Thesis (MScMedSc (Biomedical Sciences))--University of Stellenbosch, 2010. / Thesis presented in partial fulfilment of the requirements for the degree Master of Medical Science (Human Genetics) at the University of Stellenbosch. / Bibliography / ENGLISH ABSTRACT: The infectious disease tuberculosis (TB) remains the leading cause of death worldwide by a single infectious agent, despite significant advances in biomedical sciences. The idea that host genetics plays a role in the development of disease was proposed by Haldane in 1949. The observation that only 10% of immunocompetent individuals develop disease while others are able to successfully contain it, further suggests that host genetics plays an important role. TB is thus a complex disease, with the causative bacterium, Mycobacterium tuberculosis, host genetic factors and environment all contributing to the development of disease. To date several genes have been implicated in TB susceptibility, albeit with small effect. Genome-wide association studies (GWAS) offer the means to identify novel susceptibility variants and pathways through their ability to interrogate polymorphisms throughout the genome without being limited by our understanding of the immune processes involved in TB infection and disease progression. TB and sarcoidosis are both granulomatous diseases, and we therefore hypothesized that the genes and their associated variants identified in recent GWAS conducted in West Africa for TB, and Germany for sarcoidosis, could alter susceptibility to TB in the South African Coloured (SAC) population. In the sarcoidosis GWAS, ANXA11 was shown to alter susceptibility to sarcoidosis; whereas in the TB GWAS, CADM1 was found to alter susceptibility to TB. This study tested the association with TB of 16 polymorphisms in 5 potential TB host susceptibility genes in the SAC population. A well designed case-control study was employed, using the TaqMan® genotyping system to type the various polymorphisms. Any polymorphism that was found to be significantly associated with susceptibility to TB was then subjected to further analysis to determine the functional effect of the polymorphism. Promoter methylation patterns were also investigated in ANXA11 as another mechanism to elucidate its role in TB susceptibility. A 3’ UTR ANXA11 polymorphism was found to be strongly associated with susceptibility to TB, including 3 haplotypes. The gene expression analysis identified differential transcriptional levels between individual with the different genotypes, with individuals homozygous for the A-allele exhibiting a 1.2-fold increase in gene expression relative to those homozygous for the G-allele. Methylation analysis however found no differences between cases and controls. In addition, 16 novel polymorphisms were also identified, 15 of which occurred in the 3’UTR of ANXA11. The mechanism of action of ANXA11 in TB susceptibility is hypothesised to be in the area of endocytosis, autophagy or apoptosis. A weak association was noted with one of the 5’ UTR polymorphisms of CADM3, which did not hold up to further analysis in the GWAS study, and no functional work was therefore done. This work facilitates our understanding of the role of host genetics in susceptibility to TB and adds to the growing amount of information available. Proper understanding of the role that host genetics plays in TB susceptibility could result in better treatment regimens and prediction of individuals who are at a greater risk of developing TB, a disease that still kills millions of individuals annually. / AFRIKAANSE OPSOMMING: Tuberkulose is verantwoordelik vir meer sterftes as enige ander aansteeklike siekte, ten spyte van die voortuitgang wat die Biomediese Wetenskappe tans beleef. In 1949 het Haldane voorgestel dat die genetiese samestelling van die gasheer ‘n rol speel in vatbaarheid vir aansteeklike siektes. Vir tuberkulose word hierdie aanname gesteun deur die feit dat slegs 10% van individue wat geïnfekteer word aktiewe simptome ontwikkel, terwyl 90% die siekte suksesvol sal afweer. Tuberkulose is dus ‘n komplekse siekte wat veroorsaak word deur Mycobacterium tuberculosis, maar wat beïnvloed word deur genetiese sowel as omgewingsfaktore. Verskeie gene is al geïdentifiseer wat ‘n rol speel in vatbaarheid vir tuberkulose, tog is hul invloed betreklik klein. Genoom-wye assosiasiestudies (GWAS) bied unieke geleenthede vir die identifisering van nuwe polimorfismes wat genetiese vatbaarheid kan beïnvloed. Hierdie tegniek kan die hele genoom fynkam, sonder dat enige vooropgestelde idees oor die immuunrespons teen tuberkulose ‘n invloed sal hê. Tuberkulose en sarkoïdose is albei siektes wat die vorming van granulomas veroorsaak. Verskeie gene met hul geassosieerde variante is geïdentifiseer in ‘n onlangse GWAS, wat gefokus het op populasies in Wes-Afrika en Duitsland. Ons hipotese was dat die polimorfismes wat in hierdie studie geïdentifiseer is, ‘n invloed kan hê op genetiese vatbaarheid vir TB in die Suid-Afrikaanse Kleurlingbevolking (SAK). Die sarkoïdose GWAS het bevind dat ANXA11 vatbaarheid vir die siekte beïnvloed, terwyl CADM1 in die tuberkulose GWAS geïdentifiseer is. Die studie het die assosiasie tussen 16 variante en tuberkulose vatbaarheid ondersoek in die SAK populasie. Die variante strek oor 5 potensiële tuberkulose vatbaarheidsgene. Goedbeplande pasiënt-kontrole assosiasiestudies is gedoen en die polimorfismes is gegenotipeer deur gebruik te maak van die TaqMan® genotiperingsisteem. Enige polimorfisme wat beduidend met tuberkulose geassosieer was, is verder geanaliseer om die moontlike funksionele invloed daarvan te bepaal. Promotormetileringspatrone van ANXA11 is ook geanaliseer, om ‘n addisionele meganisme in tuberkulose vatbaarheidheid te ondersoek. Na genotipering van die polimorfismes is ‘n 3’ UTR ANXA11 variant geïdentifiseer wat beduidend met tuberkulose vatbaarheid geassosieer was. Drie haplotipes is ook geïdentifiseer. Geenuitdrukkingsanalise het aangedui dat verskille in transkripsie vlakke voorkom in individue met verskillende genotipes. Individue wat homosigoties was vir die A-alleel het ‘n verhoging van 1.2 in geenuitdrukking gehad, relatief tot individue wat homosigoties was vir die G-alleel. Metileringsanalise het egter geen verskil aangedui tussen pasiënte en kontroles nie. Addisioneel, is 16 nuwe variante ontdek, waarvan 15 in die 3’UTR van ANXA11 geleë was. Die meganisme waarmee ANAX11 genetiese vatbaarheid vir tuberkulose beïnvloed, blyk in die area van endositose, apoptose of outofagie, te wees. ‘n Swak assosiasie is gevind vir ‘n 5’ UTR variant van CADM3 en is nie verder opgevolg in die GWAS nie. Gevolglik is geen funksionele studies op hierdie polimorfisme gedoen nie. Hierdie studie dra by tot ons kennis oor die rol wat die genetiese samestelling van die gasheer speel in vatbaarheid vir tuberkulose. Indien die rol van mensgenetika in tuberkulose vatbaarheid korrek verstaan word, kan behandeling van die siekte verbeter word en kan individue wat ‘n hoër risiko loop om tuberkulose te ontwikkel geïdentifiseer word.

Thesis (MScMedSc)--Stellenbosch University, 2012. / Bibliography / ENGLISH ABSTRACT: The communicable disease tuberculosis (TB) is responsible for millions of deaths each year, on a global scale. At present the contribution of host genetics in TB is generally accepted and, together with environmental aspects (e.g. nutrition and crowding) and the causative bacterium, Mycobacterium tuberculosis (M. tuberculosis); it will possibly have a hand in the outcome of disease. Clearly, TB is a multifaceted disease and the repercussions for studying genetic susceptibility are that many genes will potentially be implicated. To date a variety of genes such as NRAMP1 and HLA have been implicated in influencing the host response to TB, albeit with varying effects in different populations. Some of the more recently implicated genes are the pattern recognition receptors, the Toll-like receptors (TLRs). Genetic variation in theses genes has been associated with a myriad of different diseases, including those of an infectious nature, such as TB. In the case of TB, TLR2 is the most prominent candidate with TLR8 and 9 more recently implicated. One of the more well known genes implicated with TB is the vitamin D receptor (VDR), as the antimicrobial gene cathelicidin (CAMP), one of the most important agents of mycobacterial killing, has a VDR response element in its promoter. TLR2, VDR and CAMP are all connected in a complex pathway essential for the host defence against M. tuberculosis. Nine single nucleotide polymorphisms (SNPs) in three TLR genes (TLR2,8 & 9) were investigated via a case-control approach to determine their potential role in human genetic susceptiblity to TB in the Coloured population of South Africa. The effect of the VDR polymorphism Cdx2 on the expression of cathelicidin mRNA and protein expression was also investigated. Three genes were found to contribute significantly to genetic host susceptibility in the Coloured population of South Africa. An allelic association (p = 0.031) was observed for the TLR8 (located on the X-chromosome) SNP rs3761624, with the A-allele being more prominent in females. Four haplotypes of TLR8 were found to be significantly linked to TB susceptibility with the three SNP haplotype rs3761624-rs3764879-rs3764880, specifically the allelic combination of G/C/A [p = 0.004, OR = 2.67(95% CI: 1.90-3.74)], showing a marked association (p = 0.001). The TLR9 introexon2 boundary SNP rs352139 was significantly associated with TB susceptiblity on a genotypic (P = 0.02) and allelic scale [p = 0.05, OR=0.70; (95% CI: 0.55–0.90)], with the T allele more frequent in controls. The TLR9 two SNP haplotype consisting of rs5743836 and rs352139 was linked (p = 0.037) to TB susceptibility, specifically the combination of the alleles A/T [p = 0.013, OR=0.71; (95% CI: 0.55–0.92)]. No gene-gene interaction between TLR2, TLR8 and TLR9 was observed. No significant conclusions could be drawn from the analysis of the mRNA and protein expression of CAMP in samples harbouring the different genotypes of the VDR polymorphism Cdx2. Genetic variations in the TLR8 and 9 genes were identified as potential factors that influence genetic host susceptibility to tuberculosis in the Coloured population of South Africa. / AFRIKAANSE OPSOMMING: Die oordragbare siekte tuberkulose (TB) is elke jaar verantwoordelik vir miljoene sterftes wêreldwyd. Die invloed van die gasheer genoom op TB vatbaarheid word huidiglik aanvaar, tesame met die invloed van omgewingsfaktore (dieet, oorbevolking ens.) en die bakterium Mycobacterium tuberculosis (M. tuberculosis). Dit is duidelik dat TB ‘n veelvlakkigesiekte is wat beïnvloed sal word deur ‘n menigte verskillende gene. ‘n Verskeidenheid gene is al betrek by TB genetiese vatbaarheid, onder andere NRAMP1 en HLA, hoewel hul effekte in uiteenlopende bevolkings verskil. Sommige van die onlangse gene wat betrek is in TB genetiese vatbaarheid is die Toll-like reseptore (TLRs). Genetiese variasie in hierdie gene is geassosieer met ‘n wye verskeidenheid van siektes, insluitend aansteeklik van aard, onder andere TB. In die geval van TB speel TLR2 ‘n prominente rol, terwyl TLR8 en TLR9 meer onlangs geïmpliseer is. Een van die meer bestudeerde TB vatbaarheidsgene is die vitamiene D reseptor geen (VDR). VDR is direk betrokke in die uitdrukking van die anti-mikrobiale geen cathelicidin (CAMP),’n integrale komponent in die vernietiging van mikobakterieë. Die CAMP geen het ‘n VDR respons-element in sy promotor. Die TLR2, VDR en CAMP gene word verbind deur ‘n komplekse netwerk wat integraal is tot die liggaam se vermoë om TB af te weer. Nege enkel nukleotied polimorfismes (ENPs) in drie gene (TLR2,8 & 9) is vir hierdie studie ondersoek, deur gebruik te maak van ‘n pasiënt-kontrole assosiasiestudies, om te bepaal watter rol hul speel in genetiese vatbaarheid vir TB in die Kleurling bevoling van Suid-Afrika, al dan nie. Die invloed van die VDR polimorfisme Cdx2 op die uitdrukking van die mRNS (boodskapper ribonukleïensuur) en proteïen van die geen CAMP is ook ondersoek. Ons het gevind dat drie gene beduidend bygedra het tot genetiese vatbaarheid vir TB in die Kleurling populasie. ‘n Alleel verwante assosiasie (p = 0.031) was gevind vir die TLR8 SNP rs3761624, waar die A-alleel meer algemeen was in vroue. Vier haplotipes vir TLR8 het beduidende assosiasies met TB vatbaarheid getoon. Die drie SNP haplotipe rs3761624-rs3764879- rs3764880, spesifiek die alleel kombinasie C/G/A [p = 0.004, OR = 2.67(95% CI: 1.90-3.74)] het sterk assosiasie (p = 0.001) met TB getoon. Die TLR9 intron-ekson2 grens SNP, rs352139 het beduidende assosiasie met TB getoon op ‘n genotipiese (p = 0.02) sowel as alleliese skaal [p = 0.05, OR=0.70; (95% CI: 0.55–0.90)], met die T alleel meer algemeen in kontroles. Die twee SNP haplotipe bestaande uit rs5743836 en rs352139 het TB vatbaarheid beïnvloed (p = 0.037), spesifiek die alleliese kombinasie van A/T [p = 0.013, OR=0.71; (95% CI: 0.55–0.92)]. Geen noemenswaardige interaksies tussen TLR2, 8 en 9 is gevind nie. So ook is geen beduidende resultate gevind vir die effek van die VDR SNP Cdx2 op die uitdrukking van CAMP mRNS en proteïen nie. Genetiese variasie in die TLR8 en 9 gene is geïdentifiseer as moontlike faktore wat gasheer genetiese vatbaarheid vir TB in die Kleurlingbevolking van Suid-Afrika beïnvloed. / WW Roome Trust

Over 9 million new cases of tuberculosis (TB) were reported worldwide in 2013. While the TB rate is much lower in the US, its uneven distribution and associated explanatory variables require interrogation in order to determine effective strategies for intervention and control. However, paucity of case data at fine geographic scales precludes such research. This research, using zip code level data from 837 confirmed TB cases in Tarrant County obtained from Texas Department of State Health Services, explores and attempts to explain the spatial patterns of TB and related risk markers within a framework of place vulnerability. Readily available census data is then used to characterize the spatial variations in TB risk. The resulting model will enable estimations of the geographic differences in TB case variables using this readily available census data instead of time-consuming and expensive individual data collection.

Introduction: Despite being one of the most preventable diseases, TB still remains a serious and largely neglected disease. Nurses as compared to the general population are at greater risk of acquiring nosocomial TB. This study was conducted to describe the perceptions of nurses on the underlying contributory factors that may lead to the spread of TB in the clinics treating TB patients. Methods: Quantitative, non – experimental, descriptive, exploratory and cross sectional design was used. A structured and pretested questionnaire was used. Findings: The key contributory factors identified were insufficient TB training for staff and lack of knowledge on the TB legislative framework and TB policy directives. Conclusion: The findings indicate the need for a comprehensive TB infection prevention and control policy, with associated standards for provision and practice. / Health Studies / M.A. (Public Health)

Introduction: Despite being one of the most preventable diseases, TB still remains a serious and largely neglected disease. Nurses as compared to the general population are at greater risk of acquiring nosocomial TB. This study was conducted to describe the perceptions of nurses on the underlying contributory factors that may lead to the spread of TB in the clinics treating TB patients. Methods: Quantitative, non – experimental, descriptive, exploratory and cross sectional design was used. A structured and pretested questionnaire was used. Findings: The key contributory factors identified were insufficient TB training for staff and lack of knowledge on the TB legislative framework and TB policy directives. Conclusion: The findings indicate the need for a comprehensive TB infection prevention and control policy, with associated standards for provision and practice. / Health Studies / M.A. (Public Health)