Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study.

The mortality impact of COVID-19 in Africa remains controversial because most countries lack vital registration. We analysed excess mortality in Kilifi Health and Demographic Surveillance System, Kenya, using 9 years of baseline data. SARS-CoV-2 seroprevalence studies suggest most adults here were infected before May 2022. During 5 waves of COVID-19 (April 2020-May 2022) an overall excess mortality of 4.8% (95% PI 1.2%, 9.4%) concealed a significant excess (11.6%, 95% PI 5.9%, 18.9%) among older adults ( ≥ 65 years) and a deficit among children aged 1-14 years (-7.7%, 95% PI -20.9%, 6.9%). The excess mortality rate for January 2020-December 2021, age-standardised to the Kenyan population, was 27.4/100,000 person-years (95% CI 23.2-31.6). In Coastal Kenya, excess mortality during the pandemic was substantially lower than in most high-income countries but the significant excess mortality in older adults emphasizes the value of achieving high vaccine coverage in this risk group.

Quantifying previous SARS-CoV-2 infection through mixture modelling of antibody levels.

As countries decide on vaccination strategies and how to ease movement restrictions, estimating the proportion of the population previously infected with SARS-CoV-2 is important for predicting the future burden of COVID-19. This proportion is usually estimated from serosurvey data in two steps: first the proportion above a threshold antibody level is calculated, then the crude estimate is adjusted using external estimates of sensitivity and specificity. A drawback of this approach is that the PCR-confirmed cases used to estimate the sensitivity of the threshold may not be representative of cases in the wider population-e.g., they may be more recently infected and more severely symptomatic. Mixture modelling offers an alternative approach that does not require external data from PCR-confirmed cases. Here we illustrate the bias in the standard threshold-based approach by comparing both approaches using data from several Kenyan serosurveys. We show that the mixture model analysis produces estimates of previous infection that are often substantially higher than the standard threshold analysis.

Comparison of bedside inoculation of culture media with conventional cerebrospinal fluid culture method in patients with bacterial meningitis.

BACKGROUND: The yield of bacterial cultures from cerebrospinal fluid (CSF) at Kenyatta National Hospital (KNH) is very low. Bedside inoculation of culture media with CSF may improve yields. OBJECTIVE: To compare the culture yield of CSF inoculated onto culture medium at the bedside to that of CSF inoculated onto culture medium in the microbiology laboratory. DESIGN: Cross-sectional comparative study. SETTING: Accident and Emergency Department and medical wards at Kenyatta National Hospital. SUBJECTS: Cerebrospinal fluid from patients at KNH with a clinical diagnosis of acute meningitis. RESULTS: Two hundred and twenty CSF specimens were obtained during a four month period. S. pneumaniae was isolated from 24 CSF samples and H. influenzae from one. Bacterial cultures were positive in 25 (11.4%, 95% CI 7.0-15.6%) samples inoculated at the bedside and 23 (10.5%, 95% CI 6.5-14.5%) samples inoculated at the laboratory. Bacteria were isolated 5 hours earlier in samples inoculated at the bedside (95% CI 4.34-6.86 hrs, p < 0.05). Four per cent of S. pneumaniae isolates were resistant to crystalline penicillin. CONCLUSION: There was no significant difference in culture yield after bedside inoculation of culture media with CSF compared to traditional CSF culture method. Bedside inoculation of culture media with CSF resulted in faster time to positive culture.