What capacity exists to provide essential inpatient care to small and sick newborns in a high mortality urban setting? - A cross-sectional study in Nairobi City County, Kenya.

Introduction: Appropriate demand for, and supply of, high quality essential neonatal care is key to improving newborn survival but evaluating such provision has received limited attention in low- and middle-income countries. Moreover, specific local data are needed to support healthcare planning for this vulnerable population.

Methods: We conducted health facility assessments between July 2015-April 2016, with retrospective review of admission events between 1st July 2014 and 30th June 2015, and used estimates of population-based incidence of neonatal conditions in Nairobi to explore access and evaluate readiness of public, private not-for-profit (mission), and private-for-profit (private) sector facilities providing 24/7 inpatient neonatal care in Nairobi City County.

Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya.

Background: Africa has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR).

Methods: Whole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya.

Two complement receptor one alleles have opposing associations with cerebral malaria and interact with αthalassaemia.

Malaria has been a major driving force in the evolution of the human genome. In sub-Saharan African populations, two neighbouring polymorphisms in the Complement Receptor One () gene, named and , occur at high frequencies, consistent with selection by malaria. Previous studies have been inconclusive.

Continuous Invasion by Respiratory Viruses Observed in Rural Households During a Respiratory Syncytial Virus Seasonal Outbreak in Coastal Kenya.

Background: Households are high-intensity close-contact environments favorable for transmission of respiratory viruses, yet little is known for low-income settings.

Methods: Active surveillance was completed on 47 households in rural coastal Kenya over 6 months during a respiratory syncytial virus (RSV) season. Nasopharyngeal swabs (NPSs) were taken from 483 household members twice weekly irrespective of symptoms.

Human challenge trials in vaccine development, Rockville, MD, USA, September 28-30, 2017.

The International Alliance for Biological Standardization organized the second workshop on human challenge trials (HCT) in Rockville, MD, in September 2017. The objective of this meeting was to examine the use of HCT, in response to the continuing human suffering caused by infectious diseases, preventable by the development of new and improved vaccines. For this, the approach of HCT could be valuable, as HCT can provide key safety, tolerability, immunogenicity, and efficacy data, and can be used to study host-pathogen biology.

Late Presentation With HIV in Africa: Phenotypes, Risk, and Risk Stratification in the REALITY Trial.

Background: Severely immunocompromised human immunodeficiency virus (HIV)-infected individuals have high mortality shortly after starting antiretroviral therapy (ART). We investigated predictors of early mortality and "late presenter" phenotypes.

Methods: The Reduction of EArly MortaLITY (REALITY) trial enrolled ART-naive adults and children ≥5 years of age with CD4 counts <100 cells/µL initiating ART in Uganda, Zimbabwe, Malawi, and Kenya.

Causes and Timing of Mortality and Morbidity Among Late Presenters Starting Antiretroviral Therapy in the REALITY Trial.

Background: In sub-Saharan Africa, 20%-25% of people starting antiretroviral therapy (ART) have severe immunosuppression; approximately 10% die within 3 months. In the Reduction of EArly mortaLITY (REALITY) randomized trial, a broad enhanced anti-infection prophylaxis bundle reduced mortality vs cotrimoxazole. We investigate the contribution and timing of different causes of mortality/morbidity.

Using non-exceedance probabilities of policy-relevant malaria prevalence thresholds to identify areas of low transmission in Somalia.

Background: Countries planning malaria elimination must adapt from sustaining universal control to targeted intervention and surveillance. Decisions to make this transition require interpretable information, including malaria parasite survey data. As transmission declines, observed parasite prevalence becomes highly heterogeneous with most communities reporting estimates close to zero.

Reflections on the ethics of participatory visual methods to engage communities in global health research.

There is a growing body of literature describing conceptual frameworks for working with participatory visual methods (PVM). Through a global health lens, this paper examines some key themes within these frameworks. We reflect on our experiences of working with with an array of PVM to engage community members in Vietnam, Kenya, the Philippines and South Africa in biomedical research and public health.

True malaria prevalence in children under five: Bayesian estimation using data of malaria household surveys from three sub-Saharan countries.

Background: Malaria is one of the major causes of childhood death in sub-Saharan countries. A reliable estimation of malaria prevalence is important to guide and monitor progress toward control and elimination. The aim of the study was to estimate the true prevalence of malaria in children under five in the Democratic Republic of the Congo, Uganda and Kenya, using a Bayesian modelling framework that combined in a novel way malaria data from national household surveys with external information about the sensitivity and specificity of the malaria diagnostic methods used in those surveys-i.

Tuberculous meningitis is associated with higher cerebrospinal HIV-1 viral loads compared to other HIV-1-associated meningitides.

To gain a better understanding of the immunopathogenesis of tuberculous meningitis (TBM) and identify potential diagnostic biomarkers that may discriminate TBM from other HIV-1-associated meningitides, we assessed HIV-1 viral load levels, drug resistance patterns in antiretroviral therapy (ART)-experienced patients with persistent viremia and soluble immunological analytes in peripheral blood and cerebrospinal fluid (CSF) of HIV-1 infected patients with TBM versus other meningitides. One hundred and three matched blood and CSF samples collected from HIV-1 infected patients with TBM or other meningitides presenting at a hospital in Durban, South Africa, from January 2009 to December 2011 were studied. HIV-1 RNA and 28 soluble immunological potential biomarkers were quantified in blood plasma and CSF.

A hidden burden of neonatal illness? A cross-sectional study of all admissions aged less than one month across twelve Kenyan County hospitals.

Small and sick newborns need high quality specialised care within health facilities to address persistently high neonatal mortality in low-income settings, including Kenya. We examined neonatal admissions in 12 public-sector County (formerly District) hospitals in Kenya between November 2014 and November 2016. Using data abstracted from newborn unit (NBU) admission registers and paediatric ward (PW) medical records, we explore the magnitude and distribution of admissions.

Health worker knowledge of Integrated Disease Surveillance and Response standard case definitions: a cross-sectional survey at rural health facilities in Kenya.

Background: The correct knowledge of standard case definition is necessary for frontline health workers to diagnose suspected diseases across Africa. However, surveillance evaluations commonly assume this prerequisite. This study assessed the knowledge of case definitions for health workers and their supervisors for disease surveillance activities in rural Kenya.

The influence of maternal psychosocial circumstances and physical environment on the risk of severe wasting in rural Gambian infants: a mixed methods approach.

Background: Severe wasting affects 16 million under 5's and carries an immediate risk of death. Prevalence remains unacceptably high in sub-Saharan Africa and early infancy is a high-risk period. We aimed to explore risk factors for severe wasting in rural Gambian infants.

Coverage of routine reporting on malaria parasitological testing in Kenya, 2015-2016.

Background: Following the launch of District Health Information System 2 across facilities in Kenya, more health facilities are now capable of carrying out malaria parasitological testing and reporting data as part of routine health information systems, improving the potential value of routine data for accurate and timely tracking of rapidly changing disease epidemiology at fine spatial resolutions.

Objectives: This study evaluates the current coverage and completeness of reported malaria parasitological testing data in DHIS2 specifically looking at patterns in geographic coverage of public health facilities in Kenya.

Methods: Monthly facility level data on malaria parasitological testing were extracted from Kenya DHIS2 between November 2015 and October 2016.

Adaptation of Plasmodium falciparum to its transmission environment.

Success in eliminating malaria will depend on whether parasite evolution outpaces control efforts. Here, we show that Plasmodium falciparum parasites (the deadliest of the species causing human malaria) found in low-transmission-intensity areas have evolved to invest more in transmission to new hosts (reproduction) and less in within-host replication (growth) than parasites found in high-transmission areas. At the cellular level, this adaptation manifests as increased production of reproductive forms (gametocytes) early in the infection at the expense of processes associated with multiplication inside red blood cells, especially membrane transport and protein trafficking.

Malaria prevalence metrics in low- and middle-income countries: an assessment of precision in nationally-representative surveys.

Background: One pillar to monitoring progress towards the Sustainable Development Goals is the investment in high quality data to strengthen the scientific basis for decision-making. At present, nationally-representative surveys are the main source of data for establishing a scientific evidence base, monitoring, and evaluation of health metrics. However, little is known about the optimal precisions of various population-level health and development indicators that remains unquantified in nationally-representative household surveys.

Comparative effectiveness of injectable penicillin versus a combination of penicillin and gentamicin in children with pneumonia characterised by indrawing in Kenya: a retrospective observational study.

Objectives: Kenyan guidelines for antibiotic treatment of pneumonia recommended treatment of pneumonia characterised by indrawing with injectable penicillin alone in inpatient settings until early 2016. At this point, they were revised becoming consistent with WHO guidance after results of a Kenyan trial provided further evidence of equivalence of oral amoxicillin and injectable penicillin. This change also made possible use of oral amoxicillin for outpatient treatment in this patient group.

Plasmodium falciparum variant erythrocyte surface antigens: a pilot study of antibody acquisition in recurrent natural infections.

Background: During intra-erythrocytic replication Plasmodium falciparum escapes the human host immune system by switching expression of variant surface antigens (VSA). Piecemeal acquisition of variant specific antibody responses to these antigens as a result of exposure to multiple re-infections has been proposed to play a role in acquisition of naturally acquired immunity.

Methods: Immunofluorescence was used to explore the dynamics of anti-VSA IgG responses generated by children to (i) primary malaria episodes and (ii) recurrent P.

Using data from a multi-hospital clinical network to explore prevalence of pediatric rickets in Kenya.

Nutritional rickets is a public health concern in developing countries despite tropical climates and a re-emerging issue in developed countries. In this study, we reviewed pediatric admission data from the Clinical Information Network (CIN) to help determine hospital and region based prevalence of rickets in three regions of Kenya (Central Kenya, Western Kenya and Nairobi County). We also examine the association of rickets with other diagnosis, such as malnutrition and pneumonia, and study the effect of rickets on regional hospital stays.

Plasma But Not Cerebrospinal Fluid Interleukin 7 and Interleukin 5 Levels Pre-Antiretroviral Therapy Commencement Predict Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome.

Background: Patients with human immunodeficiency virus/AIDS-associated cryptococcal meningitis (CM) frequently experience clinical deterioration, known as cryptococcosis-associated immune reconstitution inflammatory syndrome (C-IRIS), upon initiation of antiretroviral therapy (ART). The immunological mechanisms underlying C-IRIS are incompletely defined and no reliable predictive biomarkers exist. We investigated whether plasma or cerebrospinal fluid (CSF) levels of cytokines and chemokines predicted C-IRIS and are potential predictive biomarkers.

Handling missing data in propensity score estimation in comparative effectiveness evaluations: a systematic review.

Aim: Even though systematic reviews have examined how aspects of propensity score methods are used, none has reviewed how the challenge of missing data is addressed with these methods. This review therefore describes how missing data are addressed with propensity score methods in observational comparative effectiveness studies.

Methods: Published articles on observational comparative effectiveness studies were extracted from MEDLINE and EMBASE databases.

Conflict in Somalia: impact on child undernutrition.

Introduction: In Somalia, protracted conflict and drought have caused population displacement and livelihood destruction. There is also widespread childhood undernutrition. We aimed to determine the independent effects of conflict on wasting and stunting among children aged 6-59 months nationwide in Somalia.

Geographic-genetic analysis of parasite populations from surveys of primary school children in Western Kenya.

Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs. In order to determine the geographic-genetic patterns of parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya.

Univariate and multivariate spatial models of health facility utilisation for childhood fevers in an area on the coast of Kenya.

Background: Precise quantification of health service utilisation is important for the estimation of disease burden and allocation of health resources. Current approaches to mapping health facility utilisation rely on spatial accessibility alone as the predictor. However, other spatially varying social, demographic and economic factors may affect the use of health services.