BACKGROUN:Shigella is an important cause of diarrheal morbidity and mortality globally. Data on disease burden across age groups, in different epidemiologic settings, and over time are needed to guide preventive strategies. We examined shigellosis in two sites in Kenya over a 10-year period. METHODS:We used data from the Population-Based Infectious Disease Surveillance (PBIDS) platform in a rural (Asembo, population ~35,000) and urban (Kibera, population ~23,000) setting. PBIDS participants presenting to surveillance clinics with diarrhea (≥3 loose stools in 24-hour period) had stool collected and cultured; Shigella isolates underwent antimicrobial susceptibility testing. We estimated incidence by dividing Shigella cases by person-years- observation, adjusting for the proportion of diarrhea cases with stool collected and for care-seeking outside surveillance clinics. RESULTS:From January 1, 2010 to December 31, 2019, we isolated Shigella from 23% and 15% of 2,017 and 4,074 stool specimens collected in Asembo and Kibera, respectively; S. flexneri accounted for 61% and 67%, respectively. In Asembo, the adjusted shigellosis incidence was 684/100,000; it was highest in ages 12-23 months (1,873/100,000) and ≥50 years (1,502/100,000). In Kibera, the adjusted incidence was 647/100,000, highest in ages 12-23 (2,828/100,000) and 24-59 months (936/100,000). Incidence declined significantly in Asembo (p = 0.009), but not in Kibera (p = 0.53). Overall, ≥ 97% of isolates were susceptible to ciprofloxacin and ceftriaxone. CONCLUSION:The shigellosis burden was greatest among young toddlers in both urban and rural areas and was high among older adults in the rural setting. Although resistance to first-line antibiotics was infrequent, continued susceptibility monitoring is warranted.

Use of 10-valent pneumococcal conjugate vaccine in Kenya has led to substantial reductions in vaccine-type pneumococcal carriage and invasive pneumococcal disease. However, analysis of recent surveillance data indicates an outbreak of vaccine-type serotype 1 in 2023 in Kibera, Kenya. Continued monitoring of invasive pneumococcal disease in Kenya is warranted.

The Kenya Multi Site Serosurveillance (KEMIS) collaboration set out to implement an integrated, nationally representative, population-based program of serological surveillance for past infection for a number of important infectious diseases in Kenya. The project started in December 2021 and built on a portfolio of SARS-CoV-2 research conducted in 2020 and 2021. In this profile paper, we describe the background of the KEMIS collaboration, its aim and objectives, the Health and Demographic Surveillance System sites that were involved in data collection, and the key activities undertaken. We also explain how we established governance and management of the KEMIS collaboration, and reflect on opportunities, challenges, lessons learned, and future directions.

Post-COVID-19 conditions (PCC) or Long COVID, will linger due to continued circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the burden and risk factors of PCC could guide development of management guidelines for affected persons. Using Population-Based Infectious Disease Surveillance platforms established in Nairobi and Siaya Counties in Kenya, we followed up participants previously infected with SARS-CoV-2 between 01/05/2020 and 30/09/2021 to evaluate the presence and risk factors for PCC. Interviews were conducted from 13/10/2021 to 22/11/2021 to elicit information on the presence of four primary outcome categories: (i) presence of respiratory symptoms, (ii) self-reported non-recovery after SARS-CoV-2 infection, (iii) psychological distress, and (iv) worsening disability. The latter two were evaluated for persons ≥ 18 years old. Risk factors assessed included participants’ demographic and clinical characteristics. Logistic regression models were developed for each outcome adjusted for household-level clustering. Characteristics of the 832 participants from both sites were as follows; 82.7

Background: Successful introduction, high uptake and program effectiveness of new maternal vaccines aimed to prevent disease among infants require prior knowledge of their safety during pregnancy. We aimed to identify background adverse birth outcomes and their predictors in Kenya by which to aid future interpretation of outcomes for new maternal vaccination programs. Methods: A cross-sectional survey was conducted to assess birth outcomes from women residents within the health and demographic surveillance systems of Kilifi, Siaya and Nairobi, Kenya. All selected women had pregnancies registered in the years 2017-2020 through census rounds and had a birth outcome recorded by the time of data collection. They were traced at home for interviews and abstraction of birth outcome records from mother and child health booklets. Multivariable logistic regression was used to identify independent predictors of adverse birth outcomes. Results: A total of 2702 women were interviewed. Adverse birth outcomes occurred in 788/2702 (29.2%) of pregnancies: 433 (16.0%) were preterm (gestational age <37 weeks), 298 (11.0%) low birth weight (<2500 g), 99 (3.7%) macrosomic (>4000 g) and 41 (1.5%) stillbirths. Predictors of adverse birth outcomes were gestational diabetes [adjusted Odds Ratio (aOR): 3.32 (1.53-7.20)], malaria during pregnancy [aOR: 1.74 (1.232.48)], not attending antenatal care [aOR: 12.89 (2.17-76.68)] and home delivery [aOR: 1.58 (1.18-2.12)]. Conclusions: In 3 Kenyan settings, almost a third of pregnancies had adverse birth outcomes. Recognizing this baseline prevalence and the factors associated with adverse birth outcomes will be important in validating the safety of new maternal vaccines.

The Kenya Multi Site Serosurveillance (KEMIS) collaboration set out to implement an integrated, nationally representative, population-based program of serological surveillance for past infection for a number of important infectious diseases in Kenya. The project started in December 2021 and built on a portfolio of SARS-CoV-2 research conducted in 2020 and 2021. In this profile paper, we describe the background of the KEMIS collaboration, its aim and objectives, the Health and Demographic Surveillance System sites that were involved in data collection, and the key activities undertaken. We also explain how we established governance and management of the KEMIS collaboration, and reflect on opportunities, challenges, lessons learned, and future directions.

The COVID-19 pandemic caused widespread changes and disruptions to healthcare seeking behavior. There are limited studies on the effect of the COVID-19 pandemic on healthcare seeking patterns in low-and middle-income countries (LMICs), especially in settings with inequitable access to healthcare in rural and urban informal settlements. We investigated the effect of the COVID-19 pandemic on reported healthcare seeking at health facilities and chemists using morbidity data from participants in an ongoing population-based infectious disease surveillance platform in Asembo in Siaya County, a rural setting in western Kenya and Kibera, an urban informal settlement in Nairobi County. We described healthcare seeking patterns before (from 1st January 2016 to 12th March 2020) and during the pandemic (from 13th March 2020 to 31st August 2022) by gender and age for any reported illness and select clinical syndromes using frequencies and percentages. We used a generalized estimating equation with an exchangeable correlation structure to assess the effect of the pandemic on healthcare seeking adjusting for gender and age. Overall, there was a 19% (adjusted odds ratio, aOR: 0.81; 95% Confidence Interval, CI: 0.79-0.83) decline in odds of seeking healthcare at health facilities for any illness in Asembo during the pandemic, and a 30% (aOR: 0.70; 95% CI: 0.67-0.73) decline in Kibera. Similarly, there was a decline in seeking healthcare by clinical syndromes, e.g., for ARI, aOR: 0.76; 95% CI:0.73-0.79 in Asembo, and aOR: 0.68; 95% CI:0.64-0.72 in Kibera. The pandemic resulted in increased healthcare seeking at chemists (aOR: 1.23; 95% CI: 1.20-1.27 in Asembo, and aOR: 1.40; 95% CI: 1.35-1.46 in Kibera). This study highlights interruptions to healthcare seeking in resource-limited settings due to the COVID-19 pandemic. The pandemic resulted in a substantial decline in seeking care at health facilities, and an increase of the same at chemists.

BACKGROUND:Kenya introduced Synflorix™ (GlaxoSmithKline, PCV10-GSK), a 10-valent pneumococcal conjugate vaccine, in 2011, using three primary doses and, in select areas, catch-up campaigns. Surveys conducted 1-2 years post-introduction showed a stable prevalence of pneumococcal colonization, with declines in vaccine-type carriage. However, little is known about the long-term impact of PCV10-GSK in Kenya. METHODS:We conducted a cross-sectional survey of pneumococcal carriage among children aged <5 years in November-December 2017 in Kibera (Nairobi informal settlement, no catch-up) and Asembo (rural western Kenya, 2-dose catch-up for children 1-4 years), using the same methods and settings as prior annual surveys from 2009 to 2013. Participants were randomly selected from an ongoing population-based surveillance platform. Nasopharyngeal swabs were frozen in skim milk-tryptone-glucose-glycerin media within 4 h and underwent culture with broth enrichment for pneumococcus. Isolates were serotyped by polymerase chain reaction and Quellung. RESULTS:We enrolled 504 children, including 252 from each site; >90 % of participants had received 3 doses of PCV10-GSK. Pneumococcal colonization was detected in 210 (83.3 %) participants in Kibera and 149 (59.1 %) in Asembo, which was significantly lower than the prevalence observed in 2013 (92.9 % and 85.7 %, respectively). PCV10-GSK serotypes were detected in 35/252 (13.9 %) participants in Kibera and 23/252 (9.1 %) in Asembo, respectively; these prevalences were lower, but not statistically different, from vaccine-type carriage prevalences in 2013 (17.3 % and 13.3 %, respectively). In 2017 in both sites, serotypes 3, 6A, 19A, 19F, and 35B were among the most common serotypes. CONCLUSION:Six years post-PCV10-GSK introduction, the prevalence of pneumococcal carriage among children has decreased, and the impact of PCV10-GSK on vaccine-type carriage has plateaued. Kenya recently changed from PCV10-GSK to Pneumosil™ (Serum Institute of India), a 10-valent PCV that includes serotypes 6A and 19A; these data provide historical context for interpreting changes in vaccine-type carriage following the PCV formulation switch.

Background Reliable mortality data are important for evaluating the impact of health interventions. However, data on mortality patterns among populations living in urban informal settlements are limited. Objectives To examine the mortality patterns and trends in an urban informal settlement in Kibera, Nairobi, Kenya, Methods Using data from a population-based surveillance platform we estimated overall and cause-specific mortality rates for all age groups using person-year-observation (pyo) denominators and using Poisson regression tested for trends in mortality rates over time. We compared associated mortality rates across groups using incidence rate ratios (IRR). Assignment of probable cause(s) of death was done using the InterVA-4 model. Results We registered 1134 deaths from 2009 to 2018, yielding a crude mortality rate of 4.4 (95% Confidence Interval [CI]4.2-4.7) per 1,000 pyo. Males had higher overall mortality rates than females (incidence rate ratio [IRR], 1.44; 95% CI, 1.28-1.62). The highest mortality rate was observed among children aged < 12 months (41.5 per 1,000 pyo; 95% CI 36.6-46.9). All-cause mortality rates among children < 12 months were higher than that of children aged 1-4 years (IRR, 8.5; 95% CI, 6.95-10.35). The overall mortality rate significantly declined over the period, from 6.7 per 1,000 pyo (95% CI, 5.7-7.8) in 2009 to 2.7 (95% CI, 2.0-3.4) per 1,000 pyo in 2018. The most common cause of death was acute respiratory infections (ARI)/pneumonia (18.1%). Among children < 5 years, the ARI/pneumonia deaths rate declined significantly over the study period (5.06 per 1,000 pyo in 2009 to 0.61 per 1,000 pyo in 2018; p = 0.004). Similarly, death due to pulmonary tuberculosis among persons 5 years and above significantly declined (0.98 per 1,000 pyo in 2009 to 0.25 per 1,000 pyo in 2018; p = 0.006). Conclusions Overall and some cause-specific mortality rates declined over time, representing important public health successes among this population.

ABSTRACT. Typhoid fever burden can vary over time. Long-term data can inform prevention strategies; however, such data are lacking in many African settings. We reexamined typhoid fever incidence and antimicrobial resistance (AMR) over a 10-year period in Kibera, a densely populated urban informal settlement where a high burden has been previously described. We used data from the Population Based Infectious Diseases Surveillance platform to estimate crude and adjusted incidence rates and prevalence of AMR in nearly 26,000 individuals of all ages. Demographic and healthcare-seeking information was collected through household visits. Blood cultures were processed for patients with acute fever or lower respiratory infection. Between 2010 and 2019, 16,437 participants were eligible for blood culture and 11,848 (72.1%) had a culture performed. Among 11,417 noncontaminated cultures (96.4%), 237 grew Salmonella enterica serovar Typhi (2.1%). Overall crude and adjusted incidences were 95 and 188 cases per 100,000 person-years of observation (pyo), respectively. Annual crude incidence varied from 144 to 233 between 2010 and 2012 and from 9 to 55 between 2013 and 2018 and reached 130 per 100,000 pyo in 2019. Children 5–9 years old had the highest overall incidence (crude, 208; adjusted, 359 per 100,000 pyo). Among isolates tested, 156 of 217 were multidrug resistant (resistant to chloramphenicol, ampicillin, and trimethoprim/sulfamethoxazole [71.9%]) and 6 of 223 were resistant to ciprofloxacin (2.7%). Typhoid fever incidence resurged in 2019 after a prolonged period of low rates, with the highest incidence among children. Typhoid fever control measures, including vaccines, could reduce morbidity in this setting.

Robust data on the impact of the COVID-19 pandemic on mortality in Africa are relatively scarce. Using data from two well-characterized populations in Kenya we aimed to estimate excess mortality during the COVID-19 pandemic period. The mortality data arise from an ongoing population-based infectious disease surveillance (PBIDS) platform, which has been operational since 2006 in rural western Kenya (Asembo, Siaya County) and an urban informal settlement (Kibera, Nairobi County), Kenya. PBIDS participants were regularly visited at home (2–3 times a year) by field workers who collected demographic data, including deaths. In addition, verbal autopsy (VA) interviews for all identified deaths are conducted. We estimated all-cause and cause-specific mortality rates before and during the height of the COVID-19 pandemic, and we compared associated mortality rates between the periods using incidence rate ratios. Excess deaths during the COVID-19 period were also estimated by modelling expected deaths in the absence of COVID-19 by applying a negative binomial regression model on historical mortality data from January 2016. Overall and monthly excess deaths were determined using the P-score metric. Spearman correlation was used to assess whether there is a relationship between the generated P-score and COVID-19 positivity rate. The all-cause mortality rate was higher during the COVID-19 period compared to the pre-COVID-19 period in Asembo [9.1 (95% CI, 8.2–10.0) vs. 7.8 (95% CI, 7.3–8.3) per 1000 person-years of observation, pyo]. In Kibera, the all-cause mortality rate was slightly lower during the COVID-19 period compared to the pre-COVID-19 period [2.6 (95% CI, 2.2–3.2 per 1000 pyo) vs. 3.1; 95% CI, 2.7–3.4 per 1000 pyo)]. An increase in all-cause mortality was observed (incidence rate ratio, IRR, 1.16; 95% CI, 1.04–1.31) in Asembo, unlike in Kibera (IRR, 0.88; 95% CI, 0.71–1.09). The notable increase in mortality rate in Asembo was observed among persons aged 50 to 64 years (IRR, 2.62; 95% CI, 1.95–3.52), persons aged 65 years and above (5.47; 95% CI, 4.60–6.50) and among females (IRR, 1.25; 95% CI, 1.07–1.46). These age and gender differences were not observed in Kibera. We observed an increase in the mortality rate due to acute respiratory infection, including pneumonia (IRR, 1.45;95% CI, 1.03–2.04), and a reduction in the mortality rate due to pulmonary tuberculosis (IRR, 0.22; 95% CI, 0.05–0.87) among older children and adults in Asembo. There was no statistically significant change in mortality rates due to leading specific causes of death in Kibera. Overall, during the COVID-19 period observed deaths were higher than expected deaths in Asembo (P-score = 6.0%) and lower than expected in Kibera (P-score = -22.3%).Using well-characterized populations in the two diverse geographic locations, we demonstrate a heterogenous impact of the COVID-19 pandemic on all-cause and cause-specific mortality rates in Kenya. We observed more deaths than expected during the COVID-19 period in our rural site in western Kenya contrary to the urban site in Nairobi, the capital city in Kenya.

Background Understanding the age patterns of disease is necessary to target interventions to maximise cost-effective impact. New malaria chemoprevention and vaccine initiatives target young children attending routine immunisation services. Here we explore the relationships between age and severity of malaria hospitalisation versus malaria transmission intensity. Methods Clinical data from 21 surveillance hospitals in East Africa were reviewed. Malaria admissions aged 1 month to 14 years from discrete administrative areas since 2006 were identified. Each site-time period was matched to a model estimated community-based age-corrected parasite prevalence to provide predictions of prevalence in childhood ( Pf PR 2–10 ). Admission with all-cause malaria, severe malaria anaemia (SMA), respiratory distress (RD) and cerebral malaria (CM) were analysed as means and predicted probabilities from Bayesian generalised mixed models. Results 52,684 malaria admissions aged 1 month to 14 years were described at 21 hospitals from 49 site-time locations where Pf PR 2–10 varied from < 1 to 48.7%. Twelve site-time periods were described as low transmission ( Pf PR 2–10 < 5%), five low-moderate transmission ( Pf PR 2–10 5–9%), 20 moderate transmission ( Pf PR 2–10 10–29%) and 12 high transmission ( Pf PR 2–10 ≥ 30%). The majority of malaria admissions were below 5 years of age (69–85%) and rare among children aged 10–14 years (0.7–5.4%) across all transmission settings. The mean age of all-cause malaria hospitalisation was 49.5 months (95% CI 45.1, 55.4) under low transmission compared with 34.1 months (95% CI 30.4, 38.3) at high transmission, with similar trends for each severe malaria phenotype. CM presented among older children at a mean of 48.7 months compared with 39.0 months and 33.7 months for SMA and RD, respectively. In moderate and high transmission settings, 34% and 42% of the children were aged between 2 and 23 months and so within the age range targeted by chemoprevention or vaccines. Conclusions Targeting chemoprevention or vaccination programmes to areas where community-based parasite prevalence is ≥10% is likely to match the age ranges covered by interventions (e.g. intermittent presumptive treatment in infancy to children aged 2–23 months and current vaccine age eligibility and duration of efficacy) and the age ranges of highest disease burden.

An important step towards COVID-19 pandemic control is adequate knowledge and adherence to mitigation measures, including vaccination. We assessed the level of COVID-19 knowledge, attitudes, and practices (KAP) among residents from an urban informal settlement in the City of Nairobi (Kibera), and a rural community in western Kenya (Asembo). A cross-sectional survey was implemented from April to May 2021 among randomly selected adult residents from a population-based infectious diseases surveillance (PBIDS) cohort in Nairobi and Siaya Counties. KAP questions were adopted from previous studies. Factors associated with the level of COVID-19 KAP, were assessed using multivariable regression methods. COVID-19 vaccine acceptance was 83.6% for the participants from Asembo and 59.8% in Kibera. The reasons cited for vaccine hesitancy in Kibera were safety concerns (34%), insufficient information available to decide (18%), and a lack of belief in the vaccine (21%), while the reasons in Asembo were safety concerns (55%), insufficient information to decide (26%) and lack of belief in the vaccine (11%). Our study findings suggest the need for continued public education to enhance COVID-19 knowledge, attitudes, and practices to ensure adherence to mitigation measures. Urban informal settlements require targeted messaging to improve vaccine awareness, acceptability, and uptake.

Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >= 69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care- seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats.

Background Maternal immunisation to prevent respiratory syncytial virus (RSV) associated disease among infants is in focus. However, little is known about adverse birth outcomes and associated factors occurring in a setting with high morbidities of malaria, HIV infection and undernutrition. Quantifying these ahead of introduction of a maternal vaccine would assist in assessing an association between RSV vaccination and adverse birth outcomes. Methods A cross-sectional survey was conducted to collect data on birth outcomes from women residents of the health and demographic surveillance systems (HDSS) of Siaya and Kilifi, Kenya and from the maternity wards of Siaya County referral hospital and Bondo sub-county hospital. Participants of the HDSS sites had pregnancies registered in the years 2017 to 2020 through census rounds and were traced at home for interview. All women had a birth outcome by the time of data collection. Multiple logistic regression was used to determine independent predictors of adverse birth outcomes. Results A total of 2219 women were interviewed. Median age during pregnancy was 27.7yrs (range: 22.7-32.4), 1857 (83.7%) attended antenatal care clinic (ANC), 1,979 (89.2%) delivered at a health facility and 2204 (99.3%) reported they would take up a new maternal vaccine. Adverse birth outcomes occurred in 781 (35%) of pregnancies; 490 (62.7%) were preterm, 247 (31.6%) low birth weight, 189 (24.2%) macrosomia and 42 (5.4%) still births. Predictors of adverse birth outcomes were, eclampsia (AOR 6.86 (1.40-33.60); p=0.017), gestational diabetes (AOR 3.01 (1.24-7.30; p=0.015), and home delivery (AOR 2.48 (1.20-5.13); p=0.014). Being multiparous (AOR 0.52 (0.33-0.81); p=0.004) was protective. Home delivery was significantly associated with older maternal age 40-49 years (p=0.001), multiparous >5 (p=0.001), level of formal education below primary (p=0.001) and Islamic religion (p=0.001). Conclusions In this maternal population, about a third of pregnancies have adverse birth outcomes. Recognizing this baseline prevalence will be important in validating safety of a new maternal vaccine. Monitoring of the actual safety outcomes of the maternal RSV vaccine, will require integrated initiatives to mitigate against factors affecting utilization of maternal healthcare services and individual factors associated with adverse birth outcomes.

BACKGROUND:Kenya introduced 10-valent pneumococcal conjugate vaccine (PCV10) among children <1 year in 2011 with catch-up vaccination among children 1-4 years in some areas. We assessed changes in pneumococcal carriage and antibiotic susceptibility patterns in children <5 years and adults. METHODS:During 2009-2013, we performed annual cross-sectional pneumococcal carriage surveys in 2 sites: Kibera (children <5 years) and Lwak (children <5 years, adults). Only Lwak had catch-up vaccination. Nasopharyngeal and oropharyngeal (adults only) swabs underwent culture for pneumococci; isolates were serotyped. Antibiotic susceptibility testing was performed on isolates from 2009 and 2013; penicillin nonsusceptible pneumococci (PNSP) was defined as penicillin-intermediate or -resistant. Changes in pneumococcal carriage by age (<1 year, 1-4 years, adults), site, and human immunodeficiency virus (HIV) status (adults only) were calculated using modified Poisson regression, with 2009-2010 as baseline. RESULTS:We enrolled 2962 children (2073 in Kibera, 889 in Lwak) and 2590 adults (2028 HIV+, 562 HIV-). In 2013, PCV10-type carriage was 10.3% (Lwak) to 14.6% (Kibera) in children <1 year and 13.8% (Lwak) to 18.7% (Kibera) in children 1-4 years. This represents reductions of 60% and 63% among children <1 year and 52% and 60% among children 1-4 years in Kibera and Lwak, respectively. In adults, PCV10-type carriage decreased from 12.9% to 2.8% (HIV+) and from 11.8% to 0.7% (HIV-). Approximately 80% of isolates were PNSP, both in 2009 and 2013. CONCLUSIONS:PCV10-type carriage declined in children <5 years and adults post-PCV10 introduction. However, PCV10-type and PNSP carriage persisted in children regardless of catch-up vaccination.

The incidence and spread of dengue virus (DENV) have increased rapidly in recent decades.Dengue is underreported in Africa, but recent outbreaks and seroprevalence data suggest that DENV is widespread there.A lack of ongoing surveillance limits knowledge about its spatial reach and hinders disease control planning.We sought to add data on dengue distribution in Kenya through diagnostic testing of serum specimens from persons with an acute febrile illness (AFI) attending an outpatient clinic in rural western Kenya (Asembo) during rainy seasons.Patients with symptoms not likely to be misclassified as dengue (e.g., diarrhea and anemia), those with a positive diagnostic laboratory results which explained their febrile illness, or those with serum collected more than 5 days after fever onset were excluded.However, febrile patients with a positive malaria smear were included in the study.We used reverse transcription polymerase chain reaction (RT-PCR) to test for DENV and IgM anti-DENV to test for recent infection.Of the 615 serum specimens available for testing, none were dengue positive by either RT-PCR or IgM anti-DENV testing.Dengue did not appear to be a cause of febrile illness in this area of western Kenya, although our relatively small sample size may not have identified DENV infections occurring at low incidence.A more widespread AFI surveillance system that includes dengue diagnostic testing by RT-PCR and antibody-based methods is required to more definitively gauge the size and geographic distribution of DENV infection in western Kenya.

Multidrug-resistant non-typhoidal Salmonella (NTS) infection has emerged as a prominent cause of invasive infections in Africa. We investigated the prevalence of ceftriaxone-resistant invasive NTS infections, conducted exploratory analysis of risk factors for resistance, and described antimicrobial use in western Kenya. We conducted a secondary analysis of existing laboratory, epidemiology, and clinical data from three independent projects, a malaria vaccine trial, a central nervous system (CNS) study, and the International Emerging Infections Program morbidity surveillance (surveillance program) during 2009-2014. We calculated odds ratios (OR) with 95% confidence intervals (CI) for ceftriaxone-resistant NTS infections compared with ceftriaxone-susceptible infections. We surveyed hospitals, pharmacies, and animal drug retailers about the availability and use of antimicrobials. In total, 286 invasive NTS infections were identified in the three projects; 43 NTS isolates were ceftriaxone-resistant. The absolute prevalence of ceftriaxone resistance varied among these methodologically diverse projects, with 18% (16/90) of isolates resistant to ceftriaxone in the vaccine trial, 89% (16/18) in the CNS study, and 6% (11/178) in the surveillance program. Invasive ceftriaxone-resistant infections increased over time. Most ceftriaxone-resistant isolates were co-resistant to multiple other antimicrobials. Having an HIV-positive mother (OR = 3.7; CI = 1.2-11.4) and taking trimethoprim-sulfamethoxazole for the current illness (OR = 9.6, CI = 1.2-78.9) were significantly associated with acquiring ceftriaxone-resistant invasive NTS infection. Ceftriaxone and other antibiotics were widely prescribed; multiple issues related to prescription practices and misuse were identified. In summary, ceftriaxone-resistant invasive NTS infection is increasing and limiting treatment options for serious infections. Efforts are ongoing to address the urgent need for improved microbiologic diagnostic capacity and an antimicrobial surveillance system in Kenya.

Antibiotics are essential to treat for many childhood bacterial infections; however inappropriate antibiotic use contributes to antimicrobial resistance. For childhood diarrhea, empiric antibiotic use is recommended for dysentery (bloody diarrhea) for which first-line therapy is ciprofloxacin. We assessed inappropriate antibiotic prescription for childhood diarrhea in two primary healthcare facilities in Kenya. We analyzed data from the Kenya Population Based Infectious Disease Surveillance system in Asembo (rural, malaria-endemic) and Kibera (urban slum, non-malaria-endemic). We examined records of children aged 2–59 months with diarrhea (≥3 loose stools in 24 h) presenting for care from August 21, 2009 to May 3, 2016, excluding visits with non-diarrheal indications for antibiotics. We examined the frequency of antibiotic over-prescription (antibiotic prescription for non-dysentery), under-prescription (no antibiotic prescription for dysentery), and inappropriate antibiotic selection (non-recommended antibiotic). We examined factors associated with over-prescription and under-prescription using multivariate logistic regression with generalized estimating equations. Of 2808 clinic visits with diarrhea in Asembo, 2685 (95.6%) were non-dysentery visits and antibiotic over-prescription occurred in 52.5%. Of 4697 clinic visits with diarrhea in Kibera, 4518 (96.2%) were non-dysentery and antibiotic over-prescription occurred in 20.0%. Antibiotic under-prescription was noted in 26.8 and 73.7% of dysentery cases in Asembo and Kibera, respectively. Ciprofloxacin was used for 11% of dysentery visits in Asembo and 0% in Kibera. Factors associated with over- and under-prescription varied by site. In Asembo a discharge diagnosis of gastroenteritis was associated with over-prescription (adjusted odds ratio [aOR]:8.23, 95% confidence interval [95%CI]: 3.68–18.4), while malaria diagnosis was negatively associated with antibiotic over-prescription (aOR 0.37, 95%CI: 0.25–0.54) but positively associated with antibiotic under-prescription (aOR: 1.82, 95%CI: 1.05–3.13). In Kibera, over-prescription was more common among visits with concurrent signs of respiratory infection (difficulty breathing; aOR: 3.97, 95%CI: 1.28–12.30, cough: aOR: 1.42, 95%CI: 1.06–1.90) and less common among children aged < 1 year (aOR: 0.82, 95%CI: 0.71–0.94). Inappropriate antibiotic prescription was common in childhood diarrhea management and efforts are needed to promote rational antibiotic use. Interventions to improve antibiotic use for diarrhea should consider the influence of malaria diagnosis on clinical decision-making and address both over-prescription, under-prescription, and inappropriate antibiotic selection.

Background. Data on pneumococcal conjugate vaccine (PCV) indirect effects in low-income countries with high human immunodeficiency virus (HIV) burden are limited. We examined adult pneumococcal pneumonia incidence before and after PCV introduction in Kenya in 2011. Methods. From 1 January 2008 to 31 December 2016, we conducted surveillance for acute respiratory infection (ARI) among similar to 12 000 adults (>= 18 years) in western Kenya, where HIV prevalence is similar to 17%. ARI cases (cough or difficulty breathing or chest pain, plus temperature >= 38.0 degrees C or oxygen saturation <90%) presenting to a clinic underwent blood culture and pneumococcal urine antigen testing (UAT). We calculated ARI incidence and adjusted for healthcare seeking. The proportion of ARI cases with pneumococcus detected among those with complete testing (blood culture and UAT) was multiplied by adjusted ARI incidence to estimate pneumococcal pneumonia incidence. Results. Pre-PCV (2008-2010) crude and adjusted ARI incidences were 3.14 and 5.30/100 person-years-observation (pyo), respectively. Among ARI cases, 39.0% (340/872) had both blood culture and UAT; 21.2% (72/340) had pneumococcus detected, yielding a baseline pneumococcal pneumonia incidence of 1.12/100 pyo (95% confidence interval [CI]: 1.0-1.3). In each post-PCV year (2012-2016), the incidence was significantly lower than baseline; with incidence rate ratios (IRRs) of 0.53 (95% CI: 0.31-0.61) in 2012 and 0.13 (95% CI: 0.09-0.17) in 2016. Similar declines were observed in HIV-infected (IRR: 0.13; 95% CI: 0.08-0.22) and HIV-uninfected (IRR: 0.10; 95% CI: 0.05-0.20) adults. Conclusions. Adult pneumococcal pneumonia declined in western Kenya following PCV introduction, likely reflecting vaccine indirect effects. Evidence of herd protection is critical for guiding PCV policy decisions in resource-constrained areas.