Transmission of SARS-CoV-2 among underserved pastoralist communities in Kajiado County, Kenya: 2020-2022.

Initial transmission of severe acute respiratory syndrome virus-2 (SARS-CoV-2) was highest in densely populated regions of Kenya. Transmission gradually trickled down to the less densely populated, remote and underserved regions such as the pastoral regions of Kajiado County which are characterized by poor healthcare systems. Molecular assays that were pivotal for COVID-19 diagnosis were not available in these regions. Serology is an alternative method for retrospectively tracking the transmission of SARS-CoV-2 in such populations. Dry blood spots (DBS) were prepared from consenting patients attending six health facilities in Kajiado County from March 2020 to March 2022. Upon elution, we conducted an enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-Cov-2 IgG antibodies. Of the 908 DBSs we analyzed, 706 (78%) were from female participants. The overall seropositivity to SARS-Cov-2 antibodies was 7.3% (95% CI 5.7-9.1). The elderly (over 60 years) and male participants had a high likelihood of testing positive for SAR-CoV-2 infections. Mashuru (15.6%, 14/90) and Meto (15%, 19/127) health facilities registered the highest proportion of seropositive participants. Evidence of SARS-CoV-2 transmission among pastoralists in the remote and underserved regions of Kajiado County was established by DBS sampling and serologic testing.

Genetic characterization of group A rotavirus in children with acute gastroenteritis in Kericho County Referral Hospital, Kenya.

Introduction: approximately over 80% of mortalities due to rotavirus occur in countries that have limited resources, especially in sub-Saharan Africa and South Asia. The study was intended to determine the genetic characteristics of rotavirus A in children exhibiting gastroenteritis at Kericho County Referral Hospital. Methods: the study design was cross-sectional. Consecutive sampling was engaged obtaining a sample size of 200 stool samples. Genetic characterization of group A rotavirus strains was done using Enzyme-Linked Immunosorbent Assay. Positive samples underwent Sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Afterwards viewing of the RNA double strands of the rotavirus genome in gels was done using Silver Nitrate. The positive samples underwent RT-PCR amplification followed by sequencing on the pieces of the VP7 or VP4 gene obtained. Results: one hundred and six (53%) samples from males and 94 (47%) from females. Twenty-three samples were positive hence a prevalence of 11.5%. The most affected demographics were children of guardians with secondary school education (51%). The most affected social economic status was housewives (46.5%). The most affected age was 21-30 months at 26.5%. Long electropherotypes were in 22 samples (96%). The G3 genotype of rotavirus A was prevalent 16/23 (69.57%). Conclusion: rotavirus prevalence was 11.5%. The G3 genotype was the most prevalent in circulation. The occurrence of non-typable strains indicated that the strains may be diversified emphasizing the need to include emerging strains within the vaccines in use. Hence the need to continuously monitor the effects in older children.

Profiling IgG and IgA antibody responses during vaccination and infection in a high-risk gonorrhoea population.

Development of a vaccine against gonorrhoea is a global priority, driven by the rise in antibiotic resistance. Although Neisseria gonorrhoeae (Ng) infection does not induce substantial protective immunity, highly exposed individuals may develop immunity against re-infection with the same strain. Retrospective epidemiological studies have shown that vaccines containing Neisseria meningitidis (Nm) outer membrane vesicles (OMVs) provide a degree of cross-protection against Ng infection. We conducted a clinical trial (NCT04297436) of 4CMenB (Bexsero, GSK), a licensed Nm vaccine containing OMVs and recombinant antigens, comprising a single arm, open label study of two doses with 50 adults in coastal Kenya who have high exposure to Ng. Data from a Ng antigen microarray established that serum IgG and IgA reactivities against the gonococcal homologs of the recombinant antigens in the vaccine peaked at 10 but had declined by 24 weeks. For most reactive OMV-derived antigens, the reverse was the case. A cohort of similar individuals with laboratory-confirmed gonococcal infection were compared before, during, and after infection: their reactivities were weaker and differed from the vaccinated cohort. We conclude that the cross-protection of the 4CMenB vaccine against gonorrhoea could be explained by cross-reaction against a diverse selection of antigens derived from the OMV component.

Plasmodium falciparum population dynamics in East Africa and genomic surveillance along the Kenya-Uganda border.

East African countries accounted for ~ 10% of all malaria prevalence worldwide in 2022, with an estimated 23.8 million cases and > 53,000 deaths. Despite recent increases in malaria incidence, high-resolution genome-wide analyses of Plasmodium parasite populations are sparse in Kenya, Tanzania, and Uganda. The Kenyan-Ugandan border region is a particular concern, with Uganda confirming the emergence and spread of artemisinin resistant P. falciparum parasites. To establish genomic surveillance along the Kenyan-Ugandan border and analyse P. falciparum population dynamics within East Africa, we generated whole-genome sequencing (WGS) data for 38 parasites from Bungoma, Western Kenya. These sequences were integrated into a genomic analysis of available East African isolate data (n = 599) and revealed parasite subpopulations with distinct genetic structure and diverse ancestral origins. Ancestral admixture analysis of these subpopulations alongside isolates from across Africa (n = 365) suggested potential independent ancestral populations from other major African populations. Within isolates from Western Kenya, the prevalence of biomarkers associated with chloroquine resistance (e.g. Pfcrt K76T) were significantly reduced compared to wider East African populations and a single isolate contained the PfK13 V568I variant, potentially linked to reduced susceptibility to artemisinin. Overall, our work provides baseline WGS data and analysis for future malaria genomic surveillance in the region.

Outcomes of different steroid dosing regimens in critical Covid-19 pneumonia at a Kenyan hospital: A retrospective cohort study.

BACKGROUND: Among therapeutic options for severe and critical COVID- 19 infection, dexamethasone six milligrams once daily for ten days has demonstrated mortality benefit and is guideline recommended at this dose. In practice, variable doses of steroids have been used, especially in critical care settings. Our study aimed to determine the pattern of steroid dosing and outcomes in terms of critical care mortality, occurrence of dysglycaemias, and occurrence of superadded infections in patients with critical COVID-19. METHODS: A retrospective cohort study was carried out on all eligible patients admitted to the Aga Khan University Hospital, Nairobi, with critical COVID-19 between 1st March 2020 and 31st December 2021. The intervention of interest was corticosteroids quantified as the average daily dose in milligrams of dexamethasone. A steroid dose of six milligrams once a day was compared to high dose steroid dosing, which was defined as any dose greater than this. The primary outcome measure was ICU mortality and secondary outcomes included occurrence of dysglycaemias, superadded infections and duration of critical care admission. RESULTS: The study included 288 patients. The median age was 61.2 years (IQR: 49.7, 72.5), with 71.2% of patients being male. The most common comorbidities were diabetes mellitus (60.7%), hypertension (58%), and heart disease (12.2%). The average oxygen saturation and C-reactive protein at admission were 82% [IQR: 70.0-89.0]and 113.0 [IQR: 54.0-186.0], respectively. Fifty-eight percent of patients received a standard dose (6mg) of steroids. The mortality rate was higher in the high-dose group compared to the standard-dose group; however, the difference was not statistically significant (47.9% vs 43.7% p = 0.549). The two most common steroid associated adverse effects were uncomplicated hyperglycemia (62.2%) and superimposed bacterial pneumonia (20.1%). The high-dose group had a higher incidence of uncomplicated hyperglycemia compared to the standard-dose group (63.6% vs 61.1%). However, the incidence of diabetic ketoacidosis was lower in the high dose group (0.6% vs 6.6%). Oxygen saturation at admission was associated with survival where it was lower among non-survivor patients with critical COVID-19. CONCLUSION: The study found that high-dose steroids in the treatment of critically ill patients with COVID-19 pneumonia did not confer any mortality benefit and were associated with an increased risk of dysglycemia and superimposed infections.

Factors Associated With Non-Uptake of Implantable Cardioverter-Defibrillator (ICD) Among Eligible Patients at a Tertiary Hospital in Kenya.

Background: Efficacy of Implantable Cardioverter-Defibrillator (ICD) implantation in both primary and secondary prevention of Sudden Cardiac Death (SCD) in at-risk population is well established. ICD implantation rates remain low particularly in Africa with a paucity of data regarding factors associated with non-uptake. Objectives: The primary study objective was to determine the factors associated with non-uptake of ICD among heart failure (HF) patients with reduced ejection fraction (EF<35%). Reasons for ICD refusal among eligible patients were reviewed as a secondary objective. Methods: This was a retrospective study among HF patients eligible for ICD implantation evaluated between 2018 to 2020. Comparison between ICD recipient and non-recipient categories was made to establish determinants of non-uptake. Results: Of 206 eligible patients, only 69 (33.5%) had an ICD. Factors independently associated with non-uptake were lack of private insurance (42.3% vs 63.8%; p = 0.005), non-cardiology physician (16.1% vs 5.8%; p = 0.045) and non-ischemic cardiomyopathy (54.7% vs 36.4% p = 0.014). The most common (75%) reason for ICD refusal was inability to pay for the device. Conclusion: ICDs are underutilized among eligible HF with reduced EF patients in Kenya. The majority of patients without ICD had no private insurance, had non-ischemic cardiomyopathy and non-cardiology primary physician. Early referral of HF with reduced EF patients to HF specialists to optimize guideline-directed medical therapy and make ICD recommendation is needed.

Yellow fever vaccine coverage and associated factors among under-five children in Kenya: Data from Kenyan Demographic and Health Survey 2022.

Yellow fever is a vaccine preventable hemorrhagic disease that leads to morbidity and mortality in the affected individuals. The only options for preventing and controlling its spread are through vaccination. Therefore, this study was conducted to estimate yellow fever vaccination coverage and associated factors among under-five children in Kenya. The total weighted samples of 2,844 children aged under-five were included in this study. The data were taken from the Kenyan Demographic and Health Survey 2022. In the multivariable analysis, the adjusted odds ratio with a 95% CI was used to declare significant associations of yellow fever vaccine. The yellow fever vaccine coverage among children aged under-five in Kenya was 18.50%. The significant factors associated with yellow fever vaccine coverage were: the age of the child older than 24 months (AOR = 1.7; 95% CI (1.17-2.58)); higher odds of yellow fever vaccination coverage was observed among older children, place of residence (AOR = 1.76; 95% CI (1.04-2.97)); higher odds was observed among urban residents, maternal education; primary education (AOR = 1.99; 95% CI (1.04-2.97)), secondary education (AOR = 2.85; 95% CI (1.41-5.76)), mothers who attended primary or secondary education have higher odds of yellow fever vaccination coverage, wealth index (AOR = 2.38; 95% CI (1.15-4.91)); higher odds of vaccination coverage was observed among poor households. Yellow fever vaccine coverage among under-five children in Kenya was low and has become an important public health concern. Policymakers and other stakeholders are recommended to focus on vaccination programs to prevent yellow fever disease.

Lactoferrin and lysozyme to promote nutritional, clinical and enteric recovery: a protocol for a factorial, blinded, placebo-controlled randomised trial among children with diarrhoea and malnutrition (the Boresha Afya trial).

INTRODUCTION: Children with moderate or severe wasting are at particularly high risk of recurrent or persistent diarrhoea, nutritional deterioration and death following a diarrhoeal episode. Lactoferrin and lysozyme are nutritional supplements that may reduce the risk of recurrent diarrhoeal episodes and accelerate nutritional recovery by treating or preventing underlying enteric infections and/or improving enteric function. METHODS AND ANALYSIS: In this factorial, blinded, placebo-controlled randomised trial, we aim to determine the efficacy of lactoferrin and lysozyme supplementation in decreasing diarrhoea incidence and improving nutritional recovery in Kenyan children convalescing from comorbid diarrhoea and wasting. Six hundred children aged 6-24 months with mid-upper arm circumference <12.5 cm who are returning home after an outpatient visit or inpatient hospital stay for diarrhoea will be enrolled. Children will be randomised to 16 weeks of lactoferrin, lysozyme, a combination of the two, or placebo and followed for 24 weeks, with biweekly home visits by community health workers and clinic visits at 4, 10, 16 and 24 weeks. The primary analysis will compare the incidence of moderate-to-severe diarrhoea and time to nutritional recovery between each intervention arm and placebo. The trial will also test whether these interventions reduce enteric pathogen carriage, decrease enteric permeability and/or increase haemoglobin concentration in enrolled children. Finally, we will evaluate the acceptability, adherence and cost-effectiveness of lactoferrin and/or lysozyme. ETHICS AND DISSEMINATION: The trial has been approved by the institutional review boards of the Kenya Medical Research Institute, the University of Washington, the Kenyan Pharmacy and Poisons Board, and the Kenyan National Commission on Science, Technology and Innovation. The results of this trial will be shared with local and international stakeholders and published in peer-reviewed journals, and the key findings will be presented at relevant conferences. TRIAL REGISTRATION NUMBER: NCT05519254, PACTR202108480098476.

HIV Self-Testing for Efficient PrEP Delivery Is Highly Acceptable and Feasible in Public Health HIV Clinics in Kenya: A Mixed Methods Study.

HIV self-testing (HIVST) has the potential to reduce barriers associated with clinic-based preexposure prophylaxis (PrEP) delivery. We conducted a substudy nested in a prospective, pilot implementation study evaluating patient-centered differentiated care services. Clients chose either a blood-based or oral fluid HIVST kit at the first refill visit. Data were abstracted from program files and surveys were administered to clients. We purposively sampled a subset of PrEP clients and their providers to participate in in-depth interviews. We surveyed (n = 285). A majority (269/285, 94%) reported HIV risk. Blood-based HIVST was perceived as easy to use (76/140, 54%), and (41/140, 29%) perceived it to be more accurate. Oral fluid-based HIVST was perceived to be easy to use (95/107, 89%), but almost all (106/107, 99%) perceived it as less accurate. HIVST improved privacy, reduced workload, and saved time. HIVST demonstrates the potential to streamline facility-based PrEP care in busy African public health facilities.

Molecular Detection of Virulence-Associated Markers in Campylobacter coli and Campylobacter jejuni Isolates From Water, Cattle, and Chicken Faecal Samples From Kajiado County, Kenya.

Campylobacter is a zoonotic foodborne pathogen that is often linked with gastroenteritis and other extraintestinal infections in humans. This study is aimed at determining the genetic determinants of virulence-encoding genes responsible for flagellin motility protein A (flaA), Campylobacter adhesion to fibronectin F (cadF), Campylobacter invasion antigen B (ciaB) and cytolethal distending toxin (cdt) A (cdtA) in Campylobacter species. A total of 29 Campylobacter coli isolates (16 from cattle, 9 from chicken, and 4 from water samples) and 74 Campylobacter jejuni isolates (38 from cattle, 30 from chicken, and 6 from water samples) described in an earlier study in Kajiado County, Kenya, were examined for the occurrence of virulence-associated genes using polymerase chain reaction (PCR) and amplicon sequencing. The correlations among virulence genes were analyzed using Pearson's correlation coefficient (R) method. Among the 103 Campylobacter strains screened, 89 were found to harbour a single or multiple virulence gene(s), giving an overall prevalence of 86.4%. C. jejuni strains had the highest prevalence of multivirulence at 64.9% (48/74), compared to C. coli (58.6%, 17/29). The ciaB and flaA genes were the most common virulence genes detected in C. jejuni (81.1% [60/74] and 62.2% [46/74], respectively) and in C. coli (each at 62.1%; 18/29). Campylobacter isolates from chicken harboured the most virulence-encoding genes. C. jejuni strains from chicken and cattle harboured the highest proportions of the cdtA and ciaB genes, respectively. All the C. coli strains from water samples harboured the cadF and flaA genes. The results obtained further revealed a significant positive correlation between cadF and flaA (R = 0.733). C. jejuni and C. coli strains from cattle, chicken, and water harbour virulence markers responsible for motility/colonization, invasion, adherence, and toxin production, evoking their important role in campylobacteriosis development among humans and livestock. The identification of cattle, chicken, and water samples as reservoirs of virulent Campylobacter spp. highlights the possible risk to human health. These data on some virulence genes of Campylobacter will assist food safety and public health officials in formulating policy statements.

Landscape analysis of the Kenyan policy on the treatment and prevention of diarrheal disease among under-5 children.

OBJECTIVE: Diarrhoea remains a leading cause of morbidity and death among under-5 children in Kenya, despite multipronged policy and programme initiatives to increase access to treatment. This study interrogates the comprehensiveness and adequacy of Kenya's policies, frameworks and action plans for diarrheal management and prevention. The study seeks to identify policy and practice gaps that need to be filled to strengthen diarrhoea treatment and prevention among under-5 children in Kenya. DESIGN: Our study is a landscape analysis, which seeks to identify the gaps in the current Kenya diarrheal policy, frameworks and action plans. The critical questions included their comprehensiveness, the availability of elaborate treatment, management and prevention solutions, together with updatedness, building on evidence from extant literature on key pathways to infection relating to man-animal environmental interaction, which are critical in enteric infection prevention initiatives. DATA SOURCES: We conducted an internet search of databases of Government of Kenya's Ministry of Health; relevant websites/publications of international organisations and groups (Centre for Disease Control and Prevention, UNICEF and WHO) and published and grey literature (Google searches, Google Scholar and PubMed). ELIGIBILITY CRITERIA: Included are publicly available key national diarrheal policy frameworks, plans, strategies, laws, institutional frameworks and operational guidelines that inform pertinent questions on the adequacy of policy and practice and preventive policy updates and actions. Further, peer-reviewed and grey literature on diarrheal morbidity and mortality and diarrheal prevention and management are included. The analysis excluded any information that was not referenced on the internet nor obtained from the internet. DATA EXTRACTION AND SYNTHESIS: The review team extracted the key provisions of the policy guidelines guided by a checklist and questions around the adequacy of existing national policies in addressing the determinants, prevention and treatment interventions of enteric infections and diarrhoea among under-5 children in the country. The checklist covered Kenyan background and diarrhoea situation analysis, policy objectives, policy strategies and policy implementation. RESULTS: The analysis identified a corpus of strategies for the management of diarrhoea at multiple levels: health facilities, communities and households. The policies highlighted advocacy, health communication and social mobilisation, as well as logistics management and prevention strategies. However, the triangulation of evidence from the policy provisions and extant literature identified critical policy gaps in diarrhoea prevention and management in Kenya, particularly the lack of focus on zoonotic pathways to enteric infection, environment-pathogen linkages and operationalisation of the roles of social determinants of health and related services. The policy documents had limited focus on rapid diagnosis, vaccine development and deployment, together with weak funding commitment towards implementation and unclear pathways to funding responsibilities. CONCLUSION: Policies are central to guiding programmatic actions towards effective enteric and diarrhoea prevention and management measures in Kenya. This study shows the need for policy updates to reflect pathways to enteric infections not covered in the current policy guidelines. Further, there is a need to strengthen the treatment and management of infection through rapid diagnosis, vaccine development and deployment, and strong funding commitment towards implementation together with clear funding responsibilities. Together, these will be vital in strengthening the current policy provisions and addressing other pathways to the prevention of enteric infections relating to zoonotic, environment-pathogen linkages and social determinants of health in Kenya and other low-income and middle-income countries. TRIAL REGISTRATION NUMBER: NCT05322655.

Tracing the origin of NDM-1-producing and extensively drug-resistant Pseudomonas aeruginosa ST357 in the Netherlands.

BACKGROUND: In the hospital environment, carbapenemase-producing Pseudomonas aeruginosa (CPPA) may lead to fatal patient infections. However, the transmission routes of CPPA often remain unknown. Therefore, this case study aimed to trace the origin of CPPA ST357, which caused a hospital-acquired pneumonia in a repatriated critically ill patient suffering from Guillain-Barré Syndrome in 2023. METHODS: Antimicrobial susceptibility of the CPPA isolate for 30 single and combination therapies was determined by disk-diffusion, Etest or broth microdilution. Whole-genome sequencing was performed for three case CPPA isolates (one patient and two sinks) and four distinct CPPA ST357 patient isolates received in the Dutch CPPA surveillance program. Furthermore, 193 international P. aeruginosa ST357 assemblies were collected via three genome repositories and analyzed using whole-genome multi-locus sequence typing in combination with antimicrobial resistance gene (ARG) characterization. RESULTS: A Dutch patient who carried NDM-1-producing CPPA was transferred from Kenya to the Netherlands, with subsequent dissemination of CPPA isolates to the local sinks within a month after admission. The CPPA case isolates presented an extensively drug-resistant phenotype, with susceptibility only for colistin and cefiderocol-fosfomycin. Phylogenetic analysis showed considerable variation in allelic distances (mean = 150, max = 527 alleles) among the ST357 isolates from Asia (n = 92), Europe (n = 58), Africa (n = 21), America (n = 16), Oceania (n = 2) and unregistered regions (n = 4). However, the case isolates (n = 3) and additional Dutch patient surveillance program isolates (n = 2) were located in a sub-clade of isolates from Kenya (n = 17; varying 15-49 alleles), the United States (n = 7; 21-115 alleles) and other countries (n = 6; 14-121 alleles). This was consistent with previous hospitalization in Kenya of 2/3 Dutch patients. Additionally, over half of the isolates (20/35) in this sub-clade presented an identical resistome with 9/17 Kenyan, 5/5 Dutch, 4/7 United States and 2/6 other countries, which were characterized by the blaNDM-1, aph(3')-VI, ARR-3 and cmlA1 ARGs. CONCLUSION: This study presents an extensively-drug resistant subclone of NDM-producing P. aeruginosa ST357 with a unique resistome which was introduced to the Netherlands via repatriation of critically ill patients from Kenya. Therefore, the monitoring of repatriated patients for CPPA in conjunction with vigilance for the risk of environmental contamination is advisable to detect and prevent further dissemination.

Causes of pre and post-donation deferrals among blood donors, at Kwale Satellite Blood Transfusion Center, Kwale County, Kenya, 2018-2022.

BACKGROUND: Both pre-donation and post-donation deferrals pose challenges to blood safety and availability. This study delved into the deferral rates before donations and their underlying reasons, as, transfusion transmissible infections (TTIs) leading to post-donation deferrals among potential blood donors at the Kwale Satellite Blood Transfusion Centre (KSBTC) in Kenya. METHODS: We performed a retrospective electronic record review of pre- and post-donation deferrals among blood donors at KSBTC, 2018-2022. The pre-donations deferral rate and reasons for deferral were analyzed. Accepted donations were analyzed to determine the prevalence of HIV, hepatitis B (HBV), hepatitis C (HCV), and syphilis. Descriptive statistics were calculated and both crude odds ratio (COR) and adjusted odds ratio (AOR), and their 95% confidence intervals (CI) were calculated. Variables with p < 0.05 were considered statistically significant. RESULTS: A review was conducted on 12,633 blood donation records. Among these, individuals 2,729/12,633 (21.60%) were deferred from donating with the primary reason being low hemoglobin levels, constituting 51.86% of deferrals. Around 773/9,904 (7.80%) of blood units, were discarded due to at least one TTI. Among these, HBV accounted for 4.73%, HIV for 2.01%, HCV for 1.21%, and Syphilis for 0.59% of cases. The adjusted odds ratio for male donors were, (aOR = 1.3, 95% CI 1.01-1.57), donors with none or primary education level (aOR = 1.4 95% CI 1.11-1.68), first-timer donors (aOR = 1.2, 95% CI 1.01-1.44), and static strategy for blood collection (aOR = 1.4, 95%CI 1.12-1.63) were independently potentially associated with testing positive for at least one TTI. CONCLUSION: The study indicates that TTIs continue to pose a risk to the safety of Kenya's bloodstock, with a notable prevalence of HBV infections. Male donors, individuals with limited education, first-time donors, and utilizing a fixed strategy for blood collection were identified as potential risk factors independently associated with TTIs.

Acute febrile illness in Kenya: Clinical characteristics and pathogens detected among patients hospitalized with fever, 2017-2019.

Acute febrile illness (AFI) is a common reason for healthcare seeking and hospitalization in Sub-Saharan Africa and is often presumed to be malaria. However, a broad range of pathogens cause fever, and more comprehensive data on AFI etiology can improve clinical management, prevent unnecessary prescriptions, and guide public health interventions. We conducted surveillance for AFI (temperature ≥38.0°C <14 days duration) among hospitalized patients of all ages at four sites in Kenya (Nairobi, Mombasa, Kakamega, and Kakuma). For cases of undifferentiated fever (UF), defined as AFI without diarrhea (≥3 loose stools in 24 hours) or lower respiratory tract symptoms (cough/difficulty breathing plus oxygen saturation <90% or [in children <5 years] chest indrawing), we tested venous blood with real-time PCR-based TaqMan array cards (TAC) for 17 viral, 8 bacterial, and 3 protozoal fever-causing pathogens. From June 2017 to March 2019, we enrolled 3,232 AFI cases; 2,529 (78.2%) were aged <5 years. Among 3,021 with outcome data, 131 (4.3%) cases died while in hospital, including 106/2,369 (4.5%) among those <5 years. Among 1,735 (53.7%) UF cases, blood was collected from 1,340 (77.2%) of which 1,314 (98.1%) were tested by TAC; 715 (54.4%) had no pathogens detected, including 147/196 (75.0%) of those aged <12 months. The most common pathogen detected was Plasmodium, as a single pathogen in 471 (35.8%) cases and in combination with other pathogens in 38 (2.9%). HIV was detected in 51 (3.8%) UF cases tested by TAC and was most common in adults (25/236 [10.6%] ages 18-49, 4/40 [10.0%] ages ≥50 years). Chikungunya virus was found in 30 (2.3%) UF cases, detected only in the Mombasa site. Malaria prevention and control efforts are critical for reducing the burden of AFI, and improved diagnostic testing is needed to provide better insight into non-malarial causes of fever. The high case fatality of AFI underscores the need to optimize diagnosis and appropriate management of AFI to the local epidemiology.

Prevalence of all epilepsies in urban informal settlements in Nairobi, Kenya: a two-stage population-based study.

BACKGROUND: WHO estimates that more than 50 million people worldwide have epilepsy and 80% of cases are in low-income and middle-income countries. Most studies in Africa have focused on active convulsive epilepsy in rural areas, but there are few data in urban settings. We aimed to estimate the prevalence and spatial distribution of all epilepsies in two urban informal settlements in Nairobi, Kenya. METHODS: We did a two-stage population-based cross-sectional study of residents in a demographic surveillance system covering two informal settlements in Nairobi, Kenya (Korogocho and Viwandani). Stage 1 screened all household members using a validated epilepsy screening questionnaire to detect possible cases. In stage 2, those identified with possible seizures and a proportion of those screening negative were invited to local clinics for clinical and neurological assessments by a neurologist. Seizures were classified following the International League Against Epilepsy recommendations. We adjusted for attrition between the two stages using multiple imputations and for sensitivity by dividing estimates by the sensitivity value of the screening tool. Complementary log-log regression was used to assess prevalence differences by participant socio-demographics. FINDINGS: A total of 56 425 individuals were screened during stage 1 (between Sept 17 and Dec 23, 2021) during which 1126 were classified as potential epilepsy cases. A total of 873 were assessed by a neurologist in stage 2 (between April 12 and Aug 6, 2022) during which 528 were confirmed as epilepsy cases. 253 potential cases were not assessed by a neurologist due to attrition. 30 179 (53·5%) of the 56 425 individuals were male and 26 246 (46·5%) were female. The median age was 24 years (IQR 11-35). Attrition-adjusted and sensitivity-adjusted prevalence for all types of epilepsy was 11·9 cases per 1000 people (95% CI 11·0-12·8), convulsive epilepsy was 8·7 cases per 1000 people (8·0-9·6), and non-convulsive epilepsy was 3·2 cases per 1000 people (2·7-3·7). Overall prevalence was highest among separated or divorced individuals at 20·3 cases per 1000 people (95% CI 15·9-24·7), unemployed people at 18·8 cases per 1000 people (16·2-21·4), those with no formal education at 18·5 cases per 1000 people (16·3-20·7), and adolescents aged 13-18 years at 15·2 cases per 1000 people (12·0-18·5). The epilepsy diagnostic gap was 80%. INTERPRETATION: Epilepsy is common in urban informal settlements of Nairobi, with large diagnostic gaps. Targeted interventions are needed to increase early epilepsy detection, particularly among vulnerable groups, to enable prompt treatment and prevention of adverse social consequences. FUNDING: National Institute for Health Research using Official Development Assistance.

Circulating 25-hydroxycholecalciferol and calcium levels, and alkaline phosphatase activity among people living with and without human immunodeficiency virus and injecting drugs in kenya.

BACKGROUND: People who inject drugs (PWID) and living with the human immunodeficiency virus (PLHIV) are at higher risk of suffering marked derangements in micronutrient levels, leading to poor disease and treatment outcomes. Consequently, this can be monitored by measuring key biomarkers, such as total circulating (serum) 25-hydroxycholecalciferol (25(OH)D3), calcium, and alkaline phosphatase (ALP) for timely intervention. Therefore, circulating levels of 25(OH)D3 and calcium, and ALP activity were determined in PWID and are highly active anti-retroviral treatment (HAART)-experienced or -naive, along with those without HIV infection. METHODS: This cross-sectional study compared serum concentrations of 25(OH)D3, calcium, and ALP in Kenyan PLHIV and were HAART-naive (n = 30) or -experienced (n = 61), PWID and without HIV (n = 132). RESULTS: Circulating 25(OH)D3 levels were significantly different amongst the study groups (P < 0.001), and were significantly lower in the HAART-experienced (median, 17.3; IQR, 18.3 ng/ml; P < 0.001) and -naive participants (median, 21.7; IQR, 12.8 ng/ml; P = 0.015) relative to uninfected (median, 25.6; IQR, 6.8 ng/ml) PWID. In addition, the proportions of vitamin D deficiency (55.7%, 40.0%, and 17.4%) and insufficiency (31.1%, 53.3%, and 63.6%) compared to sufficiency (13.1%, 6.7%, and 18.9%; P < 0.001) were greater amongst HAART-experienced, -naive, and uninfected study groups, respectively. Likewise, serum total calcium concentrations were lower in the HAART-experienced relative to HIV-negative (P = 0.019) individuals. Serum ALP activity was also lower in the HAART-experienced in contrast to HIV-negative PWID (P = 0.048). Regression analysis indicated that predictors of circulating 25(OH)D3 were: age (ß = 0.287; R2 = 8.0%; P = 0.017) and serum ALP (ß = 0.283; R2 = 6.4%; P = 0.033) in the HAART-experienced PWID, and serum ALP (ß = 0.386; R2 = 14.5%; P < 0.001) in the HIV-negative PWID. CONCLUSION: This study suggests that HIV-1 infection and HAART, including injection substance use, decrease circulating 25(OH)D3, calcium and ALP activity. In addition, age and ALP activity are associated with low circulating vitamin D levels in HAART-experienced PWID. The results highlight the importance of incorporating vitamin D and calcium supplementation in treatment and rehabilitation protocols for PLHIV.

Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya.

Rabies, a viral disease that causes lethal encephalitis, kills ≈59,000 persons worldwide annually, despite availability of effective countermeasures. Rabies is endemic in Kenya and is mainly transmitted to humans through bites from rabid domestic dogs. We analyzed 164 brain stems collected from rabid animals in western and eastern Kenya and evaluated the phylogenetic relationships of rabies virus (RABV) from the 2 regions. We also analyzed RABV genomes for potential amino acid changes in the vaccine antigenic sites of nucleoprotein and glycoprotein compared with RABV vaccine strains commonly used in Kenya. We found that RABV genomes from eastern Kenya overwhelmingly clustered with the Africa-1b subclade and RABV from western Kenya clustered with Africa-1a. We noted minimal amino acid variances between the wild and vaccine virus strains. These data confirm minimal viral migration between the 2 regions and that rabies endemicity is the result of limited vaccine coverage rather than limited efficacy.

Characterization of genital chlamydia amongst female sex workers in Nairobi, Kenya.

Introduction: genital chlamydia, which is caused by diverse Chlamydia trachomatis (C. trachomatis) genotypes, is largely asymptomatic. We aimed to identify C. trachomatis genotypes causing genital chlamydia among female sex workers attending a sex workers outreach program clinic in Nairobi, Kenya. Methods: this cross-sectional study was conducted between 18th April 2017 and 19th March 2021. Genitourinary complaints from eligible female sex workers were documented using a structured questionnaire. Endocervical swabs were collected for laboratory analysis. C. trachomatis plasmid DNA was extracted, PCR-amplified, and sequenced. Consensus sequences were generated and aligned with reference sequences to determine the C. trachomatis genotypes. Bivariate analysis was used to determine the association between genitourinary complaints and genital chlamydia. Results: endocervical swabs were collected from a total of 348 participants. Of these, 46 (13.2%) were positive for C. trachomatis. Most (297, 85.3%) of the participants presented with pelvic discharge with or without other symptoms. Fifteen (15, 4.3%) had abdominal pain and 3 (0.9%) had an itchy vulva. There was no statistically significant relationship between clinical presentation and genital chlamydia. Twenty-three samples were successfully sequenced. Each sequence was at least 90% identical to each of the 13 references C. trachomatis genotypes A, B, C, D, E, F, G, Ia, J, L1, L2, L2b and L3. Conclusion: we found no significant association between individual genitourinary complaints and genital chlamydia infection. The C. trachomatis genotypes circulating amongst female sex workers in Nairobi could be related to genotypes A, B, C, D, E, F, G, Ia, J, L1, L2, L2b, and L3.

Temporal changes in cause of death among adolescents and adults in six countries in eastern and southern Africa in 1995-2019: a multi-country surveillance study of verbal autopsy data.

BACKGROUND: The absence of high-quality comprehensive civil registration and vital statistics systems across many settings in Africa has led to little empirical data on causes of death in the region. We aimed to use verbal autopsy data to provide comparative, population-based estimates of cause-specific mortality among adolescents and adults in eastern and southern Africa. METHODS: In this surveillance study, we harmonised verbal autopsy and residency data from nine health and demographic surveillance system (HDSS) sites in Kenya, Malawi, Tanzania, South Africa, Uganda, and Zimbabwe, each with variable coverage from Jan 1, 1995, to Dec 31, 2019. We included all deaths to adolescents and adults aged 12 or over that were residents of the study sites and had a verbal autopsy conducted. InSilicoVA, a probabilistic model, was used to assign cause of death on the basis of the signs and symptoms reported in the verbal autopsy. Levels and trends in all-cause and cause-specific mortality rates and cause-specific mortality fractions were calculated, stratified by HDSS site, sex, age, and calendar periods. FINDINGS: 52 484 deaths and 5 157 802 person-years were reported among 1 071 913 individuals across the nine sites during the study period. 47 961 (91·4%) deaths had a verbal autopsy, of which 46 570 (97·1%) were assigned a cause of death. All-cause mortality generally decreased across the HDSS sites during this period, particularly for adults aged 20-59 years. In many of the HDSS sites, these decreases were driven by reductions in HIV and tuberculosis-related deaths. In 2010-14, the top causes of death were: road traffic accidents, HIV or tuberculosis, and meningitis or sepsis in adolescents (12-19 years); HIV or tuberculosis in adults aged 20-59 years; and neoplasms and cardiovascular disease in adults aged 60 years and older. There was greater between-HDSS and between-sex variation in causes of death for adolescents compared with adults. INTERPRETATION: This study shows progress in reducing mortality across eastern and southern Africa but also highlights age, sex, within-HDSS, and between-HDSS differences in causes of adolescent and adult deaths. These findings highlight the importance of detailed local data to inform health needs to ensure continued improvements in survival. FUNDING: National Institute of Child Health and Human Development of the US National Institutes of Health.

Assessment of Heat Exposure and Health Outcomes in Rural Populations of Western Kenya by Using Wearable Devices: Observational Case Study.

BACKGROUND: Climate change increasingly impacts health, particularly of rural populations in sub-Saharan Africa due to their limited resources for adaptation. Understanding these impacts remains a challenge, as continuous monitoring of vital signs in such populations is limited. Wearable devices (wearables) present a viable approach to studying these impacts on human health in real time. OBJECTIVE: The aim of this study was to assess the feasibility and effectiveness of consumer-grade wearables in measuring the health impacts of weather exposure on physiological responses (including activity, heart rate, body shell temperature, and sleep) of rural populations in western Kenya and to identify the health impacts associated with the weather exposures. METHODS: We conducted an observational case study in western Kenya by utilizing wearables over a 3-week period to continuously monitor various health metrics such as step count, sleep patterns, heart rate, and body shell temperature. Additionally, a local weather station provided detailed data on environmental conditions such as rainfall and heat, with measurements taken every 15 minutes. RESULTS: Our cohort comprised 83 participants (42 women and 41 men), with an average age of 33 years. We observed a positive correlation between step count and maximum wet bulb globe temperature (estimate 0.06, SE 0.02; P=.008). Although there was a negative correlation between minimum nighttime temperatures and heat index with sleep duration, these were not statistically significant. No significant correlations were found in other applied models. A cautionary heat index level was recorded on 194 (95.1%) of 204 days. Heavy rainfall (>20 mm/day) occurred on 16 (7.8%) out of 204 days. Despite 10 (21%) out of 47 devices failing, data completeness was high for sleep and step count (mean 82.6%, SD 21.3% and mean 86.1%, SD 18.9%, respectively), but low for heart rate (mean 7%, SD 14%), with adult women showing significantly higher data completeness for heart rate than men (2-sided t test: P=.003; Mann-Whitney U test: P=.001). Body shell temperature data achieved 36.2% (SD 24.5%) completeness. CONCLUSIONS: Our study provides a nuanced understanding of the health impacts of weather exposures in rural Kenya. Our study's application of wearables reveals a significant correlation between physical activity levels and high temperature stress, contrasting with other studies suggesting decreased activity in hotter conditions. This discrepancy invites further investigation into the unique socioenvironmental dynamics at play, particularly in sub-Saharan African contexts. Moreover, the nonsignificant trends observed in sleep disruption due to heat expose the need for localized climate change mitigation strategies, considering the vital role of sleep in health. These findings emphasize the need for context-specific research to inform policy and practice in regions susceptible to the adverse health effects of climate change.