Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Community-directed treatment of lymphatic filariasis in Kenya and its role in the national programmes for elimination of lymphatic filariasis

We conducted a prospective, cross-sectional study to examine and compare treatment coverage of lymphatic filariasis by the health system (HST) and a health system implemented, community-directed treatment for the control of lymphatic filariasis (ComDT/HS) in 44 randomly selected villages in coastal Kenya. Demographic information on the villages and peripheral health facilities to guide design and implementation was obtained from a situation analysis phase of this study. A series of interactive training sessions on basic biology of lymphatic filariasis, concept and philosophy of ComDT/HS were given to members of the District Health Management Team (DHMT), peripheral health staff, community leaders and community drug distributors (CDDs) prior to ivermectin distribution. An intensive sensitization process of the community by the trained peripheral health staff and community leaders followed before selection of the CDDs. Quantitative and qualitative data for evaluation of the study were collected by coverage surveys of randomly selected households, focus group discussions and interviews, immediately after the drug distribution. Treatment coverage of all eligible persons was 46.5 and 88% in HST and ComDT/HS villages, respectively, P < 0.001. In comparing treatment coverage by the two study arms in relationship to the distance from a health facility, coverage among HST and not ComDT/HS villages was influenced by distance. In Kenya, ComDT/HS can effectively be implemented by the regular health system and can attain coverage levels compatible with the global filariasis elimination goal. African Journal of Health Sciences Vol. 13 (1-2) 2008: pp. 69-7

Oxacillin resistant Staphlococcus aureus among HIV infected and non-infected Kenyan patients

Background: Infections due to methicillin resistant S. aureus (MRSA) present global challenges to clinicians since therapeutic options are limited and suboptimal dosing contributes to heightened mortality and increased length of hospital stay particularly among the HIV infected patients.Objectives: To assess the prevalence and relative risk of MRSA infections in HIV infected patients.Design: Cross sectional analytical study.Setting: Kenya Medical Research Institute, Opportunistic Infection Laboratories in Nairobi.Subjects: Four hundred and thirty six male and female patients aged one to 65 years, of whom 220 were HIV-infected and 216 were non-infected.Results: There was 436 male (57.1%) and female (42.9%) respondents. The prevalence of MRSA was 26.3% with majority infecting the HIV infected patients (P=0.046). Likewise, the overall Staphylococcal infections were more common in HIV patients (

An integrated study of human and animal infectious disease in the Lake Victoria crescent small-holder crop-livestock production system, Kenya

Background: The neglected zoonotic diseases (NZD) are an understudied group that are a major cause of illness throughout the developing world. In general, little is known about the prevalence and burden of NZDs in affected communities, particularly in relation to other infectious diseases with which they are often co-endemic. We describe the design and descriptive epidemiological outputs from an integrated study of human and animal zoonotic and non-zoonotic disease in a rural farming community in western Kenya. Methods: This cross-sectional survey involved 2113 people, their cattle (n = 983) and pigs (n = 91). People and animals were tested for infection or exposure to a wide range of zoonotic and non-zoonotic pathogens. Prevalence estimates, with adjustment for the complex study design, were derived. Evidence for spatial clustering in exposure or infection was identified using the spatial scan statistic. Results: There was a high prevalence of human parasitism in the community, particularly with hookworm (Ancylostoma duodenale or Necator americanus) (36.3% (95% CI 32.8–39.9)), Entamoeba histolytica/dispar (30.1% (95% CI 27.5–32.8)), and Plasmodium falciparum (29.4% (95% CI 26.8–32.0)). Human infection with Taenia spp. was also prevalent (19.7% (95% CI 16. 7–22.7)), while exposure to other zoonotic pathogens was comparatively rarer (Brucella spp., 0.6% (95% CI 0.2–0.9); Coxiella burnetii, 2.2% (95% CI 1.5–2.9); Rift Valley fever, 0.5% (95% CI 0.2–0.8)). A low prevalence of exposure to Brucella spp. was observed in cattle (0.26% (95% CI 0–0.56). This was higher for Rift Valley fever virus (1.4% (95% CI 0.5–2.22)) and C. burnetii (10.0% (95% CI 7.7–12.2)). The prevalence of Taenia spp. cysticercosis was 53.5% (95% CI 48.7–58.3) in cattle and 17.2% (95% CI 9.1–25.3) in pigs. Mycobacterium bovis infection was found in 2.2% of cattle (95% CI 1.3–3.2), while the prevalence of infection with Mycobacterium spp. was 8.2% (95% CI 6.8–9.6) in people. Conclusion: Zoonotic infections in people and animals occur in the context of a wide range of co-endemic pathogens in a rural community in western Kenya. The wide diversity of pathogens under study provides a unique opportunity to explore the distribution and determinants of infection in a multi-pathogen, multi-host system

Understanding the relationship between prevalence of microfilariae and antigenaemia using a model of lymphatic filariasis infection.

BACKGROUND: Lymphatic filariasis is a debilitating neglected tropical disease that affects impoverished communities. Rapid diagnostic tests of antigenaemia are a practical alternative to parasitological tests of microfilaraemia for mapping and surveillance. However the relationship between these two methods of measuring burden has previously been difficult to interpret. METHODS: A statistical model of the distribution of worm burden and microfilariae (mf) and resulting antigenaemic and mf prevalence was developed and fitted to surveys of two contrasting sentinel sites undergoing interventions. The fitted model was then used to explore the relationship in various pre- and post-intervention scenarios. RESULTS: The model had good quantitative agreement with the data and provided estimates of the reduction in mf output due to treatment. When extrapolating the results to a range of prevalences there was good qualitative agreement with published data. CONCLUSIONS: The observed relationship between antigenamic and mf prevalence is a natural consequence of the relationship between prevalence and intensity of adult worms and mf production. The method described here allows the estimation of key epidemiological parameters and consequently gives insight into the efficacy of an intervention programme

Understanding the relationship between prevalence of microfilariae and antigenaemia using a model of lymphatic filariasis infection

Background: Lymphatic filariasis is a debilitating neglected tropical disease that affects impoverished communities. Rapid diagnostic tests of antigenaemia are a practical alternative to parasitological tests of microfilaraemia for mapping and surveillance. However the relationship between these two methods of measuring burden has previously been difficult to interpret. Methods: A statistical model of the distribution of worm burden and microfilariae (mf) and resulting antigenaemic and mf prevalence was developed and fitted to surveys of two contrasting sentinel sites undergoing interventions. The fitted model was then used to explore the relationship in various pre- and post-intervention scenarios. Results: The model had good quantitative agreement with the data and provided estimates of the reduction in mf output due to treatment. When extrapolating the results to a range of prevalences there was good qualitative agreement with published data. Conclusions: The observed relationship between antigenamic and mf prevalence is a natural consequence of the relationship between prevalence and intensity of adult worms and mf production. The method described here allows the estimation of key epidemiological parameters and consequently gives insight into the efficacy of an intervention programme

Household socio-economic position and individual infectious disease risk in rural Kenya

The importance of household socio-economic position (SEP) in shaping individual infectious disease risk is increasingly recognised, particularly in low income settings. However, few studies have measured the extent to which this association is consistent for the range of pathogens that are typically endemic among the rural poor in the tropics. This cross-sectional study assessed the relationship between SEP and human infection within a single community in western Kenya using a set of pathogens with diverse transmission routes. The relationships between household SEP and individual infection with Plasmodium falciparum, hookworm (Ancylostoma duodenale and/or Necator americanus), Entamoeba histolytica/dispar, Mycobacterium tuberculosis, and HIV, and co-infections between hookworm, P. falciparum and E. histolytica/dispar, were assessed using multivariable logistic and multinomial regression. Individuals in households with the lowest SEP were at greatest risk of infection with P. falciparum, hookworm and E. histolytica/dispar, as well as co-infection with each pathogen. Infection with M. tuberculosis, by contrast, was most likely in individuals living in households with the highest SEP. There was no evidence of a relationship between individual HIV infection and household SEP. We demonstrate the existence of a household socio-economic gradient within a rural farming community in Kenya which impacts upon individual infectious disease risk. Structural adjustments that seek to reduce poverty, and therefore the socio-economic inequalities that exist in this community, would be expected to substantially reduce overall infectious disease burden. However, policy makers and researchers should be aware that heterogeneous relationships can exist between household SEP and infection risk for different pathogens in low income settings

Community-directed Treatment of Lymphatic Filariasis in Kenya and its Role in the National Programmes for Elimination of Lymphatic Filariasis

We conducted a prospective, cross-sectional study to examine and compare treatment coverage of lymphatic filariasis by the health system (HST) and a health system implemented, community-directed treatment for the control of lymphatic filariasis (ComDT/HS) in 44 randomly selected villages in coastal Kenya. Demographic information on the villages and peripheral health facilities to guide design and implementation was obtained from a situation analysis phase of this study. A series of interactive training sessions on basic biology of lymphatic filariasis, concept and philosophy of ComDT/HS were given to members of the District Health Management Team (DHMT), peripheral health staff, community leaders and community drug distributors (CDDs) prior to ivermectin distribution. An intensive sensitization process of the community by the trained peripheral health staff and community leaders followed before selection of the CDDs. Quantitative and qualitative data for evaluation of the study were collected by coverage surveys of randomly selected households, focus group discussions and interviews, immediately after the drug distribution. Treatment coverage of all eligible persons was 46.5 and 88% in HST and ComDT/HS villages, respectively, P &lt; 0.001. In comparing treatment coverage by the two study arms in relationship to the distance from a health facility, coverage among HST and not ComDT/HS villages was influenced by distance. In Kenya, ComDT/HS can effectively be implemented by the regular health system and can attain coverage levels compatible with the global filariasis elimination goal

General contextual effects on neglected tropical disease risk in rural Kenya

The neglected tropical diseases (NTDs) are characterized by their tendency to cluster within groups of people, typically the poorest and most marginalized. Despite this, measures of clustering, such as within-group correlation or between-group heterogeneity, are rarely reported from community-based studies of NTD risk. We describe a general contextual analysis that uses multi-level models to partition and quantify variation in individual NTD risk at multiple grouping levels in rural Kenya. The importance of general contextual effects (GCE) in structuring variation in individual infection with Schistosoma mansoni, the soil-transmitted helminths, Taenia species, and Entamoeba histolytica/dispar was examined at the household-, sublocation- and constituency-levels using variance partition/intra-class correlation co-efficients and median odds ratios. These were compared with GCE for HIV, Plasmodium falciparum and Mycobacterium tuberculosis. The role of place of residence in shaping infection risk was further assessed using the spatial scan statistic. Individuals from the same household showed correlation in infection for all pathogens, and this was consistently highest for the gastrointestinal helminths. The lowest levels of household clustering were observed for E. histolytica/dispar, P. falciparum and M. tuberculosis. Substantial heterogeneity in individual infection risk was observed between sublocations for S. mansoni and Taenia solium cysticercosis and between constituencies for infection with S. mansoni, Trichuris trichiura and Ascaris lumbricoides. Large overlapping spatial clusters were detected for S. mansoni, T. trichiura, A. lumbricoides, and Taenia spp., which overlapped a large cluster of elevated HIV risk. Important place-based heterogeneities in infection risk exist in this community, and these GCEs are greater for the NTDs and HIV than for TB and malaria. Our findings suggest that broad-scale contextual drivers shape infectious disease risk in this population, but these effects operate at different grouping-levels for different pathogens. A general contextual analysis can provide a foundation for understanding the complex ecology of NTDs and contribute to the targeting of interventions

Assessment of lymphatic filariasis prior to re-starting mass drug administration campaigns in coastal Kenya.

BACKGROUND: Lymphatic filariasis (LF) is a debilitating disease associated with extensive disfigurement and is one of a diverse group of diseases referred to as neglected tropical diseases (NTDs) which mainly occur among the poorest populations. In line with global recommendations to eliminate LF, Kenya launched its LF elimination programme in 2002 with the aim to implement annual mass drug administration (MDA) in order to interrupt LF transmission. However, the programme faced financial and administrative challenges over the years such that sustained annual MDA was not possible. Recently, there has been renewed interest to eliminate LF and the Kenyan Ministry of Health, through support from World Health Organization (WHO), restarted annual MDA in 2015. The objective of this study was to evaluate the current status of LF infection in the endemic coastal region of Kenya before MDA campaigns were restarted. RESULTS: Ten sentinel sites in Kwale, Kilifi, Tana River, Lamu, and Taita-Taveta counties in coastal Kenya were selected for participation in a cross-sectional survey of LF infection prevalence. At least 300 individuals in each sentinel village were sampled through random house-to-house visits. During the day, the point-of-care immunochromatographic test (ICT) was used to detect the presence of Wuchereria bancrofti circulating filarial antigen in finger prick blood samples collected from residents of the selected sentinel villages. Those individuals who tested positive with the ICT test were requested to provide a night-time blood sample for microfilariae (MF) examination. The overall prevalence of filarial antigenaemia was 1.3% (95% CI: 0.9-1.8%). Ndau Island in Lamu County had the highest prevalence (6.3%; 95% CI: 4.1-9.7%), whereas sites in Kilifi and Kwale counties had prevalences?<?1.7%. Mean microfilarial density was also higher in Ndau Island (234 MF/ml) compared to sentinel sites in Kwale and Kilifi counties (< 25 MF/ml). No LF infection was detected in Tana River and Taita-Taveta counties. Overall, more than 88% of the study participants reported to have used a bed net the previous night. CONCLUSIONS: Prevalence of LF infection is generally very low in coastal Kenya, but there remain areas that require further rounds of MDA if the disease is to be eliminated as a public health problem in line with the ongoing global elimination efforts. However, areas where there was no evidence of LF transmission should be considered for WHO-recommended transmission assessment surveys in view of stopping MDA