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Sexual risk-taking behavior amongst emerging adults in a tertiary institution of learning in Coastal Kenya: A qualitative study of stakeholders' perspectives using causal loop mapping. PLoS One 2023; 18:e0284550. [PMID: 37816016 PMCID: PMC10564131 DOI: 10.1371/journal.pone.0284550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND It is known from previous studies that university students in sub-Saharan Africa (sSA) engage in sexual risk-taking behaviour (SRTB). However, there is paucity of data on factors contributing to SRTB among university students (emerging adults) at the Kenyan Coast thus hindering intervention planning. This study seeks to provide an in-depth qualitative understanding of the factors contributing to SRTB and their interconnectedness among university students at the Kenyan Coast combining qualitative research with a systems thinking approach. METHODS Using the ecological model, and employing in-depth interviews, we explored the perceptions of twenty-six key informants (twenty-one emerging adults and five other stakeholders) on what constitutes and influences SRTB among emerging adults at a tertiary institution of learning in Coastal Kenya. Data were analysed using a thematic framework approach. A causal loop diagram (CLD) was developed to map the interconnectedness of the correlates of SRTB. RESULTS Our findings show that unprotected sex, transactional sex, cross-generational sex, multiple sex partnerships, gender-based violence, sex under influence of alcohol/drugs, early sex debut, and sharing sex toys were common SRTBs. Based on the ecological model and CLD, most of the reported risk factors were interconnected and operated at the individual level. CONCLUSION Our study shows that emerging adults are frequently engaging in unprotected sex. Enhancing sexuality education programs for students in Kenyan universities and strengthening support systems including counselling for those using alcohol/drugs may help reduce SRTB among emerging adults in Kenyan universities.
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Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Achieving the health and well-being Sustainable Development Goals among adolescent mothers and their children in South Africa: Cross-sectional analyses of a community-based mixed HIV-status cohort. PLoS One 2022; 17:e0278163. [PMID: 36480550 PMCID: PMC9731463 DOI: 10.1371/journal.pone.0278163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
The Sustainable Development Goals (SDGs) are a visionary and multi-sectoral agenda for human development. With less than a decade left to reach these targets, it is important to identify those at greatest risk of not meeting these ambitious targets. Adolescent mothers and their children are a highly vulnerable group. We mapped 35 SGD-related targets among 1,046 adolescent mothers and their oldest child (n = 1046). Questionnaires using validated scales were completed by 10- to 24-year-old adolescent girls and young women who had their first child before age 20 in an HIV-endemic district in the Eastern Cape province of South Africa. Maternal outcomes included 26 SDG-aligned indicators, while child-related outcomes included 9 indicators. Data was collected by trained researchers, following informed voluntary consent by the adolescent mothers and their caregivers. Frequencies and chi-square tests were conducted to compare progress along SDG-aligned indicators among adolescent mothers by HIV status. Overall, adolescent mothers reported low attainment of SDG-aligned indicators. While four in five adolescent mothers lived in poor households, nearly 93% accessed at least one social cash transfer and 80% accessed a child support grant for their children. Food security rates among adolescent mothers (71%) were lower than among their children (91%). Only two-thirds of adolescent mothers returned to school after childbirth, and only one-fifth were either studying or employed. Over half of adolescent mothers had experienced at least one type of violence (domestic, sexual or community). HIV-positive status was associated with higher rates of hunger and substance use, poorer school attendance, and higher rates of exposure to violence. Understanding progress and gaps in meeting the SDGs among highly vulnerable groups is critical, particularly for adolescent mothers and their children. These complex vulnerabilities suggest that programming for adolescent mothers must address their unique needs.
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Antiretroviral Drug Detection in a Community-Randomized Trial of Universal HIV Testing and Treatment: HPTN 071 (PopART). Open Forum Infect Dis 2022; 9:ofac576. [PMID: 36447611 PMCID: PMC9697607 DOI: 10.1093/ofid/ofac576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/28/2022] [Indexed: 08/19/2023] Open
Abstract
Background Antiretroviral therapy (ART) reduces human immunodeficiency virus (HIV) transmission risk. The primary aim of this study was to evaluate ART uptake in a trial in Zambia and South Africa that implemented a community-wide universal testing and treatment package to reduce HIV incidence. Methods Study communities were randomized to 3 arms: A, combination-prevention intervention with universal ART; B, combination-prevention intervention with ART according to local guidelines; and C, standard of care. Samples were collected from people with HIV (PWH) during a survey visit conducted 2 years after study implementation: these samples were tested for 22 antiretroviral (ARV) drugs. Antiretroviral therapy uptake was defined as detection of ≥1 ARV drug. Resistance was evaluated in 612 randomly selected viremic participants. A 2-stage, cluster-based approach was used to assess the impact of the study intervention on ART uptake. Results Antiretroviral drugs were detected in 4419 of 6207 (71%) samples (Arm A, 73%; Arm B, 70%; Arm C, 60%); 4140 (94%) of samples with ARV drugs had viral loads <400 copies/mL. Drug resistance was observed in 237 of 612 (39%) viremic participants (95 of 102 [93%] with ARV drugs; 142 of 510 [28%] without drugs). Antiretroviral therapy uptake was associated with older age, female sex, enrollment year, seroconverter status, and self-reported ART (all P < .001). The adjusted risk ratio for ART uptake was similar for Arm A versus C (1.21; 95% confidence interval [CI], .94-1.54; P = .12) and Arm B versus C (1.14; 95% CI, .89-1.46; P = .26). Conclusions At the 2-year survey, 71% of PWH were on ART and 94% of those participants were virally suppressed. Universal testing and treatment was not significantly associated with increased ART uptake in this cohort.
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The development of children born to young mothers with no, first- or second-generation HIV acquisition in the Eastern Cape province, South Africa: a cross-sectional study. BMJ Open 2022; 12:e058340. [PMID: 36229140 PMCID: PMC9562751 DOI: 10.1136/bmjopen-2021-058340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The intergenerational effects of HIV require long-term investigation. We compared developmental outcomes of different generations impacted by HIV-children of mothers not living with HIV, the 'second generation' (ie, with recently infected mothers) and the 'third generation' (ie, children of perinatally infected mothers). METHODS A cross-sectional community sample of N=1015 young mothers (12-25 years) and their first children (2-68 months, 48.2% female), from South Africa's Eastern Cape Province. 71.3% (n=724) of children were born to mothers not living with HIV; 2.7% (n=27; 1 living with HIV) were third-generation and 26.0% (n=264; 11 living with HIV) second-generation children. Child scores on the Mullen Scales of Early Learning (MSEL), the WHO Ten Questions Screen for Disability and maternal demographics were compared between groups using χ2 tests and univariate approach, analysis of variance analysis. Hierarchical linear regressions investigated predictive effects of familial HIV infection patterns on child MSEL composite scores, controlling for demographic and family environment variables. RESULTS Second-generation children performed poorer on gross (M=47.0, SD=13.1) and fine motor functioning (M=41.4, SD=15.2) and the MSEL composite score (M=90.6, SD=23.0) than children with non-infected mothers (gross motor: M=50.4, SD=12.3; fine motor: M=44.4, SD=14.1; composite score: M=94.1, SD=20.7). The third generation performed at similar levels to non-exposed children (gross motor: M=52.4, SD=16.1; fine motor: M=44.3, SD=16.1, composite score: M=94.7, SD=22.2), though analyses were underpowered for definite conclusions. Hierarchical regression analyses suggest marginal predictive effects of being second-generation child compared with having a mother not living with HIV (B=-3.3, 95% CI=-6.8 to 0 .1) on MSEL total scores, and non-significant predictive effects of being a third-generation child (B=1.1, 5% CI=-7.5 to 9.7) when controlling for covariates. No group differences were found for disability rates (26.9% third generation, 27.7% second generation, 26.2% non-exposed; χ2=0.02, p=0.90). CONCLUSION Recently infected mothers and their children may struggle due to the disruptiveness of new HIV diagnoses and incomplete access to care/support during pregnancy and early motherhood. Long-standing familial HIV infection may facilitate care pathways and coping, explaining similar cognitive development among not exposed and third-generation children. Targeted intervention and fast-tracking into services may improve maternal mental health and socioeconomic support.
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Association of impaired kidney function with mortality in rural Uganda: results of a general population cohort study. BMJ Open 2022; 12:e051267. [PMID: 35473721 PMCID: PMC9045120 DOI: 10.1136/bmjopen-2021-051267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To determine the association between baseline kidney function and subsequent all-cause mortality. DESIGN AND SETTING A general population-based cohort study from rural Uganda. PARTICIPANTS People aged 18 years and above with measured baseline estimated glomerular filtration rate (eGFR), recruited from survey rounds in 2011-2012 or 2014-2015 and followed up to March 2019. OUTCOME MEASURE The primary outcome was all-cause mortality, identified through reports from community health workers and verified by verbal autopsy. The association between baseline eGFR category and mortality was determined using multivariable Cox regression. RESULTS Of 5812 participants in both rounds, we included 5678 (97.7%) participants with kidney function and mortality data; the median age was 36 years (IQR 24-50), 60.7% were female, 10.3% were hypertensive, 9.8% were HIV-positive and 1.5% were diabetic. During a median follow-up of 5.0 years (IQR 3.7-6.0) there were 140 deaths. In age-adjusted and sex-adjusted analyses, eGFR <45 mL/min/1.73 m2 at baseline was associated with a 5.97 (95% CI 2.55 to 13.98) increased risk of mortality compared with those with baseline eGFR >90 mL/min/1.73 m2. After inclusion of additional confounders (HIV, body mass index, diabetes, hypertension, alcohol and smoking status) into the model, eGFR <45 mL/min/1.73 m2 at baseline remained strongly associated with mortality (HR 6.12, 95% CI 2.27 to 16.45), although the sample size fell to 3102. Test for trend showed strong evidence (p<0.001) that the rate of mortality increased progressively as the category of baseline kidney function decreased. When very high eGFR was included as a separate category in age-adjusted and sex-adjusted analyses, baseline eGFR ≥120 mL/min/1.73 m2 was associated with increased risk of mortality (HR 2.68, 95% CI 1.47 to 4.87) compared with the reference category of 90-119 mL/min/1.73 m2. CONCLUSION In a prospective cohort in rural Uganda we found that impaired baseline kidney function was associated with subsequently increased total mortality. Improved understanding of the determinants of kidney disease and its progression is needed in order to inform interventions for prevention and treatment.
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A computationally tractable birth-death model that combines phylogenetic and epidemiological data. PLoS Comput Biol 2022; 18:e1009805. [PMID: 35148311 PMCID: PMC8903285 DOI: 10.1371/journal.pcbi.1009805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 03/08/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.
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Abstract
BACKGROUND Chronic aflatoxin (AF) exposure has been shown to occur at high levels in children from sub-Saharan Africa (SSA), and has been associated with growth retardation and immune dysfunction. Our objective was to investigate the impact of AF exposure on immune development in early infancy using thymic size and antibody (Ab) response to vaccination as indicators of immune function. METHODS A total of 374 infants born between May 2011 and December 2012 were enrolled into the current study. These infants were recruited from a larger, randomised trial examining the impact of nutritional supplementation of mothers and infants on infant immune development (the Early Nutrition and Immune Development Trial). Thymic size (Thymic Index, TI) was measured by sonography at 1 week, 8 weeks, 24 weeks and 52 weeks of infant age. Infants were given the diphtheria-tetanus-pertussis (DTP) vaccine at 8 weeks, 12 weeks and 16 weeks of age, and Ab responses to each vaccine measured at 12 weeks and 24 weeks of age. AF-albumin (AF-alb) adduct levels in infant blood were measured by ELISA as the biomarker of AF exposure. RESULTS The geometric mean (GM) level of AF-alb increased with age. Only half of infants had detectable AF-alb with a GM of 3.52 pg/mg at 24 weeks, increasing to 25.39 pg/mg at 52 weeks, when 98% of infants had AF-alb >limit of detection. Significant negative association of AF-alb level with TI was seen in infants during the first 24 weeks, especially at 8 weeks of age (p<0.001), which is the time point of fastest thymus growth. There were no associations between AF exposure level and Ab response to pertussis and tetanus, but a significant positive correlation was observed between AF-alb level and Ab titre to diphtheria (p<0.005). CONCLUSIONS High levels of AF exposure during early infancy may impact on infant immune development. TRIAL REGISTRATION NUMBER ISRCTN49285450.
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Estimating ventilation rates in rooms with varying occupancy levels: Relevance for reducing transmission risk of airborne pathogens. PLoS One 2021; 16:e0253096. [PMID: 34166388 PMCID: PMC8224849 DOI: 10.1371/journal.pone.0253096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In light of the role that airborne transmission plays in the spread of SARS-CoV-2, as well as the ongoing high global mortality from well-known airborne diseases such as tuberculosis and measles, there is an urgent need for practical ways of identifying congregate spaces where low ventilation levels contribute to high transmission risk. Poorly ventilated clinic spaces in particular may be high risk, due to the presence of both infectious and susceptible people. While relatively simple approaches to estimating ventilation rates exist, the approaches most frequently used in epidemiology cannot be used where occupancy varies, and so cannot be reliably applied in many of the types of spaces where they are most needed. METHODS The aim of this study was to demonstrate the use of a non-steady state method to estimate the absolute ventilation rate, which can be applied in rooms where occupancy levels vary. We used data from a room in a primary healthcare clinic in a high TB and HIV prevalence setting, comprising indoor and outdoor carbon dioxide measurements and head counts (by age), taken over time. Two approaches were compared: approach 1 using a simple linear regression model and approach 2 using an ordinary differential equation model. RESULTS The absolute ventilation rate, Q, using approach 1 was 2407 l/s [95% CI: 1632-3181] and Q from approach 2 was 2743 l/s [95% CI: 2139-4429]. CONCLUSIONS We demonstrate two methods that can be used to estimate ventilation rate in busy congregate settings, such as clinic waiting rooms. Both approaches produced comparable results, however the simple linear regression method has the advantage of not requiring room volume measurements. These methods can be used to identify poorly-ventilated spaces, allowing measures to be taken to reduce the airborne transmission of pathogens such as Mycobacterium tuberculosis, measles, and SARS-CoV-2.
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The use of a speaking book® to enhance vaccine knowledge among caregivers in The Gambia: A study using qualitative and quantitative methods. BMJ Open 2021; 11:e040507. [PMID: 34006021 PMCID: PMC7942236 DOI: 10.1136/bmjopen-2020-040507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To measure the usefulness of a Speaking Book (SB) as an educational tool for enhancing knowledge, understanding and recall of key vaccine-related information among caregivers in The Gambia, as well as its acceptability and relevance as a health promotion tool for caregivers and healthcare workers. DESIGN AND SETTING We developed a multimedia educational tool, the vaccine Speaking Book, which contained prerecorded information about vaccines provided in The Gambia's Expanded Programme on Immunization. Using qualitative and quantitative methods, we then conducted a sequential study assessing the use of this tool among caregivers andhealthcare workers in The Gambia.Participants200 caregivers attending primary healthcare centres in The Gambia for routine immunisation services for their infants, and 15 healthcare workers employed to provide immunisation services at these clinics. OUTCOME MEASURES We calculated the median knowledge scores on vaccine-related information obtained at baseline, 1-month and 3-month follow-up visits. Wilcoxon's matched-pairs signed-rank test was used to compare the difference in the median knowledge scores between baseline and 1-month, and between baseline and 3-month follow-up visits. RESULTS Of the 113 caregivers who participated, 104 (92%) completed all three study visits, 108 (95.6%) completed the baseline and 1-month follow-up visits, and 107 (94.7%) completed the baseline and 3-month follow-up visits. The median knowledge score increased from 6.0 (IQR 5.0-7.0) at baseline to 11.0 (IQR 8.0-14.0) at 1-month visit (p<0.001), and 15.0 (IQR 10.0-20.0) at 3-month visit (p<0.001). Qualitative results showed high acceptability and enthusiasm for the Speaking Book among both caregivers and healthcare workers. The Speaking Book was widely shared in the community and this facilitated communication with healthcare workers at the primary healthcare centres. CONCLUSIONS Context-specific and subject-specific Speaking Books are a useful communication and educational tool to increase caregiver vaccine knowledge in low/middle-income countries.
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Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling. Mol Biol Evol 2021; 38:274-289. [PMID: 32898225 PMCID: PMC7783189 DOI: 10.1093/molbev/msaa225] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilize these methodologies for malaria, we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterized using estimated relationships between complexity of infection and age from five regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterize the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance.
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Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models. Syst Biol 2020; 69:1163-1179. [PMID: 32333789 PMCID: PMC7584150 DOI: 10.1093/sysbio/syaa035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/12/2022] Open
Abstract
Estimating temporal changes in a target population from phylogenetic or count data is an important problem in ecology and epidemiology. Reliable estimates can provide key insights into the climatic and biological drivers influencing the diversity or structure of that population and evidence hypotheses concerning its future growth or decline. In infectious disease applications, the individuals infected across an epidemic form the target population. The renewal model estimates the effective reproduction number, R, of the epidemic from counts of observed incident cases. The skyline model infers the effective population size, N, underlying a phylogeny of sequences sampled from that epidemic. Practically, R measures ongoing epidemic growth while N informs on historical caseload. While both models solve distinct problems, the reliability of their estimates depends on p-dimensional piecewise-constant functions. If p is misspecified, the model might underfit significant changes or overfit noise and promote a spurious understanding of the epidemic, which might misguide intervention policies or misinform forecasts. Surprisingly, no transparent yet principled approach for optimizing p exists. Usually, p is heuristically set, or obscurely controlled via complex algorithms. We present a computable and interpretable p-selection method based on the minimum description length (MDL) formalism of information theory. Unlike many standard model selection techniques, MDL accounts for the additional statistical complexity induced by how parameters interact. As a result, our method optimizes p so that R and N estimates properly and meaningfully adapt to available data. It also outperforms comparable Akaike and Bayesian information criteria on several classification problems, given minimal knowledge of the parameter space, and exposes statistical similarities among renewal, skyline, and other models in biology. Rigorous and interpretable model selection is necessary if trustworthy and justifiable conclusions are to be drawn from piecewise models. [Coalescent processes; epidemiology; information theory; model selection; phylodynamics; renewal models; skyline plots].
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The Safe Start trial to assess the effect of an infant hygiene intervention on enteric infections and diarrhoea in low-income informal neighbourhoods of Kisumu, Kenya: a study protocol for a cluster randomized controlled trial. BMC Infect Dis 2019; 19:1066. [PMID: 31856747 PMCID: PMC6923833 DOI: 10.1186/s12879-019-4657-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/22/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Symptomatic and asymptomatic enteric infections in early childhood are associated with negative effects on childhood growth and development, especially in low and middle-income countries, and food may be an important transmission route. Although basic food hygiene practices might reduce exposure to faecal pathogens and resulting infections, there have been few rigorous interventions studies to assess this, and no studies in low income urban settings where risks are plausibly very high. The aim of this study is to evaluate the impact of a novel infant food hygiene intervention on infant enteric infections and diarrhoea in peri-urban settlements of Kisumu, Kenya. METHODS This is a cluster randomized control trial with 50 clusters, representing the catchment areas of Community Health Volunteers (CHVs), randomly assigned to intervention or control, and a total of 750 infants recruited on a rolling basis at 22 weeks of age and then followed for 15 weeks. The intervention targeted four key caregiver behaviours related to food hygiene: 1) hand washing with soap before infant food preparation and feeding; 2) bringing all infant food to the boil before feeding, including when reheating or reserving; 3) storing all infant food in sealed containers; and, 4) using only specific utensils for infant feeding which are kept separate and clean. RESULTS The primary outcome of interest is the prevalence of one or more of 23 pre-specified enteric infections, determined using quantitative real-time polymerase chain reaction for enteric pathogen gene targets. In addition, infant food samples were collected at 33 weeks, and faecal indicator bacteria (Enterococcus) isolated and enumerated to assess the impact of the intervention on infant food contamination. CONCLUSION To our knowledge this is the first randomized controlled trial to assess the effect of an infant food hygiene intervention on enteric infections in a high burden, low income urban setting. Our trial responds to growing evidence that food may be a key pathway for early childhood enteric infection and disease and that basic food hygiene behaviours may be able to mitigate these risks. The Safe Start trial seeks to provide new evidence as to whether a locally appropriate infant food hygiene intervention delivered through the local health extension system can improve the health of young children. TRIAL REGISTRATION The trial was registered at clinicaltrial.gov on March 16th 2018 before enrolment of any participants (https://clinicaltrials.gov/ct2/show/NCT03468114).
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Accountability mechanisms and the value of relationships: experiences of front-line managers at subnational level in Kenya and South Africa. BMJ Glob Health 2018; 3:e000842. [PMID: 30002921 PMCID: PMC6038841 DOI: 10.1136/bmjgh-2018-000842] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/01/2022] Open
Abstract
Resource constraints, value for money debates and concerns about provider behaviour have placed accountability ‘front and centre stage’ in health system improvement initiatives and policy prescriptions. There are a myriad of accountability relationships within health systems, all of which can be transformed by decentralisation of health system decision-making from national to subnational level. Many potential benefits of decentralisation depend critically on the accountability processes and practices of front-line health facility providers and managers, who play a central role in policy implementation at province, county, district and facility levels. However, few studies have examined these responsibilities and practices in detail, including their implications for service delivery. In this paper we contribute to filling this gap through presenting data drawn from broader ongoing research collaborations between researchers and health managers in Kenya and South Africa. These collaborations are aimed at understanding and strengthening day-to-day micropractices of health system governance, including accountability processes. We illuminate the multiple directions and forms of accountability operating at the subnational level across three sites. Through detailed illustrative examples we highlight some of the unintended consequences of bureaucratic forms of accountability, the importance of relational elements in enabling effective bureaucratic accountability, and the ways in which front-line managers can sometimes creatively draw upon one set of accountability requirements to challenge another set to meet their goals. Overall, we argue that interpersonal interactions are key to appropriate functioning of many accountability mechanisms, and that policies and interventions supportive of positive relationships should complement target-based and/or audit-style mechanisms to achieve their intended effects. Where this is done systematically and across key elements and actors of the health system, this offers potential to build everyday health system resilience.
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Enhancing evidence informed policymaking in complex health systems: lessons from multi-site collaborative approaches. Health Res Policy Syst 2016; 14:20. [PMID: 26983405 PMCID: PMC4794922 DOI: 10.1186/s12961-016-0089-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is an increasing interest worldwide to ensure evidence-informed health policymaking as a means to improve health systems performance. There is a need to engage policymakers in collaborative approaches to generate and use knowledge in real world settings. To address this gap, we implemented two interventions based on iterative exchanges between researchers and policymakers/implementers. This article aims to reflect on the implementation and impact of these multi-site evidence-to-policy approaches implemented in low-resource settings. METHODS The first approach was implemented in Mexico and Nicaragua and focused on implementation research facilitated by communities of practice (CoP) among maternal health stakeholders. We conducted a process evaluation of the CoPs and assessed the professionals' abilities to acquire, analyse, adapt and apply research. The second approach, called the Policy BUilding Demand for evidence in Decision making through Interaction and Enhancing Skills (Policy BUDDIES), was implemented in South Africa and Cameroon. The intervention put forth a 'buddying' process to enhance demand and use of systematic reviews by sub-national policymakers. The Policy BUDDIES initiative was assessed using a mixed-methods realist evaluation design. RESULTS In Mexico, the implementation research supported by CoPs triggered monitoring by local health organizations of the quality of maternal healthcare programs. Health programme personnel involved in CoPs in Mexico and Nicaragua reported improved capacities to identify and use evidence in solving implementation problems. In South Africa, Policy BUDDIES informed a policy framework for medication adherence for chronic diseases, including both HIV and non-communicable diseases. Policymakers engaged in the buddying process reported an enhanced recognition of the value of research, and greater demand for policy-relevant knowledge. CONCLUSIONS The collaborative evidence-to-policy approaches underline the importance of iterations and continuity in the engagement of researchers and policymakers/programme managers, in order to account for swift evolutions in health policy planning and implementation. In developing and supporting evidence-to-policy interventions, due consideration should be given to fit-for-purpose approaches, as different needs in policymaking cycles require adapted processes and knowledge. Greater consideration should be provided to approaches embedding the use of research in real-world policymaking, better suited to the complex adaptive nature of health systems.
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