Molecular typing is increasingly essential to tuberculosis (TB) control programmes, providing public health practitioners with a tool to characterize transmission patterns, track the emergence and spread of strains of M. tuberculosis complex (MTC) in populations. While molecular typing is already used extensively as a tool for TB control in many developed settings across the globe, its use in resource-poor settings is still limited. Moreover, information on the role, contribution and burden of nontuberculous mycobacteria (NTM) and other pathogens in aetiology of TB-like syndromes is also lacking in such settings. The broad objective of this dissertation was to determine the genetic diversity of MTC and their drug resistance profiles as well as the prevalence of NTM and other potentially pathogenic bacteria among TB suspects in Northeastern, Tanzania in order to generate insights that may inform the design of a rational TB control programmes. A total of 18 distinct spoligotypes were identified in this study area, with CAS1-KILI and EAI8 being the most predominant families. Major lineages prediction by conformal Bayesian network (CBN) revealed that 70% of TB infections in this area is due to modern lineages, whereas 30% of TB infections is due to the ancestral lineages mainly of Indo-oceanic lineage. The study also revealed that the overall proportions of any drug resistance and MDR-TB were 12.7% and 6.3% respectively. With the prevalence of any drug resistance and MDR-TB among new cases being 11.4% and 4.3% respectively, among previously, treated cases were 22.2%. The prevalence of NTM was found to be 9.7 %, with HIV being a significant predictor of NTM detection (P < 0.001). Four out of 30 patients with NTM diagnosed by culture received 1st line anti-TB treatment suggesting that a proportion of patients diagnosed by smear microscopy (4/65, 6.2%) were mistreated as TB patients. Our findings further showed that 17 (4.6%) out of 372 TB suspects were due to pulmonary nocardiosis. Overall this dissertation has revealed that TB is still a major problem in Tanga and is characterized by a diverse array of MTB strains. Additionally, modern MTB strains contribute significantly to TB infections in this area. High proportions of anti-TB drug resistance among new treated cases observed suggest that more efforts need to be done to identify individual cases at facility level for improved TB control programmes. Inefficient screening of TB patients and a prevalent increase of NTM may contribute to both unrealistic and mismanagement of TB cases. A diverse array of pathogenic Nocardia species among TB suspects further indicates that they are likely cause of human disease in this population. Therefore, need to integrate NTM and pathogens causing TB-like syndromes in diagnosis and management of TB is urgent. Results of these investigations contribute to the understanding of the dynamics of TB transmission in resource poor settings of Tanzania and highlight key factors that should be considered in the development of rational approaches to design effective TB prevention and control programmes in the country.

Molecular typing is increasingly essential to tuberculosis (TB) control programmes, providing public health practitioners with a tool to characterize transmission patterns, track the emergence and spread of strains of M. tuberculosis complex (MTC) in populations. While molecular typing is already used extensively as a tool for TB control in many developed settings across the globe, its use in resource-poor settings is still limited. Moreover, information on the role, contribution and burden of nontuberculous mycobacteria (NTM) and other pathogens in aetiology of TB-like syndromes is also lacking in such settings. The broad objective of this dissertation was to determine the genetic diversity of MTC and their drug resistance profiles as well as the prevalence of NTM and other potentially pathogenic bacteria among TB suspects in Northeastern, Tanzania in order to generate insights that may inform the design of a rational TB control programmes. A total of 18 distinct spoligotypes were identified in this study area, with CAS1-KILI and EAI8 being the most predominant families. Major lineages prediction by conformal Bayesian network (CBN) revealed that 70% of TB infections in this area is due to modern lineages, whereas 30% of TB infections is due to the ancestral lineages mainly of Indo-oceanic lineage. The study also revealed that the overall proportions of any drug resistance and MDR-TB were 12.7% and 6.3% respectively. With the prevalence of any drug resistance and MDR-TB among new cases being 11.4% and 4.3% respectively, among previously, treated cases were 22.2%. The prevalence of NTM was found to be 9.7 %, with HIV being a significant predictor of NTM detection (P < 0.001). Four out of 30 patients with NTM diagnosed by culture received 1st line anti-TB treatment suggesting that a proportion of patients diagnosed by smear microscopy (4/65, 6.2%) were mistreated as TB patients. Our findings further showed that 17 (4.6%) out of 372 TB suspects were due to pulmonary nocardiosis. Overall this dissertation has revealed that TB is still a major problem in Tanga and is characterized by a diverse array of MTB strains. Additionally, modern MTB strains contribute significantly to TB infections in this area. High proportions of anti-TB drug resistance among new treated cases observed suggest that more efforts need to be done to identify individual cases at facility level for improved TB control programmes. Inefficient screening of TB patients and a prevalent increase of NTM may contribute to both unrealistic and mismanagement of TB cases. A diverse array of pathogenic Nocardia species among TB suspects further indicates that they are likely cause of human disease in this population. Therefore, need to integrate NTM and pathogens causing TB-like syndromes in diagnosis and management of TB is urgent. Results of these investigations contribute to the understanding of the dynamics of TB transmission in resource poor settings of Tanzania and highlight key factors that should be considered in the development of rational approaches to design effective TB prevention and control programmes in the country.

Descrição: As doenças causadas por actinomicetos patógenos, aeróbios e anaeróbios facultativos, diferem consideravelmente no que diz respeito à sua etiologia, patogênese, apresentação clínica e epidemiologia. Objetivos: Analisar a distribuição etária, manifestações clínicas, doenças de base e condições associadas, achados radiológicos, microbiológicos, tratamento e evolução, nos pacientes com actinomicetoses (actinomicose, nocardiose, rodococose). Delineamento: Foram analisados, retrospectivamente, prontuários de pacientes com achados microbiológicos positivos para infecções por actinomicetos. Local do estudo: Um hospital universitário de atendimento terciário em Porto Alegre, Rio Grande do Sul, Brasil. Pacientes e métodos: Foram incluídos neste estudo, pacientes com diagnóstico de actinomicose, nocardiose e rodococose, num período de 1978 a 2009. Os critérios microscópicos para o diagnóstico de actinomicetose foram os seguintes: actinomicose - composto por grânulos actinomicóticos, filamentos Gram-positivos, não ácido-resistentes; nocardiose - bactérias filamentosas ramificadas, Gram-positivas, e ácido-resistentes; rodococose - cocobacilos Gram-positivos, ácido resistentes. Resultados: Foram incluídos 59 pacientes com actinomicetose. Actinomicose foi obervada em 27 pacientes entre 8 e 65 anos (idade média de 39,9 anos), 22 do sexo masculino (81,5%). Doença oral (cárie dentária, a doença periodontal) esteve frequentemente associada, sendo procedimento odontológico o fator de risco mais importante. A apresentação clínica foi actinomicose torácica em 24 casos, em dois facial e em um cérvico-facial e mediastinal. O diagnóstico microscópico foi positivo em 25, com o isolamento do organismo em cultivo anaeróbico em um, e, pelo teste de imunofluorescência direta em um. Estes dois últimos casos foi identificado como A. israelii. O tratamento mais utilizado consiste na administração prolongada de penicilina e esteve associado a boa evolução na maioria dos casos. Nocardiose foi observada em 27 pacientes, a idade variou entre 21 e 84 anos, idade média de 51,8 anos. A manifestação mais comum foi pneumonia cavitária, apresentado no paciente imunossuprimido, especialmente recebendo altas doses de corticoterapia. Todos os casos foram positivos para filamentos bacterianos ramificados Gram-positivos, ácido resistentes, sugestivos de espécies de Nocardia. Nocardia sp foi isolada em 14 casos, ―N. asteroides” em 7, N. farcinica em 2, N. brasiliensis em 1, N. pseudobrasiliensis em 1, N. abscessus em 1 e N. cyriacigeorgica em 1. Doze pacientes foram a óbito e os restantes tiveram melhora clínica. A rodococose foi diagnosticada em 5 pacientes, com idade, no momento do diagnóstico, de 22-69 anos (média de 45,6). Rhodococcus foi isolado em todos os 5 casos, três pacientes imunodeprimidos apresentaram infecção pulmonar pelo R. equi. O caso do paciente com HIV/AIDS foi fatal. Conclusões: Esta experiência, indica que a informação clínica associada ao Gram e a ácido-resistência em amostras clínicas é útil no reconhecimento da infecção por actinomicetos. A actinomicetose deve ser sempre considerada em pacientes apresentando doença febril supurativa ou radiografia de tórax anormal, em paciente com estado imune alterado causado por determinadas drogas (corticoterapia) e condições associadas (HIV/AIDS). / Background: Diseases caused by pathogenic aerobic and facultative anaerobic actinomycetes differ considerably with respect to their etiology, pathogenesis, clinical appearence and epidemiology. Objectives: To analyse the age distribution, clinical manifestations, underlying diseases and associated medical conditions, radiographic findings, microbiology, treatment and outcome, in patients with actinomycetosis (actinomycosis, nocardiosis, rhodococcosis). Design: The medical records of patients with positive microbiology findings to actinomycetes infections were retrospectively analysed. Settings: A university-based tertiary care hospital in Porto Alegre, Rio Grande do Sul, Brazil. Patients and methods: From 1978 through 2009 patients diagnosed with actinomycosis, nocardiosis, and rhodococcosis were included in this study. The microscopic criteria for diagnosis of actinomycetosis were as follow: actinomycosis –granules composed by branching Gram-positive organisms non acid-fast stained; nocardiosis - branched filamentous, Gram-positive, and acid-fast bacteria; rhodococcosis - coccobacilli Gram-positive, and acid-fast organism. Results: Sixty-five patients with actinomycetosis were included. Actinomycosis was oberved in 27 patients between 8 and 65 years old (mean age, 39,9 years), 22 were male (81,5%). Oral disease (poor dentition, periodontal disease) frequently associated with dental procedure was the most important risk factor. The clinical presentation was thoracic actinomycosis in 24 cases, facial in two, and cervico-facial and mediastinal one. Microcopic diagnosis were positive in 25, recovery of organism in anaerobic culture in one, and by fluorescent antibody test in one. These last two cases was identified as A. israelii. Treatment most commonly consisted of prolonged administration of penicillin and was associated with good outcome in the majority of cases. Nocardiosis was observed in 27 patients, aged 21 to 84 years old, with a mean age of 51,8 years. Cavitary pneumonia was the most common manifestation, presented in immunosuppresed patient, especially receiving high-dose corticotherapy. All cases were positive for branching Gram-positive, acid-fast bacterial filaments, suggestive of a Nocardia species. Nocardia sp was isolated in 14 cases, ―N. asteroides” in 7, N. farcinica in 2, N. brasiliensis in 1, N. pseudobrasiliensis in 1, N. abscessus in 1 and N. cyriacigeorgica in 1. Twelve patients died and the remaining cases were well improved. The diagnosis of rhodococcosis was made in five patients, ranged in age at time of diagnosis from 22 to 69 years, with a mean age of 45,6 years. Rhodococcus was isolated in all 5 cases, three immunocompromised patients showed pulmonary infection by R. equi. The case with HIV/AIDS was fatal. Conclusions: This experience, indicates that clinical information with Gram and acid-fast stains on clinical specimens is helpful in recognizing the possibility os actinomycetes should always be considered as a cause os suppurative febrile illness or abnormal chest roentgenograms in patient who may have an altered immune status caused by certain drugs (corticotherapy) and underlying conditions (HIV/AIDS).

Descrição: As doenças causadas por actinomicetos patógenos, aeróbios e anaeróbios facultativos, diferem consideravelmente no que diz respeito à sua etiologia, patogênese, apresentação clínica e epidemiologia. Objetivos: Analisar a distribuição etária, manifestações clínicas, doenças de base e condições associadas, achados radiológicos, microbiológicos, tratamento e evolução, nos pacientes com actinomicetoses (actinomicose, nocardiose, rodococose). Delineamento: Foram analisados, retrospectivamente, prontuários de pacientes com achados microbiológicos positivos para infecções por actinomicetos. Local do estudo: Um hospital universitário de atendimento terciário em Porto Alegre, Rio Grande do Sul, Brasil. Pacientes e métodos: Foram incluídos neste estudo, pacientes com diagnóstico de actinomicose, nocardiose e rodococose, num período de 1978 a 2009. Os critérios microscópicos para o diagnóstico de actinomicetose foram os seguintes: actinomicose - composto por grânulos actinomicóticos, filamentos Gram-positivos, não ácido-resistentes; nocardiose - bactérias filamentosas ramificadas, Gram-positivas, e ácido-resistentes; rodococose - cocobacilos Gram-positivos, ácido resistentes. Resultados: Foram incluídos 59 pacientes com actinomicetose. Actinomicose foi obervada em 27 pacientes entre 8 e 65 anos (idade média de 39,9 anos), 22 do sexo masculino (81,5%). Doença oral (cárie dentária, a doença periodontal) esteve frequentemente associada, sendo procedimento odontológico o fator de risco mais importante. A apresentação clínica foi actinomicose torácica em 24 casos, em dois facial e em um cérvico-facial e mediastinal. O diagnóstico microscópico foi positivo em 25, com o isolamento do organismo em cultivo anaeróbico em um, e, pelo teste de imunofluorescência direta em um. Estes dois últimos casos foi identificado como A. israelii. O tratamento mais utilizado consiste na administração prolongada de penicilina e esteve associado a boa evolução na maioria dos casos. Nocardiose foi observada em 27 pacientes, a idade variou entre 21 e 84 anos, idade média de 51,8 anos. A manifestação mais comum foi pneumonia cavitária, apresentado no paciente imunossuprimido, especialmente recebendo altas doses de corticoterapia. Todos os casos foram positivos para filamentos bacterianos ramificados Gram-positivos, ácido resistentes, sugestivos de espécies de Nocardia. Nocardia sp foi isolada em 14 casos, ―N. asteroides” em 7, N. farcinica em 2, N. brasiliensis em 1, N. pseudobrasiliensis em 1, N. abscessus em 1 e N. cyriacigeorgica em 1. Doze pacientes foram a óbito e os restantes tiveram melhora clínica. A rodococose foi diagnosticada em 5 pacientes, com idade, no momento do diagnóstico, de 22-69 anos (média de 45,6). Rhodococcus foi isolado em todos os 5 casos, três pacientes imunodeprimidos apresentaram infecção pulmonar pelo R. equi. O caso do paciente com HIV/AIDS foi fatal. Conclusões: Esta experiência, indica que a informação clínica associada ao Gram e a ácido-resistência em amostras clínicas é útil no reconhecimento da infecção por actinomicetos. A actinomicetose deve ser sempre considerada em pacientes apresentando doença febril supurativa ou radiografia de tórax anormal, em paciente com estado imune alterado causado por determinadas drogas (corticoterapia) e condições associadas (HIV/AIDS). / Background: Diseases caused by pathogenic aerobic and facultative anaerobic actinomycetes differ considerably with respect to their etiology, pathogenesis, clinical appearence and epidemiology. Objectives: To analyse the age distribution, clinical manifestations, underlying diseases and associated medical conditions, radiographic findings, microbiology, treatment and outcome, in patients with actinomycetosis (actinomycosis, nocardiosis, rhodococcosis). Design: The medical records of patients with positive microbiology findings to actinomycetes infections were retrospectively analysed. Settings: A university-based tertiary care hospital in Porto Alegre, Rio Grande do Sul, Brazil. Patients and methods: From 1978 through 2009 patients diagnosed with actinomycosis, nocardiosis, and rhodococcosis were included in this study. The microscopic criteria for diagnosis of actinomycetosis were as follow: actinomycosis –granules composed by branching Gram-positive organisms non acid-fast stained; nocardiosis - branched filamentous, Gram-positive, and acid-fast bacteria; rhodococcosis - coccobacilli Gram-positive, and acid-fast organism. Results: Sixty-five patients with actinomycetosis were included. Actinomycosis was oberved in 27 patients between 8 and 65 years old (mean age, 39,9 years), 22 were male (81,5%). Oral disease (poor dentition, periodontal disease) frequently associated with dental procedure was the most important risk factor. The clinical presentation was thoracic actinomycosis in 24 cases, facial in two, and cervico-facial and mediastinal one. Microcopic diagnosis were positive in 25, recovery of organism in anaerobic culture in one, and by fluorescent antibody test in one. These last two cases was identified as A. israelii. Treatment most commonly consisted of prolonged administration of penicillin and was associated with good outcome in the majority of cases. Nocardiosis was observed in 27 patients, aged 21 to 84 years old, with a mean age of 51,8 years. Cavitary pneumonia was the most common manifestation, presented in immunosuppresed patient, especially receiving high-dose corticotherapy. All cases were positive for branching Gram-positive, acid-fast bacterial filaments, suggestive of a Nocardia species. Nocardia sp was isolated in 14 cases, ―N. asteroides” in 7, N. farcinica in 2, N. brasiliensis in 1, N. pseudobrasiliensis in 1, N. abscessus in 1 and N. cyriacigeorgica in 1. Twelve patients died and the remaining cases were well improved. The diagnosis of rhodococcosis was made in five patients, ranged in age at time of diagnosis from 22 to 69 years, with a mean age of 45,6 years. Rhodococcus was isolated in all 5 cases, three immunocompromised patients showed pulmonary infection by R. equi. The case with HIV/AIDS was fatal. Conclusions: This experience, indicates that clinical information with Gram and acid-fast stains on clinical specimens is helpful in recognizing the possibility os actinomycetes should always be considered as a cause os suppurative febrile illness or abnormal chest roentgenograms in patient who may have an altered immune status caused by certain drugs (corticotherapy) and underlying conditions (HIV/AIDS).

Descrição: As doenças causadas por actinomicetos patógenos, aeróbios e anaeróbios facultativos, diferem consideravelmente no que diz respeito à sua etiologia, patogênese, apresentação clínica e epidemiologia. Objetivos: Analisar a distribuição etária, manifestações clínicas, doenças de base e condições associadas, achados radiológicos, microbiológicos, tratamento e evolução, nos pacientes com actinomicetoses (actinomicose, nocardiose, rodococose). Delineamento: Foram analisados, retrospectivamente, prontuários de pacientes com achados microbiológicos positivos para infecções por actinomicetos. Local do estudo: Um hospital universitário de atendimento terciário em Porto Alegre, Rio Grande do Sul, Brasil. Pacientes e métodos: Foram incluídos neste estudo, pacientes com diagnóstico de actinomicose, nocardiose e rodococose, num período de 1978 a 2009. Os critérios microscópicos para o diagnóstico de actinomicetose foram os seguintes: actinomicose - composto por grânulos actinomicóticos, filamentos Gram-positivos, não ácido-resistentes; nocardiose - bactérias filamentosas ramificadas, Gram-positivas, e ácido-resistentes; rodococose - cocobacilos Gram-positivos, ácido resistentes. Resultados: Foram incluídos 59 pacientes com actinomicetose. Actinomicose foi obervada em 27 pacientes entre 8 e 65 anos (idade média de 39,9 anos), 22 do sexo masculino (81,5%). Doença oral (cárie dentária, a doença periodontal) esteve frequentemente associada, sendo procedimento odontológico o fator de risco mais importante. A apresentação clínica foi actinomicose torácica em 24 casos, em dois facial e em um cérvico-facial e mediastinal. O diagnóstico microscópico foi positivo em 25, com o isolamento do organismo em cultivo anaeróbico em um, e, pelo teste de imunofluorescência direta em um. Estes dois últimos casos foi identificado como A. israelii. O tratamento mais utilizado consiste na administração prolongada de penicilina e esteve associado a boa evolução na maioria dos casos. Nocardiose foi observada em 27 pacientes, a idade variou entre 21 e 84 anos, idade média de 51,8 anos. A manifestação mais comum foi pneumonia cavitária, apresentado no paciente imunossuprimido, especialmente recebendo altas doses de corticoterapia. Todos os casos foram positivos para filamentos bacterianos ramificados Gram-positivos, ácido resistentes, sugestivos de espécies de Nocardia. Nocardia sp foi isolada em 14 casos, ―N. asteroides” em 7, N. farcinica em 2, N. brasiliensis em 1, N. pseudobrasiliensis em 1, N. abscessus em 1 e N. cyriacigeorgica em 1. Doze pacientes foram a óbito e os restantes tiveram melhora clínica. A rodococose foi diagnosticada em 5 pacientes, com idade, no momento do diagnóstico, de 22-69 anos (média de 45,6). Rhodococcus foi isolado em todos os 5 casos, três pacientes imunodeprimidos apresentaram infecção pulmonar pelo R. equi. O caso do paciente com HIV/AIDS foi fatal. Conclusões: Esta experiência, indica que a informação clínica associada ao Gram e a ácido-resistência em amostras clínicas é útil no reconhecimento da infecção por actinomicetos. A actinomicetose deve ser sempre considerada em pacientes apresentando doença febril supurativa ou radiografia de tórax anormal, em paciente com estado imune alterado causado por determinadas drogas (corticoterapia) e condições associadas (HIV/AIDS). / Background: Diseases caused by pathogenic aerobic and facultative anaerobic actinomycetes differ considerably with respect to their etiology, pathogenesis, clinical appearence and epidemiology. Objectives: To analyse the age distribution, clinical manifestations, underlying diseases and associated medical conditions, radiographic findings, microbiology, treatment and outcome, in patients with actinomycetosis (actinomycosis, nocardiosis, rhodococcosis). Design: The medical records of patients with positive microbiology findings to actinomycetes infections were retrospectively analysed. Settings: A university-based tertiary care hospital in Porto Alegre, Rio Grande do Sul, Brazil. Patients and methods: From 1978 through 2009 patients diagnosed with actinomycosis, nocardiosis, and rhodococcosis were included in this study. The microscopic criteria for diagnosis of actinomycetosis were as follow: actinomycosis –granules composed by branching Gram-positive organisms non acid-fast stained; nocardiosis - branched filamentous, Gram-positive, and acid-fast bacteria; rhodococcosis - coccobacilli Gram-positive, and acid-fast organism. Results: Sixty-five patients with actinomycetosis were included. Actinomycosis was oberved in 27 patients between 8 and 65 years old (mean age, 39,9 years), 22 were male (81,5%). Oral disease (poor dentition, periodontal disease) frequently associated with dental procedure was the most important risk factor. The clinical presentation was thoracic actinomycosis in 24 cases, facial in two, and cervico-facial and mediastinal one. Microcopic diagnosis were positive in 25, recovery of organism in anaerobic culture in one, and by fluorescent antibody test in one. These last two cases was identified as A. israelii. Treatment most commonly consisted of prolonged administration of penicillin and was associated with good outcome in the majority of cases. Nocardiosis was observed in 27 patients, aged 21 to 84 years old, with a mean age of 51,8 years. Cavitary pneumonia was the most common manifestation, presented in immunosuppresed patient, especially receiving high-dose corticotherapy. All cases were positive for branching Gram-positive, acid-fast bacterial filaments, suggestive of a Nocardia species. Nocardia sp was isolated in 14 cases, ―N. asteroides” in 7, N. farcinica in 2, N. brasiliensis in 1, N. pseudobrasiliensis in 1, N. abscessus in 1 and N. cyriacigeorgica in 1. Twelve patients died and the remaining cases were well improved. The diagnosis of rhodococcosis was made in five patients, ranged in age at time of diagnosis from 22 to 69 years, with a mean age of 45,6 years. Rhodococcus was isolated in all 5 cases, three immunocompromised patients showed pulmonary infection by R. equi. The case with HIV/AIDS was fatal. Conclusions: This experience, indicates that clinical information with Gram and acid-fast stains on clinical specimens is helpful in recognizing the possibility os actinomycetes should always be considered as a cause os suppurative febrile illness or abnormal chest roentgenograms in patient who may have an altered immune status caused by certain drugs (corticotherapy) and underlying conditions (HIV/AIDS).