Bayesian (hierarchical) spatial modeling in epidemiology

Paper presented at Strathmore International Math Research Conference on July 23 - 27, 2012Paper presented at Strathmore International Maths Research Conference on July 23 - 27, 201

Trends and correlates of HIV testing amongst women: lessons learnt from Kenya

BACKGROUND: A majority of women in Kenya do not know their HIV status and are therefore unable to take preventive measures or medication in order to prolong their lives. OBJECTIVES: This study investigates the key determinants of HIV testing in Kenya and documents how these changed over the 1998-2008 period. METHOD: This study uses data from the 1998, 2003 and 2008 Kenya Demographic and Health surveys. Principal components analysis was used to compute indices of HIV knowledge, HIV-related stigma, media exposure and decision making. Survey logistic regression analysis was used to determine factors that had a statistically-significant association with ever having been tested for HIV. RESULTS: Testing was significantly higher in 2008 compared with the previous surveys. In 1998, 14.7% of the women had tested for HIV. The rate increased to 15.0% in 2003 and then to 59.2% in 2008. In the 1998 and 2003 Kenya Demographic and Health surveys, respondents' age, region of residence, education, knowledge of someone who had died from HIV-related illness and media exposure were the main determinants of testing. In the 2008 study, HIV-related stigma, occupation and the partner's level of education were found to be associated with HIV testing. CONCLUSION: Despite efforts to scale up voluntary counselling and testing in Kenya over the 1998-2008 period, HIV testing amongst women is still quite low. Prevention and control programmes in Kenya need to focus on reducing HIV-related stigma, increasing access to testing in rural areas and increasing access amongst women with little or no education.DHE

Spatiotemporal patterns of successful TB treatment outcomes among HIV co-infected patients in Kenya

Paper presented at the 5th Strathmore International Mathematics Conference (SIMC 2019), 12 - 16 August 2019, Strathmore University, Nairobi, KenyaConvergence of the Tuberculosis (TB) and HIV epidemics threatens the management of TB treatment. These has been evidenced by various studies describing how HIV cc-infection propagates unsuccessful TB treatment outcomes. Information on the spatiotemporal patterns of successful TB treatment outcomes remain less understood despite the multi-organizational TB treatment efforts. This study uses case notification data to evaluate the spatiotemporal patterns of successful TB treatment outcomes for HIV co-infected patients in Kenya. This study used the case notification data from the Kenya National TB control program to investigate successful TB treatment outcomes in forty-seven counties in the period 2012 - 2017. The population of study was HIV co-infected cases with known TB treatment outcome. Achi-squre test was performed to determine the association between treatment outcomes and risk factors; TB- type, age, gender, ART therapy and patient type. The study also assessed the geographic patterns and temporal trends by mapping the TB treatment success rate in each county for the six-year period. Using the Integrated Nested Laplace Approach (INLA), the TB treatment success of HIV co-infected patients was modeled. The spatial parameters assumed the BesagYork-Mollie (BYM) specification. The temporally structured effect was represented through a neighboring structure and the temporally unstructured effects using a Gaussian exchangeable prior. Among the 172233 HIV co-infected cases included in the analysis, 135973 (78.9%) achieved successful TB treatment outcomes. Female cases registered higher treatment success rates (80.1%) compared to the male cases (77.8%). The cases on Anti-Retroviral Therapy (ART) recorded a success rate of 79.9% against 69.1% for their counterpart not on ART. The spatial trend depicted increased treatment success in some parts of the country with a relatively high level of associated certainty, characterized by a spatial relative success above 1 and posterior probabilities above 0.8. The temporal trend of treatment success showed an increase in the treatment success of TB in HIV coinfected cases. Overall, the success rate was still below 85% particularly for Homabay, Siaya, Kisumu, Migori and Busia counties in western Kenya. The successful TB treatment outcomes for HIV coinfected cases in Kenya were slightly below the 85% standard threshold set by the World Health Organization. Our study showed that even though co-infected cases have an increased risk of unsuccessful treatment outcomes, enhanced treatment monitoring improved the treatment outcome in most counties for the six-year period.Department of Mathematical Sciences, Pan African University Institute of Basic Sciences Technology and Innovation, Nairobi, Kenya Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa. School of Mathematics, Statistics Computer Science, University of Kwa-Zulu Natal, Pietermaritzburg, South Africa

Clinical-pathological presentation, treatment and outcomes of ovarian cancer cases at moi teaching and referral hospital (mtrh), eldoret

Introduction: Ovarian cancer is the third most frequent cause of death amongst gynecological cancers both locally and globally. It presents with vague nonspecific symptoms and is histologically heterogeneous. Ovarian cancer management is primarily surgical followed by adjuvant chemotherapy depending on the histological type and the surgical stage. Objectives: To determine the clinical-pathological presentation, treatment and outcomes of ovarian cancer patients at Moi Teaching and Referral Hospital (MTRH), Eldoret. Methods: This was a retrospective chart review of ovarian cancer patients managed between January 2010 and August 2017 at MTRH. Data were analyzed using STATA version 15. Survival trends were generated using Kaplan Meier method. Results: A total of 124 medical charts of patients with ovarian cancer were retrieved, 29 had incomplete data and were excluded, and 95 were evaluable and included in this review. Over half, (63%) presented in stage 3 and 4 though there was no significant association between histology and stage of disease [X2(6) =4.72, p=0.58]. The median age at diagnosis was 47 years with 55-80 years being the modal age group (36%). Majority (57%) were married and 83.9% were unemployed. Only 66% had documented histopathology, with Epithelial Ovarian Cancer (EOC) being most common (70%), [serous (50%) and mucinous (11.4%)]. Sex cord stromal tumors 11%. Germ cell tumors amounted to 11% (dygerminomas 50%and Yolk sac tumors (25%) Bivariate analysis revealed significant association only between histology and parity [X2 (6) = 28.8, p\u3c0.001]. Those reviewed contributed a total of 138.2 person-years to the study and 11(12%) died, giving a diseasespecific mortality rate of 79.6 per 1,000 person years (95% CI: 44.1-143.8). Mortality was highest among those with epithelial histology 109 (95% CI: 48.8-241.9) per 1,000 person years and those who had neoadjuvant chemotherapy then surgery as a treatment option, 373.1 (95% CI: 93.3-1491.8) per 1,000 person years. Those who underwent upfront surgery followed by adjuvant chemotherapy and sex cord stromal cancer had higher survival probability. Conclusion: Ovarian cancer at MTRH is diagnosed at advanced stages III and IV of disease and has a lower median age at presentation. EOC is the commonest histological type and serous subtype is the most lethal. Mortality was highest among those with EOC and those who underwent neoadjuvant chemotherapy. Granulosa cell tumor is the only sex cord stromal type reported in our setting and it exhibited a higher survival probability. Germ cell tumors were mainly found in nulliparous women

Epidemiological profile and clinico-pathological features of pediatric gynecological cancers at Moi Teaching & Referral Hospital, Kenya

Background: The main pediatric (0–18 years) gynecologic cancers include stromal carcinomas (juvenile granulosa cell tumors and Sertoli-Leydig cell tumors), genital rhabdomyosarcomas and ovarian germ cell. Outcomes depend on time of diagnosis, stage, tumor type and treatment which can have long-term effects on the reproductive career of these patients. This study seeks to analyze the trends in clinical-pathologic presentation, treatment and outcomes in the cases seen at our facility. This is the first paper identifying these cancers published from sub-Saharan Africa. Method: Retrospective review of clinico-pathologic profiles and treatment outcomes of pediatric gynecologic oncology patients managed at MTRH between 2010 and 2020. Data was abstracted from gynecologic oncology database and medical charts. Results: Records of 40 patients were analyzed. Most, (92.5%, 37/40) of the patients were between 10 and 18 years. Ovarian germ cell tumors were the leading histological diagnosis in 72.5% (29/40) of the patients; with dysgerminomas being the commonest subtype seen in 12 of the 37 patients (32.4%). The patients received platinum-based chemotherapy in 70% of cases (28/40). There were 14 deaths among the 40 patients (35%) Conclusion: Surgery remains the main stay of treatment and fertility-sparing surgery with or without adjuvant platinum-based chemotherapy are the standard of care with excellent prognosis following early detection and treatment initiation. LMICs face several challenges in access to quality care and that affects survival of these patients. Due to its commonality, ovarian germ cell cancers warrant a high index of suspicion amongst primary care providers attending to adnexal masses in this age group

Where Are the Newly Diagnosed HIV Positives in Kenya? Time to Consider Geo-Spatially Guided Targeting at a Finer Scale to Reach the “First 90”

Background: The UNAIDS 90-90-90 Fast-Track targets provide a framework for assessing coverage of HIV testing services (HTS) and awareness of HIV status – the “first 90.” In Kenya, the bulk of HIV testing targets are aligned to the five highest HIV-burden counties. However, we do not know if most of the new HIV diagnoses are in these five highest-burden counties or elsewhere. Methods: We analyzed facility-level HTS data in Kenya from 1 October 2015 to 30 September 2016 to assess the spatial distribution of newly diagnosed HIV-positives. We used the Moran's Index (Moran's I) to assess global and local spatial auto-correlation of newly diagnosed HIV-positive tests and Kulldorff spatial scan statistics to detect hotspots of newly diagnosed HIV-positive tests. For aggregated data, we used Kruskal-Wallis equality-of-populations non-parametric rank test to compare absolute numbers across classes. Results: Out of 4,021 HTS sites, 3,969 (98.7%) had geocodes available. Most facilities (3,034, 76.4%), were not spatially autocorrelated for the number of newly diagnosed HIV-positives. For the rest, clustering occurred as follows; 438 (11.0%) were HH, 66 (1.7%) HL, 275 (6.9%) LH, and 156 (3.9%) LL. Of the HH sites, 301 (68.7%) were in high HIV-burden counties. Over half of 123 clusters with a significantly high number of newly diagnosed HIV-infected persons, 73(59.3%) were not in the five highest HIV-burden counties. Clusters with a high number of newly diagnosed persons had twice the number of positives per 1,000,000 tests than clusters with lower numbers (29,856 vs. 14,172). Conclusions: Although high HIV-burden counties contain clusters of sites with a high number of newly diagnosed HIV-infected persons, we detected many such clusters in low-burden counties as well. To expand HTS where most needed and reach the “first 90” targets, geospatial analyses and mapping make it easier to identify and describe localized epidemic patterns in a spatially dispersed epidemic like Kenya's, and consequently, reorient and prioritize HTS strategies.publishedVersio

Geographic variation and factors associated with female genital mutilation among reproductive age women in Ethiopia: A national population based survey

Background: Female genital mutilation (FGM) is a common traditional practice in developing nations including Ethiopia. It poses complex and serious long-term health risks for women and girls and can lead to death. In Ethiopia, the geographic distribution and factors associated with FGM practices are poorly understood. Therefore, we assessed the spatial distribution and factors associated with FGM among reproductive age women in the country. Method: We used population based national representative surveys. Data from two (2000 and 2005) Ethiopian demographic and health surveys (EDHS) were used in this analysis. Briefly, EDHS used a stratified, two-stage cluster sampling design. A total of 15,367 (from EDHS 2000) and 14,070 (from EDHS 2005) women of reproductive age (15-49 years) were included in the analysis. Three outcome variables were used (prevalence of FGM among women, prevalence of FGM among daughters and support for the continuation of FGM). The data were weighted and descriptive statistics (percentage change), bivariate and multivariable logistic regression analyses were carried out. Multicollinearity of variables was assessed using variance inflation factors (VIF) with a reference value of 10 before interpreting the final output. The geographic variation and clustering of weighted FGM prevalence were analyzed and visualized on maps using ArcGIS. Z-scores were used to assess the statistical difference of geographic clustering of FGM prevalence spots. Result: The trend of FGM weighted prevalence has been decreasing. Being wealthy, Muslim and in higher age categories are associated with increased odds of FGM among women. Similarly, daughters from Muslim women have increased odds of experiencing FGM. Women in the higher age categories have increased odds of having daughters who experience FGM. The odds of FGM among daughters decrease with increased maternal education. Mass media exposure, being wealthy and higher paternal and maternal education are associated with decreased odds of women's support of FGM continuation. FGM prevalence and geographic clustering showed variation across regions in Ethiopia. Conclusion: Individual, economic, socio-demographic, religious and cultural factors played major roles in the existing practice and continuation of FGM. The significant geographic clustering of FGM was observed across regions in Ethiopia. Therefore, targeted and integrated interventions involving religious leaders in high FGM prevalence spot clusters and addressing the socio-economic and geographic inequalities are recommended to eliminate FGM. © 2016 Setegn et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Developing excellence in biostatistics leadership, training and science in Africa: How the Sub-Saharan Africa Consortium for Advanced Biostatistics (SSACAB) training unites expertise to deliver excellence

The increase in health research in sub-Saharan Africa (SSA) has generated large amounts of data and led to a high demand for biostatisticians to analyse these data locally and quickly.  Donor-funded initiatives exist to address the dearth in statistical capacity, but few initiatives have been led by African institutions. The Sub-Saharan African Consortium for Advanced Biostatistics (SSACAB) aims to improve biostatistical capacity in Africa according to the needs identified by African institutions, through (collaborative) masters and doctoral training in biostatistics. We describe the SSACAB Consortium, which comprises 11 universities and four research institutions- supported by four European universities. SSACAB builds on existing resources to strengthen biostatistics for health research with a focus on supporting biostatisticians to become research leaders; building a critical mass of biostatisticians, and networking institutions and biostatisticians across SSA.  In 2015 only four institutions had established Masters programmes in biostatistics and SSACAB supported the remaining institutions to develop Masters programmes. In 2019 the University of the Witwatersrand became the first African institution to gain Royal Statistical Society accreditation for a Biostatistics MSc programme. A total of 150 fellows have been awarded scholarships to date of which 123 are Masters fellowships (41 female) of which with 58 have already graduated. Graduates have been employed in African academic (19) and research (15) institutions and 10 have enrolled for PhD studies. A total of 27 (10 female) PhD fellowships have been awarded; 4 of them are due to graduate by 2020. To date, SSACAB Masters and PhD students have published 17 and 31 peer-reviewed articles, respectively. SSACAB has also facilitated well-attended conferences, face-to-face and online short courses. Pooling the limited biostatistics resources in SSA, and combining with co-funding from external partners is an effective strategy for the development and teaching of advanced biostatistics methods, supervision and mentoring of PhD candidates

Spatial modelling and mapping of female genital mutilation in Kenya

BACKGROUND: Female genital mutilation/cutting (FGM/C) is still prevalent in several communities in Kenya and other areas in Africa, as well as being practiced by some migrants from African countries living in other parts of the world. This study aimed at detecting clustering of FGM/C in Kenya, and identifying those areas within the country where women still intend to continue the practice. A broader goal of the study was to identify geographical areas where the practice continues unabated and where broad intervention strategies need to be introduced. METHODS: The prevalence of FGM/C was investigated using the 2008 Kenya Demographic and Health Survey (KDHS) data. The 2008 KDHS used a multistage stratified random sampling plan to select women of reproductive age (15–49 years) and asked questions concerning their FGM/C status and their support for the continuation of FGM/C. A spatial scan statistical analysis was carried out using SaTScan™ to test for statistically significant clustering of the practice of FGM/C in the country. The risk of FGM/C was also modelled and mapped using a hierarchical spatial model under the Integrated Nested Laplace approximation approach using the INLA library in R. RESULTS: The prevalence of FGM/C stood at 28.2% and an estimated 10.3% of the women interviewed indicated that they supported the continuation of FGM. On the basis of the Deviance Information Criterion (DIC), hierarchical spatial models with spatially structured random effects were found to best fit the data for both response variables considered. Age, region, rural–urban classification, education, marital status, religion, socioeconomic status and media exposure were found to be significantly associated with FGM/C. The current FGM/C status of a woman was also a significant predictor of support for the continuation of FGM/C. Spatial scan statistics confirm FGM clusters in the North-Eastern and South-Western regions of Kenya (p < 0.001). CONCLUSION: This suggests that the fight against FGM/C in Kenya is not yet over. There are still deep cultural and religious beliefs to be addressed in a bid to eradicate the practice. Interventions by government and other stakeholders must address these challenges and target the identified clusters