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Background: The World Health Organization (WHO) recommends tuberculosis (TB) diagnostic evaluation for children with HIV (CHIV) who have history of TB contact, poor weight gain, cough, or fever. These screening criteria were developed based on studies of symptomatic CHIV with incomplete microbiologic confirmation. We performed routine TB microbiologic evaluation of hospitalized CHIV with and without symptoms to develop a data-driven TB symptom screen., Methods: Among hospitalized antiretroviral therapy-naive Kenyan CHIV enrolled in the Pediatric Urgent Start of Highly Active Antiretroviral Therapy (PUSH) trial, we performed Xpert MTB/RIF and mycobacterial culture of respiratory and stool specimens independent of TB symptoms. We evaluated performance of WHO and other published pediatric TB screening criteria and derived optimized criteria using a combination of symptoms., Results: Of 168 CHIV who underwent TB microbiologic evaluation, 13 (8%) had confirmed TB. WHO TB symptom screening had 100% sensitivity and 4% specificity to detect confirmed TB. Published TB screening criteria that relied on prolonged symptoms missed cases of confirmed TB (sensitivity 85%-92%). An optimized symptom screen including weight loss, cough, anorexia, or TB contact had 100% sensitivity and improved specificity (31%) compared with the WHO pediatric TB symptom screen., Conclusions: The WHO TB symptom screen was highly sensitive but resulted in a high proportion of hospitalized CHIV who would require TB diagnostic evaluation. Other published TB screening criteria missed CHIV with confirmed TB. Our optimized screening tool increased specificity while preserving sensitivity. Future multicenter studies are needed to improve TB screening tools for CHIV in both inpatient and outpatient settings., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Malaria and schistosomiasis present considerable disease burden in tropical and sub-tropical areas and severity is worsened by co-infections in areas where both diseases are endemic. Although pathogenesis of these infections separately is well studied, there is limited information on the pathogenic disease mechanisms and clinical disease outcomes in co-infections. In this study, we investigated the prevalence of malaria and schistosomiasis co-infections, and the hematologic and blood chemistry abnormalities in asymptomatic adults in a rural fishing community in western Kenya., Methods: This sub-study used samples and data collected at enrollment from a prospective observational cohort study (RV393) conducted in Kisumu County, Kenya. The presence of malaria parasites was determined using microscopy and real-time-PCR, and schistosomiasis infection by urine antigen analysis (CCA). Hematological analysis and blood chemistries were performed using standard methods. Statistical analyses were performed to compare demographic and infection data distribution, and hematologic and blood chemistry parameters based on different groups of infection categories. Clinically relevant hematologic conditions were analyzed using general linear and multivariable Poisson regression models., Results: From February 2017 to May 2018, we enrolled 671 participants. The prevalence of asymptomatic Plasmodium falciparum was 28.2% (157/556) and schistosomiasis 41.2% (229/562), with 18.0% (100/556) of participants co-infected. When we analyzed hematological parameters using Wilcoxon rank sum test to evaluate median (IQR) distribution based on malarial parasites and/or schistosomiasis infection status, there were significant differences in platelet counts (p = 0.0002), percent neutrophils, monocytes, eosinophils, and basophils (p < 0.0001 each). Amongst clinically relevant hematological abnormalities, eosinophilia was the most prevalent at 20.6% (116/562), whereas thrombocytopenia was the least prevalent at 4.3% (24/562). In univariate model, Chi-Square test performed for independence between participant distribution in different malaria parasitemia/schistosomiasis infection categories within each clinical hematological condition revealed significant differences for thrombocytopenia and eosinophilia (p = 0.006 and p < 0.0001, respectively), which was confirmed in multivariable models. Analysis of the pairwise mean differences of liver enzyme (ALT) and kidney function (Creatinine Clearance) indicated the presence of significant differences in ALT across the infection groups (parasite + /CCA + vs all other groups p < .003), but no differences in mean Creatinine Clearance across the infection groups., Conclusions: Our study demonstrates the high burden of asymptomatic malaria parasitemia and schistosomiasis infection in this rural population in Western Kenya. Asymptomatic infection with malaria or schistosomiasis was associated with laboratory abnormalities including neutropenia, leukopenia and thrombocytopenia. These abnormalities could be erroneously attributed to other diseases processes during evaluation of diseases processes. Therefore, evaluating for co-infections is key when assessing individuals with laboratory abnormalities. Additionally, asymptomatic infection needs to be considered in control and elimination programs given high prevalence documented here., (© 2021. The Author(s).)

Competing Interests: The authors have no conflicts of interest to disclose.

Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS., Competing Interests: The authors have declared that no competing interests exist.

Stakeholder engagement between researchers, policymakers and practitioners is critical for the successful translation of research into policy and practice. The Counseling and Testing for Children at Home (CATCH) study evaluated a paediatric index case testing model, targeting the children of HIV-infected adults in care in Kenya. Researchers collaborated with stakeholders in the planning, execution and evaluation, and dissemination phases of CATCH. They included a community advisory board, the national HIV programme, County health departments, institutional ethics review bodies, a paediatric bioethics group, facility heads and frontline healthcare workers . Stakeholder analysis considered the power and interest of each stakeholder in the study. All stakeholders had some power to influence the success of the project in the different phases. However, support from institutions with higher hierarchical power increased acceptance of the study by stakeholders lower in the hierarchy. During the planning, execution and evaluation, and dissemination phases, the study benefitted from deliberate stakeholder engagement. Through engagement, changes were made in the approach to recruitment to ensure high external validity, placing recruitment optimally within existing clinic flow patterns. Choices in staffing home visits were made to include the appropriate cadre of staff. Adaptations were made to the consenting process that balanced the child's evolving autonomy and risks of HIV disclosure. Dissemination involved delivering site-specific results in each HIV clinic, local and international conferences and sharing of study tools, resulting in the study approach being scaled up nationally. The deliberate engagement of stakeholders early in intervention development optimized study validity and accelerated adoption of the CATCH approach in nationwide HIV testing campaigns by the Ministry of Health and inclusion of paediatric index-case testing in national HIV testing guidelines. Involving policymakers and frontline healthcare workers throughout the study cycle builds capacity in the implementing team for quick adoption and scale-up of the evidence-based practice., (© The Author(s) 2020. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: There has been continuous debate among scholars regarding fertility transition in Africa. Two conclusions emerge: slow pace of decline because of weak facilitating social programs and high demand for large families amidst weak family planning programs. Accelerated fertility decline is expected to occur if there is both substantial decline in desired fertility and increased level of preference implementation. Despite these conclusions, there are also emergent exceptions in Africa, even among the Eastern African countries. Our motivation for the study of this region therefore lies in this context. First, the East African countries share some similarities in policy framework. Secondly, Rwanda and Kenya appear as exceptional in the drive towards accelerating further fertility decline. Fertility change therefore in any one country may have implications in the neighbouring country due to the commonalities especially in language, cultural traits, diffusion and spread new models of behaviour. Methods: With the utilization of DHS data, we analyse trends overtime in two specific features that scholars have indicated to slow or increase fertility decline. Using Bongaarts supply-demand framework, we first deduce trends in fertility preferences among women of reproductive age (15-49 years) and second, the extent to which women have been able to implement their fertility preferences during the course of fertility decline and subsequently decomposing these trends. Results: We found that with the rising aggregate of the degree of fertility preference implementation index, continuous declining trends in demand for births and subsequent increases in the contribution made by either or both the wanted fertility and the degree of fertility preference implementation index across categories that fertility transition is certainly on course in all countries albeit at different levels, thanks to the family planning. Conclusions: Family planning programs must therefore be accompanied by rigorous, consistent sensitization and public education., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Otieno V et al.)

Here, we report the genome sequences of a Staphylococcus aureus clinical isolate, strain SMA0034-04 (UGA22), which contains one chromosome and one plasmid. We also reveal that isolate SMA0034-04 (UGA22) contains loci in the genome that encode multiple exotoxins., (Copyright © 2019 Xie et al.)

Here, we report the sequence of a Staphylococcus pettenkoferi clinical isolate, strain SMA0010-04 (UGA20), which contains the PC1 beta-lactamase ( blaZ ) gene., (Copyright © 2019 Otieno et al.)

We report here the genome sequence of a Staphylococcus xylosus clinical isolate, strain SMA0341-04 (UGA5), which contains one chromosome and at least one plasmid. Notably, strain SMA0341-04 (UGA5) contains the tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ) gene., (Copyright © 2019 Cheng et al.)

Bacteremia is a leading cause of death in sub-Saharan Africa where childhood mortality rates are the highest in the world. The early diagnosis of bacteremia and initiation of treatment saves lives, especially in high-disease burden areas. However, diagnosing bacteremia is challenging for clinicians, especially in children presenting with co-infections such as malaria and HIV. There is an urgent need for a rapid method for detecting bacteremia in pediatric patients with co-morbidities to inform treatment. In this manuscript, we have developed and clinically validated a novel method for the direct detection of amphiphilic pathogen biomarkers indicative of bacteremia, directly in aqueous blood, by mimicking innate immune recognition. Specifically, we have exploited the interaction of amphiphilic pathogen biomarkers such as lipopolysaccharides (LPS) from Gram-negative bacteria and lipoteichoic acids (LTA) from Gram-positive bacteria with host lipoprotein carriers in blood, in order to develop two tailored assays - lipoprotein capture and membrane insertion - for their direct detection. Our assays demonstrate a sensitivity of detection of 4 ng/mL for LPS and 2 ng/mL for LTA using a waveguide-based optical biosensor platform that was developed at LANL. In this manuscript, we also demonstrate the application of these methods for the detection of LPS in serum from pediatric patients with invasive Salmonella Typhimurium bacteremia (n = 7) and those with Staphylococcal bacteremia (n = 7) with 100% correlation with confirmatory culture. Taken together, these results demonstrate the significance of biochemistry in both our understanding of host-pathogen biology, and development of assay methodology, as well as demonstrate a potential new approach for the rapid, sensitive and accurate diagnosis of bacteremia at the point of need.

We report the complete draft genome sequences of two Staphylococcus warneri clinical isolates, strains SMA0023-04 (UGA3) and SMA0670-05 (UGA28), each of which contains one chromosome and at least one plasmid. Isolate SMA0023-04 (UGA3) contains tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ), macrolide resistance ( msrC and mphC ), and beta-lactamase ( blaZ ) genes on its plasmids., (Copyright © 2019 Xie et al.)

Background: The blood monocyte-to-lymphocyte ratio (MLR) is associated with active tuberculosis (TB) in adults but has not been evaluated as a TB diagnostic biomarker in HIV-infected children in whom respiratory sampling is difficult., Setting: In a cohort of HIV-infected hospitalized Kenyan children initiating antiretroviral therapy, absolute monocyte and lymphocyte counts were determined at enrollment and 4, 12, and 24 weeks thereafter., Methods: Children were classified as confirmed, unconfirmed, or unlikely pulmonary TB. Receiver operating characteristic curves of MLR cutoff values were generated to distinguish children with confirmed TB from those with unconfirmed and unlikely TB. General estimating equations were used to estimate change in the MLR over time by TB status., Results: Of 160 children with median age 23 months, 13 (8.1%) had confirmed TB and 67 (41.9%) had unconfirmed TB. The median MLR among children with confirmed TB {0.407 [interquartile range (IQR) 0.378-0.675]} was higher than the MLR in children with unconfirmed [0.207 (IQR 0.148-0.348), P < 0.01] or unlikely [0.212 (IQR 0.138-0.391), P = 0.01] TB. The MLR above 0.378 identified children with confirmed TB with 77% sensitivity, 78% specificity, 24% positive predictive value, and 97% negative predictive value. After TB treatment, the median MLR declined in children with confirmed TB and levels were similar to children with unlikely TB after 12 weeks., Conclusions: The blood MLR distinguished HIV-infected children with confirmed TB from those with unlikely TB and declined with TB treatment. The MLR may be a useful diagnostic tool for TB in settings where respiratory-based microbiologic confirmation is inaccessible.

Background: Late human immunodeficiency virus (HIV) diagnosis after severe co-morbidity remains common in resource-limited settings. Neurodevelopmental recovery during antiretroviral therapy (ART) for late-diagnosed children is understudied. We determined 6-month neurodevelopmental trajectories in HIV-infected children initiating ART during hospitalization., Methods: HIV-infected children initiated ART after HIV diagnosis during hospitalization in Kenya. The Malawi Developmental Assessment Tool was administered after clinical stabilization within 1 month and at 6 months post-ART initiation. Baseline versus 6-month Z scores for each developmental domain were compared; cofactors for change in Z scores were evaluated using linear regression., Results: Among 74 children, median age was 1.7 years (interquartile range, 0.8-2.4) and median Z scores for gross motor, fine motor, social and language domains were -1.34, -1.04, -0.53 and -0.95, respectively. At baseline, children with higher plasma viremia had lower social Z scores (P = 0.008). Better nourished (weight-for-age Z score [WAZ] ≥-2) children had higher Z scores in all developmental domains (all P values ≤0.05). After 6 months on ART (n = 58), gross and fine motor Z scores improved significantly (mean change 0.39; P = 0.007 and 0.43; P = 0.001, respectively), but social and language did not. Children with better immune and growth response to ART had higher gains in gross motor (0.05 per unit-gain CD4%; P = 0.04; 0.34 per unit-gain WAZ; P = 0.006 and 0.44 per unit-gain height-for-age Z score; P = 0.005), social (0.37 per unit-gain WAZ; P = 0.002) and language (0.25 per unit-gain height-for-age Z score; P = 0.01)., Conclusions: Children had significant neurodevelopmental gains during 6 months of ART, and children with better growth and immune recovery had greater improvement. Prompt commencement of ART may improve neurodevelopment in addition to immunity and growth.

We compared change in HIV reservoir DNA following continued antiretroviral therapy (ART) vs short treatment interruption (TI) in early ART-treated Kenyan infants. While HIV DNA in the reservoir decayed with continued ART, HIV DNA levels were similar to pre-TI HIV DNA reservoir levels in most children after short TI.

Background: One objective of the Kenya National Malaria Strategy 2009-2017 is scaling access to prompt diagnosis and effective treatment. In 2013, a quality assurance (QA) pilot was implemented to improve accuracy of malaria diagnostics at selected health facilities in low-transmission counties of Kenya. Trends in malaria diagnostic and QA indicator performance during the pilot are described., Methods: From June to December 2013, 28 QA officers provided on-the-job training and mentoring for malaria microscopy, malaria rapid diagnostic tests and laboratory QA/quality control (QC) practices over four 1-day visits at 83 health facilities. QA officers observed and recorded laboratory conditions and practices and cross-checked blood slides for malaria parasite presence, and a portion of cross-checked slides were confirmed by reference laboratories., Results: Eighty (96%) facilities completed the pilot. Among 315 personnel at pilot initiation, 13% (n = 40) reported malaria diagnostics training within the previous 12 months. Slide positivity ranged from 3 to 7%. Compared to the reference laboratory, microscopy sensitivity ranged from 53 to 96% and positive predictive value from 39 to 53% for facility staff and from 60 to 96% and 52 to 80%, respectively, for QA officers. Compared to reference, specificity ranged from 88 to 98% and negative predictive value from 98 to 99% for health-facility personnel and from 93 to 99% and 99%, respectively, for QA officers. The kappa value ranged from 0.48-0.66 for facility staff and 0.57-0.84 for QA officers compared to reference. The only significant test performance improvement observed for facility staff was for specificity from 88% (95% CI 85-90%) to 98% (95% CI 97-99%). QA/QC practices, including use of positive-control slides, internal and external slide cross-checking and recording of QA/QC activities, all increased significantly across the pilot (p < 0.001). Reference material availability also increased significantly; availability of six microscopy job aids and seven microscopy standard operating procedures increased by a mean of 32 percentage points (p < 0.001) and 38 percentage points (p < 0.001), respectively., Conclusions: Significant gains were observed in malaria QA/QC practices over the pilot. However, these advances did not translate into improved accuracy of malaria diagnostic performance perhaps because of the limited duration of the QA pilot implementation.

Objective: Treatment interruption has been well tolerated and durable in some pediatric studies but none have compared treatment interruption with continued antiretroviral treatment (ART) following ART initiation in early HIV. The objective of this study was to compare outcomes in treatment interruption versus continued ART among early-treated infants., Design: Randomized trial (OPH-03; NCT00428116)., Methods: The trial included HIV-infected infants who initiated ART at less than 13 months of age, received ART for 24 months, and, if eligible (CD4% >25%, normal growth), were randomized to treatment interruption versus continued ART. Children in the treatment interruption group restarted ART if they met WHO ART-eligibility criteria. During 18-months postrandomization, primary outcomes were incidence of serious adverse events and growth. CD4%, viral load, morbidity, and growth were compared., Results: Of 140 infants enrolled, 121 started ART, of whom 75 completed at least 24 months ART and 42 were randomized (21 per arm). ART was initiated at median age 5 months and randomization at 30 months. Among 21 treatment interruption children, 14 met ART restart criteria within 3 months. Randomization was discontinued by Data and Safety Monitoring Board due to low treatment interruption durability. At 18 months postrandomization, growth and serious adverse events were comparable between arms; hypercholesteremia incidence was higher in the continued arm (P = 0.03). CD4% and viral load did not differ between arms [CD4% 35% and median viral load undetectable (<150 copies/ml) in both arms, P = 0.9 for each comparison]. No infants had post-treatment viral control., Conclusion: Short treatment interruption did not compromise 18-month CD4%, viral control, growth, or morbidity compared with continued ART among infants who started ART in early HIV infection.

Bacteremia and malaria coinfection is a common and life-threatening condition in children residing in sub-Saharan Africa. We previously showed that coinfection with Gram negative (G[-]) enteric Bacilli and Plasmodium falciparum (Pf[+]) was associated with reduced high-density parasitemia (HDP, >10,000 parasites/μL), enhanced respiratory distress, and severe anemia. Since inflammatory mediators are largely unexplored in such coinfections, circulating cytokines were determined in four groups of children (n = 206, aged <3 yrs): healthy; Pf[+] alone; G[-] coinfected; and G[+] coinfected. Staphylococcus aureus and non-Typhi Salmonella were the most frequently isolated G[+] and G[-] organisms, respectively. Coinfected children, particularly those with G[-] pathogens, had lower parasite burden (peripheral and geometric mean parasitemia and HDP). In addition, both coinfected groups had increased IL-4, IL-5, IL-7, IL-12, IL-15, IL-17, IFN-γ, and IFN-α and decreased TNF-α relative to malaria alone. Children with G[-] coinfection had higher IL-1β and IL-1Ra and lower IL-10 than the Pf[+] group and higher IFN-γ than the G[+] group. To determine how the immune response to malaria regulates parasitemia, cytokine production was investigated with a multiple mediation model. Cytokines with the greatest mediational impact on parasitemia were IL-4, IL-10, IL-12, and IFN-γ. Results here suggest that enhanced immune activation, especially in G[-] coinfected children, acts to reduce malaria parasite burden.

Arthropod-borne viruses (arboviruses) may cause severe emerging and re-emerging infectious diseases, which pose a significant threat to human and animal health in the world today. These infectious diseases range from mild febrile illnesses, arthritis, and encephalitis to haemorrhagic fevers. It is postulated that certain environmental factors, vector competence, and host susceptibility have a major impact on the ecology of arboviral diseases. Presently, there is a great interest in the emergence of Alphaviruses because these viruses, including Chikungunya virus, O'nyong'nyong virus, Sindbis virus, Ross River virus, and Mayaro virus, have caused outbreaks in Africa, Asia, Australia, Europe, and America. Some of these viruses are more common in the tropics, whereas others are also found in temperate regions, but the actual factors driving Alphavirus emergence and re-emergence remain unresolved. Furthermore, little is known about the transmission dynamics, pathophysiology, genetic diversity, and evolution of circulating viral strains. In addition, the clinical presentation of Alphaviruses may be similar to other diseases such as dengue, malaria, and typhoid, hence leading to misdiagnosis. However, the typical presence of arthritis may distinguish between Alphaviruses and other differential diagnoses. The absence of validated diagnostic kits for Alphaviruses makes even routine surveillance less feasible. For that purpose, this review describes the occurrence, genetic diversity, clinical characteristics, and the mechanisms involving Alphaviruses causing arthritis in humans. This information may serve as a basis for better awareness and detection of Alphavirus-caused diseases during outbreaks and in establishing appropriate prevention and control measures.

Background: Rift Valley fever (RVF) is a fatal arthropod-borne zoonotic disease of livestock and humans. Since the identification of RVF in Kenya in the 1930s, repeated epizootics and epidemics coinciding with El Niño events have occurred in several locations in Africa and Saudi Arabia, causing mass deaths of livestock and humans. RVF is of great interest worldwide because of its negative effect on international livestock trade and its potential to spread globally. The latter is due to the increasing incidence of extreme climatic phenomena caused by global warming, as well as to the increase in global trade and international travel. How RVF is maintained and sustained between epidemics and epizootics is not clearly understood, but it has been speculated that wildlife reservoirs and trans-ovarian transmission in the vector may be important. Several studies have examined the role of wildlife and livestock in isolation or in a limited geographical location within the one country over a short time (usually less than a year). In this study, we examined the seroprevalence of anti-RVF antibodies in cattle and several wildlife species from several locations in Kenya over an inter-epidemic period spanning up to 7 years., Methods: A serological survey of immunoglobulin G (IgG) antibodies to RVF using competitive ELISA was undertaken on 297 serum samples from different wildlife species at various locations in Kenya. The samples were collected between 2008 and 2015. Serum was also collected in 2014 from 177 cattle from Ol Pejeta Conservancy; 113 of the cattle were in close contact with wildlife and the other 64 were kept separate from buffalo and large game by an electric fence., Results: The seroprevalence of RVF virus (RVFV) antibody was 11.6% in wildlife species during the study period. Cattle that could come in contact with wildlife and large game were all negative for RVFV. The seroprevalence was relatively high in elephants, rhinoceros, and buffalo, but there were no antibodies in zebras, baboons, vervet monkeys, or wildebeest., Conclusions: Diverse species in conservation areas are exposed to RVFV. RVFV exposure in buffalo may indicate distribution of the virus over wide geographical areas beyond known RVFV foci in Kenya. This finding calls for thorough studies on the epizootology of RVFV in specific wildlife species and locations.

Objectives: To evaluate final year medical students' access to new medical information., Method: Cross-sectional survey of final year medical students at the University of Nairobi using anonymous, self-administered questionnaires., Results: Questionnaires were distributed to 85% of a possible 343 students and returned by 44% (152). Half reported having accessed some form of new medical information within the previous 12 months, most commonly from books and the internet. Few students reported regular access; and specific, new journal articles were rarely accessed. Absence of internet facilities, slow internet speed and cost impeded access to literature; and current training seems rarely to encourage students to seek new information., Conclusion: Almost half the students had not accessed any new medical information in their final year in medical school. This means they are ill prepared for a career that may increasingly demand life-long, self-learning.