A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand , in fulfillment of the requirements for the degree of Master of Science in Medicine, 2013 / Sequence analysis from HIV-1 (human immunodeficiency virus type 1) subtype B and more recently subtype C infected patients has revealed that mutations in the HIV-1 protease region that confer drug resistance to boosted protease inhibitor (PIs) are rarely detected at the time of virological failure. Mutations in the HIV-1 subtype B gag-pol cleavage sites are thought to be compensatory mutations which arise as a result of PI use. This study investigated the presence of compensatory mutations in the HIV-1 subtype C gag-pol cleavage sites and matched pol genotypes from South African patients failing a boosted PI-based regimen, as compared to antiretroviral drug naïve patients. A new amplification protocol encompassing the near full-length gag, PR and partial RT was established and used to sequence the HIV-1 gag-pol cleavage sites from 23 proviral DNA samples (p24 antigen cultured peripheral blood mononuclear cells; PBMCs), and 51 patient samples (23 antiretroviral drug-naïve, 26 failing second-line lopinavir/ritonavir containing regimens), all attending the Charlotte Maxeke Johannesburg Hospital. Nucleotide sequences were aligned and codon positions S373Q, A431V, I437T/V, L449P or P453L associated with known gag-pol cleavage site mutations were analysed and compared. The pol genotypes were established using an in house assay. Antiretroviral drug resistant primary virus isolates were grown from samples from patients enrolled on the CIPRA-SA study, and propagated in coculture with PHA-activated, IL-2 stimulated PBMCs. HIV-1 gag-pol cleavage sites and pol genotypes for all primary virus isolates were established as described above. Fifty one of 74 patient samples, used to establish the in-house gag-pol cleavage site assay, were successfully amplified and sequenced. Detailed analysis of the five known gag-pol cleavage sites revealed that 5 patient samples (4 PI-exposed, 1 unknown regimen) encoded for the previously described mutations that impact on gag-pol cleavage in the absence of any major PR mutations. A further five samples from patients on the failing PI-based regimen had major PR mutations. No known mutations in the gag-pol region were identified in patients failing a first line regimen. The pol mutations described in this study were similar to the findings reported for treatment failures in South African HIV-1 subtype C infected patients. Primary virus was grown from only 25 of the 91 PBMC CIPRA samples. None of the 25 CIPRA-SA primary virus isolates had gag-pol cleavage site mutations, and only 9 harboured known RT antiretroviral drug resistant mutations. Overall, the presence of HIV-1 gag-pol cleavage site mutations may account for virological treatment failure in 5 of the South African patient samples analysed. Although the gag-pol cleavage site mutations detected in the current study are only present in a small proportion of treatment-experienced South African patients, this may increase due to more patients accessing second line PI-containing regimens. Thus, future genotyping work incorporating the analysis of the gag-pol cleavage sites in addition to the PR and RT regions is warranted. The antiretroviral drug resistant primary viruses obtained provide valuable reagents for future phenotyping studies.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 42-48).

Magister Public Health - MPH / Introduction: Zambia is among the countries in the sub-Saharan African region most severely affected with HIV/AIDS. Approximately 1.2 million (14%) Zambians were living with HIV in 2010. Zambia introduced antiretroviral therapy (ART) in the public sector in 2002, starting with two pilot sites, and rolling it out throughout the country in 2004 and 2005. To date,approximately 350,000 people have accessed HIV treatment. The long-term success of ART programs depends on optimal adherence to ART by patients.In 2010 Livingstone General Hospital (LGH), the setting for the current research had over 7,000 enrolled for HIV care of whom 3,880 patients were on ART. By the end of June 2011, it was reported that 343 patients in this hospital were between 2 to 30 days late for their medication refill appointments. This meant that these patients had missed more than one dose, and thus not meeting the required 95% of medication for viral suppression. This study explored the barriers to medication adherence experienced by ART patients at Livingstone General Hospital (LGH). Methodology: An exploratory qualitative study was conducted. Six focus group discussions(FGD) were conducted with 42 patients on ART, and follow up semi-structured interviews with 7 patients identified during the FGDs. FGDs and semi-structured interviews were audio-tape recorded and transcribed verbatim. Thematic and content analysis of transcribed data was done. Results: The study found that the barriers to ART adherence included socio-economic factors such as poverty, use of traditional complementary and alternative medicines (TCAM) and religious beliefs. Patient related factors reported to negatively affect adherence were HIV related-stigma and discrimination, alcohol use, low literacy and education levels, busy daily schedules and forgetfulness. Regimen related factors included experiencing side effects to medication and complexity of treatment regimen. Negative staff attitudes, traveling long distances to health facility, long waiting times, lack of confidentiality, poor health information and poor patient-health provider relationships were the health system factors that negatively impacted on ART adherence. Conclusion: The combination and complexity of factors affecting adherence identified in this study have posed a challenge to adherence to ART. People have been forced to make adjustments to their routine lives in order to accommodate ART. The most problematic factor identified was the use of TCAM in combination with ART or as replacement of ART.

Magister Chirurgiae Dentium (MChD) / TI and T2 squamous cell carcinomas of the head and neck have an unpredictable prognosis that often pose therapeutic problems. Sophisticated methods such as cytometric DNA analysis, immunocytochemistry and detection of cellular growth factors, have been applied with varying success rates for predicting recurrences, metastatic rates and overall prognoses. However, with the general lack of resources in Africa, devising a simple, reliable, reproducible and cost-effective method of predicting tumour behaviour to aid optimal treatment planning is imperative. Surgical excision specimens of forty-eight primary Tl and T2 squamous cell carcinomas of the floor of the mouth and tongue were histologically evaluated by two individual pathologists (double-blinded study) who had no prior knowledge of clinical course or outcome.

The Clinical Support Tools (CST) was developed to help therapists organize and target potential problems that might account for negative outcomes in psychotherapy. The core of CST feedback is The Assessment for Signal Clients (ASC). The purpose of this study was to describe and identify patterns of problems that typically characterize off-track cases. A cluster analysis of 107 off-track clients revealed three client types: those whose problems were characterized by alliance and motivational difficulties; those characterized by social support and life event difficulties; and those whose problems had an indistinguishable pattern. Loglinear modeling showed that if patients had less therapeutic alliance problems they were also less likely to have motivational problems. Findings were also consistent with the cluster analysis, which showed that a relatively higher percentage of not-on-track participants received signal alerts for the social support items and scale. Individuals whose progress goes off-track appear to have their greatest difficulty with social support, losses, and therapy task agreement.

Southern Africa has the highest prevalence of HIV worldwide, and South Africa has the highest number of HIV infected people. South Africa and other resource-limited countries provide antiretroviral therapy (ART) for people with HIV, with limited, standardized regimens for first line and second line. Patients who fail first line treatment are put on second line regimens, yet options for third line are very limited. The first study looks at predictors of first line treatment failure in South Africa and develops a predictive model that can estimate absolute risk of treatment failure over 5 years on ART, given a baseline profile of clinical and demographic factors. The model was developed with accelerated failure time models, using predictors that maximized discrimination between patients. The model can be used to identify patients who need adherence interventions, and to estimate how changes in baseline parameters in the population influence long-term need for second line ART. The second study explores whether delays from detection of first line treatment failure until second line treatment initiation, which are widespread in South Africa, decrease the effectiveness of second line ART. Marginal structural models were used to include patients who never switched to second line after failure in analysis. This study shows that, despite potency of second line drugs, short delays in second line among very sick patients can lead to worse outcomes. These findings may be due to drug resistance, immune system damage, and/or lack of adherence to medication. The third study examines whether switch in type of NRTI (nucleoside reverse transcriptase inhibitor, which is a drug class used in both first and second line regimens) from first line to second line improves outcomes on second line ART. While a switch in NRTI is recommended by treatment guidelines, it cannot always occur due to contraindications to some NRTIs. Using clinical data from South Africa and Zambia and adjusting for propensity scores, we see that switching from zidovudine in first line to a different NRTI in second line leads to less treatment failure on second line, suggesting that NRTI resistance may play a role in second line outcomes.

Racional: Aproximadamente um de cada cinco pacientes hospitalizados por pneumonia adquirida na comunidade (PAC) apresenta uma resposta clínica inadequada, sendo a mortalidade nestes pacientes de 40%. Os objetivos do estudo foram: determinar a incidência e as variáveis de associação independente com fracasso terapêutico da PAC, e os fatores prognósticos da PAC tratada em ambiente hospitalar. Métodos: Estudo de coorte, prospectivo, multicêntrico, com 425 pacientes hospitalizados por PAC. Os pacientes foram acompanhados de forma sistemática para identificação do fracasso terapêutico e seguidos até a alta hospitalar. Resultados: A incidência de fracasso terapêutico foi de 14,6% (62/425). Os preditores independentes de risco para o fracasso foram: insuficiência renal aguda à admissão (OR 2,9; IC 95% 1,2-7,2; p=0,017), progressão radiológica (OR 29,8; IC 95 8,1-109,7%; p<0,001), derrame pleural (OR 3,4; IC 95% 1,3-8,6; p=0,010), relação PaO2/FiO2 inferior a 250 à admissão (OR 2,7; IC 95% 1,1-6,7; p=0,017) e PSI classe V (OR 2,7; IC 95% 1,1-7,0; p=0,042). A mortalidade geral foi de 7,5%, e de 40,3% nos pacientes com fracasso. O fracasso terapêutico foi o principal fator independente de mortalidade na PAC (OR 85,3, IC 95% 18,8-387,4, p<0,0001). Conclusão: O fracasso terapêutico da PAC é freqüente, está associado a marcadores clínicos, radiológicos e laboratoriais identificáveis desde a admissão hospitalar (ou nos primeiros dias de acompanhamento), sendo o principal preditor independente de mortalidade. / Rational: One out of five patients hospitalized for community-acquired pneumonia (CAP) might have an inadequate response to empirical antimicrobial treatment, and the mortality among these patients may reach rates of up to 40%. The aims of the study were to: quantify the incidence of empirical treatment failure in CAP, identify risk factors for therapeutic failure and prognostic factors in CAP. Methods: Prospective, multicenter cohort study of 425 hospitalized patients for CAP. The systematic identification of treatment failure required a daily follow-up until hospital discharge. Results: The incidence of treatment failure was 14.6% (62/425). The independent risk factors associated with therapeutic failure in a logistic analysis were: acute renal failure (OR 2.9; 95% CI 1.2-7.2; p=0.017), radiological progression (OR 29.8; IC 95 8.1-109.7%; p<0.001), pleural effusion (OR 3.4; 95% CI 1.3-8.6; p=0.010), PaO2/FiO2 ratio < 250 (OR 2.7; 95% CI 1.1-6.7; p=0.017) e pneumonia severity index Class V (OR 2.7; 95% CI 1.1-7.0; p=0.042). Mortality was significantly higher in patients with therapeutic failure (40.3% vs. 7.5%). Treatment failure was the main prognostic factor associated with CAP (OR 85.3; 95% CI 18.8-387.4, p<0.0001). Conclusion: The treatment failure is frequently found and it is associated with clinical, radiological and laboratorial markers. It is also an important independent predictor of mortality in CAP.

Racional: Aproximadamente um de cada cinco pacientes hospitalizados por pneumonia adquirida na comunidade (PAC) apresenta uma resposta clínica inadequada, sendo a mortalidade nestes pacientes de 40%. Os objetivos do estudo foram: determinar a incidência e as variáveis de associação independente com fracasso terapêutico da PAC, e os fatores prognósticos da PAC tratada em ambiente hospitalar. Métodos: Estudo de coorte, prospectivo, multicêntrico, com 425 pacientes hospitalizados por PAC. Os pacientes foram acompanhados de forma sistemática para identificação do fracasso terapêutico e seguidos até a alta hospitalar. Resultados: A incidência de fracasso terapêutico foi de 14,6% (62/425). Os preditores independentes de risco para o fracasso foram: insuficiência renal aguda à admissão (OR 2,9; IC 95% 1,2-7,2; p=0,017), progressão radiológica (OR 29,8; IC 95 8,1-109,7%; p<0,001), derrame pleural (OR 3,4; IC 95% 1,3-8,6; p=0,010), relação PaO2/FiO2 inferior a 250 à admissão (OR 2,7; IC 95% 1,1-6,7; p=0,017) e PSI classe V (OR 2,7; IC 95% 1,1-7,0; p=0,042). A mortalidade geral foi de 7,5%, e de 40,3% nos pacientes com fracasso. O fracasso terapêutico foi o principal fator independente de mortalidade na PAC (OR 85,3, IC 95% 18,8-387,4, p<0,0001). Conclusão: O fracasso terapêutico da PAC é freqüente, está associado a marcadores clínicos, radiológicos e laboratoriais identificáveis desde a admissão hospitalar (ou nos primeiros dias de acompanhamento), sendo o principal preditor independente de mortalidade. / Rational: One out of five patients hospitalized for community-acquired pneumonia (CAP) might have an inadequate response to empirical antimicrobial treatment, and the mortality among these patients may reach rates of up to 40%. The aims of the study were to: quantify the incidence of empirical treatment failure in CAP, identify risk factors for therapeutic failure and prognostic factors in CAP. Methods: Prospective, multicenter cohort study of 425 hospitalized patients for CAP. The systematic identification of treatment failure required a daily follow-up until hospital discharge. Results: The incidence of treatment failure was 14.6% (62/425). The independent risk factors associated with therapeutic failure in a logistic analysis were: acute renal failure (OR 2.9; 95% CI 1.2-7.2; p=0.017), radiological progression (OR 29.8; IC 95 8.1-109.7%; p<0.001), pleural effusion (OR 3.4; 95% CI 1.3-8.6; p=0.010), PaO2/FiO2 ratio < 250 (OR 2.7; 95% CI 1.1-6.7; p=0.017) e pneumonia severity index Class V (OR 2.7; 95% CI 1.1-7.0; p=0.042). Mortality was significantly higher in patients with therapeutic failure (40.3% vs. 7.5%). Treatment failure was the main prognostic factor associated with CAP (OR 85.3; 95% CI 18.8-387.4, p<0.0001). Conclusion: The treatment failure is frequently found and it is associated with clinical, radiological and laboratorial markers. It is also an important independent predictor of mortality in CAP.

Racional: Aproximadamente um de cada cinco pacientes hospitalizados por pneumonia adquirida na comunidade (PAC) apresenta uma resposta clínica inadequada, sendo a mortalidade nestes pacientes de 40%. Os objetivos do estudo foram: determinar a incidência e as variáveis de associação independente com fracasso terapêutico da PAC, e os fatores prognósticos da PAC tratada em ambiente hospitalar. Métodos: Estudo de coorte, prospectivo, multicêntrico, com 425 pacientes hospitalizados por PAC. Os pacientes foram acompanhados de forma sistemática para identificação do fracasso terapêutico e seguidos até a alta hospitalar. Resultados: A incidência de fracasso terapêutico foi de 14,6% (62/425). Os preditores independentes de risco para o fracasso foram: insuficiência renal aguda à admissão (OR 2,9; IC 95% 1,2-7,2; p=0,017), progressão radiológica (OR 29,8; IC 95 8,1-109,7%; p<0,001), derrame pleural (OR 3,4; IC 95% 1,3-8,6; p=0,010), relação PaO2/FiO2 inferior a 250 à admissão (OR 2,7; IC 95% 1,1-6,7; p=0,017) e PSI classe V (OR 2,7; IC 95% 1,1-7,0; p=0,042). A mortalidade geral foi de 7,5%, e de 40,3% nos pacientes com fracasso. O fracasso terapêutico foi o principal fator independente de mortalidade na PAC (OR 85,3, IC 95% 18,8-387,4, p<0,0001). Conclusão: O fracasso terapêutico da PAC é freqüente, está associado a marcadores clínicos, radiológicos e laboratoriais identificáveis desde a admissão hospitalar (ou nos primeiros dias de acompanhamento), sendo o principal preditor independente de mortalidade. / Rational: One out of five patients hospitalized for community-acquired pneumonia (CAP) might have an inadequate response to empirical antimicrobial treatment, and the mortality among these patients may reach rates of up to 40%. The aims of the study were to: quantify the incidence of empirical treatment failure in CAP, identify risk factors for therapeutic failure and prognostic factors in CAP. Methods: Prospective, multicenter cohort study of 425 hospitalized patients for CAP. The systematic identification of treatment failure required a daily follow-up until hospital discharge. Results: The incidence of treatment failure was 14.6% (62/425). The independent risk factors associated with therapeutic failure in a logistic analysis were: acute renal failure (OR 2.9; 95% CI 1.2-7.2; p=0.017), radiological progression (OR 29.8; IC 95 8.1-109.7%; p<0.001), pleural effusion (OR 3.4; 95% CI 1.3-8.6; p=0.010), PaO2/FiO2 ratio < 250 (OR 2.7; 95% CI 1.1-6.7; p=0.017) e pneumonia severity index Class V (OR 2.7; 95% CI 1.1-7.0; p=0.042). Mortality was significantly higher in patients with therapeutic failure (40.3% vs. 7.5%). Treatment failure was the main prognostic factor associated with CAP (OR 85.3; 95% CI 18.8-387.4, p<0.0001). Conclusion: The treatment failure is frequently found and it is associated with clinical, radiological and laboratorial markers. It is also an important independent predictor of mortality in CAP.

I NTRODUÇÃO: A refratariedade aos inibidores da bomba de prótons (IBP) tem sido o grande desafio dos gastroenterologistas. Este trabalho visa caracterizar os pacientes que persistem com sintomas típicos de doença do refluxo gastroesofágico (DRGE), em uso de inibidores de bomba de prótons em doses de, pelo menos 40mg/dia, quanto aos aspectos demográficos, clínicos e laboratoriais, determinando-se a freqüência da persistência de refluxo ácido pela pH-metria esofágica de 24h. Secundariamente procurouse determinar a freqüência da esofagite eosinofílica nessa população. MÉTODO: Foram entrevistados 110 pacientes que apresentavam persistência de sintomas de pirose e/ou regurgitação em uso de pelo menos 40 mg de IBP por pelo menos 6 semanas. Os mesmos foram submetidos à endoscopia digestiva alta (EDA) com biópsia esofágica, manometria, pHmetria esofágica de duplo canal e exames laboratoriais. RESULTADOS: Dos pacientes avaliados, 77,3% eram do sexo feminino, com média de 46 anos e predomínio de baixa escolaridade. Apenas 10,9% eram tabagistas, 55% apresentavam índice de massa corpórea (IMC) acima de 25Kg/m2, sendo o IMC médio de 27Kg/m2. Entre as comorbidades, as mais freqüentes foram: alergias (72,7%); hipertensão arterial (34,5%), asma (18,2%), depressão (29,1%) e fibromialgia (8,2%), sendo estas duas últimas maiores que a encontrada na população geral. Observou-se freqüência elevada de sintomas dispépticos (70% dos pacientes relataram epigastralgia e 70% plenitude pós-prandial), disfagia (60,9%); globus (37,3%), tosse (37,3%) e dor torácia não cardíaca (30,9%). Apenas 16,4% evidenciavam à endoscopia, lesão em corpo esofágico e 23,6% hérnia de hiato. A maioria dos pacientes (61,8%) apresentava alguma alteração à manometria esofágica. Encontrou-se, entre os pacientes estudados, 24,6% com pHmetria positiva (8,1% no canal distal e 16,45% no proximal) e 75,4% com pH-metria normal. Comparando-se os resultados desses dois grupos de pacientes (pH-metria positiva e normal), segundo as variáveis estudadas, apenas a presença de lesão no corpo esofágico à endoscopia e a elevada escolaridade evidenciaram associação com persistência de pH-metria positiva (p: 0,0061 OR: 4,11 IC: 1,43:11,84 e p: 0,0237 OR: 2,74 IC: 1,13: 6,67 respectivamente). Ao se comparar presença de sintomas atípicos com a presença de refluxo ácido (no esôfago proximal versus distal), apenas globus apresentou associação com pH-metria positiva no canal proximal. Foi diagnosticado um único caso de esofagite eosinofílica entre os pacientes com sintomas típicos de DRGE refratários ao IBP. CONCLUSÃO: DRGE refratária predomina em mulheres de meia idade, associada à alta freqüência de história de alergia, depressão, fibromialgia e sintomas dispépticos. Segundo os resultados da pH-metria, a presença de esofagite erosiva em uso do IBP ou elevada escolaridade foram os únicos fatores de risco para a persistência de refluxo ácido nos dois canais, e globus no canal proximal. Não se observou diferença entre os pacientes com pH-metria positiva ou normal quanto às demais variáveis, até mesmo sintomas dispépticos. É baixa a freqüência de esofagite eosinofílica entre pacientes com pirose e/ou regurgitação refratários ao inibidor da bomba de próton / BACKGROUND: Proton pump inhibitor (PPI) refractory patients have been a big challenge to gastroenterologists. The aim of this study was to characterize the patients that had gastroesophageal reflux disease (GERD) persistent typical symptoms, undergoing PPI medication, administered at a dose of at least 40 mg/day, according to demographic, clinical and laboratory aspects. The primary outcome was to determine the frequency of acid reflux persistence based on the 24-hour esophageal pH-metry result. The secondary outcome was to determine, the frequency of eosinophilic esophagitis in the same population. METHODS: We interviewed 110 patients that presented persistence of heartburn and/or regurgitation symptoms and were undergoing treatment with PPI at a minimum dose of 40 mg/day for at least six weeks. They underwent upper gastrointestinal endoscopy with esophageal mucosa biopsy, esophageal manometry and double probe 24- hour esophageal pH-metry, as well as laboratory tests. RESULTS: 77.3% of the evaluated patients were female, with mean age of 46 years old, and most of them with low educational level. Only 10.9% were tobacco smokers and 55% had body mass index (BMI) greater than 25Kg/m2, showing mean BMI of 27Kg/m2. The most frequent comorbidities were allergy (72.7%), arterial systemic hypertension (34.5%), asthma (18.2%), depression (29.1%) and fibromyalgia (8.2%). Comparing the general population and the group of patients, a higher frequency of depression and fibromyalgia was observed. Some symptoms were found in high frequency: dyspeptic symptoms (70% associated with epigastric pain and 70% with postprandial fullness), dysphagia (60.9%), globus and cough (37.3% each) and no-cardiac chest pain (30.9%). By endoscopy, only 16.4% showed esophageal body lesion and 23.6% hiatal hernia. Most patients (61.8%) presented some alteration in esophageal manometry. Among studied patients, 24.6% had abnormal pHmetry (8.1% in distal probe and 16.45% in the upper probe) and 75.4%, a normal result. When comparing normal to abnormal pH-metry patients according to studied variables only the presence of esophageal body lesion, observed by endoscopy, and high educational level were associated to the persistence of abnormal pH-metry (p: 0.0061; OR: 4.11; IC: 1.43:11.84; and p: 0.0237; OR: 2.74; IC: 1.13: 6.67; respectively). When comparing atypical symptoms with the presence of acid reflux (proximal versus distal esophagus) only globus was associated with abnormal upper probe pHmetry. Only one patient was diagnosed with eosinophilic esophagitis among the total sample with typical gastroesophageal reflux symptoms refractory to PPI treatment. CONCLUSION: Refractory GERD was predominant in middleaged females, associated with high frequency of previous allergy, depression, fibromyalgia and dyspeptics symptoms. The risk factors to the persistence of acid reflux in the two pH-metry probes and to the symptom of globus in the upper pH-metry probe were the persistence of erosive esophagitis in patients undergoing treatment with PPI an a higher educational level. No differences between abnormal or normal pH-metry results patients were found regarding the other variables, such as dyspeptic symptoms. The frequency of eosinophilic esophagitis was low in heartburn and/or regurgitation in PPI refractory patients