A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in part fulfillment of the requirements for the degree of MSc (Med) (Pharmaceutical Affairs) Johannesburg, 25 March 2013 / The emergence of resistant forms of tuberculosis (TB) has not only caused continuous challenges on the world populations’ health, but has also attracted increased costs of primary health care for the infected and society at large. In 2005, when the South African public came to learn about another resistant form of TB other than multi-drug resistant (MDR), 53 patients had just died in a rural hospital in KwaZulu-Natal (KZN). The reports (SA DoH, 2006) came to announce this form of TB as extreme drug resistant tuberculosis (XDR-TB).

by Cheung Wah. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1994. / Includes bibliographical references (leaves 64-68). / Tuberculosis in the Elderly : Presentation and Therapeutic Problems -a Clinical and Pharmacological Study / Contents / Chapter 1. --- Summary --- p.6 / Chapter 2. --- Introduction --- p.7 / Chapter 3. --- Aims of the Study --- p.11 / Chapter 4. --- Subjects and Methods --- p.12 / Chapter 5. --- Results --- p.36 / Chapter 6. --- Discussion --- p.55 / Chapter 7. --- Conclusion --- p.61 / Chapter 8. --- Acknowledgement --- p.63 / Chapter 9. --- References --- p.64

Objectives: We aimed to assess the variation in patient body weight over time according to the treatment outcome among multidrug-resistant tuberculosis (MDR-TB) cases. Methods: This was a retrospective cohort study. The data of patients commencing MDR-TB therapy were analyzed. Data were collected from different public TB treatment facilities located in peri-urban areas to the south of Lima, Peru. The outcome was patient body weight (kilograms) from treatment commencement, measured monthly. A random effects model was fitted using robust standard errors to calculate 95% confidence intervals. Results: Of a total of 1242 TB cases, 243 (19.6%) were MDR-TB. Only 201 cases were included in the analysis; 127 (63.2%) were males and the mean patient age was 33.6 (standard deviation 16.2) years. Weight changes over time among the patients who were cured differed from changes in those who died during therapy (p < 0.001). Weight curve divergence was important at the end of the third, fourth, and fifth treatment months: on average, the weight difference was 2.18 kg (p < 0.001), 3.27 kg (p = 0.007), and 3.58 kg (p = 0.03), respectively, when cured patients were compared to those who died. Conclusions: Our results show that weight variation during treatment can be a useful surrogate for the treatment outcome, specifically death during therapy. MDR-TB patients with weight loss should be followed more closely, as they are at greater risk of death. / Revisión por pares

Magister Artium - MA (Anthropology/Sociology) / Biomedicine positively maintains that tuberculosis transmission occurs due to close contact with a diseased individual (Coovadia and Benatar, 1991). Consequently, this refers to a direct mode of transmission where individuals are at direct risk of becoming infected. It is often taken for granted that when one speaks of contact within the context of tuberculosis, one is necessarily referring to contact or interactions among tuberculosis patients and people in the community with whom they have contact of any nature. It is then assumed that tuberculosis is transmitted in this manner. However, there are also indirect modes of transmission which are often neglected to be explored, but have an equally serious effect on transmission in high incidence areas. This paper also addresses other contact patterns that are also role-players in the tuberculosis epidemic.

Wang, Xingyan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 126-131). / Abstracts in English and Chinese. / ACKNOWLEDGEMENT --- p.I / ABBREVIATIONS --- p.II / ABSTRACT --- p.V / 摘要 --- p.VIII / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- CLINICAL DISEASE CAUSED BY M.TB --- p.1 / Chapter 1.1.1 --- Tuberculosis (TB) --- p.1 / Chapter 1.1.2 --- Pathogen: Mycobacteria tuberculosis (M. TB) --- p.2 / Chapter 1.2 --- HOST DEFENSE AGAINST M.TB --- p.4 / Chapter 1.2.1 --- Overview --- p.4 / Chapter 1.2.2 --- Specific pathways --- p.6 / Chapter 1.3 --- GENETIC PREDISPOSITION OF HOST TO INFECTION --- p.12 / Chapter CHAPTER 2 --- OVERVIEW AND AIM OF THIS PROJECT --- p.14 / Chapter 2.1 --- GWAS REPLICATION --- p.14 / Chapter 2.2 --- CANDIDATE GENES REVEALED IN GWAS OF OTHER GRANULOMATOUS INFLAMMATORY DISEASES (GLD) --- p.14 / Chapter 2.3 --- CHROMOSOME 17 CHEMOKINE CLUSTER REGION --- p.15 / Chapter CHAPTER 3 --- REPLICATION STUDY OF TB GWAS --- p.16 / Chapter 3.1 --- INTRODUCTION --- p.16 / Chapter 3.1.1 --- TB GWAS study --- p.16 / Chapter 3.1.2 --- Aims of this part --- p.16 / Chapter 3.2 --- MATERIAL AND METHODS --- p.17 / Chapter 3.2.1 --- Case and control samples --- p.17 / Chapter 3.2.2 --- DNA extraction --- p.18 / Chapter 3.2.3 --- Genotyping of the SNPs --- p.19 / Chapter 3.2.4 --- Statistical analysis --- p.21 / Chapter 3.3 --- RESULTS --- p.23 / Chapter 3.3.1 --- Description of studied samples --- p.23 / Chapter 3.3.2 --- Results of case-control study for replication studies of TB GWAS --- p.23 / Chapter 3.4 --- DISCUSSION --- p.28 / Chapter CHAPTER 4 --- GENETIC VARIANTS IN GRANULOMATOUS INFLAMMATORY DISEASES --- p.32 / Chapter 4.1 --- INTRODUCTION --- p.32 / Chapter 4.1.1 --- Granulomatous inflammation --- p.32 / Chapter 4.1.2 --- Diseases characterized by granulomatous inflammatory --- p.34 / Chapter 4.1.3 --- Shared immune mechanisms in GiDs --- p.38 / Chapter 4.1.4 --- Genome-wide Association Studies (GWAS) in GiD --- p.38 / Chapter 4.1.5 --- Hypothesis of this part --- p.41 / Chapter 4.2 --- MATERIAL AND METHODS --- p.43 / Chapter 4.2.1 --- Case and control samples --- p.43 / Chapter 4.2.2 --- DNA extraction --- p.44 / Chapter 4.2.3 --- Tag SNP selection --- p.44 / Chapter 4.2.4 --- Genotyping of tagging SNPs --- p.45 / Chapter 4.2.5 --- Statisitical analysis --- p.45 / Chapter 4.3 --- RESULTS --- p.55 / Chapter 4.3.1 --- Description of TB case samples --- p.55 / Chapter 4.3.2 --- Primary endpoint case-control results --- p.56 / Chapter 4.3.3 --- Secondary endpoint case-only studies results --- p.67 / Chapter 4.3.4 --- Haplotype analysis --- p.78 / Chapter 4.4 --- DISCUSSION --- p.83 / Chapter 4.4.1 --- ATG16L1 gene with TB susceptibility --- p.83 / Chapter 4.4.2 --- Associations in case-only studies (Interaction effects) --- p.83 / Chapter 4.4.2.1 --- Age and pathogenesis of TB --- p.83 / Chapter CHAPTER 5 --- STUDIES IN THE CHEMOKINE-GENE CLUSTER AND A MIRNA SNP STUDY --- p.89 / Chapter 5.1 --- INTRODUCTION --- p.89 / Chapter 5.1.1 --- Genetic susceptibility to TB in familial cases --- p.89 / Chapter 5.1.2 --- Familial studies suggested linkage at 17qll.2 --- p.89 / Chapter 5.1.3 --- Chemokines --- p.90 / Chapter 5.1.4 --- Studies of SNP rs2910164 of microRNA-146a (miRNA-146a) --- p.91 / Chapter 5.2 --- MATERIAL AND METHODS --- p.92 / Chapter 5.2.1 --- Case and control samples --- p.92 / Chapter 5.2.2 --- DNA extraction --- p.92 / Chapter 5.2.3 --- TagSNP selection --- p.92 / Chapter 5.2.4 --- Genotyping of tagging SNPs --- p.93 / Chapter 5.2.5 --- PCR-RFLP --- p.93 / Chapter 5.2.6 --- Statistical analysis --- p.94 / Chapter 5.3 --- RESULTS --- p.100 / Chapter 5.3.1 --- PCR-RFLP results of the three SNPs --- p.100 / Chapter 5.3.2 --- Description of TB case samples --- p.102 / Chapter 5.3.3 --- Primary endpoint case-control results --- p.103 / Chapter 5.3.4 --- Secondary endpoint case-only studies results of CCL genes --- p.109 / Chapter 5.4 --- DISCUSSION --- p.120 / Chapter 5.4.1 --- Genetic association of SNPs with severity of TB --- p.120 / Chapter 5.4.2 --- Smoking and immunity --- p.121 / Chapter CHAPTER 6 --- FINAL CONCLUSION AND PROSPECT FOR FUTURE WORK --- p.122 / Chapter 6.1 --- CONCLUSION --- p.122 / Chapter 6.2 --- LIMITATION OF THE STUDIES --- p.124 / Chapter 6.3 --- FUTURE WORKS AND PROSPECT --- p.125 / REFERENCES --- p.126

泛基因组的概念来源于比较分析同一微生物物种的多个基因组。泛基因组分析已经被用于研究病原微生物基因组的变化，并且揭示了与菌株进化和宿主适应相关的特异基因。目前泛基因组研究主要集中在估计不同物种的泛基因组大小。但是对泛基因组的结构进行进化分析的生物信息方法还有待开发，以便研究不同基因在不同菌株的进化，比如基因的获得或者丢失，或者共同进化的基因簇。这样的分析方法可以把基因和菌株之间的表型关联起来，为进一步的生物学实验提供线索。 / 为了研究结核分枝杆菌种和分枝杆菌属泛基因组进化的规律并揭示其生物学意义，本论文开发了两种泛基因组数据分析的生物信息学方法。第一个是基于局部最大简约计算的祖先状态重构算法。它被用来分析结核分枝杆菌北京型全基因组水平插入／缺失序列（indels）的进化。分析表明基因组退化不仅塑造了该物种不同亚种的形成，并且也塑造了同一亚种不同亚型的分化，比如北京型。该分析还找出了北京型全基因组水平的RD区域和各种被中断的基因，这些基因可能同北京型的毒力进化相关。同时，该算法提供了另一个理解简约分析的视角；该视角可以把统计分析引入到该算法中。本论文提出的第二个模型是基于泛基因组进化的基因聚类模型。通过计算泛基因组中不同基因家族的分布频率，结合基于图论的聚类算法，该模型可以找出泛基因组中共同进化的基因聚类。对分枝杆菌属的泛基因组进行聚类分析发现了不同类别的基因簇，它们与不同分枝杆菌种的表型进化相关。这些结果说明了，一方面结核分枝杆菌在进化过程中丢失大量环境相关的基因；另一方面，它可能通过水平基因转移获得一些基因，特别是PE/PPE基因家族。因此，结核分枝杆菌可能是通过不断的基因组收缩，从一个环境菌种进化为与宿主共进化的病原菌。 / 总地来说，上面的两种方法能够被有效地用于结核分枝杆菌种和分枝杆菌属的泛基因组分析。 将来的工作可以考虑进一步引进随机模型；同时需要建立分枝杆菌的泛基因组数据库，以面对大规模测序的需求。 / Comparative analysis of multiple genomes of the same microbial species has led to the concept of pangenome to characterize the variations of gene content in different strains and to study their relationship to strain phenotype variations. Pangenome studies of microbial pathogens have identified strain-specific genes that may play roles in the evolution and adaptation of the pathogens. In previous studies, much attention was paid to estimate the size of the pangenome of different microbial species. But it is also important to develop bioinformatic methods for analyzing the evolution of the pangenome of a species, such as gene gain and loss or coevolution of clusters of genes, which may help to associate genotype variations with phenotype variations of a microbial species, and thus provides biological insights for further studies. / In this thesis, to analyze the pangenome consisting of complete mycobacterial genomes from public database and additional five Mycobacterium tuberculosis (MTB) Beijing genotype genomes sequenced by our own project, two bioinformatic approaches have been developed. The first is a local parsimony ancestral state reconstruction method, which was used to analyze genome-wide indels evolution of the MTB Beijing genotype. The key finding was that reductive evolution shaped the formation of not only different MTB species, but also different subspecies or genotypes, such as the Beijing genotype, for which genome-wide deletions of large RDs and disruption of individual genes were identified. This finding might have implications for the virulence evolution of the Beijing genotype. The method also provides an alternative perspective to understand parsimony analysis in phylogenetics, which can be used to incorporate statistical analysis into the method. / The second approach developed is a pangenome phyletic model for analyzing the coevolution of genes in the pangenome of a microbial species. This phyletic model calculates coevolution scores of gene frequencies in a pangenome. And graph-based clustering is used to identify coevolved clusters of genes. Applying this method to the genus Mycobacterium helped us to identify various gene clusters, from conserved core clusters of housekeeping genes to species-specific clusters, including genes related to pathogenesis. The key finding was that different MTB species have arose from their mycobacterial ancestor mainly by loss of many environmental related genes. On the other hand, gain of genes has also occurred within the MTB genomes, especially the clusters of the PE/PPE genes. This finding implied that the MTB species have undergone reductive evolution from an environmental species to adapt to and coevolve with their specific hosts. / In conclusion, the two methods were shown to be powerful in analyzing the pangenome of the MTB species and also of the Mycobacterium genus, and have provided useful insights into their genome and virulence evolution for further studies, including both pathogenesis related genes and genotyping genetic markers. Future works in that direction is to introduce stochastic models of gene evolution into these two methods. Finally, this work indicated that pangenome modeling is critical and can provide a good starting point for comprehensive pangenome sequencing of mycobacteria. Therefore, a database of Mycobacterial genomes for integrative pangenome annotation and evolutionary analysis should be developed. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Zhou, Haokui. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 121-135). / Abstracts also in Chinese.

La tuberculosis (TB) es un desafío en la actualidad peruana debido a las elevadas tasas de incidencia y prevalencia; así como la creciente incidencia de tuberculosis drogorresistente. Por ello la preocupación en la eficacia del tratamiento y su adecuada adherencia. Objetivos: Determinar el grado de malestar psicológico en pacientes con tuberculosis atendidos en tres centros de salud de Lima y los factores relacionados a mayor malestar psicológico. Diseño: Estudio descriptivo transversal, con muestreo no probabilístico. Escenario: Los centros de salud San Cosme. Max Arias-Schereiber y El Pino Métodos: En el periodo agosto –diciembre 2014 se entrevistó a 125 pacientes con diagnóstico de TB y en tratamiento. Se aplicó el test de Malestar psicológico de Kessler 10. Se determinó frecuencias, porcentajes, cuadros de doble entrada y análisis de independencia mediante la prueba de Chi2 con un nivel de significancia de 0.05. Se usó SPSS versión 22.Principales medidas de los Resultados: Grado de Malestar Psicológico Kessler 10 y factores socio-demográfico, clínicos, consumo de sustancias psicoactivas y período de tratamiento en el que se aplicó el Test. Resultados: Se estudió 125 paciente, 40 mujeres (32%) y 85 varones (68%) con edad media de 32 ±13. El 82% fueron pacientes con diagnóstico de TB pulmonar o pleural, el 12% con TB-MDR; con pocas comorbilidades, enfermedades asociadas o RAFA. Consumo de sustancias psicoactivas en un 50%. Hubo 15 pacientes (12%) con grado de malestar bajo, 44 (35%) con grado moderado, 46 (37%) con grado alto y 20 (16%) con grado muy alto. Se encontró que existe relación entre el estado civil y el grado de malestar psicológico (Chi2=10.8,p=0.029;∞=0.05) Conclusiones: Más de la mitad de los pacientes con TB presentan grado de malestar psicológico entre los rangos de alto y muy alto. Se encontró relación significativa entre el estado civil de paciente y el grado de malestar psicológico: los pacientes casados presentaron mayor nivel de malestar psicológico. No se encontró relaciones significativas entre el grado de malestar psicológico y las otras variables medidas en este estudio. / Tesis

Introducción: La Tuberculosis, según la OMS, es la segunda causa de muerte en el mundo causada por un agente infeccioso, después del SIDA, más del 95% de estas muertes ocurren en países con ingresos bajos. En el Perú según la OMS y el MINSA, cada año se diagnostican 35,000 casos de Tuberculosis, una de las cifras más elevadas, de todos ellos el 10% contrae la tuberculosis multidrogo-resistente (TB MDR), producidas por las cepas resistentes a las drogas más efectivas para curar la TB como son la isoniacida y la rifampicina. Esta situación se considera a nivel mundial sólo el comienzo de un problema de consecuencias imprevisibles, ya que la población portadora de esta infección puede ser la fuente de una epidemia de TB incurable en el planeta. Objetivo: El presente trabajo tiene como objetivo evaluar el nivel de conocimientos sobre la Tuberculosis multidrogo-resistente en la población usuaria del Centro de Salud Mirones Bajo del Cercado de Lima, para lo cual toma en cuenta su edad, sexo, grado de instrucción, entre otros. Metodología: Este estudio se basa en una encuesta, que se aplicó del 1 de marzo al 1 de abril del 2014. El tipo de diseño es no experimental, descriptivo de corte transversal. Se obtuvo una muestra de 112 pobladores usuarios del Centro de Salud y durante la aplicación del instrumento se usó el criterio por conveniencia. Resultados y Conclusiones:Finalmente una de las conclusiones a la que se llega, es que la población joven, la que según diversos estudios es la más afectada por esta enfermedad, tiene un nivel de conocimientos entre medio y bajo en todas las áreas evaluadas, como signos y síntomas, factores de riesgo, prevención y tratamiento. Recomendaciones: Por ello las recomendaciones van dirigidas a proveer de conocimientos documentados, a la luz de lo que hoy se sabe de la enfermedad, tal como consta en las Normas Técnicas que rigen el trabajo de las instituciones del estado, lo que permitirá afrontar este problema sanitario en mejores condiciones. / Tesis

Thesis (M.Sc. (Medical Microbiology)) --University Limpopo, 2013 / Genotyping of TB is essential to investigate and confirm transmission of the multi-drug resistant tuberculosis and of great value in optimizing strategies for the determination of strains causing the increased mortality rates of TB outbreaks. Sputum samples (207) were collected from National Health Laboratory Services in Polokwane laboratory for determining mutations and genotypes of the Mycobacterium tuberculosis strains using GenoType®MTBDRplus (Hain LifeScience, Germany) and Real-Time PCR (Roche, South Africa) techniques. Of the 207 samples, 28 (13.5%) exhibited drug resistance. Thirteen of the 28 (46%) MDR-TB strains belonged to the non-Beijing family, with mutations at codons rpoB 516 and rpoB 526 for RIF and katG 315 and inhA 15 for INH resistance. The Non-Beijing strains 75% (21/28) were monoresistant to RIF 14% (3/21) at codons 516, 526, 531 of rpoB gene and INH 19% (4/21) at codon 315 of katG and codon 15 of inhA 5% (1/21). Of the eight Beijing strains, 3(8%) were INH- resistant at codon 315 for katG and codon 15 for inhA and 3(8%) were RIF-resistant with mutations at codons 516 and 526. Two samples were typed as MDR for the Beijing strains with codon 315 for INH and codons 526 and 531 for RIF. The sample with a co-infection for Beijing and non-Beijing was an MDR-TB strain with mutations in rpoB codons 526, 531, katG 315 and inhA 8, 15 and16. The study showed a high rate of drug resistance with the non-Beijing compared to Beijing strains and mutations in specific codons for RIF and INH are variable for the TB families.

ABSTRACT INTRODUCTION: Multi-drug resistant tuberculosis (MDR-TB) poses a great threat to the eradication of TB. In the US, MDR-TB is faced with inadequate diagnostic tools and long and expensive treatment regimens. Therefore, preventing the disease is the key to saving lives and resources. Social and behavioral variables play a big part in this prevention. It is important to determine the social factors that may lead to MDR-TB in order to set up prevention programs and more efficient treatment regimens. AIM: This study was conducted to ascertain the social determinants of MDR-TB in the US between the years of 2005 and 2009 to better equip public health officials to deal with this growing threat. METHODS: This study used the Centers for Disease Control and Prevention (CDC) Online Tuberculosis Information System (OTIS) database to find associations between certain social variables and MDR-TB. The variables that were tested were whether or not the individual had lived in a correctional facility for the past year; HIV status; homelessness; whether or not the individual had an occupation; and whether the individual was foreign-born or US-born. An unadjusted odds ratio (OR) was calculated to find this association. The variables were then stratified with age; sex; race; age and race; age and sex; and age, sex, and race to see whether or not the strata were confounders. RESULTS: The variables of having lived in a correctional facility and homelessness were found to be associated with MDR-TB. However, all of the strata were found to be confounders for this relationship. Having HIV and being US-born were not found to be associated with MDR-TB. All of the strata for HIV were found to be confounders. But for place of birth, stratifying by age, sex, and both age and sex were not confounders. The rest of the strata were. The OR for occupation versus MDR-TB was almost at 1, meaning that those with a job and those without a job had almost equal odds of having MDR-TB. Effect modification was present for the strata in all variables, meaning that the risk of having MDR-TB varied with each different age, sex, and racial group. DISCUSSION: Results from this study showed which variables were more likely to be associated with MDR-TB in the US between the years of 2005 and 2009. However, when compared to the literature that exists, the results showed that more research needs to be done to properly ascertain this relationship. Using this study, public health officials can identify which populations to focus prevention efforts on.