The impact of the COVID-19 pandemic on vaccine coverage in Kilifi, Kenya: A retrospective cohort study.

The COVID-19 pandemic caused unprecedented disruption in health service delivery, globally. This study sought to provide evidence on the impact of the pandemic on vaccine coverage in Kilifi County, Kenya. We conducted a vaccine coverage survey between April and June 2021 within the Kilifi Health and Demographic Surveillance System (KHDSS). Simple random sampling was used to identify 1500 children aged 6 weeks-59 months. Participants were grouped into three retrospective cohorts based on when they became age-eligible for vaccination: before the pandemic, during the first year, or during the second year of the pandemic. Survival analysis with Cox regression was used to evaluate the association between the time-period at which participants became age-eligible for vaccination and the rate of vaccination within a month of age-eligibility for the third dose of pentavalent vaccine (Pentavalent-3) and within three months of age-eligibility for the first dose of Measles vaccine (MCV-1). A total of 1,341 participants were included in the survey. Compared to the pre-COVID-19 baseline period, the rate of vaccination within a month of age-eligibility for Pentavalent-3 was not significantly different in the first year of the pandemic (adjusted hazard ratio [aHR] 1.03, 95 % confidence interval [CI] 0.90-1.18) and was significantly higher during the second year of the pandemic (aHR 1.33, 95 % CI 1.07-1.65). The rate of vaccination with MCV-1 within three months of age-eligibility was not significantly different among those age-eligible for vaccination during the first year of the pandemic (aHR 1.04, 95 % CI 0.88-1.21) and was 35 % higher during the second year of the pandemic (95 % CI 1.11-1.64), compared to those age-eligible pre-COVID-19. After adjusting for known determinants of vaccination, the COVID-19 pandemic did not adversely affect the rate of vaccination within the KHDSS

Exclusive breastfeeding in first-time mothers in rural Kenya: a longitudinal observational study of feeding patterns in the first six months of life

Background: Exclusive breastfeeding up to 6 months of age is recommended by the World Health Organization as the optimal mode of infant feeding, providing adequate nutrition for the baby and protection against infectious diseases. Breastfeeding can be adversely affected by individual, cultural and socio-economic factors. The study aimed to explore barriers of exclusive breastfeeding in the first 6 months of life among first-time mothers in rural Kenya. Methods: An observational longitudinal design aimed to provide rich data on breastfeeding behaviour. Twenty pregnant first-time mothers were recruited through antenatal clinics and snowballing. Mothers were visited nine times at home from late pregnancy, at 1 week and 2 weeks post-delivery, then monthly until the baby was aged 6 months. Visits were conducted between November 2016 and April 2018. At the first visit, participants were asked about breastfeeding intentions and infant feeding education received. At each postnatal visit, direct observation of breastfeeding, a recorded semi-structured interview on feeding, mother’s and baby’s health was performed. Interviews were transcribed, checked, content was grouped into categories and analyzed using a qualitative descriptive approach. Results: Most participants were adolescent (75%) and unmarried (65%). All 20 mothers intended to and did breastfeed, however additional fluids and semi-solids were commonly given. Only two mothers exclusively breastfed from birth up to 6 months of age. Prelacteal feeds, home remedies and traditional medicine were given by over a third of mothers in the first week of life. Concern over babies’ bowel habits and persistent crying perceived as abdominal colic led to several mothers receiving advice to give gripe water and traditional remedies. Early introduction of maize porridge from 3 months of age because of perceived hunger of the child was recommended by other family members. Breastfeeding observation showed persistent problems with positioning and attachment of infants. Conclusions: Exclusive breastfeeding from birth to 6 months was uncommon. Prioritization of capacity to detect mothers with breastfeeding problems and provide breastfeeding education and support is necessary, particularly during the antenatal and early postnatal period. It is important to engage with other women resident in the household who may offer conflicting feeding advice.</br

Spatial-temporal clustering of malaria using routinely collected health facility data on the Kenyan Coast

Background The over-distributed pattern of malaria transmission has led to attempts to define malaria “hotspots” that could be targeted for purposes of malaria control in Africa. However, few studies have investigated the use of routine health facility data in the more stable, endemic areas of Africa as a low-cost strategy to identify hotspots. Here the objective was to explore the spatial and temporal dynamics of fever positive rapid diagnostic test (RDT) malaria cases routinely collected along the Kenyan Coast. Methods Data on fever positive RDT cases between March 2018 and February 2019 were obtained from patients presenting to six out-patients health-facilities in a rural area of Kilifi County on the Kenyan Coast. To quantify spatial clustering, homestead level geocoded addresses were used as well as aggregated homesteads level data at enumeration zone. Data were sub-divided into quarterly intervals. Kulldorff’s spatial scan statistics using Bernoulli probability model was used to detect hotspots of fever positive RDTs across all ages, where cases were febrile individuals with a positive test and controls were individuals with a negative test. Results Across 12 months of surveillance, there were nine significant clusters that were identified using the spatial scan statistics among RDT positive fevers. These clusters included 52% of all fever positive RDT cases detected in 29% of the geocoded homesteads in the study area. When the resolution of the data was aggregated at enumeration zone (village) level the hotspots identified were located in the same areas. Only two of the nine hotspots were temporally stable accounting for 2.7% of the homesteads and included 10.8% of all fever positive RDT cases detected. Conclusion Taking together the temporal instability of spatial hotspots and the relatively modest fraction of the malaria cases that they account for; it would seem inadvisable to re-design the sub-county control strategies around targeting hotspots

Long-lasting insecticide-treated net use and malaria infections on the Kenyan coast

Background A study was conducted to examine the impact of long-lasting insecticide-treated net (LLIN) use on the prevalence of malaria infections across all ages, 25 y after a trial of insecticide-treated nets was conducted in the same area along the Kenyan coast. Methods The study comprised four community-based infection surveys and a simultaneous 12-month surveillance at six government outpatient health facilities (March 2018–February 2019). Logistic regression was used to examine the effect of LLIN use on malaria infections across all ages. Results There was a high level of reported LLIN use by the community (72%), notably among children <5 y of age (84%). Across all ages, the adjusted odds ratio of LLIN use against asymptomatic parasitaemia in community surveys was 0.45 (95% confidence interval [CI] 0.36 to 0.57; p<0.001) and against fevers associated with infection presenting to health facilities was 0.63 (95% CI 0.58 to 0.68; p<0.001). Conclusions There was significant protection of LLIN use against malaria infections across all ages

The relationship between facility-based malaria test positivity rate and community-based parasite prevalence.

INTRODUCTION:Malaria surveillance is a key pillar in the control of malaria in Africa. The value of using routinely collected data from health facilities to define malaria risk at community levels remains poorly defined. METHODS:Four cross-sectional parasite prevalence surveys were undertaken among residents at 36 enumeration zones in Kilifi county on the Kenyan coast and temporally and spatially matched to fever surveillance at 6 health facilities serving the same communities over 12 months. The age-structured functional form of the relationship between test positivity rate (TPR) and community-based parasite prevalence (PR) was explored through the development of regression models fitted by alternating the linear, exponential and polynomial terms for PR. The predictive ranges of TPR were explored for PR endemicity risk groups of control programmatic value using cut-offs of low (PR &lt;5%) and high (PR &#x2265; 30%) transmission intensity. RESULTS:Among 28,134 febrile patients encountered for malaria diagnostic testing in the health facilities, 12,143 (43.2%: 95% CI: 42.6%, 43.7%) were positive. The overall community PR was 9.9% (95% CI: 9.2%, 10.7%) among 6,479 participants tested for malaria. The polynomial model was the best fitting model for the data that described the algebraic relationship between TPR and PR. In this setting, a TPR of &#x2265; 49% in all age groups corresponded to an age-standardized PR of &#x2265; 30%, while a TPR of &lt; 40% corresponded to an age-standardized PR of &lt; 5%. CONCLUSION:A non-linear relationship was observed between the relative change in TPR and changes in the PR, which is likely to have important implications for malaria surveillance programs, especially at the extremes of transmission. However, larger, more spatially diverse data series using routinely collected TPR data matched to community-based infection prevalence data are required to explore the more practical implications of using TPR as a replacement for community PR

Shocks, stress and everyday health system resilience: experiences from the Kenyan coast

Health systems are faced with a wide variety of challenges. As complex adaptive systems, they respond differently and sometimes in unexpected ways to these challenges. We set out to examine the challenges experienced by the health system at a sub-national level in Kenya, a country that has recently undergone rapid devolution, using an 'everyday resilience' lens. We focussed on chronic stressors, rather than acute shocks in examining the responses and organizational capacities underpinning those responses, with a view to contributing to the understanding of health system resilience. We drew on learning and experiences gained through working with managers using a learning site approach over the years. We also collected in-depth qualitative data through informal observations, reflective meetings and in-depth interviews with middle-level managers (sub-county and hospital) and peripheral facility managers (n&#x2009;=&#x2009;29). We analysed the data using a framework approach. Health managers reported a wide range of health system stressors related to resource scarcity, lack of clarity in roles and political interference, reduced autonomy and human resource management. The health managers adopted absorptive, adaptive and transformative strategies but with mixed effects on system functioning. Everyday resilience seemed to emerge from strategies enacted by managers drawing on a varying combination of organizational capacities depending on the stressor and context

Malaria infection, disease and mortality among children and adults on the coast of Kenya

BACKGROUND:Malaria transmission has recently fallen in many parts of Africa, but systematic descriptions of infection and disease across all age groups are rare. Here, an epidemiological investigation of parasite prevalence, the incidence of fevers associated with infection, severe hospitalized disease and mortality among children older than 6&#xA0;months and adults on the Kenyan coast is presented. METHODS:A prospective fever surveillance was undertaken at 6 out-patients (OPD) health-facilities between March 2018 and February 2019. Four community-based, cross sectional surveys of fever history and infection prevalence were completed among randomly selected homestead members from the same communities. Paediatric and adult malaria at Kilifi county hospital was obtained for the 12&#xA0;months period. Rapid Diagnostic Tests (CareStart&#x2122; RDT) to detect HRP2-specific to Plasmodium falciparum was used in the community and the OPD, and microscopy in the hospital. Crude and age-specific incidence rates were computed using Poisson regression. RESULTS:Parasite prevalence gradually increased from childhood, reaching 12% by 9&#xA0;years of age then declining through adolescence into adulthood. The incidence rate of RDT positivity in the OPD followed a similar trend to that of infection prevalence in the community. The incidence of hospitalized malaria from the same community was concentrated among children aged 6&#xA0;months to 4&#xA0;years (i.e. 64% and 70% of all hospitalized and severe malaria during the 12&#xA0;months of surveillance, respectively). Only 3.7% (12/316) of deaths were directly attributable to malaria. Malaria mortality was highest among children aged 6&#xA0;months-4&#xA0;years at 0.57 per 1000 person-years (95% CI 0.2, 1.2). Severe malaria and death from malaria was negligible above 15&#xA0;years of age. CONCLUSION:Under conditions of low transmission intensity, immunity to disease and the fatal consequences of infection appear to continue to be acquired in childhood and faster than anti-parasitic immunity. There was no evidence of an emerging significant burden of severe malaria or malaria mortality among adults. This is contrary to current modelled approaches to disease burden estimation in Africa and has important implications for the targeting of infection prevention strategies based on chemoprevention or vector control

Coverage and timeliness of vaccination and the validity of routine estimates: Insights from a vaccine registry in Kenya

Background The benefits of childhood vaccines are critically dependent on vaccination coverage. We used a vaccine registry (as gold standard) in Kenya to quantify errors in routine coverage methods (surveys and administrative reports), to estimate the magnitude of survivor bias, contrast coverage with timeliness and use both measures to estimate population immunity. Methods Vaccination records of children in the Kilifi Health and Demographic Surveillance System (KHDSS), Kenya were combined with births, deaths, migration and residence data from 2010 to 17. Using inverse survival curves, we estimated up-to-date and age-appropriate vaccination coverage, calculated mean vaccination coverage in infancy as the area under the inverse survival curves, and estimated the proportion of fully immunised children (FIC). Results were compared with published coverage estimates. Risk factors for vaccination were assessed using Cox regression models. Results We analysed data for 49,090 infants and 48,025 children aged 12–23 months in 6 birth cohorts and 6 cross-sectional surveys respectively, and found 2nd year of life surveys overestimated coverage by 2% compared to birth cohorts. Compared to mean coverage in infants, static coverage at 12 months was exaggerated by 7–8% for third doses of oral polio, pentavalent (Penta3) and pneumococcal conjugate vaccines, and by 24% for the measles vaccine. Surveys and administrative coverage also underestimated the proportion of the fully immunised child by 10–14%. For BCG, Penta3 and measles, timeliness was 23–44% higher in children born in a health facility but 20–37% lower in those who first attended during vaccine stock outs. Conclusions Standard coverage surveys in 12–23 month old children overestimate protection by ignoring timeliness, and survivor and recall biases. Where delayed vaccination is common, up-to-date coverage will give biased estimates of population immunity. Surveys and administrative methods also underestimate FIC prevalence. Better measurement of coverage and more sophisticated analyses are required to control vaccine preventable diseases

Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study

BACKGROUND: Ten-valent pneumococcal conjugate vaccine (PCV10), delivered at 6, 10, and 14 weeks of age was introduced in Kenya in January, 2011, accompanied by a catch-up campaign in Kilifi County for children aged younger than 5 years. Coverage with at least two PCV10 doses in children aged 2-11 months was 80% in 2011 and 84% in 2016; coverage with at least one dose in children aged 12-59 months was 66% in 2011 and 87% in 2016. We aimed to assess PCV10 effect against nasopharyngeal carriage and invasive pneumococcal disease (IPD) in children and adults in Kilifi County. METHODS: This study was done at the KEMRI-Wellcome Trust Research Programme among residents of the Kilifi Health and Demographic Surveillance System, a rural community on the Kenyan coast covering an area of 891 km2. We linked clinical and microbiological surveillance for IPD among admissions of all ages at Kilifi County Hospital, Kenya, which serves the community, to the Kilifi Health and Demographic Surveillance System from 1999 to 2016. We calculated the incidence rate ratio (IRR) comparing the prevaccine (Jan 1, 1999-Dec 31, 2010) and postvaccine (Jan 1, 2012-Dec 31, 2016) eras, adjusted for confounding, and reported percentage reduction in IPD as 1 minus IRR. Annual cross-sectional surveys of nasopharyngeal carriage were done from 2009 to 2016. FINDINGS: Surveillance identified 667 cases of IPD in 3 211 403 person-years of observation. Yearly IPD incidence in children younger than 5 years reduced sharply in 2011 following vaccine introduction and remained low (PCV10-type IPD: 60·8 cases per 100 000 in the prevaccine era vs 3·2 per 100 000 in the postvaccine era [adjusted IRR 0·08, 95% CI 0·03-0·22]; IPD caused by any serotype: 81·6 per 100 000 vs 15·3 per 100 000 [0·32, 0·17-0·60]). PCV10-type IPD also declined in the post-vaccination era in unvaccinated age groups (<2 months [no cases in the postvaccine era], 5-14 years [adjusted IRR 0·26, 95% CI 0·11-0·59], and ≥15 years [0·19, 0·07-0·51]). Incidence of non-PCV10-type IPD did not differ between eras. In children younger than 5 years, PCV10-type carriage declined between eras (age-standardised adjusted prevalence ratio 0·26, 95% CI 0·19-0·35) and non-PCV10-type carriage increased (1·71, 1·47-1·99). INTERPRETATION: Introduction of PCV10 in Kenya, accompanied by a catch-up campaign, resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. Although the catch-up campaign is likely to have brought forward the benefits by several years, the study suggests that routine infant PCV10 immunisation programmes will provide substantial direct and indirect protection in low-income settings in tropical Africa. FUNDING: Gavi, The Vaccine Alliance and The Wellcome Trust of Great Britain