Browsing by Author "Schomaker, Michael"

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    Open Access
    Baseline Predictors of Sputum Culture Conversion in Pulmonary Tuberculosis: Importance of Cavities, Smoking, Time to Detection and W-Beijing Genotype
    (Public Library of Science, 2012) Visser, Marianne E; Stead, Michael C; Walzl, Gerhard; Warren, Rob; Schomaker, Michael; Grewal, Harleen M S; Swart, Elizabeth C; Maartens, Gary
    BACKGROUND: Time to detection (TTD) on automated liquid mycobacterial cultures is an emerging biomarker of tuberculosis outcomes. The M. tuberculosis W-Beijing genotype is spreading globally, indicating a selective advantage. There is a paucity of data on the association between baseline TTD and W-Beijing genotype and tuberculosis outcomes. Aim To assess baseline predictors of failure of sputum culture conversion, within the first 2 months of antitubercular therapy, in participants with pulmonary tuberculosis. Design Between May 2005 and August 2008 we conducted a prospective cohort study of time to sputum culture conversion in ambulatory participants with first episodes of smear and culture positive pulmonary tuberculosis attending two primary care clinics in Cape Town, South Africa. Rifampicin resistance (diagnosed on phenotypic susceptibility testing) was an exclusion criterion. Sputum was collected weekly for 8 weeks for mycobacterial culture on liquid media (BACTEC MGIT 960). Due to missing data, multiple imputation was performed. Time to sputum culture conversion was analysed using a Cox-proportional hazards model. Bayesian model averaging determined the posterior effect probability for each variable. RESULTS: 113 participants were enrolled (30.1% female, 10.5% HIV-infected, 44.2% W-Beijing genotype, and 89% cavities). On Kaplan Meier analysis 50.4% of participants underwent sputum culture conversion by 8 weeks. The following baseline factors were associated with slower sputum culture conversion: TTD (adjusted hazard ratio (aHR) = 1.11, 95% CI 1.02; 1.2), lung cavities (aHR = 0.13, 95% CI 0.02; 0.95), ever smoking (aHR = 0.32, 95% CI 0.1; 1.02) and the W-Beijing genotype (aHR = 0.51, 95% CI 0.25; 1.07). On Bayesian model averaging, posterior probability effects were strong for TTD, lung cavitation and smoking and moderate for W-Beijing genotype. CONCLUSION: We found that baseline TTD, smoking, cavities and W-Beijing genotype were associated with delayed 2 month sputum culture. Larger studies are needed to confirm the relationship between the W-Beijing genotype and sputum culture conversion.
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    A comparison of death recording by health centres and civil registration in South Africans receiving antiretroviral treatment
    (Journal of the International AIDS Society, 2015-12-16) Johnson, Leigh F; Dorrington, Rob E; Laubscher, Ria; Hoffmann, Christopher J; Wood, Robin; Fox, Matthew P; Cornell, Morna; Schomaker, Michael; Prozesky, Hans; Tanser, Frank; Davies, Mary-Ann; Boulle, Andrew
    Introduction: There is uncertainty regarding the completeness of death recording by civil registration and by health centres in South Africa. This paper aims to compare death recording by the two systems, in cohorts of South African patients receiving antiretroviral treatment (ART). Methods: Completeness of death recording was estimated using a capture-recapture approach. Six ART programmes linked their patient record systems to the vital registration system using civil ID numbers, and provided data comparing the outcomes recorded in patient files and in the vital registration. Patients were excluded if they had missing/invalid IDs or had transferred to other ART programmes. Results: After exclusions, 91 548 patient records were included. Of deaths recorded in patients files after 2003, 94.0% (95% CI: 93.3-94.6%) were recorded by civil registration, with completeness being significantly higher in urban areas, older adults and females. Of deaths recorded by civil registration after 2003, only 35.0% (95% CI: 34.2-35.8%) were recorded in patient files, with this proportion dropping from 60% in 2004-2005 to 30% in 2010 and subsequent years. Recording of deaths in patient files was significantly higher in children and in locations within 50km of the health centre. When the information from the two systems was combined, an estimated 96.2% of all deaths were recorded (93.5% in children and 96.2% in adults). Conclusions: South Africa’s civil registration system has achieved a high level of completeness in the recording of mortality. However, the fraction of deaths recorded by health centres is low and information from patient records is insufficient by itself to evaluate levels and predictors of ART patient mortality. Previously-documented improvements in ART mortality over time may be biased if based only on data from patient records.
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    Effectiveness of patient adherence groups as a model of care for stable patients on antiretroviral therapy in Khayelitsha, Cape Town, South Africa
    (Public Library of Science, 2013) Luque-Fernandez, Miguel Angel; Cutsem, Gilles Van; Goemaere, Eric; Hilderbrand, Katherine; Schomaker, Michael; Mantangana, Nompumelelo; Mathee, Shaheed; Dubula, Vuyiseka; Ford, Nathan; Hernán, Miguel A
    BACKGROUND: Innovative models of care are required to cope with the ever-increasing number of patients on antiretroviral therapy in the most affected countries. This study, in Khayelitsha, South Africa, evaluates the effectiveness of a group-based model of care run predominantly by non-clinical staff in retaining patients in care and maintaining adherence. Methods and FINDINGS: Participation in "adherence clubs" was offered to adults who had been on ART for at least 18 months, had a current CD4 count >200 cells/ml and were virologically suppressed. Embedded in an ongoing cohort study, we compared loss to care and virologic rebound in patients receiving the intervention with patients attending routine nurse-led care from November 2007 to February 2011. We used inverse probability weighting to estimate the intention-to-treat effect of adherence club participation, adjusted for measured baseline and time-varying confounders. The principal outcome was the combination of death or loss to follow-up. The secondary outcome was virologic rebound in patients who were virologically suppressed at study entry. Of 2829 patients on ART for >18 months with a CD4 count above 200 cells/µl, 502 accepted club participation. At the end of the study, 97% of club patients remained in care compared with 85% of other patients. In adjusted analyses club participation reduced loss-to-care by 57% (hazard ratio [HR] 0.43, 95% CI = 0.21-0.91) and virologic rebound in patients who were initially suppressed by 67% (HR 0.33, 95% CI = 0.16-0.67). DISCUSSION: Patient adherence groups were found to be an effective model for improving retention and documented virologic suppression for stable patients in long term ART care. Out-of-clinic group-based models facilitated by non-clinical staff are a promising approach to assist in the long-term management of people on ART in high burden low or middle-income settings.
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    Elevation and cholera: an epidemiological spatial analysis of the cholera epidemic in Harare, Zimbabwe, 2008-2009
    (BioMed Central Ltd, 2012) Luque-Fernandez, Miguel Angel; Schomaker, Michael; Mason, Peter; Fesselet, Jean; Baudot, Yves; Boulle, Andrew; Maes, Peter
    BACKGROUND: In highly populated African urban areas where access to clean water is a challenge, water source contamination is one of the most cited risk factors in a cholera epidemic. During the rainy season, where there is either no sewage disposal or working sewer system, runoff of rains follows the slopes and gets into the lower parts of towns where shallow wells could easily become contaminated by excretes. In cholera endemic areas, spatial information about topographical elevation could help to guide preventive interventions. This study aims to analyze the association between topographic elevation and the distribution of cholera cases in Harare during the cholera epidemic in 2008 and 2009. METHODS: We developed an ecological study using secondary data. First, we described attack rates by suburb and then calculated rate ratios using whole Harare as reference. We illustrated the average elevation and cholera cases by suburbs using geographical information. Finally, we estimated a generalized linear mixed model (under the assumption of a Poisson distribution) with an Empirical Bayesian approach to model the relation between the risk of cholera and the elevation in meters in Harare. We used a random intercept to allow for spatial correlation of neighboring suburbs. RESULTS: This study identifies a spatial pattern of the distribution of cholera cases in the Harare epidemic, characterized by a lower cholera risk in the highest elevation suburbs of Harare. The generalized linear mixed model showed that for each 100 meters of increase in the topographical elevation, the cholera risk was 30% lower with a rate ratio of 0.70 (95% confidence interval=0.66-0.76). Sensitivity analysis confirmed the risk reduction with an overall estimate of the rate ratio between 20% and 40%. CONCLUSION: This study highlights the importance of considering topographical elevation as a geographical and environmental risk factor in order to plan cholera preventive activities linked with water and sanitation in endemic areas. Furthermore, elevation information, among other risk factors, could help to spatially orientate cholera control interventions during an epidemic.
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    Gender differences in survival among adult patients starting antiretroviral therapy in South Africa: a multicentre cohort study
    (Public Library of Science, 2012) Cornell, Morna; Schomaker, Michael; Garone, Daniela Belen; Giddy, Janet; Hoffmann, Christopher J; Lessells, Richard; Maskew, Mhairi; Prozesky, Hans; Wood, Robin; Johnson, Leigh F
    Morna Cornell and colleagues investigate differences in mortality for HIV-positive men and women on antiretroviral therapy in South Africa.
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    Growth and mortality outcomes for different antiretroviral therapy initiation criteria in children ages 1–5 Years: a causal modeling analysis
    (Lippincott, Williams & Wilkins, 2016) Schomaker, Michael; Davies, Mary-Ann; Malateste, Karen; Renner, Lorna; Sawry, Shobna; N’Gbeche, Sylvie; Technau, Karl-Günter; Eboua, François; Tanser, Frank; Sygnaté-Sy, Haby; Phiri, Sam; Madeleine, Amorissani-Folquet; Cox, Vivian; Koueta, Fla; Chimbete, Cleophas; Lawson-Evi, Annette; Giddy, Janet; Amani-Bosse, Clarisse; Wood, Robin; Egger, Matthias; Leroy, Valeriane
    Background: There is limited evidence regarding the optimal timing of initiating antiretroviral therapy (ART) in children. We conducted a causal modeling analysis in children ages 1–5 years from the International Epidemiologic Databases to Evaluate AIDS West/Southern-Africa collaboration to determine growth and mortality differences related to different CD4-based treatment initiation criteria, age groups, and regions. Methods: ART-naïve children of ages 12–59 months at enrollment with at least one visit before ART initiation and one follow-up visit were included. We estimated 3-year growth and cumulative mortality from the start of follow-up for different CD4 criteria using g-computation. Results: About one quarter of the 5,826 included children was from West Africa (24.6%).The median (first; third quartile) CD4% at the first visit was 16% (11%; 23%), the median weight-for-age z-scores and height-for-age z-scores were −1.5 (−2.7; −0.6) and −2.5 (−3.5; −1.5), respectively. Estimated cumulative mortality was higher overall, and growth was slower, when initiating ART at lower CD4 thresholds. After 3 years of follow-up, the estimated mortality difference between starting ART routinely irrespective of CD4 count and starting ART if either CD4 count <750 cells/mm3 or CD4% <25% was 0.2% (95% CI = −0.2%; 0.3%), and the difference in the mean height-for-age z-scores of those who survived was −0.02 (95% CI = −0.04; 0.01). Younger children ages 1–2 and children in West Africa had worse outcomes. Conclusions: Our results demonstrate that earlier treatment initiation yields overall better growth and mortality outcomes, although we could not show any differences in outcomes between immediate ART and delaying until CD4 count/% falls below 750/25%.
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    MAMI: An R-package for model selection and model averaging after multiple imputation
    (2015-09-07) Schomaker, Michael
    The package performs model selection/averaging on multiply imputed datasets and combines the resulting estimates. The package also provides access to less frequently used model averaging techniques and offers integrated bootstrap estimation.
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    Mortality in patients with HIV-1 infection starting antiretroviral therapy in South Africa, Europe, or North America: a collaborative analysis of prospective studies
    (Public Library of Science, 2014) Boulle, Andrew; Schomaker, Michael; May, Margaret T; Hogg, Robert S; Shepherd, Bryan E; Monge, Susana; Keiser, Olivia; Lampe, Fiona C; Giddy, Janet; Ndirangu, James
    Analyzing survival in HIV treatment cohorts, Andrew Boulle and colleagues find mortality rates in South Africa comparable to or better than those in North America by 4 years after starting antiretroviral therapy. Please see later in the article for the Editors' Summary
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    The feasibility and effectiveness of universal antiretroviral therapy provision in adults: The Treat-All approach in the public-sector in rural Swaziland
    (2021) Kerschberger, Bernhard; Boulle, Andrew; Schomaker, Michael
    The World Health Organization (WHO) recommends antiretroviral therapy (ART) initiation at the time of HIV diagnosis irrespective of immunological criteria – known as Treat-All – aiming at improving individual level health outcomes and reducing HIV transmission. However, concerns were raised about the feasibility of further treatment expansion in already fragile health systems in resource-limited settings (RLS). This thesis evaluates the feasibility of ART expansion under the Treat-All approach in a public sector setting in Eswatini. A wide range of HIV care expansion outcomes were explored at patient, programme, and population level. The studies were conducted in outpatient departments of primary and secondary care facilities of the predominantly rural Shiselweni region of Eswatini, from 2007 to 2016. The study population consisted of people living with HIV (PLHIV) who were offered ART under Treat-All and standard of care (SOC) as well as HIV co-infected tuberculosis (TB) patients. The result section of this thesis presents the findings through submitted and published manuscripts. The first paper describes the feasibility of rapid public sector ART expansion before the Treat-All approach became policy. The active ART cohort and treatment coverage among PLHIV expanded approximately 8-fold. Attrition decreased over time, which was most pronounced in the most recent treatment cohort. Attrition remained high for previously described higher risk socio-demographic (e.g. young age, men), clinical (e.g. higher WHO clinical stage, lower CD4 cell count), and programme factors (e.g. toxic drug regimens). The second paper investigates the feasibility of ART initiation under Treat-All compared with SOC. ART initiation was higher and quicker under Treat-All, mainly because more patients with high baseline CD4 cell count initiated treatment under the policy of universal ART. ART initiation was delayed for patients co-infected with TB disease under Treat-All, but was higher overall after 1 month compared with patients without TB. Patients presenting with advanced HIV disease (CD4 < 200 cells/mm3 and/or WHO III/IV clinical stage) had similar cumulative ART initiation rates with both interventions, although initiation was faster under Treat-All during the first month after care enrolment. The third paper assesses treatment outcomes of patients initiated on ART under Treat-All compared with SOC. Patients under Treat-All initiated ART with a higher median CD4 cell count and were more likely to achieve viral suppression. The risk of an unfavourable treatment outcome and viral failure was similar between both interventions. Under Treat-All, previously described higher risk socio-demographic (e.g. younger age, pregnancy) and clinical factors (e.g. low CD4 cell count, higher WHO clinical staging) increased the risk of the unfavourable outcome. The fourth paper evaluated the effectiveness and efficacy of ART initiation on the day of facility-based HIV care enrolment under Treat-All compared with patients initiated 1 to 14 days after care enrolment. Among patients initiated on treatment, same-day ART initiation increased the risk of an unfavourable outcome. This effect was mainly seen during the first months of ART after HIV care enrolment. The fifth paper describes temporal trends in HIV-associated TB during rapid ART expansion including the time-period of Treat-All. Notifications of TB disease decreased by 5-fold over a period of 8 years, and the decline was most pronounced in HIV-associated TB disease compared with HIV-negative TB. The main population-level predictor of TB disease was HIV disease, and the decline in TB coincided with increased access to ART in PLHIV. The thesis concludes that ART expansion and Treat-All are feasible in this RLS, by achieving favourable HIV care outcomes in terms of ART initiation and treatment, for patients with high CD4 cell counts as well for patients presenting late to HIV care. It also highlights the potential population level impact of rapid ART expansion on reducing the burden of HIV-associated TB disease over time. It cautions however against the assumption that outcomes will be improved through ART initiation on the same day as facility-based HIV care enrolment under the Treat-All approach.
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    When to start antiretroviral therapy in children aged 2-5 years: a collaborative causal modelling analysis of cohort studies from southern Africa
    (Public Library of Science, 2013) Schomaker, Michael; Egger, Matthias; Ndirangu, James; Phiri, Sam; Moultrie, Harry; Technau, Karl; Cox, Vivian; Giddy, Janet; Chimbetete, Cleophas; Wood, Robin
    Michael Schomaker and colleagues estimate the mortality associated with starting ART at different CD4 thresholds among children aged 2-5 years using observational data collected in cohort studies in Southern Africa. Please see later in the article for the Editors' Summary