Challenges of setting up flow cytometry for diagnosis of leukemia and lymphoma at Moi Teaching and Referral Hospital, Eldoret, Kenya

The bone marrow (BM) is a complex tissue containing cells of multiple hematopoietic cell lineages in all stages of development. Flow cytometricimmunophenotyping evaluates the frequencies of the various leukocyte (sub) populations in BM and blood that then helps in the diagnosis of leukemia's. The aim of this study was to identify challenges of setting up an advanced diagnostic tool like flow cytometry in a resource strained country like Kenya. This is based on a 2 year experience of use of flow cytometry for diagnosis of leukemia, the challenges faced by both the pathologists and the technical team

Sensitivity and specificity of cryptococcal antigen lateral flow assay for the diagnosis of HIV-associated cryptococcal meningitis in western Kenya

Background: HIV-associated cryptococcal meningitis carries a high case-fatality-rate in sub-Saharan Africa. Diagnostic delays partly contribute to this. Rapid point-of-care tests may facilitate speedy diagnosis. This study aimed to determine the sensitivity and specificity of urine, serum and cerebrospinal fluid (CSF) cryptococcal antigen lateral flow assay for the diagnosis of HIV-associated cryptococcal meningitis compared with the gold standard CSF culture.Methods: A cross-sectional study was conducted in the medical wards of Moi Teaching and Referral Hospital, Eldoret, Kenya. Adult (≥18years) HIV-infected in-patients suspected to have meningitis had paired samples of urine, serum and CSF collected and tested real time using the cryptococcal antigen lateral flow assay (rapid point of care test). CSF cultures were also conducted. Data were analyzed using STATA ® (Statacorp Texas USA®). Descriptive statistics were used to summarize demographic, clinical and laboratory parameters. Sensitivity and specificity of the rapid test were calculated with the CSF culture as the gold standard.Results: Of the 302 participants included 172 (57%) were female, median age 37 years (IQR 30-45). The median CD4+ cell count was 183/ul (IQR 54-333). Among 288 participants with available CSF culture results, 50(17%) had culture-confirmed cryptococcal meningitis. Urine rapid test had a sensitivity and specificity of 86 %( 95% CI 73-94) and 95.7% (95% CI 92-98) respectively. Serum rapid test had a sensitivity and specificity of 92% (95%CI 81-98) and 94.9% (95%CI 91-97) respectively. CSF rapid test had a sensitivity and specificity of 92% (95%CI 81-98%) and 94.5% (95% CI 91-97) respectively. Conclusion: Serum and CSF cryptococcal antigen lateral flow assay are highly sensitive and specific for the diagnosis of HIV-associated cryptococcal meningitis. Urine is relatively sensitive and specific. Serum and CSF cryptococcal antigen lateral flow assay can be used as a less expensive alternative to cryptococcal antigen latex agglutination method. Urine cryptococcal antigen lateral flow assay could be adopted as a rapid point of care diagnostic test in primary care clinics in low income settings without experience in handling CSF or serum, to fast track diagnosis of cryptococcal meningitis

The cost‐effectiveness of prophylaxis strategies for individuals with advanced HIV starting treatment in Africa

Introduction Many HIV‐positive individuals in Africa have advanced disease when initiating antiretroviral therapy (ART) so have high risks of opportunistic infections and death. The REALITY trial found that an enhanced‐prophylaxis package including fluconazole reduced mortality by 27% in individuals starting ART with CD4 <100 cells/mm3. We investigated the cost‐effectiveness of this enhanced‐prophylaxis package versus other strategies, including using cryptococcal antigen (CrAg) testing, in individuals with CD4 <200 cells/mm3 or <100 cells/mm3 at ART initiation and all individuals regardless of CD4 count. Methods The REALITY trial enrolled from June 2013 to April 2015. A decision‐analytic model was developed to estimate the cost‐effectiveness of six management strategies in individuals initiating ART in the REALITY trial countries. Strategies included standard‐prophylaxis, enhanced‐prophylaxis, standard‐prophylaxis with fluconazole; and three CrAg testing strategies, the first stratifying individuals to enhanced‐prophylaxis (CrAg‐positive) or standard‐prophylaxis (CrAg‐negative), the second to enhanced‐prophylaxis (CrAg‐positive) or enhanced‐prophylaxis without fluconazole (CrAg‐negative) and the third to standard‐prophylaxis with fluconazole (CrAg‐positive) or without fluconazole (CrAg‐negative). The model estimated costs, life‐years and quality‐adjusted life‐years (QALY) over 48 weeks using three competing mortality risks: cryptococcal meningitis; tuberculosis, serious bacterial infection or other known cause; and unknown cause. Results Enhanced‐prophylaxis was cost‐effective at cost‐effectiveness thresholds of US$300 and US$500 per QALY with an incremental cost‐effectiveness ratio (ICER) of US$157 per QALY in the CD4 <200 cells/mm3 population providing enhanced‐prophylaxis components are sourced at lowest available prices. The ICER reduced in more severely immunosuppressed individuals (US$113 per QALY in the CD4 <100 cells/mm3 population) and increased in all individuals regardless of CD4 count (US$722 per QALY). Results were sensitive to prices of the enhanced‐prophylaxis components. Enhanced‐prophylaxis was more effective and less costly than all CrAg testing strategies as enhanced‐prophylaxis still conveyed health gains in CrAg‐negative patients and savings from targeting prophylaxis based on CrAg status did not compensate for costs of CrAg testing. CrAg testing strategies did not become cost‐effective unless the price of CrAg testing fell below US$2.30. Conclusions The REALITY enhanced‐prophylaxis package in individuals with advanced HIV starting ART reduces morbidity and mortality, is practical to administer and is cost‐effective. Efforts should continue to ensure that components are accessed at lowest available prices

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

This article has been accepted for publication in Clinical Infectious Diseases Published by Oxford University PressBackground: 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 .1). Results: Among 1711 included participants, 203 (12%) died. Mortality was independently higher with older age; lower CD4 count, albumin, hemoglobin, and grip strength; presence of World Health Organization stage 3/4 weight loss, fever, or vomiting; and problems with mobility or self-care at baseline (all P < .04). Receiving enhanced antimicrobial prophylaxis independently reduced mortality (P = .02). Of five late-presenter phenotypes, Group 1 (n = 355) had highest mortality (25%; median CD4 count, 28 cells/µL), with high symptom burden, weight loss, poor mobility, and low albumin and hemoglobin. Group 2 (n = 394; 11% mortality; 43 cells/µL) also had weight loss, with high white cell, platelet, and neutrophil counts suggesting underlying inflammation/infection. Group 3 (n = 218; 10% mortality) had low CD4 counts (27 cells/µL), but low symptom burden and maintained fat mass. The remaining groups had 4%-6% mortality. Conclusions: Clinical and laboratory features identified groups with highest mortality following ART initiation. A screening tool could identify patients with low CD4 counts for prioritizing same-day ART initiation, enhanced prophylaxis, and intensive follow-up. Clinical Trials Registration: ISRCTN43622374.REALITY was funded by the Joint Global Health Trials Scheme (JGHTS) of the UK Department for International Development, the Wellcome Trust, and Medical Research Council (MRC) (grant number G1100693). Additional funding support was provided by the PENTA Foundation and core support to the MRC Clinical Trials Unit at University College London (grant numbers MC_UU_12023/23 and MC_UU_12023/26). Cipla Ltd, Gilead Sciences, ViiV Healthcare/GlaxoSmithKline, and Merck Sharp & Dohme donated drugs for REALITY, and ready-to-use supplementary food was purchased from Valid International. A. J. P. is funded by the Wellcome Trust (grant number 108065/Z/15/Z). J. A. B. is funded by the JGHTS (grant number MR/M007367/1). The Malawi-Liverpool–Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine (grant number 101113/Z/13/Z) and the Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi (grant number 203077/Z/16/Z) are supported by strategic awards from the Wellcome Trust, United Kingdom. Permission to publish was granted by the Director of KEMRI. This supplement was supported by funds from the Bill & Melinda Gates Foundation

Immunopathological Features Developing in the Mosquito Midgut after Feeding on Anopheles gambiae Mucin-1 / Interleukin-12 cDNA Immunized Mice

The mosquito midgut is the organ into which the blood meal passes and in which, within a peritrophic membrane secreted by the epithelium, the blood is retained during digestion and absorption. The mosquito midgut is lined with an actin filled microvilli that are exposed to the harsh environment of the gut lumen such as food particle abrasion, digestive hydrolases and attack by pathogens and parasites that are taken in by the blood meal. These microvilli are protected them these effects by the peritrophic matrix, the glycocalyx and the mucin proteins that line their epithelial surfaces. Immunization of BALB/c mice with AgMUC1/IL-12 cDNA has been shown to kill mosquitoes when fed on these mice. Mucin is one of the proteins produced in the mosquito midgut after a blood meal. The fine structure of the mosquito midgut epithelium interacting with immune factors such as antibodies or immune cells is of special significance for interpreting early events in the interaction between the mosquito midgut lining and the specific immune components present in the blood of AgMUC1/IL-12 cDNA immunized BALB/c mice. Following bright light microscopy, scanning electron and transmission electron microscopic observations of the features seen in mosquito midgut sections from An. gambiae mosquitoes fed on BALB/c mice immunized with AgMUC1/IL-12 cDNA, the most likely immune mechanisms responsible for mosquito killing could be cell mediated, most likely antibody dependent cellular cytotoxicity. Both necrotic and apoptotic processes that could be the cause of mosquito death were seen to take place in the cells lining the midgut epithelium

Induction of Mosquitocidal Activity in Mice Immunized with Anopheles gambiae Midgut cDNA

Vaccines that induce mosquito-killing (mosquitocidal) activity could substantially reduce the transmission of certain mosquito-borne diseases, especially vaccines against African malaria vectors, such as the mosquito Anopheles gambiae. To generate and characterize antimosquito immunity we immunized groups of mice with two individual A. gambiae midgut cDNAs, Ag-Aper1 (a secreted peritrophic matrix protein) and AgMuc1 (a midgut-bound mucin), and an A. gambiae midgut cDNA library from blood-fed mosquitoes. We observed significantly increased mortality among mosquitoes that fed on either the AgMuc1- or the cDNA library-immunized mice compared to that of controls, but no differences were observed among those fed on Ag-Aper1-immunized mice. Analysis of the humoral and cellular immune responses from mice showed that the induced mosquitocidal effect was associated with immune profiles characterized by elevated tumor necrosis factor alpha and gamma interferon cytokine levels and very low antibody titers. Furthermore, an additional immunization of cDNA library-immunized mice with midgut protein shifted immunity toward a Th2-type immune response, characterized by elevated antibody titers and high interleukin-5 and interleukin-10 cytokine levels; importantly, mosquitoes feeding on these mice exhibited no undo mortality. Finally, when immune sera was ingested by mosquitoes through a membrane feeder, no effect on mosquito mortality was observed, indicating that serum factors alone were not responsible for the mosquitocidal effect. Our results demonstrate that mosquitocidal immunity in mice can be consistently generated by midgut cDNA immunization and suggest this cDNA-induced mosquitocidal immunity is cell mediated

Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa

Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations

Genetic studies in underrepresented populations identify disproportionate numbers of novel associations. However, most genetic studies use genotyping arrays and sequenced reference panels that best capture variation most common in European ancestry populations. To compare data generation strategies best suited for underrepresented populations, we sequenced the whole genomes of 91 individuals to high coverage as part of the Neuropsychiatric Genetics of African Population-Psychosis (NeuroGAP-Psychosis) study with participants from Ethiopia, Kenya, South Africa, and Uganda. We used a downsampling approach to evaluate the quality of two cost-effective data generation strategies, GWAS arrays versus low-coverage sequencing, by calculating the concordance of imputed variants from these technologies with those from deep whole-genome sequencing data. We show that low-coverage sequencing at a depth of ≥4× captures variants of all frequencies more accurately than all commonly used GWAS arrays investigated and at a comparable cost. Lower depths of sequencing (0.5–1×) performed comparably to commonly used low-density GWAS arrays. Low-coverage sequencing is also sensitive to novel variation; 4× sequencing detects 45% of singletons and 95% of common variants identified in high-coverage African whole genomes. Low-coverage sequencing approaches surmount the problems induced by the ascertainment of common genotyping arrays, effectively identify novel variation particularly in underrepresented populations, and present opportunities to enhance variant discovery at a cost similar to traditional approaches