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BackgroundVaccination against coronavirus disease 2019 (COVID-19) is a cost-effective mitigation strategy against the pandemic. As the COVID-19 vaccine becomes more available, low uptake is now a global threat and understanding the underpinnings in local contexts is a priority for intervention development. We aimed to evaluate behavioural determinants of COVID-19 vaccine acceptance that could inform engagement strategies to improve vaccine uptake in Makoko, an urban slum in Lagos, Nigeria.MethodsA population-based case–control study utilized the barrier analysis (BA) approach to evaluate the beliefs and behaviours of 45 ‘doers’ and 45 ‘non-doers’. The standardized BA tabulation sheet was used to assess differences in the proportions between the two groups to identify significant factors that could be addressed through a behaviour change strategy.ResultsPerceived social norms (family, friend, healthcare workers) that approve the vaccine and expected vaccine protection against diseases among doers were determinants of behaviour. Perceived poor accessibility, safety concerns, lack of trust, low vaccine efficacy and low susceptibility to the infection were the most important determinants of behaviour among non-doers.ConclusionsMeasures to improve COVID-19 vaccine acceptance in Makoko should include improvement in accessibility and exposing myths and misinformation through clear, concise and evidence-based community education delivered by trusted persons such as healthcare workers and religious leaders.

Background Few studies have assessed the seroprevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among healthcare workers (HCWs) in Africa. We report findings from a survey among HCWs in 3 counties in Kenya. Methods We recruited 684 HCWs from Kilifi (rural), Busia (rural), and Nairobi (urban) counties. The serosurvey was conducted between 30 July and 4 December 2020. We tested for immunoglobulin G antibodies to SARS-CoV-2 spike protein, using enzyme-linked immunosorbent assay. Assay sensitivity and specificity were 92.7 (95% CI, 87.9-96.1) and 99.0% (95% CI, 98.1-99.5), respectively. We adjusted prevalence estimates, using bayesian modeling to account for assay performance. Results The crude overall seroprevalence was 19.7% (135 of 684). After adjustment for assay performance, seroprevalence was 20.8% (95% credible interval, 17.5%–24.4%). Seroprevalence varied significantly (P < .001) by site: 43.8% (95% credible interval, 35.8%–52.2%) in Nairobi, 12.6% (8.8%–17.1%) in Busia and 11.5% (7.2%–17.6%) in Kilifi. In a multivariable model controlling for age, sex, and site, professional cadre was not associated with differences in seroprevalence. Conclusion These initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.

BACKGROUND: Population-level health and mortality data are crucial for evidence-informed policy but scarce in Nigeria. To fill this gap, we undertook a comprehensive assessment of the burden of disease in Nigeria and compared outcomes to other west African countries. METHODS: In this systematic analysis, using data and results of the Global Burden of Diseases, Injuries, and Risk Factors Study 2019, we analysed patterns of mortality, years of life lost (YLLs), years lived with disability (YLDs), life expectancy, healthy life expectancy (HALE), and health system coverage for Nigeria and 15 other west African countries by gender in 1998 and 2019. Estimates of all-age and age-standardised disability-adjusted life-years for 369 diseases and injuries and 87 risk factors are presented for Nigeria. Health expenditure per person and gross domestic product were extracted from the World Bank repository. FINDINGS: Between 1998 and 2019, life expectancy and HALE increased in Nigeria by 18% to 64·3 years (95% uncertainty interval [UI] 62·2-66·6), mortality reduced for all age groups for both male and female individuals, and health expenditure per person increased from the 11th to third highest in west Africa by 2018 (US$18·6 in 2001 to $83·75 in 2018). Nonetheless, relative outcomes remained poor; Nigeria ranked sixth in west Africa for age-standardised mortality, seventh for HALE, tenth for YLLs, 12th for health system coverage, and 14th for YLDs in 2019. Malaria (5176·3 YLLs per 100 000 people, 95% UI 2464·0-9591·1) and neonatal disorders (4818·8 YLLs per 100 000, 3865·9-6064·2) were the leading causes of YLLs in Nigeria in 2019. Nigeria had the fourth-highest under-five mortality rate for male individuals (2491·8 deaths per 100 000, 95% UI 1986·1-3140·1) and female individuals (2117·7 deaths per 100 000, 1756·7-2569·1), but among the lowest mortality for men older than 55 years. There was evidence of a growing non-communicable disease burden facing older Nigerians. INTERPRETATION: Health outcomes remain poor in Nigeria despite higher expenditure since 2001. Better outcomes in countries with equivalent or lower health expenditure suggest health system strengthening and targeted intervention to address unsafe water sources, poor sanitation, malnutrition, and exposure to air pollution could substantially improve population health. FUNDING: The Bill & Melinda Gates Foundation.

Funder: Wellcome Trust, Health is central to the development of any country. Nigeria’s gross domestic product is the largest in Africa, but its per capita income of about ₦770 000 (US$2000) is low with a highly inequitable distribution of income, wealth, and therefore, health. It is a picture of poverty amidst plenty. Nigeria is both a wealthy country and a very poor one. About 40% of Nigerians live in poverty, in social conditions that create ill health, and with the ever-present risk of catastrophic expenditures from high out-of-pocket spending for health. Even compared with countries of similar income levels in Africa, Nigeria’s population health outcomes are poor, with national statistics masking drastic differences between rich and poor, urban and rural populations, and different regions.

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya (∼75% June 1st) have implications for a fourth wave and future control strategies.One Sentence SummaryCOVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure

Background Early diagnosis and treatment of tuberculosis (TB) are the mainstay of global and national TB control efforts. However, the gap between expected and reported cases persists for various reasons attributable to the TB services and care-seeking sides of the TB care cascade. Understanding individual and collective perspectives of knowledge, attitudes, beliefs and other social circumstances around TB can inform an evidence-based approach in engaging communities and enhance their participation in TB case detection and treatment. Methods The study was conducted during the Gambian survey of TB prevalence. This was a nationwide cross-sectional multistage cluster survey with 43,100 participants aged ≥15 years in 80 clusters. The study sample, a random selection of 10% of the survey population within each cluster responded to a semi-structured questionnaire administered by trained fieldworkers to assess the knowledge, attitudes and practice of the participants towards TB. Overall knowledge, attitude and practice scores were dichotomised using the computed mean scores and analysed using descriptive, univariable and multivariable logistic regression. Results All targeted participants (4309) were interviewed. Majority were females 2553 (59.2%), married 2614 (60.7%), had some form of education 2457 (57%), and were unemployed 2368 (55%). Although 3617 (83.9%) of the participants had heard about TB, only 2883 (66.9%) were considered to have good knowledge of TB. Overall 3320 (77%) had unfavourable attitudes towards TB, including 1896 (44%) who indicated a preference for staying away from persons with TB rather than helping them. However, 3607(83.7%) appeared to have the appropriate health-seeking behaviours with regard to TB as 4157 (96.5%) of them were willing to go to the health facility if they had symptoms suggestive of TB. Conclusions About 3 in 10 Gambians had poor knowledge on TB, and significant stigma towards TB and persons with TB persists. Interventions to improve TB knowledge and address stigma are required as part of efforts to reduce the burden of undiagnosed TB in the country.

Highlights • Systematic review and meta-analysis of 18 studies and more than 6000 participants. • Adults over the age of 60 had a pooled prevalence of pneumococcal carriage of 9%. • Risk factors: contact with children, smoking and residing in a nursing home., Summary Background Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous. Methods This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70). Interpretation Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding No funding was required.

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., The proportion of a population that has previously been infected by a pathogen is typically estimated using antibody thresholds adjusted for sensitivity and specificity. Here, the authors present a model-based alternative to threshold methods which accounts for antibody waning and other sources of spectrum bias.

This study examines the prevalence of SARS-CoV-2 antibodies among blood donors aged 16 to 64 years in Kenya from January to March 2021.

Background Pneumococcal disease contributes significantly to childhood morbidity and mortality and treatment is costly. Nigeria recently introduced the Pneumococcal Conjugate Vaccine (PCV) to prevent pneumococcal disease. The aim of this study is to estimate health provider and household costs for the treatment of pneumococcal disease in children aged Methods We recruited U5s with clinical pneumonia, pneumococcal meningitis or pneumococcal septicaemia from a tertiary and a secondary level hospital in Kano, Nigeria. We obtained resource utilisation data from medical records to estimate costs of treatment to provider, and household expenses and income loss data from caregiver interviews to estimate costs of treatment to households. We defined catastrophic health expenditure (CHE) as household costs exceeding 25% of monthly household income and estimated the proportion of households that experienced it. We compared CHE across tertiles of household income (from the poorest to least poor). Results Of 480 participants recruited, 244 had outpatient pneumonia, and 236 were hospitalised with pneumonia (117), septicaemia (66) and meningitis (53). Median (IQR) provider costs were US$17 (US$14-22) for outpatients and US$272 (US$271-360) for inpatients. Median household cost was US$51 (US$40-69). Overall, 33% of households experienced CHE, while 53% and 4% of the poorest and least poor households, experienced CHE respectively. The odds of CHE increased with admission at the secondary hospital, a diagnosis of meningitis or septicaemia, higher provider costs, and caregiver having a non-salaried job. Conclusion Provider costs are substantial, and households incur treatment expenses that considerably impact on their income and this is particularly so for the poorest households. Sustaining the PCV programme and ensuring high and equitable coverage to lower disease burden will reduce the economic burden of pneumococcal disease to the healthcare provider and households. What is already known? Children Pneumococcal conjugate vaccine (PCV) was introduced in Nigeria in 2016 to reduce the burden of pneumococcal disease PCV is currently subsidised through Gavi financial support and Nigeria will transition to full self-financing in a few of years There is no contextual evidence in Nigeria on economic burden of IPD to the health system and society that can support longer term investments in PCV when Gavi co-financing terminates What are the new findings? Treatment of one hospitalised episode of pneumococcal disease cost on average, US$300 to the provider, and US$83 to the household with significant variation by clinical syndrome and level of care Overall, a third of the households encountered costs that were catastrophic (i.e., >25% of household income) Burden of CHE varied by household income tertile ranging from 4% in the least poor households (highest income tertile) to 53% in the poorest households (lowest income tertile) Despite the short illness duration, pneumococcal disease syndromes result in huge economic costs to providers and households What do the new findings imply? Sustaining the PCV programme and achieving high PCV coverage has the potential of saving resources at both provider and household level Households are at risk of further impoverishment from catastrophic expenses associated with treatment of pneumococcal disease. This risk can also be significantly reduced by PCV.

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.

In tropical Africa, SARS-CoV-2 epidemiology is poorly described because of lack of access to testing and weak surveillance systems. Since April 2020, we followed SARS-CoV-2 seroprevalence in plasma samples across the Kenya National Blood Transfusion Service. We developed an IgG ELISA against full length spike protein. Validated in locally-observed, PCR-positive COVID-19 cases and in pre-pandemic sera, sensitivity was 92.7% and specificity was 99.0%. Using sera from 9,922 donors, we estimated national seroprevalence of SARS-CoV-2 antibodies at 4.3% in April-June 2020 and 9.1% in August-September 2020. Kenya’s second COVID-19 wave peaked in November 2020. Here we estimate national seroprevalence in early 2021.Between January 3 and March 15, 2021, we collected 3,062 samples from donors aged 16-64 years. Among 3,018 samples that met our study criteria, 1,333 were seropositive (crude seroprevalence 44.2%, 95% CI 42.4-46.0%). After Bayesian test-performance adjustment and population weighting to represent the national population distribution, the national estimate of seroprevalence was 48.5% (95% CI 45.2-52.1%). Seroprevalence varied little by age or sex but was higher in Nairobi (61.8%), the capital city, and lower in two rural regions.Almost half of Kenya’s adult donors had evidence of past SARS-CoV-2 infection by March 2021. Although high, the estimate is corroborated by other population-specific estimates in country. Between March and June, 2% of the population were vaccinated against COVID-19 and the country experienced a third epidemic wave. Natural infection is outpacing vaccine delivery substantially in Africa, and this reality needs to be considered as objectives of the vaccine programme are set.

In October 2020, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among healthcare workers and blood donors. Truck drivers and their assistants transport essential supplies during the coronavirus disease 2019 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 over a wide geographical area.

As countries decide on vaccination strategies and how to ease movement restrictions, estimates of cumulative incidence of SARS-CoV-2 infection are essential in quantifying the extent to which populations remain susceptible to COVID-19. Cumulative incidence is usually estimated from seroprevalence data, where seropositives are defined by an arbitrary threshold antibody level, and adjusted for sensitivity and specificity at that threshold. This does not account for antibody waning nor for lower antibody levels in asymptomatic or mildly symptomatic cases. Mixture modelling can estimate cumulative incidence from antibody-level distributions without requiring adjustment for sensitivity and specificity. To illustrate the bias in standard threshold-based seroprevalence estimates, we compared both approaches using data from several Kenyan serosurveys. Compared to the mixture model estimate, threshold analysis underestimated cumulative incidence by 31% (IQR: 11 to 41) on average. Until more discriminating assays are available, mixture modelling offers an approach to reduce bias in estimates of cumulative incidence.One-Sentence SummaryMixture models reduce biases inherent in the standard threshold-based analysis of SARS-CoV-2 serological data.

BackgroundFew studies have assessed the seroprevalence of antibodies against SARS-CoV-2 among Health Care Workers (HCWs) in Africa. We report findings from a survey among HCWs in three counties in Kenya.MethodsWe recruited 684 HCWs from Kilifi (rural), Busia (rural) and Nairobi (urban) counties. The serosurvey was conducted between 30th July 2020 and 4th December 2020. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. We adjusted prevalence estimates using Bayesian modeling to account for assay performance.ResultsCrude overall seroprevalence was 19.7% (135/684). After adjustment for assay performance seroprevalence was 20.8% (95% CI 17.5-24.4%). Seroprevalence varied significantly (pConclusionThese initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.

Observed SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality., The reported burden of SARS-CoV-2 has been relatively low in tropical Africa compared to Europe and the Americas, but estimating true infection rates is challenging. Here, the authors screen blood donors in Kenya for SARS-CoV-2 antibodies and describe spatiotemporal seroprevalence dynamics.

In October 2020, anti-SARS-CoV-2 IgG seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among other key populations. TDA transport essential supplies during the COVID-19 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 infection over a wide geographical area.

Observed SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality.

BackgroundThere are no data on SARS-CoV-2 seroprevalence in Africa though the COVID-19 epidemic curve and reported mortality differ from patterns seen elsewhere. We estimated the anti-SARS-CoV-2 antibody prevalence among blood donors in Kenya.MethodsWe measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. Assay sensitivity and specificity were 83% (95% CI 59-96%) and 99.0% (95% CI 98.1-99.5%), respectively. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance.ResultsComplete data were available for 3098 of 3174 donors, aged 15-64 years. By comparison with the Kenyan population, the sample over- represented males (82% versus 49%), adults aged 25-34 years (40% versus 27%) and residents of coastal Counties (49% versus 9%). Crude overall seroprevalence was 5.6% (174/3098). Population-weighted, test- adjusted national seroprevalence was 5.2% (95% CI 3.7– 7.1%). Seroprevalence was highest in the 3 largest urban Counties - Mombasa (9.3% [95% CI 6.4-13.2%)], Nairobi (8.5% [95% CI 4.9-13.5%]) and Kisumu (6.5% [95% CI 3.3-11.2%]).ConclusionsWe estimate that 1 in 20 adults in Kenya had SARS-CoV-2 antibodies during the study period. By the median date of our survey, only 2093 COVID-19 cases and 71 deaths had been reported through the national screening system. This contrasts, by several orders of magnitude, with the numbers of cases and deaths reported in parts of Europe and America when seroprevalence was similar.

Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.

Background Monovalent rotavirus vaccine, Rotarix (GlaxoSmithKline), was introduced in Kenya in July 2014 and is recommended to infants as oral doses at ages 6 and 10 weeks. A multisite study was established in 2 population-based surveillance sites to evaluate vaccine impact on the incidence of rotavirus-associated hospitalizations (RVHs). Methods Hospital-based surveillance was conducted from January 2010 to June 2017 for acute diarrhea hospitalizations among children aged Results Between January 2010 and June 2017 there were 1513 and 1652 diarrhea hospitalizations in Kilifi and Siaya; among those tested for rotavirus, 28% (315/1142) and 23% (197/877) were positive, respectively. There was a 57% (95% confidence interval [CI], 8–80%) reduction in RVHs observed in the first year post–vaccine introduction in Kilifi and a 59% (95% CI, 20–79%) reduction in Siaya. In the second year, RVHs decreased further at both sites, 80% (95% CI, 46–93%) reduction in Kilifi and 82% reduction in Siaya (95% CI. 61–92%); this reduction was sustained at both sites into the third year. Conclusions A substantial reduction in RVHs and all-cause diarrhea was observed in 2 demographic surveillance sites in Kenya within 3 years of vaccine introduction.

Pulmonary non-tuberculous mycobacterial (NTM) disease epidemiology in sub-Saharan Africa is not as well described as for pulmonary tuberculosis. Earlier reviews of global NTM epidemiology only included subject-level data from one sub-Saharan Africa country. We systematically reviewed the literature and searched PubMed, Embase, Popline, OVID and Africa Wide Information for articles on prevalence and clinical relevance of NTM detection in pulmonary samples in sub-Saharan Africa. We applied the American Thoracic Society/Infectious Disease Society of America criteria to differentiate between colonisation and disease. Only 37 articles from 373 citations met our inclusion criteria. The prevalence of pulmonary NTM colonization was 7.5% (95% CI: 7.2%–7.8%), and 75.0% (2325 of 3096) occurred in males, 16.5% (512 of 3096) in those previously treated for tuberculosis and Mycobacterium avium complex predominated (27.7% [95% CI: 27.2–28.9%]). In seven eligible studies, 27.9% (266 of 952) of participants had pulmonary NTM disease and M. kansasii with a prevalence of 69.2% [95% CI: 63.2–74.7%] was the most common cause of pulmonary NTM disease. NTM species were unidentifiable in 29.2% [2,623 of 8,980] of isolates. In conclusion, pulmonary NTM disease is a neglected and emerging public health disease and enhanced surveillance is required.

Tobacco use is a major risk factor for tuberculosis (TB). Secondhand smoke (SHS) is also a risk factor for TB and to a lesser extent, Mycobacterium tuberculosis infection without disease. We investigated the added risk of M. tuberculosis infection due to SHS exposure in childhood contacts of TB cases in The Gambia. Participants were childhood household contacts aged ≤ 14 years of newly diagnosed pulmonary TB (PTB) cases. The intensity of exposure to the case was categorized according to whether contacts slept in the same room, same house, or a different house as the case. Contacts were tested with an enzyme-linked immunospot interferon gamma release assay. In multivariate regression models, M. tuberculosis infection was associated with increasing exposure to a case (odds ratios [OR]: 3.9, 95% confidence interval [CI]: 2.11–71.4, P < 0.001]) and with male gender (OR: 1.5 [95% CI: 1.12–2.11], P = 0.008). Tobacco use caused a 3-fold increase in the odds of M. tuberculosis infection in children who slept closest to a case who smoked within the same home compared with a nonsmoking case (OR: 8.0 [95% CI: 2.74–23.29] versus 2.4 [95% CI: 1.17–4.92], P < 0.001). SHS exposure as an effect modifier appears to greatly increase the risk of M. tuberculosis infection in children exposed to PTB cases. Smoking cessation campaigns may be important for reducing transmission of M. tuberculosis to children within households.

Highlights • We predict a substantial decline in the carriage prevalence of vaccine serotypes. • About a 56% reduction in invasive pneumococcal disease is also predicted. • The decline is predicted to be sustainable ten years post-vaccination. • The current vaccination schedule is unlikely to achieve elimination of vaccine serotypes., Background In 2011, Kenya introduced the 10-valent pneumococcal conjugate vaccine together with a catch-up campaign for children aged

Background Many parts of Africa have witnessed reductions in Plasmodium falciparum transmission over the last 15 years. Since immunity to malaria is acquired more rapidly at higher transmission, the slower acquisition of immunity at lower transmission may partially offset the benefits of reductions in transmission. We examined the clinical spectrum of disease and predictors of mortality after sustained changes in transmission intensity, using data collected from 1989 to 2016. Methods We conducted a temporal observational analysis of 18,000 children, aged 14 days to 14 years old, who were admitted to Kilifi County Hospital, Kenya, from 1989 to 2016 with malaria. We describe the trends over time of the clinical and laboratory criteria for severe malaria and associated risk of mortality. Results During the time periods 1989–2003, 2004–2008, and 2009–2016, Kilifi County Hospital admitted averages of 657, 310, and 174 cases of severe malaria per year including averages of 48, 14, and 12 malaria-associated deaths per year, respectively. The median ages in years of children admitted with cerebral malaria, severe anaemia, and malaria-associated mortality were 3.0 (95% confidence interval (CI) 2.2–3.9), 1.1 (95% CI 0.9–1.4), and 1.1 (95% CI 0.3–2.2) in the year 1989, rising to 4.9 (95% CI 3.9–5.9), 3.8 (95% CI 2.5–7.1), and 5 (95% CI 3.3–6.3) in the year 2016. The ratio of children with cerebral malaria to severe anaemia rose from 1:2 before 2004 to 3:2 after 2009. Hyperparasitaemia was a risk factor for death after 2009 but not in earlier time periods. Conclusion Despite the evidence of slower acquisition of immunity, continued reductions in the numbers of cases of severe malaria resulted in lower overall mortality. Our temporal data are limited to a single site, albeit potentially applicable to a secular trend present in many parts of Africa. Electronic supplementary material The online version of this article (10.1186/s12916-019-1359-9) contains supplementary material, which is available to authorized users.

Summary Background In 2009, Gavi, the World Bank, and donors launched the pneumococcal Advance Market Commitment, which helped countries access more affordable pneumococcal vaccines. As many low-income countries begin to reach the threshold at which countries transition from Gavi support to self-financing (3-year average gross national income per capita of US$1580), they will need to consider whether to continue pneumococcal conjugate vaccine (PCV) use at full cost or to discontinue PCV in their childhood immunisation programmes. Using Kenya as a case study, we assessed the incremental cost-effectiveness of continuing PCV use. Methods In this modelling and cost-effectiveness study, we fitted a dynamic compartmental model of pneumococcal carriage to annual carriage prevalence surveys and invasive pneumococcal disease (IPD) incidence in Kilifi, Kenya. We predicted disease incidence and related mortality for either continuing PCV use beyond 2022, the start of Kenya's transition from Gavi support, or its discontinuation. We calculated the costs per disability-adjusted life-year (DALY) averted and associated 95% prediction intervals (PI). Findings We predicted that if PCV use is discontinued in Kenya in 2022, overall IPD incidence will increase from 8·5 per 100 000 in 2022, to 16·2 per 100 000 per year in 2032. Continuing vaccination would prevent 14 329 (95% PI 6130–25 256) deaths and 101 513 (4386–196 674) disease cases during that time. Continuing PCV after 2022 will require an estimated additional US$15·8 million annually compared with discontinuing vaccination. We predicted that the incremental cost per DALY averted of continuing PCV would be $153 (95% PI 70–411) in 2032. Interpretation Continuing PCV use is essential to sustain its health gains. Based on the Kenyan GDP per capita of $1445, and in comparison to other vaccines, continued PCV use at full costs is cost-effective (on the basis of the assumption that any reduction in disease will translate to a reduction in mortality). Although affordability is likely to be a concern, our findings support an expansion of the vaccine budget in Kenya. Funding Wellcome Trust and Gavi, the Vaccine Alliance.

Background Pneumococcal conjugate vaccines (PCV) are highly protective against invasive pneumococcal disease caused by vaccine serotypes, but the burden of pneumococcal disease in low-income and middle-income countries is dominated by pneumonia, most of which is non-bacteraemic. We examined the effect of 10-valent PCV on the incidence of pneumonia in Kenya. Methods We linked prospective hospital surveillance for clinically-defined WHO severe or very severe pneumonia at Kilifi County Hospital, Kenya, from 2002 to 2015, to population surveillance at Kilifi Health and Demographic Surveillance System, comprising 45 000 children younger than 5 years. Chest radiographs were read according to a WHO standard. A 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PCV10) was introduced in Kenya in January, 2011. In Kilifi, there was a three-dose catch-up campaign for infants (aged Findings Between May 1, 2002 and March 31, 2015, 44 771 children aged 2–143 months were admitted to Kilifi County Hospital. We excluded 810 admissions between January and March, 2011, and 182 admissions during nurses' strikes. In 2002–03, the incidence of admission with clinically-defined pneumonia was 2170 per 100 000 in children aged 2–59 months. By the end of the catch-up campaign in 2011, 4997 (61·1%) of 8181 children aged 2–11 months had received at least two doses of PCV10 and 23 298 (62·3%) of 37 416 children aged 12–59 months had received at least one dose. Across the 13 years of surveillance, the incidence of clinically-defined pneumonia declined by 0·5% per month, independent of vaccine introduction. There was no secular trend in the incidence of radiologically-confirmed pneumonia over 8 years of study. After adjustment for secular trend and season, incidence rate ratios for admission with radiologically-confirmed pneumonia, clinically-defined pneumonia, and diarrhoea (control condition), associated temporally with PCV10 introduction and the catch-up campaign, were 0·52 (95% CI 0·32–0·86), 0·73 (0·54–0·97), and 0·63 (0·31–1·26), respectively. Immediately before PCV10 was introduced, the annual incidence of clinically-defined pneumonia was 1220 per 100 000; this value was reduced by 329 per 100 000 at the point of PCV10 introduction. Interpretation Over 13 years, admissions to Kilifi County Hospital for clinically-defined pneumonia decreased sharply (by 27%) in association with the introduction of PCV10, as did the incidence of radiologically-confirmed pneumonia (by 48%). The burden of hospital admissions for childhood pneumonia in Kilifi, Kenya, has been reduced substantially by the introduction of PCV10.

Background Ten-valentpneumococcal conjugate vaccine(PCV10), delivered at 6, 10, and 14 weeks ofagewas 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 andinvasive 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 DemographicSurveillance System, arural communityon the Kenyan coast covering an area of 891 km2. We linked clinical and microbiologicalsurveillancefor 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 1minusIRR. 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 followingvaccineintroduction and remained low (PCV10-type IPD: 60·8 cases per 100 000 in the prevaccine eravs3·2 per 100 000 in the postvaccine era [adjusted IRR 0·08, 95% CI 0·03–0·22]; IPD caused by anyserotype: 81·6 per 100 000vs15·3 per 100 000 [0·32, 0·17–0·60]). PCV10-type IPD also declined in the post-vaccination era in unvaccinatedage groups( 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 PCV10immunisationprogrammes will provide substantial direct and indirect protection in low-income settings in tropical Africa.

To estimate the population prevalence of active pulmonary tuberculosis in Gambia.Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence.Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tuberculosis cases (58/69) than did symptoms alone (43/71). The estimated prevalence of smear-positive and bacteriologically confirmed pulmonary tuberculosis were 90 (95% confidence interval, CI: 53-127) and 212 (95% CI: 152-272) per 100 000 population, respectively. Tuberculosis prevalence was higher in males (333; 95% CI: 233-433) and in the 35-54 year age group (355; 95% CI: 219-490).The burden of tuberculosis remains high in Gambia but lower than earlier estimates of 490 per 100 000 population in 2010. Less than half of all cases would have been identified based on smear microscopy results alone. Successful control efforts will require interventions targeting men, increased access to radiography and more accurate, rapid diagnostic tests.Estimer la prévalence de la tuberculose pulmonaire active dans la population de Gambie.Entre décembre 2011 et janvier 2013, dans le cadre d'une enquête nationale en grappes à plusieurs degrés, un dépistage de la tuberculose pulmonaire active a été réalisé au moyen d'un questionnaire sur les symptômes tuberculeux et d'une radiographie pulmonaire, chez des personnes âgées de 15 ans ou plus ayant consenti à participer. Pour confirmer le diagnostic, des échantillons d'expectoration ont été collectés pour tous les participants dont les résultats de dépistage s’étaient révélés positifs, en vue de réaliser des examens par microscopie de fluorescence et des cultures en milieu liquide. Les techniques d'imputation multiple et de pondération par l'inverse de la probabilité ont été utilisées pour estimer la prévalence de la tuberculose.Sur les 100 678 personnes recensées, 55 832 étaient éligibles pour participer à l'étude et, parmi elles, 43 100 personnes (77,2%) ont participé. La majorité des participants (42 942; 99,6%) ont effectivement répondu au questionnaire sur les symptômes et passé une radiographie pulmonaire. Seules 5 948 personnes (13,8%) ont été éligibles pour un examen des expectorations, ce qui a entraîné le dépistage de 43 cas de tuberculose confirmée bactériologiquement, de 28 cas formels de tuberculose à frottis positif et de 6 cas probables de tuberculose à frottis positif. Les radiographies pulmonaires ont permis d'identifier plus de cas de tuberculose (58/69) que le seul questionnaire sur les symptômes (43/71). Les prévalences de la tuberculose pulmonaire à frottis positif et de la tuberculose bactériologiquement confirmée ont respectivement été estimées à 90 cas (intervalle de confiance de 95%: 53–127) pour 100 000 habitants et 212 cas (IC 95%: 152–272) pour 100 000 habitants. La prévalence de la tuberculose s'est avérée plus élevée dans la population masculine (333 cas; IC 95%: 233–433) et dans la tranche des 35–54 ans (355; IC 95%: 219-490).La charge de la tuberculose reste élevée en Gambie, même si elle a baissé par rapport à la précédente estimation, réalisée en 2010, qui faisait état de 490 cas pour 100 000 habitants. En utilisant uniquement la microscopie des frottis, moins de la moitié des cas auraient été identifiés. Pour être efficaces, les efforts de lutte contre la tuberculose doivent inclure des campagnes ciblant les hommes, améliorer l'accessibilité des examens radiographiques et utiliser des tests diagnostiques rapides plus précis.Estimar la prevalencia de la tuberculosis pulmonar activa entre la población en Gambia.Entre diciembre de 2011 y enero de 2013, personas de 15 años o más que participaron en una encuesta nacional en varias etapas y a nivel de grupos fueron examinadas en busca de tuberculosis pulmonar activa mediante una radiografía de tórax y para encontrar síntomas de tuberculosis. Para confirmar el diagnóstico, se recolectaron muestras de esputo de las personas cuyo examen resultó positivo y se sometieron a microscopia de fluorescencia y cultivos líquidos de tuberculosis. Para calcular la prevalencia de la tuberculosis, se utilizaron varias asignaciones y análisis de probabilidad inversa.De las 100 678 personas enumeradas, 55 832 se consideraron aptas para participar, de las cuales 43 100 (77,2%) participaron. La mayoría de los participantes (42 942; 99,6%) fueron examinados con éxito para detectar síntomas, así como por radiografía del tórax. Solo 5 948 (13,8%) fueron aptos para pruebas de esputo, lo que dio lugar a 43 confirmados a nivel bacteriológico, 28 casos bacilíferos de tuberculosis definitivos y 6 casos bacilíferos de tuberculosis probable. Las radiografías del tórax identificaron más casos de tuberculosis (58/69) que los síntomas por sí solos (43/71). La prevalencia estimada de tuberculosis pulmonar bacilífera y confirmada a nivel bacteriológico fue de 90 (intervalo de confianza, IC, del 95%: 53–127) y 212 (IC del 95%: 152–272) por cada 100 000 habitantes, respectivamente. La prevalencia de la tuberculosis fue mayor en hombres (333; IC del 95%: 233–433) y en los grupos de edad entre 35 y 54 años (355; IC del 95%: 219–490).Los índices de tuberculosis siguen siendo altos en Gambia, pero inferiores a las estimaciones anteriores de 490 por cada 100 000 habitantes en 2010. Se identificaron menos de la mitad de todos los casos según los resultados de la microscopia de frotis por sí solos. Para que los esfuerzos de control tengan éxito, serán necesarias intervenciones enfocadas a los hombres, un mayor acceso a radiografías y pruebas de diagnóstico más rápidas y exactas.تقدير مدى تفشي مرض السل الرئوي النشط بين السكان في غامبيا.خضع الأشخاص الذين تبلغ أعمارهم 15 عامًا أو أكثر ممن شاركوا في مسح عنقودي متعدد المراحل على مستوى الدولة بأكملها في الفترة بين ديسمبر/كانون الأول 2011 ويناير 2013 لفحص للكشف عن الإصابة بالسل الرئوي النشط باستخدام تصوير الصدر بالأشعة وفحص للكشف عن أعراض السل. وللتأكد من التشخيص، تم جمع عينات من البصاق من الأشخاص الذين أظهر الفحص نتائج إيجابية لهم، وخضعت تلك العينات للفحص تحت المجهر الفلوري ولعمليات زراعة في وسط سائل للكشف عن بكتريا السل. وتمت الاستعانة بطريقة حساب القيم التعويضية المتعددة وأسلوب ترجيح الاحتمال العكسي في تقدير مدى تفشي مرض السل. ايظل عبء مرض السل بمعدل مرتفع في غامبيا، إلا أنه يقل عن التقديرات السابقة التي أشارت إلى وجود 490 حالة في كل مجموعة سكانية يبلغ عدد أفرادها 100,000 نسمة في عام 2010. وقد تم تحديد ما يقل عن النصف من الحالات بأكملها اعتمادًا على نتائج الفحص المجهري لمسحة البصاق وحده. وستتطلب الجهود الرامية للنجاح في السيطرة على المرض بعض التدخلات التي تستهدف الرجال، وزيادة فرص الخضوع للتصوير بالأشعة وتوفير المزيد من الاختبارات التشخيصية الدقيقة والسريعة.旨在预测冈比亚境内活动性肺结核患病率。.在 2011 年 12 月到 2013 年 1 月期间，研究人员采用 X 线胸片对年龄为 15 岁以及上参与全国范围内、多阶段整群调查的人员进行活动性肺结核筛查以及肺结核症状筛查。为进行确诊，研究人员采集了筛查结果阳性人员的痰液样本并对其进行荧光显微镜观察以及肺结核液体培养基培养。还采用多重填补法和逆概率加权法以估算肺结核患病率。.在选出的 100,678 人中，55 ,832 人有资格参与调查，其中 43,100 (77.2%) 人参与了调查。我们通过 X 线胸片成功地对大部分参与者（42,942 人；99.6%）进行了症状筛查。仅 5,948 (13.8%) 人有资格参加痰液检验，结果显示 43 人为细菌学检查阳性，28 人痰涂片检查为阳性，并且发现了六例痰涂片检查疑似阳性的肺结核病例。相对于单纯症状查痰法 (43/71)， X 线胸片可确诊更多肺结核病例 (58/69)。每 10 万人中，预计痰涂片阳性和细菌学检查阳性的肺结核患病人数分别为 90（95% 置信区间，CI: 53-127) 和 212 (95% 置信区间，CI: 152–272)。男性 (333; 95% CI: 233–433) 以及年龄介于 35–54 岁的人群 (355; 95% CI: 219–490) 肺结核患病率更高 。.冈比亚境内肺结核患病率居高不下，但低于 2010 年估计的每 10 万人中 490 例的患病率。在所有病例中，半数以下病例本可以仅仅通过显微镜观察痰涂片确诊。为有效控制疾病发展，需要对男性采取干预措施、进一步促进 X线胸片以及更多精确、快速诊断检测方法的普及。.Оценить популяционную распространенность активной формы туберкулеза легких в Гамбии.В период с декабря 2011 года по январь 2013 года лица в возрасте ≥□15 лет принимали участие в национальном многоэтапном исследовании с применением гнездовой выборки; их обследовали на наличие активной формы туберкулеза легких при помощи рентгенографии грудной клетки, а также проверяли наличие у них клинических симптомов туберкулеза. С целью подтверждения диагноза у лиц, для которых результаты скринингового обследования были положительными, брали пробу мокроты и подвергали ее флуоресцентной микроскопии, а также применяли ее посев на жидкую питательную среду. Для оценки распространенности туберкулеза применялся метод множественного восстановления пропущенных данных и метод весовых коэффициентов для величин, обратных вероятности.Из 100 678 человек, зарегистрированных для проведения обследования, 55 832 отвечали критериям исследования. Из них 43 100 человек (77,2%) приняли участие в исследовании. В большинстве своем участники (42 942 (99,6%)) успешно прошли скрининг симптомов и рентгенографию грудной клетки. Только 5 948 участников (13,8%) отвечали критериям для сдачи мокроты на анализ, из них в 43 случаях было получено бактериологическое подтверждение, 28 мазков были квалифицированы как достоверно положительные, шесть — как вероятные случаи туберкулеза. Рентгенография грудной клетки выявила больше случаев туберкулеза (58 из 69), чем диагностика только по симптомам (43 из 71). Оценка распространенности положительного мазка на туберкулез и бактериологически подтвержденного туберкулеза легких составила 90 (95%-й доверительный интервал, ДИ: 53–127) и 212 (95%-й ДИ: 152–272) на 100 000 населения соответственно. Туберкулез чаще встречался среди мужчин (333, 95%-й ДИ: 233–433) и лиц в возрасте 35–54 лет (355, 95%-й ДИ: 219–490).В Гамбии сохраняется высокое бремя туберкулеза, но полученные оценочные значения ниже величины, рассчитанной в 2010 году, в 490 случаях на 100 000 населения. Менее половины всех случаев могли быть выявлены только на основании микроскопического исследования мазка. Для успеха контролирующих мероприятий потребуются вмешательства, ориентированные на мужчин, более широкий доступ к рентгенографии и более точные и быстродействующие диагностические тесты.

Highlights • A high coverage is essential if the full benefits of vaccines are to be enjoyed. • A vaccine registry can help quantify the errors in coverage estimates from surveys. • Vaccination coverage obtained using a survey approach overestimates coverage by 2%. • Survey and administrative methods underestimate fully immunised children by ≥10%. • Non-hospital delivery and stock-outs were associated with failure to vaccinate., 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.

Background10-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 MethodsClinical and microbiological surveillance for invasive pneumococcal disease (IPD) among admissions of all ages at Kilifi County Hospital was linked to the Kilifi Health and Demographic Surveillance System from 1999-2016. We calculated the incidence rate ratio (IRR) comparing the pre-vaccine and post-vaccine eras, adjusted for confounding, and reported percent reduction in IPD as 1-IRR. Annual cross-sectional surveys of nasopharyngeal carriage were conducted from 2009-2016.FindingsSurveillance identified 667 IPD cases in 3,211,403 person-years of observation. IPD incidence in children InterpretationIntroduction of PCV10 in Kenya resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. These findings suggest that routine infant PCV10 immunization programmes with catch-up campaigns will provide substantial direct and indirect protection in low-income settings in tropical Africa.

IntroductionMany low income countries soon will need to consider whether to continue pneumococcal conjugate vaccine (PCV) use at full costs as they transition from Gavi support. Using Kenya as a case study we assessed the incremental cost-effectiveness of continuing PCV use.MethodsWe fitted a dynamic compartmental model of pneumococcal carriage to annual carriage prevalence surveys and invasive pneumococcal disease (IPD) incidence in Kilifi, Kenya, and predicted disease incidence and related mortality for either continuing PCV use beyond 2022, the start of Kenya’s transition from Gavi support, or its discontinuation. We calculated the costs per disability-adjusted-life-year (DALY) averted and associated prediction intervals (PI).ResultsWe predicted that overall IPD incidence will increase by 93% (PI: 72% - 114%) from 8.5 in 2022 to 16.2 per 100,000 per year in 2032, if PCV use is discontinued. Continuing vaccination would prevent 15,355 (PI: 10,196–21,125) deaths and 112,050 (PI: 79,620– 130,981) disease cases during that time. Continuing PCV after 2022 will require an estimated additional US$15.6 million annually compared to discontinuing vaccination. The incremental cost per DALY averted of continuing PCV was predicted at $142 (PI: 85 - 252) in 2032.ConclusionContinuing PCV use is essential to sustain its health gains. Based on the Kenyan GDP per capita of $1445, and in comparison to other vaccines, continued PCV use at full costs is cost-effective. These arguments support an expansion of the vaccine budget, however, affordability may be a concern.FundingFunded by the Wellcome Trust.

Changes in nasopharyngeal (NP) carriage of vaccine-type (VT) Streptococcus pneumoniae can be used to assess the effectiveness of a pneumococcal conjugate vaccine (PCV10). We conducted a baseline carriage survey in rural (Kumbotso, Kano) and urban (Pakoto, Ogun) Nigeria. In this cross-sectional study, we obtained data on demography, clinical history, risk factors, and took NP swabs for pneumococcal culture. We calculated crude and age-standardised carriage prevalence and used log-binomial regression to assess risk factors for carriage. Among children aged 40% across all ages. The age-standardized prevalence of pneumococcal carriage was 66% in Kumbotso and 40% in Pakoto. The most commonly identified serotypes were 19 F, 6 A and 23 F. Risk factors for carriage were young age, recent rhinorrhoea, cohabitation with ≥2 children aged

Objective Paragonimiasis is a foodborne trematode infection of the lungs caused by Paragonimus spp., presenting clinically with similar symptoms to active tuberculosis (TB). Worldwide, an estimated 20.7 million people are infected with paragonimiasis, but relatively little epidemiological data exists for Africa. Given a recently reported case, we sought to establish whether paragonimiasis should be considered as an important differential diagnosis for human TB in The Gambia, West Africa. Results We developed a novel PCR-based diagnostic test for Paragonimus species known to be found in West Africa, which we used to examine archived TB negative sputum samples from a cross-sectional study of volunteers with tuberculosis-like symptoms from communities in the Western coastal region of The Gambia. Based on a “zero patient” design for detection of rare diseases, 300 anonymised AFB smear negative sputum samples, randomly selected from 25 villages, were screened for active paragonimiasis by molecular detection of Paragonimus spp. DNA. No parasite DNA was found in any of the sputa of our patient group. Despite the recent case report, we found no evidence of active paragonimiasis infection masking as TB in the Western region of The Gambia. Electronic supplementary material The online version of this article (10.1186/s13104-018-3134-y) contains supplementary material, which is available to authorized users.

Rationale: Contacts of patients with tuberculosis (TB) constitute an important target population for preventive measures because they are at high risk of infection with Mycobacterium tuberculosis and progression to disease. Objectives: We investigated bio-signatures with predictive ability for incident TB. Methods: In a case-control study nested within the Grand Challenges 6-74 longitudinal HIV-negative African cohort of exposed household contacts, we employed RNA sequencing, PCR, and the pair ratio algorithm in a training/test set approach. Overall, 79 progressors who developed TB between 3 and 24 months after diagnosis of index case and 328 matched nonprogressors who remained healthy during 24 months of follow-up were investigated. Measurements and Main Results: A four-transcript signature derived from samples in a South African and Gambian training set predicted progression up to two years before onset of disease in blinded test set samples from South Africa, the Gambia, and Ethiopia with little population-associated variability, and it was also validated in an external cohort of South African adolescents with latent M. tuberculosis infection. By contrast, published diagnostic or prognostic TB signatures were predicted in samples from some but not all three countries, indicating site-specific variability. Post hoc meta-analysis identified a single gene pair, C1QC/TRAV27 (complement C1q C-chain / T-cell receptor-a variable gene 27) that would consistently predict TB progression in household contacts from multiple African sites but not in infected adolescents without known recent exposure events. Conclusions: Collectively, we developed a simple whole blood-based PCR test to predict TB in recently exposed household contacts from diverse African populations. This test has potential for implementation in national TB contact investigation programs.

Background: Africa has the lowest childhood vaccination coverage worldwide. If the full benefits of childhood vaccination programmes are to be enjoyed in sub-Saharan Africa, all countries need to improve on vaccine delivery to achieve and sustain high coverage. In this paper, we review trends in vaccination coverage, dropouts between vaccine doses and explored the country-specific predictors of complete vaccination in West Africa. Methods: We utilized datasets from the Demographic and Health Surveys Program, available for Benin, Burkina Faso, The Gambia, Ghana, Guinea, Cote d’Ivoire, Liberia, Mali, Niger, Nigeria, Senegal, Sierra Leone and Togo, to obtain coverage for Bacillus Calmette-Guerin, polio, measles, and diphtheria, pertussis and tetanus (DPT) vaccines in children aged 12 – 23 months. We also calculated the DPT1-to-DPT3 and DPT1-to-measles dropouts, and proportions of the fully immunised child (FIC). Factors predictive of FIC were explored using Chi-squared tests and multivariable logistic regression. Results: Overall, there was a trend of increasing vaccination coverage. The proportion of FIC varied significantly by country (range 24.1-81.4%, mean 49%). DPT1-to-DPT3 dropout was high (range 5.1% -33.9%, mean 16.3%). Similarly, DPT1-measles dropout exceeded 10% in all but four countries. Although no single risk factor was consistently associated with FIC across these countries, maternal education, delivery in a health facility, possessing a vaccine card and a recent post delivery visit to a health facility were the key predictors of complete vaccination. Conclusions: The low numbers of fully immunised children and high dropout between vaccine doses highlights weaknesses and the need to strengthen the healthcare and routine immunization delivery systems in this region. Country-specific correlates of complete vaccination should be explored further to identify interventions required to increase vaccination coverage. Despite the promise of an increasing trend in vaccination coverage in West African countries, more effort is required to attain and maintain global vaccination coverage targets.

Background In West Africa, penicillin, macrolide and lincosamide resistance among beta-haemolytic streptococci (BHS) isolates has rarely been described. However, such data are critical to detect and track the emergence of antibiotic resistance. Methods Beta-haemolytic streptococci were cultured from clinical specimens from patients attending the clinic at the Medical Research Council Unit The Gambia (n = 217) and kept at −70 °C. Of these, 186 were revived and tested for penicillin susceptibility by disc diffusion and E-test methods, and the D-test for determination of constitutive and inducible macrolide–lincosamide (MLSB) resistance phenotypes. Results The majority of BHS isolates from infections were group A streptococci (GAS) (126/186, 67.7%). Of these, 16% were from invasive disease (30/186). Other BHS isolated included lancefield groups B (19, 10.2%); C (9/186, 4.8%), D (3/186, 1.6%), F (5/186, 2.7%), G (16/186, 8.6%) and non-typeable (8/186, 4.3%). Prevalence of BHS isolated from blood cultures ranges from 0% (2005) to 0.5% (2010). Most (85, 45.7%) of the isolates were from wound infections. Of the 186 BHS isolates, none was resistant to penicillin and 14 (6.1%) were resistant to erythromycin. Of these, 8 (4.3%) demonstrated constitutive MLSB resistance, and 5 (2.7%) were inducible MLSB resistant. All the inducible MLSB isolates were GAS, and majority of the constitutive MLSB isolates (6/8, 75.0%) were non-GAS. Conclusions Beta-haemolytic streptococci, predominantly GAS are associated with a wide range of infections in The Gambia. It is reassuring that macrolide and lincosamide resistance is relatively low. However, monitoring of MLSB resistance is necessary with the global spread of resistant BHS strains.

In The Gambia, Mycobacterium tuberculosis (Mtb) and Mycobacterium africanum (Maf) are major causes of tuberculosis (TB). Maf is more likely to cause TB in immune suppressed individuals, implying differences in virulence. Despite this, few studies have assessed the underlying immunity to the two pathogens in human. In this study, we analyzed T-cell responses from 19 Maf- and 29 Mtb-infected HIV-negative patients before and after TB chemotherapy following overnight stimulation of whole blood with TB-specific antigens. Before treatment, percentages of early secreted antigenic target-6(ESAT-6)/culture filtrate protein-10(CFP-10) and purified protein derivative-specific single-TNF-α-producing CD4(+) and CD8(+) T cells were significantly higher while single-IL-2-producing T cells were significantly lower in Maf- compared with Mtb-infected patients. Purified protein derivative-specific polyfunctional CD4(+) T cells frequencies were significantly higher before than after treatment, but there was no difference between the groups at both time points. Furthermore, the proportion of CD3(+) CD11b(+) T cells was similar in both groups pretreatment, but was significantly lower with higher TNF-α, IL-2, and IFN-γ production in Mtb- compared with that of Maf-infected patients posttreatment. Our data provide evidence of differences in T-cell responses to two mycobacterial strains with differing virulence, providing some insight into TB pathogenesis with different Mtb strains that could be prospectively explored as biomarkers for TB protection or susceptibility.