. tuberculosis. Finally, the phylogenetic analysis based on polymorphic sites indicates that the phylogenetic grouping of M. bovis is supported by Clonal Complexes (CCs), and not by the host of M. bovis isolates, confirming that polymorphic sites can be used for phylogenetic classification of genetic lineages of this bacterial species. Furthermore, 2/28 (7.14%) genomes of M. bovis could not be classified in the currently described CCs, suggesting the existence of complexes yet to be determined. This study represents the first genome of a Brazilian strain of M. bovis to be completely sequenced and the first comparative genomic analysis of the genomes of this bacterial species.

O Mycobacterium tuberculosis é intrinsecamente resistente a diversos antimicrobianos. Esta resistência é devida, principalmente, ao envelope hidrofóbico da célula bacteriana que atua como uma barreira efetiva para diversos compostos. Outros determinantes da sua resistência intrínseca incluem enzimas hidrolíticas e bombas de efluxo de drogas. A resistência adquirida em isolados clínicos de M. tuberculosis é principalmente devida a mutações em genes que codificam alvos para os fármacos ou em seus ativadores. Apesar disso, um número entre 5–30% das cepas resistentes não têm caracterizado o seu mecanismo de resistência, considerando-se o sistema de efluxo como uma das possibilidades para esta resistência. O efluxo é o resultado da atividade de proteínas transportadoras envolvidas na extrusão de substâncias (incluindo todas as classes de relevantes antimicrobianos clínicos) de dentro da célula para o meio externo. O principal objetivo deste trabalho foi comparar a Concentração Mínima Inibitória (CMI) em condições de diferentes tratamentos (presença e ausência de inibição do sistema de efluxo) e os resultados obtidos com o seqüenciamento dos genes rpsL e rrs. Para isso foram testados 79 isolados de M. tuberculosis, destes, 43 (54%) isolados apresentaram mutações; 38 (48%) diminuíram a CMI na presença de inibidores do sistema de efluxo, sendo que isso ocorreu tanto em isolados resistentes ou sensíveis, mutados ou não-mutados. Em três isolados resistentes a estreptomicina não foram identificadas alterações nos genes rpsL e rrs e na presença de inibidores do sistema de efluxo a resistência foi diminuída. A diminuição da CMI nesses isolados resistentes, embora sem mutação, indica uma possível participação do sistema de efluxo. Nas cepas mutadas, o mecanismo de efluxo, estaria aumentando a tolerância do isolado à concentração da droga. Estas últimas possuiriam dois mecanismos de resistência atuantes (mutação nos genes alvo do fármaco e superexpressão das proteínas de membrana responsáveis pelo efluxo de drogas). / Mycobacterium tuberculosis is naturally resistant to many antimicrobials. This resistance is due mainly to the hydrophobic cell envelope acting as an effective permeability barrier for many compounds. Other determinants ones of its intrinsic resistance include hydrolytic enzymes and efflux pumps of drugs. The acquired resistance in clinical isolates of M. tuberculosis is mainly due to mutations in genes that encode targets for drugs substances or in their activators. Even so, in 5-30% of the resistant strains the resistance mechanism is not known and the efflux system has been considered as one of the possibilities for this resistance. Efflux is the result of the activity of transport proteins involved in extrusion of substances (including all classes of clinically relevant antimicrobials) from the interior of the cells into the external environment. The main goal of this study is to compare the Minimal Inibitory Concentration (MIC) in different conditions (with or without efflux system inhibitors) and the sequencing data of the rpsL and rrs genes. For that we have analized 79 M. tuberculosis isolates, and from these, 43 (54%) presented mutations; 38 (48%) decreased the MIC in presence of efflux system inhibitors. This decrease in MIC occurred in resistant or sensitive isolates, with or without mutations. Three resistant isolates did not present any mutations in rpsL and rrs genes and in presence of efflux system inhibitors the resistance decreased. The decrease of MIC in these resistant isolates, although without mutation, indicates participation of the efflux system. In the mutated isolates the efflux system could increase the tolerance to drug concentration. In these isolates two resistance mechanisms must be acting (mutation on the drug target genes and over-expression of membrane proteins responsible for the drug efflux).

A Dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. 21 May 2015 / Crystal polymorphism is the capacity of a solid crystalline form to exist in more than one structural arrangement. In the pharmaceutical setting investigations into the polymorphic forms of potential drugs are of vital importance since different crystalline forms can affect bioavailability, mechanical, thermal, and chemical properties. One such example is isonicotinic acid-(1-phenylethylidene) hydrazide (IPH), a derivative of the popular drug isoniazid (used as first line treatment against Mycobacterium tuberculosis) was found to crystallise in six different polymorphic forms. Each crystal structure was determined using X-ray diffraction techniques and including the thermal phase relationships of the polymorphic compound were delineated. In addition to polymorph elucidation, isonicotinic acid-(1-phenylethylidene) hydrazide was modified with –OH and –NH2 at various aromatic positions, creating geometric pyridyl isomers. In-depth studies of these pyridyl isomers revealed a diverse range of supramolecular aggregates. Preliminary thermal screening suggests that only a small selection of these pyridyl isomers present potential polymorphic activity for further study.

No description available.

No description available.