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.

A tuberculose bovina (bTB) é um problema sanitário importante em Moçambique e ainda a espera de uma ação organizada por parte dos Serviços Veterinários Oficiais. O presente estudo teve por objetivo investigar e mapear os genótipos de Mycobacterium bovis circulantes no país e paralelamente maximizar a utilização de abatedouros como fonte de informação epidemiológica da bTB. Durante o período de outubro de 2016 a abril de 2017 foram colhidas um total de 90 amostras de lesões sugestivas de tuberculose bovina nos abatedouros Municipais de Maputo e Maxixe e dois abatedouros privados da província de Maputo. Essas amostras, juntamente com outras 10, disponibilizadas pelo Laboratório Central de Veterinária e 72 do banco de amostras de Faculdade de Veterinária de Moçambique foram processadas para isolamento, identificação e discriminação molecular (MIRU-VNTR e spoligotyping) de micobactérias. Nos abatedouros foram coletados dados para calcular as prevalências de carcaças com lesões sugestivas de tuberculose e foi estimada em 0,63% e 80% das carcaças condenadas por tuberculose apresentaram lesões compatíveis com generalização da infecção. Foram obtidos 104 isolados identificados como gênero Mycobacterium, dos quais 80 foram compatíveis com o MTBC e 10 MNT. Destes 80 MTBC, 70 foram identificados como M. bovis. O MIRU-VNTR discriminou os 70 isolados de M. bovis em 47 perfis, agrupados em 3 complexos clonais e cinco singletons. Dos 24 loci estudados, os que apresentaram maiores polimorfismos foram MIRU 960, 2996 e QUB-4052. Em relação ao spoligotyping, foram identificados cinco perfis, dos quais o mais prevalente foi o SB0961, seguido do SB0140, SB2306, SB2481 (novo) e SB1099. Dos 70 isolados submetidos a análises dos complexos clonais africano 1, africano 2, europeu 1 e europeu 2, foram detectados apenas 18,5% de europeu. O distrito de Machanga foi o que apresentou maior diversidade de isolados e o Govuro maior número de isolados de M. bovis. Quando comparados as técnicas, o MIRU-VNTR apresentou maior poder de discriminação em relação ao spoligotyping. O complexo clonal europeu 1 está relacionado com o SB0140 que por sua vez é característico de isolados do Reino Unido e de países que tiveram trocas comerciais de bovinos com o país, incluindo os circunvizinhos a Moçambique e de onde há registros da importação de animais para Moçambique. A não identificação precisa dos complexos clonais dos spoligotyping SB0961, SB2306, SB2481 relacionados, podem ser derivados do BCG, que é sugestivo de evolução clonal própria de Moçambique e os complexos clonais até hoje existentes não são suficientes para discriminar os isolados de Moçambique. Embora os dados de abatedouros sugeriram que a prevalência da tuberculose bovina em Moçambique está entre as mais baixas dos países africanos, a predominância de carcaças com lesões generalizadas significa alto risco de exposição de animais e humanos, sobretudo das populações rurais que têm estreito contato com esses animais. Esse risco é ampliado em função da alta prevalência de humanos que vivem com HIV/AIDS no país. Assim, recomenda-se que Moçambique estruture programa de controle da doença nos animais e métodos de diagnóstico que detectem a infecção por M. bovis na população humana. / Bovine tuberculosis (bTB) is a major sanitary problem in Mozambique and awaits organized action by the Official Veterinary Services. The aim of this work was to investigate and map the circulating Mycobacterium bovis genotypes in the country and to maximize the use of slaughterhouses as a source of epidemiological information for bTB. During the period from October 2016 to April 2017, a total of 90 samples with lesions suggestive of bovine tuberculosis were collected from Maputo and Maxixe Municipal abattoirs and two private abattoirs from the province of Maputo. These samples, together with 10 others provided by the Central Veterinary Laboratory and 72 from the Veterinary Faculty sample bank were processed for isolation, identification and molecular discrimination (MIRU-VNTR and spoligotyping) of mycobacteria. Samples collected in the slaughterhouses were analyzed by calculating the prevalence of carcasses with lesions suggestive of bTB, which was estimated at 0.63% and 80% of carcasses condemned for tuberculosis presented lesions compatible with generalized infection. A total of 104 isolates were identified as M. bovis as Mycobacterium genus were obtained, of which 80 were compatible with MTBC and 10 MNT. Of these 80 MTBC, 70 were identified as M. bovis. The MIRU-VNTR discriminated the 70 isolates of M. bovis in 47 profiles, grouped in 3 clonal complexes and 5 singletons. Of the 24 loci studied, the ones with the highest polymorphisms were MIRU 960, 2996 and QUB-4052. In relation to spoligotyping, five profiles were identified; SB0961 was the most prevalent, being SB0961, followed by SB0140, SB2306, SB2481 (new) and SB1099. Of the 70 isolates submitted to analyzes of the clonal complexes African 1, African 2, European 1 and European 2, only 18.5% of European complex were detected. Machanga district presented the greatest diversity of isolates, while Govuro district had largest number of isolates of M. bovis. The MIRU-VNTR presented greater power of discrimination in relation to spoligotyping. The European clonal complex 1 was related to SB0140 which in turn is characteristic of isolates from the United Kingdom and from countries that have had commercial trade in cattle with UK including those surrounding Mozambique and where there are records of imports of animals for Mozambique. The precise identification of the clonal complexes of the SB0961, SB2306 and SB2481 related spoligotypings subject to the BCG derivatives, is suggestive of the clonal evolution of Mozambique and that the clonal complexes to date are not sufficient to discriminate against the isolates from Mozambique. Although data from slaughterhouses suggested that the prevalence of bovine tuberculosis in Mozambique is among the lowest in African countries, the predominance of carcasses with generalized lesions means a high risk of animal and human exposure, especially of rural populations that have close contact with these animals. This risk is amplified due to the high prevalence of people that living with HIV/AIDS in the country. Thus, it is recommended that Mozambique structure a disease control program in animals and diagnostic methods that detect M. bovis infection in the human population.

INTRODUÇÃO: A tuberculose é um problema grave de saúde pública, acometendo indivíduos em todas as faixas etárias e em todos os estratos socioeconômicos. Apesar de estarem sob grande risco de adoecimento, as crianças carecem de meios diagnósticos sensíveis e específicos. Neste estudo avaliou-se em crianças a acurácia de um teste baseado na dosagem de interferon-gama liberado por linfócitos após estímulo com antígenos específicos do Mycobacterium tuberculosis (QuantiFERON-TB Gold In Tube® [Cellestis, Carnegie, Austrália] ).MÉTODO: Foram incluídas no estudo 184 crianças não infectadas e 11 crianças com infecção pelo Mycobacterium tuberculosis. Todas as crianças receberam previamente o BCG. Foram excluídas crianças com comprometimento do sistema imunológico. Obteve-se amostra de sangue de cada criança, e o material foi processado conforme as instruções do laboratório fabricante. O desempenho do teste foi avaliado pela construção de uma curva de características operacionais (ROC). RESULTADOS: Do total de 184 crianças sem infecção pela micobatéria, 74 (40,2%) eram do sexo feminino, e 130 (70,6%) tinham menos de quatro anos de idade. A idade média neste grupo foi de 35 meses. Seis (3,2%) crianças apresentaram resultado indeterminado do teste, uma criança (0,5%) apresentou um resultado positivo e 177 (96,2%) apresentaram resultado negativo. No grupo de 11 crianças infectadas, sete (63,0%) eram meninas, e a idade média era de 58,5 meses. Duas (18,0%) crianças neste grupo apresentaram resultado negativo do teste. A curva ROC obtida evidenciou uma área sob a curva de 0,876 (I. C 95% - 0,82 a 0,92; p<0,001), refletindo o desempenho preditivo elevado do teste. A sensibilidade do teste foi de 81,8% (IC 95% - 48,2% a 97,2%) e a especificidade de 98,8% (IC 95% - 96,0 a 99,8%), o valor preditivo positivo foi de 81,8% (IC 95%: 46,3% a 97,4%) e o valor preditivo negativo foi de 98,9% (IC 95%: 96,0% a 99,8%). CONCLUSÕES: Neste estudo o teste mostrou ter uma boa acurácia no diagnóstico da infecção pelo Mycobaterium tuberculosis em crianças previamente vacinadas com o BCG, e sua utilização rotineira pode contribuir para a melhor avaliação de crianças expostas a um doente bacilífero e na tomada de decisões sobre a introdução de quimioprofilaxia ou tratamento. / BACKGROUND: Tuberculosis is a major public health problem, affecting people from all ages and diverse socioeconomic incomes. Despite the high risk that children have to develop the disease, accurate methods for diagnosis are not yet available. In this study the accuracy of an interferon-gamma release assay (QuantiFERON-TB Gold In Tube® [Cellestis, Carnegie, Australia]) was evaluated for the diagnosis of Mycobacterium tuberculosis infection in children. METHODS: 195 children were evaluated, 184 children without mycobacterial infection, and 11 children infected by the Mycobacterium tuberculosis. All the children had been previously vaccinated with BCG. Immunocompromised children were excluded from the study. A blood sample was obtained from each child, and it was processed according the manufacturer´s instructions. The performance of the assay was evaluated by a receiver operating characteristic (ROC) curve. RESULTS: In the group of 184 noninfected children, 74 (40.2%) were female and 130 (70.6%) were younger than four years old. The mean age in this group was 35 months. Six children (3.2%) had indeterminate test result, one child (0.5%) had a positive test result, and 177 (96.2%) children had negative test results. In the group of 11 infected children, seven (63.0%) were female, and the mean age in this group was 58.5 months. Two children (18.0%) in this group had a negative test result. The ROC curve determined an area under the curve of 0.876 (95% CI 0.82 to 0.92; p< 0.001), disclosing a high positive predictive value for the test. The assay sensibility was 81.8% (95% CI, 48.2% to 97.2%) and the assay specificity was 98.8% (95% CI, 96.0% to 99.8%), the positive predictive value was 81.8% (95% CI: 46.3% to 97.4%) and the negative predictive value was 98.9% (95% CI: 96.0% to 99.8%). CONCLUSIONS: In this study, the accuracy of the assay was high for the diagnosis of Mycobacterium tuberculosis infection in children previously vaccinated with BCG. The use of this assay for the routine evaluation of children exposed to the disease may help physicians to decide on whether to start chemoprophylaxis or tuberculosis treatment.

A biodiversidade de microrganismos encontrados nos ecossistemas constitui excelentes fontes para a descoberta de moléculas farmacologicamente ativas. Neste estudo, 32 isolados de actinobactérias coletadas do solo e 51 isolados de fungos de manguezais da costa brasileira foram avaliados quanto à ação antifúngica, antimicobacteriana, leishmanicida e tripanossomicida. Extratos orgânicos obtidos a partir do sobrenadante da cultura dos isolados foram testados e cinco apresentaram concentrações inibitórias mínimas iguais ou inferiores a 400 mg/mL sobre fungos patogênicos e dois demonstraram expressiva ação contra a forma tripomastigota de Trypanosoma cruzi. Para a forma promastigota de Leishmania amazonensis e Mycobacterium tuberculosis H37Rv, os extratos não foram efetivos. Os resultados indicam que fungos isolados de manguezais representam boas perspectivas na investigação de novos agentes antimicrobianos. / The biodiversity of microorganisms found in the ecosystems provide excellent perspectives for the discovery of pharmacologically active molecules. In this study, 32 actinobacteria from the soil and 51 fungi from the mangrove swamps of the Brazilian coast were analyzed with respect to their antifungal, antimycobacterial, leishmanicidal and trypanocidal actions. Organic extracts from the supernatant of the culture of the microorganisms were analyzed and five extracts presented MICs equal or less than 400 mg/mL over the pathogenic fungi and two presented significant action against the trypomastigote of Trypanosoma cruzi. The results indicate that fungi from mangrove swamps present promising perspectives for the research of new antimicrobial agents.

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

Apesar da incidência per capita da tuberculose (TB) ter se mantido estável em 2005, o número de novos casos que surgem a cada ano continua a aumentar no mundo todo. De acordo com a Organização Mundial de Saúde, foram estimados 9,4 milhões de novos casos de TB em 2008, dos quais 1,4 milhões eram HIV - positivos, e com 1,8 milhões de mortes - o equivalente a 4.500 mortes por dia. Fatores como migração, privação sócio-econômica, co-infecção TB-HIV e o aparecimento de cepas resistentes contribuíram para o aumento do número de casos de TB no mundo, principalmente nos países onde a TB já foi considerada erradicada, e criaram a necessidade do desenvolvimento de novas terapêuticas. Alvos moleculares específicos, que são essenciais para o patógeno, e ausentes no hospedeiro, como as enzimas da via do ácido chiquímico são alvos atraentes para o desenvolvimento de novas drogas antituberculose. Essa via leva à síntese de compostos aromáticos, como aminoácidos aromáticos, e é encontrada em plantas, fungos, bactérias e parasitas do phylum Apicomplexa, mas está ausente em humanos. No ano de 2000, foi comprovada a essencialidade dessa via para a viabilidade do bacilo, tornando todas essas enzimas alvos validados para estudo. A segunda enzima da via, deidroquinato sintase (DHQS), catalisa a conversão de 3-deoxi-D-arabino heptulosonato-7-fosfato em 3-deidroquinato, o primeiro composto cíclico. Neste trabalho, são descritos o requerimento de metais divalentes na reação e a determinação do mecanismo cinético da DHQS. Os parâmetros cinéticos verdadeiros foram determinados e, juntamente com os experimentos de ligação, o mecanismo rápido-equilíbrio aleatório foi proposto. O tratamento com EDTA aboliu completamente a atividade de DHQS, sendo que a adição de Co+2 e Zn+2 levam a recuperação total e parcial da atividade enzimática, respectivamente. O excesso de Zn+2 inibe a atividade DHQS, e os dados de ITC indicaram a presença de dois sítios seqüenciais de ligação, o que é consistente com a existência de um sítio secundário inibitório. O protocolo de cristalização foi estabelecido e experimentos em andamento proporcionarão a elucidação da estrutura tridimensional da DHQS, que irá beneficiar tanto o desenho de novos inibidores como uma análise detalhada dos rearranjos do domínio da proteína. Em conjunto, estes resultados representam um passo essencial para o desenho racional de inibidores específicos que podem fornecer uma alternativa promissora para um novo, eficaz, e mais curto de tratamento para TB. / Although the estimated per capita tuberculosis (TB) incidence was stable in 2005, the number of new cases arising each year is still increasing globally. According with World Health Organization, there were estimated 9.4 million new TB cases in 2008, from which 1.4 million were HIV-positive, with 1.8 million deaths total – equal to 4500 deaths a day. Migration, socio-economic deprivation, HIV co-infection and the emergence of extensively-resistance strains, have all contributed to the increasing number of TB cases worldwide, mainly in countries where it was once considered eradicated, and have created an urgent need for the development of new therapeutics against TB. Specific molecular targets, that are essential to the pathogen, and absent in the host, like the enzymes of the shikimate pathway, are attractive targets to development of new antitubercular drugs. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids and it is found in plant, fungi, bacteria and Apicomplexa parasites, but is absent in humans. In 2000, this pathway was proved to be essential to the viability of the pathogen, which validates all its enzymes as potential targets. The second enzyme of this pathway, dehydroquinate synthase (DHQS), catalyzes the conversion of 3-deoxy-D-arabinoheptulosonate 7-phosphate in 3-dehydroquinate, the first cyclic compound. In this work, we described the metal requirement and kinetic mechanism determination of the dehydroquinate synthase. The determination of the true kinetic parameters was performed, and, in addition to ligand binding experiments, the rapid-equilibrium random mechanism was determined. The treatment with EDTA abolished completely the activity of DHQS, and the addition of Co+2 and Zn+2 leads to full and partial recovery of enzyme activity, respectively. Excess of Zn+2 inhibits the DHQS activity, and the ITC data revealed two sequential binding sites, which is consistent with the existence of a secondary inhibitory site. The crystallization protocol was established and ongoing experiments will provide the three-dimensional structure of mtDHQS, which will benefit both the design of novel inhibitors as well as detailed analysis of domain rearrangements of protein. Taken together, these results represent an essential step for the rational design of specific inhibitors that can provide a promising alternative to a new, effective, and shorter treatment for TB.

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 &le;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&le;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.

Made available in DSpace on 2015-04-22T22:06:30Z (GMT). No. of bitstreams: 1 Kim Vinicius.pdf: 1711922 bytes, checksum: 8cc4a90994011dd026aa6483a81d0384 (MD5) Previous issue date: 2013-11-28 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Exposure to Mycobacterium tuberculosis can trigger three distinct events in the human body, which are: elimination of bacilli; latent infection, where there is infection control, but not its elimination; or development of tuberculosis, when the immune response is insufficient to contain the infection. Undergraduate nursing students can become exposed to these bacteria, due to their curricula activities. The purpose of this study was to identify latent tuberculosis infection and its associated risk factors among undergraduate nursing students according to their college year. This is an epidemiological, cross-sectional, case detection study with primary collection of data on knowledge and situation of latent tuberculosis infection among first and last year undergraduate nursing students from the Federal University of Amazonas and the University of the State of Amazonas in which were conducted test release interferon-gamma (Quantiferon TB Gold in Test) and Tuberculin Test to detect TB infection . Data were analyzed using the Statistical Package program for the Social Sciences in univariate approaches for describing the distribution of variables, and bivariate approaches to identify how variables relate to each other and the associated risk factors within latent tuberculosis infection . The first year students test results showed positive in four cases simultaneously, while the last year students results detected both positive results in a single individual. The total of 38 positive test results was obtained in correspondence to 33 students at both universities. Statistically significant differences were detected between the first and last year students, and the age group with positive result for Tuberculin Test as well as latent infection, use of Tuberculin Test to guide treatment, sharing environments with patients and mandatory reporting of case tuberculosis situation with first or last year students. Data from this study allowed a profile analysis of the students and compared it between the groups of first and last years. We suggest Nursing Schools better preparation for learning more accurately about tuberculosis. / A exposição ao Mycobacterium tuberculosis pode desencadear três eventos distintos no organismo humano, quais sejam: eliminação dos bacilos; infecção latente, onde há controle, mas não eliminação da infecção; ou adoecimento por tuberculose, quando a resposta do sistema imune é insuficiente para conter a infecção. Entre estudantes de enfermagem estas ocorrências são possíveis, visto as situações de contágio aos quais são expostos em atividades curriculares. O objetivo deste trabalho foi identificar infecção latente por tuberculose e seus fatores associados em acadêmicos do curso de graduação em enfermagem, conforme a situação de iniciante ou finalista. Trata-se de um estudo epidemiológico, transversal, de detecção de caso, com coleta primária de dados sobre conhecimentos e situação de infecção latente por tuberculose de acadêmicos iniciantes e finalistas dos cursos de enfermagem da Universidade Federal do Amazonas e da Universidade do Estado do Amazonas, nos quais foram realizados Ensaios de Liberação de Interferon-gama (Quantiferon-TB Gold In Test) e Prova Tuberculínica a fim de detectar infecção por tuberculose. Os dados foram analisados no Programa Statistical Package for the Social Sciences (SPSS) em abordagens univariadas para descrição da distribuição das variáveis, e bivariadas para identificar como as variáveis se relacionam entre si e os fatores associados à infecção latente por tuberculose. Nos estudantes iniciantes, o resultado dos dois exames foi simultaneamente positivo em quatro casos, e nos finalistas detectamos ambos os resultados positivos em um único indivíduo. No total obtivemos 38 exames positivos correspondentes a 33 estudantes de enfermagem, em ambas as instituições. Detectamos diferenças estatisticamente significativas entre as variáveis de situação no curso (iniciante ou finalista) e faixa etária com o resultado positivo de Prova Tuberculínica, bem como infecção latente, uso de Prova Tuberculínica para guiar tratamento, compartilhamento de ambientes com pacientes e notificação compulsória de caso de TB com situação de iniciante ou finalista do curso. Os dados deste estudo permitiram uma análise do perfil dos estudantes e de comparação entre os grupos de iniciantes e finalistas. Sugerimos às escolas de enfermagem melhor preparação para facilitar no processo de aprendizado um conhecimento mais acurado sobre TB.

INTRODUÇÃO: A tuberculose é um problema grave de saúde pública, acometendo indivíduos em todas as faixas etárias e em todos os estratos socioeconômicos. Apesar de estarem sob grande risco de adoecimento, as crianças carecem de meios diagnósticos sensíveis e específicos. Neste estudo avaliou-se em crianças a acurácia de um teste baseado na dosagem de interferon-gama liberado por linfócitos após estímulo com antígenos específicos do Mycobacterium tuberculosis (QuantiFERON-TB Gold In Tube® [Cellestis, Carnegie, Austrália] ).MÉTODO: Foram incluídas no estudo 184 crianças não infectadas e 11 crianças com infecção pelo Mycobacterium tuberculosis. Todas as crianças receberam previamente o BCG. Foram excluídas crianças com comprometimento do sistema imunológico. Obteve-se amostra de sangue de cada criança, e o material foi processado conforme as instruções do laboratório fabricante. O desempenho do teste foi avaliado pela construção de uma curva de características operacionais (ROC). RESULTADOS: Do total de 184 crianças sem infecção pela micobatéria, 74 (40,2%) eram do sexo feminino, e 130 (70,6%) tinham menos de quatro anos de idade. A idade média neste grupo foi de 35 meses. Seis (3,2%) crianças apresentaram resultado indeterminado do teste, uma criança (0,5%) apresentou um resultado positivo e 177 (96,2%) apresentaram resultado negativo. No grupo de 11 crianças infectadas, sete (63,0%) eram meninas, e a idade média era de 58,5 meses. Duas (18,0%) crianças neste grupo apresentaram resultado negativo do teste. A curva ROC obtida evidenciou uma área sob a curva de 0,876 (I. C 95% - 0,82 a 0,92; p<0,001), refletindo o desempenho preditivo elevado do teste. A sensibilidade do teste foi de 81,8% (IC 95% - 48,2% a 97,2%) e a especificidade de 98,8% (IC 95% - 96,0 a 99,8%), o valor preditivo positivo foi de 81,8% (IC 95%: 46,3% a 97,4%) e o valor preditivo negativo foi de 98,9% (IC 95%: 96,0% a 99,8%). CONCLUSÕES: Neste estudo o teste mostrou ter uma boa acurácia no diagnóstico da infecção pelo Mycobaterium tuberculosis em crianças previamente vacinadas com o BCG, e sua utilização rotineira pode contribuir para a melhor avaliação de crianças expostas a um doente bacilífero e na tomada de decisões sobre a introdução de quimioprofilaxia ou tratamento. / BACKGROUND: Tuberculosis is a major public health problem, affecting people from all ages and diverse socioeconomic incomes. Despite the high risk that children have to develop the disease, accurate methods for diagnosis are not yet available. In this study the accuracy of an interferon-gamma release assay (QuantiFERON-TB Gold In Tube® [Cellestis, Carnegie, Australia]) was evaluated for the diagnosis of Mycobacterium tuberculosis infection in children. METHODS: 195 children were evaluated, 184 children without mycobacterial infection, and 11 children infected by the Mycobacterium tuberculosis. All the children had been previously vaccinated with BCG. Immunocompromised children were excluded from the study. A blood sample was obtained from each child, and it was processed according the manufacturer´s instructions. The performance of the assay was evaluated by a receiver operating characteristic (ROC) curve. RESULTS: In the group of 184 noninfected children, 74 (40.2%) were female and 130 (70.6%) were younger than four years old. The mean age in this group was 35 months. Six children (3.2%) had indeterminate test result, one child (0.5%) had a positive test result, and 177 (96.2%) children had negative test results. In the group of 11 infected children, seven (63.0%) were female, and the mean age in this group was 58.5 months. Two children (18.0%) in this group had a negative test result. The ROC curve determined an area under the curve of 0.876 (95% CI 0.82 to 0.92; p< 0.001), disclosing a high positive predictive value for the test. The assay sensibility was 81.8% (95% CI, 48.2% to 97.2%) and the assay specificity was 98.8% (95% CI, 96.0% to 99.8%), the positive predictive value was 81.8% (95% CI: 46.3% to 97.4%) and the negative predictive value was 98.9% (95% CI: 96.0% to 99.8%). CONCLUSIONS: In this study, the accuracy of the assay was high for the diagnosis of Mycobacterium tuberculosis infection in children previously vaccinated with BCG. The use of this assay for the routine evaluation of children exposed to the disease may help physicians to decide on whether to start chemoprophylaxis or tuberculosis treatment.

Homologous recombination is a fundamental cellular process evolved to maintain genomic integrity and to generate genetic diversity. It plays a crucial role in DNA repair, correct segregation of meiotic chromosomes and resumption of the stalled replication forks. In vitro, the homologous recombination pathway is kinetically separable into a four step process involving initiation, homologous pairing, branch migration and junction resolution. The process of pairing and strand exchange between two homologous double-stranded DNA molecules leads to the formation of an intermediate structure called the Holliday junction (HJ). The crucial enzyme involved in this step in bacteria is RecA. In eubacteria, the junction is processed by three proteins, collectively referred to as the RuvABC protein complex. RuvA binds to the HJ, while RuvB, a helicase, binds to the RuvA-HJ complex and pumps the duplex DNA thus facilitating branch migration. The work reported here is concerned with structural studies on mycobacterial RecA and RuvA. X-ray crystallography was used to solve the protein crystal structures. The hanging drop vapour diffusion method was used for crystallization in all cases. X-ray intensity data were collected on a MAR Research imaging plate mounted on a Rigaku RU200 X-ray generator except for two data sets collected using synchrotron radiation. The data were processed mostly using Mosflm and Scala and few data sets were processed using the HKL program suite. The molecular replacement method using programs Phaser and AMoRe was used for structure solution. Structure refinements were carried out using programs CNS and PHENIX. Model building was performed using COOT and O. PROCHECK, MOLPROBITY, ALIGN and NACCESS were used for structure validation and analysis of the refined structures. Mycobacterium smegmatis RecA (MsRecA) and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals discussed in the earlier part of the thesis and the five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P61. They include one obtained by reducing the relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 61 screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported in the case of E.coli RecA, the variation in the pitch among the three forms correlate well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C-domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue Gln 196, which is believed to provide the trigger for transmitting the effect of nucleotide-binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue, in a way similar to that caused by nucleotide-binding. The ordering of the DNA-binding loops L1 and L2, which present an ensemble of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide-binding presumably on account of the movement of the switch residue which forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications to intermolecular communications within the RecA filament. The structures resulting from different orientations of the C-domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA molecule at different phases of activity and provide insights into the mechanism of action of RecA. Crystal structures of mutants of MsRecA involving changes of Gln 196 from glutamine to alanine, asparagine and glutamic acid, wild type MsRecA and several of their nucleotide complexes were subsequently determined using mostly low temperature and partly room temperature X-ray data. At both the temperatures, nucleotide binding results in a movement of Gln 196 towards the bound nucleotide in the wild type protein. This movement is abolished in the mutants, thus establishing the structural basis for the triggering action of the residue in terms of the size, shape and the chemical nature of the side chain. The 25 crystal structures reported in this thesis, along with the 5 MsRecA structures reported earlier, provide further elaboration of the relation among the pitch of the `inactive´ RecA filament, the orientation of the C-terminal domain with respect to the main domain and the location of the switch residue. The low temperature structures define one extreme of the range of positions the C-domain can occupy. The movement of the C-domain is correlated to those of the LexA binding loop and the loop that connects the main and the N-terminal domains. These elements of molecular plasticity are made use of in the transition to the `active´ filament, as evidenced by the recently reported structures of RecA-DNA complexes. The available structures of RecA resulting from X-ray and electron microscopic studies appear to represent different stages in the trajectory of the allosteric transformations of the RecA filament. This work contributes to the description of the early stages of this trajectory and provides insights into structures relevant to the later stages. The interesting results observed in the case of MsRecA prompted similar studies on the RecA from Mycobacterium tuberculosis (MtRecA). In this study, the crystals were grown at slightly different conditions and examined at different relative humidities and temperatures. Surprisingly, in spite of the 92% sequence identity between the two proteins, the structures indicated MtRecA to be substantially less plastic than MsRecA. The crystal structures do not provide an obvious explanation for this difference. Further studies are warranted to explain the molecular basis of the difference. RuvA, along with RuvB, is involved in branch migration of heteroduplex DNA in homologous recombination. The structures of four crystal forms of RuvA from Mycobacterium tuberculosis (MtRuvA) have been determined. The RuvB-binding domain is cleaved off in one of them. Detailed models of the complexes of octameric RuvA from different species with the Holliday junction have also been constructed. A thorough examination of the structures determined as part of the doctoral programme and those reported earlier bring to light the hitherto unappreciated role of the RuvB-binding domain in determining inter-domain orientation and oligomerization. These structures also permit an exploration of the interspecies variability of structural features such as oligomerization and the conformation of the loop that carries the acidic pin, in terms of amino acid substitutions. These models emphasize the additional role of the RuvB-binding domain in HJ binding. This role along with its role in oligomerization could have important biological implications. In addition to the work on RecA and RuvA, which forms the body of the thesis, the author was also involved in a structural bioinformatics study in which several carbohydrate binding proteins were probed to identify common minimum principles required for binding mannose, glucose and galactose. The study, presented in an Appendix, identified interactions that were specific to particular sugars, leading to individual fingerprints. These fingerprints were then used for exploring lead compounds, using a fragment based approach. This investigation helped the author to familiarize himself with the analysis of protein structures and ligand design based on them.