Thesis (MScMedSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: Application of molecular fingerprinting highlights transmission as the driving force behind the drug resistant epidemic in South Africa. Different strains dominate within different geographical regions, which is a reflection of micro-epidemics of drug resistance in the different regions. Cluster analysis shows that strains within the same strain family are different. The Beijing drug resistant strain family is the most dominant strain family (31%) in the Western Cape and of particular concern is the highly transmissible Beijing cluster 220 strain in the Western Cape communities. This cluster is widespread in the region and was previously identified in a MDR outbreak in a high school in Cape Town. Results suggest that the spread of Beijing drug resistant cluster 220 in the community was due to a combination of acquisition of drug resistant markers and transmission. This study also indicate that atypical Beijing can acquire drug resistance and become fit amongst HIV infected individuals. This is contrary to believe that atypical Beijing strains are not frequently associated with drug resistance and are attenuated. This implies that HIV levels the playing field for all drug resistant strains. Mechanisms leading to the evolution of MDR-TB and XDR-TB in a mine setting with a wellfunctioning TB control program which exceeds the target for cure rates set by the WHO were investigated. Despite the excellent control program, an alarming increase in the number of drug resistant cases was observed in 2003 and subsequent years. Phylogenetic analysis shows sequential acquisition of resistance to first and second-line anti-TB drugs leading to the development of MDR and XDR-TB. Contact tracing indicate extensive transmission of drug resistant TB in the shafts, hospital and place of residence. This study shows that despite exceeding the WHO cure rate target, it was not possible to control the spread and amplification of drug resistance. In summary, as a top priority, future TB control plans need to address diagnostic delay more vigorously. / AFRIKAANSE OPSOMMING: Molukulêre tegnieke toon transmissie as die hoofrede vir die toename in die anti-tuberkulose middelweerstandigheid epidemie in Suid-Afrika. Die verskillende Mikobakterium tuberkulose rasse wat domineer in verskillende areas is ‘n refleksie van middelweerstandige mikro-epidemies in verskillende gebiede. Analise van identiese rasgroepe demonstreer dat ras families bestaan uit verskillende rasse. Die Beijing middelweerstandige rasfamilie is die mees dominante familie in die Wes-Kaap (31% van monsters van middelweerstandige families) en van spesifieke belang is die hoogs oordraagbare Beijing 220 groep. Hierdie groep is die mees wydverspreide groep in die studie area en was voorheen geïdentifiseer tydens ‘n meervoudige middelweerstandige uitbreking in ‘n hoërskool in Kaapstad. Die resultate dui aan dat die Beijing middelweerstandige groep 220 in die gemeenskap versprei as gevolg van ‘n kombinasie van middelweerstand verwerwing en transmissie. Hierdie studie dui verder aan dat die atipiese Beijing ook middelweerstandigheid kan verwerf en hoogs geskik is vir infeksie veral in MIV geïnfekteerde individue. Hierdie data is in teenstelling met die algemene denke dat atipiese Beijing nie gereeld geassosieer word met middelweerstandigheid nie en dat dit dikwels geattenueer is. Dit beteken dat MIV die hoof faktor is wat alle middelweerstandige rasse kans gee om te versprei. Hierdie studie het die meganisme wat lei tot die evolusie van middelweerstandigheid en “XDRTB” in die myne ondersoek. Die myn besit ‘n goeie funksioneerde tuberkulose kontrole program wat alreeds die Wêreld Gesondheids Organisasie se mikpunt vir tuberkulose genesing oortref. Ten spyte van ‘n uitstekende tuberkulose kontrole program, is daar ‘n bekommerenswaardige toename in die aantal middelweerstandige tuberkulose gevalle waargeneem in 2003 en in die daaropvolgende jare. Filogenetiese analise wys dat opeenvolgende verwerwing van middelweerstandigheid teen eerste en tweede vlak anti-tuberkulose middels gelei het tot die ontwikkeling van meervoudige middelweerstandigheid en “XDR-TB”. Die opsporing van kontakpersone om transmissie te bewys dui aan dat transmissie van middelweerstandige tuberkulose in die werk plek, hospitaal en woon plek plaasvind. Hierdie studie wys dat ongeag die feit dat die Wêreld Gesondheids Organisasie se genesings verwagtinge oortref is, dit steeds onmoontlik was om die verspreiding en amplifisering van middelweerstandigheid te beheer. ‘n Top prioriteit vir tuberkulose kontrole planne in die toekoms behoort die vertraging van diagnose sterk aan te spreek.

This quantitative, descriptive study investigated factors that contributed to TB patients registered in four Tembisa clinics in 2001, defaulting treatment. An interview schedule with closed and open-ended questions was used for 30 patients who could be traced who had interrupted treatment. The reasons for treatment interruption were related to socio-economic, TB policy-related and health care worker-related factors. The findings illustrate that TB management requires a multi-sectoral approach and joint efforts to tackle the disease that continues to kill people even though it is curable. / Health Studies / M.A. (Health Studies)

The study investigated the knowledge levels of clients on long-term tuberculosis (TB) treatment at Kwekwe General Hospital, Zimbabwe. A quantitative, descriptive research design was chosen and data was collected using a structured questionnaire with a convenience sample of 60 clients on TB treatment and 10 professional nurses. The major findings of the study were that although clients had some knowledge about their condition, there was a lack of knowledge regarding critical aspects such as information on drug-resistant TB and the Directly Observed Therapy Short Course. The professional nurses experienced constraints such as insufficient time for appropriate health education and home visits. Based on the study findings and conclusions, several recommendations were made. / Health Studies / Thesis(M.A(Health Studies))

KwaZulu-Natal has been ranked as having the fourth highest incidence of transmitted Multiple Drug Resistant-Tuberculosis (MDR-TB) in sub-Saharan Africa. Substantial literature exists indicating the permanent damage that MDR-TB medication has on hearing abilities. The purpose of this study was to describe the hearing function of adults on long term MDR-TB treatment from Murchison Hospital MDR-TB unit in the Ugu District in rural KwaZulu-Natal. The primary aim of the study was to review the possible changes in hearing function in a group of adults on long-term treatment for MDR-TB. Secondly, the study aimed to estimate the number of adults who may present with changes following MDR-TB treatment and establish if relationships exist between the audiological findings and factors such as age and gender. The design of the study was a retrospective comparative data review of 68 patient records, all of which underwent audiological investigations from the start of MDR-TB treatment over a five-month period. The study made use of descriptive and inferential statistics to analyse the data. Specific inferential statistical analysis included analysis of covariance as well as regression analysis. Results from the study showed changes in hearing function in Distortion Product Otoacoustic Emissions (DPOAEs) and Pure Tone Audiometry (PTA) results at all five audiological sessions and across a range of frequencies. 84% of the total sample presented with overall refer readings for DPOAEs and 98.53% of the group of adults presented with criteria indicative of ototoxic hearing loss, specifically a bilateral mild-profound sloping SNHL on clinical PTA results. In the total sample of patient records reviewed in this study, all 68 records showed a change in hearing function, be that changes in DPOAE function and/or changes in PTA thresholds, following long-term treatment for MDR-TB. Variations in the effects of gender and ear difference were minimal and non-significant in all results. Similar presentation, to ototoxic hearing loss, of other degenerative conditions exists; however these conditions were accounted for as exclusion criteria in this study. Therefore the only remaining cause of possible hearing deficit was that of ototoxicity. The study provided valuable data regarding hearing function in a population of adults on long-term MDR-TB treatment in South Africa. Furthermore, the study has highlighted the need for the establishment of standardised audiological monitoring programmes sensitive to ototoxic hearing loss, within the South African context where the incidence of Tuberculosis (TB) and MDR-TB is reportedly high.

A tuberculose (TB) embora passível de tratamento efetivo, ainda é um grave problema de saúde pública em diversos países, inclusive no Brasil. Nas últimas décadas houve progressos consistentes no controle da doença, porém o avanço da resistência bacilar ainda é um desafio a ser superado, já que os mecanismos da resistência são bastante complexos e não totalmente conhecidos, o que dificulta o desenvolvimento de testes de sensibilidade com elevada acurácia. O objetivo deste trabalho foi caracterizar as mutações gênicas de cepas de Mycobacterium tuberculosis de pacientes do Brasil e de Moçambique com doença resistente a drogas através do sequenciamento genômico total, além de descrever padrões de mutações obtidos por testes moleculares comerciais e comparar estes dados com resultados de testes fenotípicos. Estudo descritivo e transversal que incluiu 30 isolados (17 do Brasil e 13 de Moçambique), submetidos aos testes moleculares comerciais Genotype MTBDRplus®, Genotype MTBDRsl®, Xpert MTB/RIF® e teste fenotípico BACTEC MGIT 960 SIRE®. Todos os isolados também foram avaliados pelo sequenciamento genômico realizado pelo Illumina MiSeq Sequencing System® e submetidos a análise de mutações que conferem resistência às drogas contra TB utilizando o TB profiler online tool. A sensibilidade e especificidade do sequenciamento genômico para detecção de resistência a rifampicina foi de 87,5% e 92,3%, respectivamente. Além disso, o sequenciamento detectou a mutação (Val170Phe) no gene rpoB em dois isolados de M. tuberculosis de Moçambique. Esta mutação não é detectada pelos testes genotípicos comerciais. A sensibilidade do sequenciamento para a isoniazida foi de 95,6% e a especificidade de 100%. Para a estreptomicina, a sensibilidade foi de 85,7% e a especificidade de 93,3%. Para o etambutol, observamos sensibilidade de 100% e especificidade de 77,2%. As mutações mais frequentes associadas à resistência à rifampicina foram a Ser450Leu e a His445Tyr no gene rpoB. Em relação à isoniazida, predominou a mutação Ser315Thr no gene katG. O sequenciamento genômico, dado seu alto poder discriminatório, tem grande potencial de fornecer informações mais acuradas sobre mecanismo gênicos da resistência bacilar, possibilitando futuramente o aprimoramento de testes diagnósticos mais precisos. / Although there is an effective treatment for tuberculosis (TB), it is still a serious public health problem in several countries, including Brazil. In the last decades, there has been consistent progress in disease control, but the increasing number of disease caused by resistant strains is still a challenge to be overcome, since the mechanisms of resistance are quite complex and not fully known, which difficult the development of susceptibility tests with high accuracy. The aim of this work was to characterize gene mutations of Mycobacterium tuberculosis strains from Brazilian and Mozambican patients with drug-resistant disease through whole genome sequencing, as well as to describe patterns of mutations obtained by commercial molecular tests and to compare these data with results of phenotypic susceptibility tests. It was a cross-sectional study that included 30 isolates (17 from Brazil and 13 from Mozambique). Commercial molecular tests Genotype MTBDRplus(TM), Genotype MTBDRsl(TM), Xpert MTB / RIF(TM) and BACTEC MGIT 960 SIRE(TM) phenotypic test were performed for all isolates. All of them were also evaluated by whole genome sequencing performed by the Illumina MiSeq Sequencing System(TM) and submitted to analysis of mutations that confer drug resistance against TB using the TB profiler online tool. The sensitivity and specificity of whole genome sequencing for detection rifampicin resistance was 87.5% and 92.3%, respectively. Also, whole genome sequencing detected the mutation (Val170Phe) in the rpoB gene in two isolates of M. tuberculosis from Mozambique. This mutation is not detected by commercial genotypic tests. The sensitivity of the whole genome sequencing for isoniazid was 95.6%, and the specificity was 100%. For streptomycin, the sensitivity was 85.7%, and the specificity was 93.3%. For ethambutol, we observed a sensitivity of 100% and specificity of 77.2%. The most frequent mutations associated with rifampicin resistance were rpoB Ser450Leu and His445Tyr. About isoniazid, the katG Ser315Thr mutation was the most frequent. Whole genome sequencing, given its high discriminatory power, has great potential to provide more accurate information about the gene mechanisms of bacilli resistance, making possible the improvement of more accurate diagnostic tests in the future.

This quantitative, descriptive study investigated factors that contributed to TB patients registered in four Tembisa clinics in 2001, defaulting treatment. An interview schedule with closed and open-ended questions was used for 30 patients who could be traced who had interrupted treatment. The reasons for treatment interruption were related to socio-economic, TB policy-related and health care worker-related factors. The findings illustrate that TB management requires a multi-sectoral approach and joint efforts to tackle the disease that continues to kill people even though it is curable. / Health Studies / M.A. (Health Studies)

The study investigated the knowledge levels of clients on long-term tuberculosis (TB) treatment at Kwekwe General Hospital, Zimbabwe. A quantitative, descriptive research design was chosen and data was collected using a structured questionnaire with a convenience sample of 60 clients on TB treatment and 10 professional nurses. The major findings of the study were that although clients had some knowledge about their condition, there was a lack of knowledge regarding critical aspects such as information on drug-resistant TB and the Directly Observed Therapy Short Course. The professional nurses experienced constraints such as insufficient time for appropriate health education and home visits. Based on the study findings and conclusions, several recommendations were made. / Health Studies / Thesis(M.A(Health Studies))

A tuberculose (TB) embora passível de tratamento efetivo, ainda é um grave problema de saúde pública em diversos países, inclusive no Brasil. Nas últimas décadas houve progressos consistentes no controle da doença, porém o avanço da resistência bacilar ainda é um desafio a ser superado, já que os mecanismos da resistência são bastante complexos e não totalmente conhecidos, o que dificulta o desenvolvimento de testes de sensibilidade com elevada acurácia. O objetivo deste trabalho foi caracterizar as mutações gênicas de cepas de Mycobacterium tuberculosis de pacientes do Brasil e de Moçambique com doença resistente a drogas através do sequenciamento genômico total, além de descrever padrões de mutações obtidos por testes moleculares comerciais e comparar estes dados com resultados de testes fenotípicos. Estudo descritivo e transversal que incluiu 30 isolados (17 do Brasil e 13 de Moçambique), submetidos aos testes moleculares comerciais Genotype MTBDRplus®, Genotype MTBDRsl®, Xpert MTB/RIF® e teste fenotípico BACTEC MGIT 960 SIRE®. Todos os isolados também foram avaliados pelo sequenciamento genômico realizado pelo Illumina MiSeq Sequencing System® e submetidos a análise de mutações que conferem resistência às drogas contra TB utilizando o TB profiler online tool. A sensibilidade e especificidade do sequenciamento genômico para detecção de resistência a rifampicina foi de 87,5% e 92,3%, respectivamente. Além disso, o sequenciamento detectou a mutação (Val170Phe) no gene rpoB em dois isolados de M. tuberculosis de Moçambique. Esta mutação não é detectada pelos testes genotípicos comerciais. A sensibilidade do sequenciamento para a isoniazida foi de 95,6% e a especificidade de 100%. Para a estreptomicina, a sensibilidade foi de 85,7% e a especificidade de 93,3%. Para o etambutol, observamos sensibilidade de 100% e especificidade de 77,2%. As mutações mais frequentes associadas à resistência à rifampicina foram a Ser450Leu e a His445Tyr no gene rpoB. Em relação à isoniazida, predominou a mutação Ser315Thr no gene katG. O sequenciamento genômico, dado seu alto poder discriminatório, tem grande potencial de fornecer informações mais acuradas sobre mecanismo gênicos da resistência bacilar, possibilitando futuramente o aprimoramento de testes diagnósticos mais precisos. / Although there is an effective treatment for tuberculosis (TB), it is still a serious public health problem in several countries, including Brazil. In the last decades, there has been consistent progress in disease control, but the increasing number of disease caused by resistant strains is still a challenge to be overcome, since the mechanisms of resistance are quite complex and not fully known, which difficult the development of susceptibility tests with high accuracy. The aim of this work was to characterize gene mutations of Mycobacterium tuberculosis strains from Brazilian and Mozambican patients with drug-resistant disease through whole genome sequencing, as well as to describe patterns of mutations obtained by commercial molecular tests and to compare these data with results of phenotypic susceptibility tests. It was a cross-sectional study that included 30 isolates (17 from Brazil and 13 from Mozambique). Commercial molecular tests Genotype MTBDRplus(TM), Genotype MTBDRsl(TM), Xpert MTB / RIF(TM) and BACTEC MGIT 960 SIRE(TM) phenotypic test were performed for all isolates. All of them were also evaluated by whole genome sequencing performed by the Illumina MiSeq Sequencing System(TM) and submitted to analysis of mutations that confer drug resistance against TB using the TB profiler online tool. The sensitivity and specificity of whole genome sequencing for detection rifampicin resistance was 87.5% and 92.3%, respectively. Also, whole genome sequencing detected the mutation (Val170Phe) in the rpoB gene in two isolates of M. tuberculosis from Mozambique. This mutation is not detected by commercial genotypic tests. The sensitivity of the whole genome sequencing for isoniazid was 95.6%, and the specificity was 100%. For streptomycin, the sensitivity was 85.7%, and the specificity was 93.3%. For ethambutol, we observed a sensitivity of 100% and specificity of 77.2%. The most frequent mutations associated with rifampicin resistance were rpoB Ser450Leu and His445Tyr. About isoniazid, the katG Ser315Thr mutation was the most frequent. Whole genome sequencing, given its high discriminatory power, has great potential to provide more accurate information about the gene mechanisms of bacilli resistance, making possible the improvement of more accurate diagnostic tests in the future.

PURPOSE: The purpose of this study was to assess factors associated with the development of drug resistant tuberculosis in Ethiopia. DESIGN: A quantitative case-control study was conducted to determine if there were any significant differences in prevalence of pre-defined factors between cases and controls. METHODS: Cases were patients with drug resistant tuberculosis who had a confirmed diagnosis by culture drug-susceptibility or gene expert tests. Successfully treated, tuberculosis symptom free patients who had been on first-line tuberculosis treatment and who were registered as cured or treatment completed were taken as controls. An equal number of cases (N=181) and controls (N=181) was selected using a systematic random sampling method and was used in the study. A structured questionnaire developed by the researcher was used to collect data. Odds ratio and multiple logistic regression were used to quantify the strength of association between dependent and independent variables. RESULTS: The development of drug resistant tuberculosis was significantly associated with two or more previous episodes of tuberculosis illness (adjusted odds ratio (AOR): 14.84; 95% CI 8.90 –24.75), previous first-line tuberculosis treatment not directly observed by a health worker for 7 to 8 weeks (AOR: 13.41; 95% CI 8.06 – 22.29) and previous first-line tuberculosis treatment outcome of failure (AOR: 39.19; 95% CI 12.05 -127.46). Interruption of first-line tuberculosis treatment for one day or more (AOR = 4.28; 95% CI 2.76 – 6.64) and history of treatment in the first-line tuberculosis treatment category for previously treated patients (AOR: 3.70; 95% CI 2.40 – 5.72) were also significantly associated with the development of drug resistant tuberculosis in the current study. CONCLUSION: Patients with a history of previous first-line tuberculosis treatment, patients who interrupted previous first-line tuberculosis treatment and patients with previous first-line tuberculosis treatment outcome of failure were at high risk of developing drug resistant tuberculosis. Therefore, the full course of first-line tuberculosis treatment should be given, following the Directly Observed Treatment (DOT) guide. Patients with recurrent tuberculosis and unfavourable first-line tuberculosis treatment outcome should be tested for drug susceptibility. / Health Studies / D. Litt. et Phil. (Health Studies)

Background: Disabling hearing loss is a global burden. This burden is worsened by the emergence of multi-drug resistant tuberculosis (MDR-TB). Some of the medications used to treat MDR-TB are damaging to the cochlea and auditory nerve (ototoxic) and can lead to permanent hearing loss and/or balance disorders. Ototoxicity monitoring aims to reduce this burden by preventing or minimising the damage caused by ototoxic treatment as it can progress and worsen speech perception difficulties. However, the proposed test battery for ototoxicity monitoring is lengthy and demands active participation which is not ideal for ill patients (such as those on MDR-TB treatment). The Sensitive Range of Ototoxicity (SRO) technique is recommended to shorten the test time. The SRO consists of seven consecutive relatively high frequencies determined from the highest frequency the participant responded to. The SRO technique is time efficient. Although the SRO technique provides the prospect of a shortened test battery, there is still a global lack of audiologists. Automated audiometry is a vital application for testing especially when audiologists are not available to physically do the test. Automated audiometry has been previously validated. Clinically, automated audiometry is objective and allows for standardisation. Even though automated audiometry helps improve access to monitoring more patients, patient preference is an important factor when using automated audiometry to ensure patient-centred care is not compromised. Aims and Objectives: This study aimed to investigate the specificity and sensitivity of the SRO technique with automated audiometry compared to the gold standard (manual audiometry). This comparison was made by firstly, determining the testing time efficiency and the correlation of thresholds obtained with the different test methods and, secondly, testing the diagnostic value of automated audiometry using the SRO technique. The incidence of an ototoxicity-induced hearing loss was described by determining the time interval between starting ototoxic MDR-TB treatment and the onset of a significant threshold shift (STS) according to ASHA's criteria. Lastly, the test method preference of the participants with MDR-TB was described and compared using a short exit survey. Study Design: A prospective repeated-measures study design was used. Participants were chosen based on a risk factor (i.e. exposure to ototoxic medication) for an outcome of interest (i.e. the presence or absence of an STS). With a repeated measures study, multiple tests using different test methods can be compared with the same sample. Participants: Twenty-seven in-patients at Brooklyn Chest Hospital and DP Marais TB Hospital with normal hearing and on MDR-TB medication were included in the study. Their age range was from 19 to 51 years old with an average age of 33 years old. Non-probability convenience sampling was used as it was cost-effective, reduced data collection time and was relatively easy to execute. Data collection materials and procedures: The procedure for data collection included weekly follow-up testing for a maximum of four weeks. The test battery was as follows: an auditory symptom questionnaire, otoscopy examination, and manual and automated audiometry using the SRO technique with a fifteen-minute break in between. Participants were tested with the KUDUwave ™ in a non-sound treated room. The frequency range was determined with the SRO technique. If an STS was obtained, the patient was discharged from the study after completing an exit survey. Statistics: Analysis included descriptive statistics and inferential statistics. A Bonferroni corrected p-value (initially p ≤ 0.05) was used. Manual and automated audiometry thresholds were compared using the Pearson's Correlation Coefficient test. Manual and automated audiometry testing time and threshold means were compared using paired sample's t-tests. The diagnostic value of automated audiometry with the SRO technique was assessed with Receiver Operating Characteristics (ROC) Curves. Results: Manual audiometry was statistically more time-efficient compared to automated audiometry by an average of one minute and ten seconds (t (94) = -5.44; p< 0.003). There was a strong positive correlation for both left and right ears between the thresholds' obtained from manual and automated audiometry at 8kHz to 16 kHz (df> 28 = r > 0.70, p< 0.003). Automated audiometry was found to be a fair diagnostic test (area under the curve was 0.75; p= 0.002). Also, the ROC curve revealed that automated audiometry had a sensitivity of 61% and specificity of 90% when compared to manual audiometry (gold standard). Only participants that started data collection within 31 days after starting their MDR-TB treatment were included in the analysis of determining the incidence of an ototoxicity-induced hearing loss (n= 24 ears). This study found that 41.67% of ears (n= 10) had an ototoxicity-induced hearing loss. A box and whisker plot revealed that data was skewed to the right (i.e. more variation in data between the median and the maximum values) and that the median number of days for an ototoxicity-induced hearing loss to appear was 33 days. Secondly, 55.55% of participants (n=15 out of 27) reported auditory symptoms before data collection commencement. Aural fullness was the most reported symptom (n= eight out of 15). Ten out of 15 (66.66%) participants that reported auditory symptoms obtained an ototoxicity-induced hearing loss. Lastly, most participants (i.e. 13 out of 19; 68.42%) that completed the exit survey had no preference between manual or automated audiometry. The common rationale among these participants was “No difference noted.” Conclusion: This research study has revealed that manual audiometry was more time-efficient compared to automated audiometry in patients with MDR-TB. Also, automated audiometry was a fair diagnostic test. It may aid in reducing the disproportionate audiologist to patient ratio, especially in a developing country. However, manual audiometry (with the SRO technique) is more clinically appropriate in patients that are difficult-to-test. Secondly, audiometric settings can be changed to accommodate testing frequencies in 1/6 octaves so that the SRO technique can be clinically adopted. An ototoxicity-induced hearing loss seems to appear 33 days after ototoxic MDR-TB treatment commencement. Aural fullness was a commonly reported symptom among participants with MDRTB. Aural fullness is omnipresent in peripheral auditory pathologies. Therefore, auditory symptoms reported by patients' needs a comprehensive audiological investigation. Lastly, more research is needed on how patients (and clinicians) experience the advances in technology innovation especially in audiology where technology innovation is continuously evolving.