Implementation of liquid culture for tuberculosis diagnosis in a remote setting: lessons learned.

Although sputum smear microscopy is the primary method for tuberculosis (TB) diagnosis in low-resource settings, it has low sensitivity. The World Health Organization recommends the use of liquid culture techniques for TB diagnosis and drug susceptibility testing in low- and middle-income countries. An evaluation of samples from southern Sudan found that culture was able to detect cases of active pulmonary TB and extra-pulmonary TB missed by conventional smear microscopy. However, the long delays involved in obtaining culture results meant that they were usually not clinically useful, and high rates of non-tuberculous mycobacteria isolation made interpretation of results difficult. Improvements in diagnostic capacity and rapid speciation facilities, either on-site or through a local reference laboratory, are crucial

Rotational effects of grain legumes on maize performance in the Rift Valley Highlands of Kenya

High fertiliser costs and declining soil fertility are among the key factors contributing to low crop yields in Kenya. The contribution of five legumes grown in the short-rains season to soil nitrogen status and performance of a succeeding maize (Zea mays L.) was studied in an experiment at Njoro and Rongai within the Rift Valley Highlands of Kenya, from 1997 to 1999. Treatments included a weedy fallow, five grain legumes and maize (H513) grown during short-rains season followed by maize in the April-August long-rains season. The legumes were chickpea (Cicer arietinum L.), field bean (Phaseolus vulgaris L.), soybean [Glycine max (L.) Merril], garden pea (Pisum sativum L.), dolichos [Lablab purpureus (L.) Sweet]. The crop residues and vegetation of the weedy fallow were incorporated in the soil during seedbed preparation for the long rains season. The maize test crop was supplied with three levels of nitrogen, 0, 30, and 60 kg ha-1 as main factor whilst fallow management options were allocated as sub-factors in a split-plot treatment arrangement of a randomised complete block design replicated three times. Results show improved soil N status following legumes, with dolichos giving highest available N. Grain yield in maize succeeding legumes was 24-68% higher than maize succeeding weed fallow. In the absence of N fertiliser input, maize succeeding dolichos gave 20-40% higher yield than maize after weed fallow treated with recommended 60 kg N ha-1 fertiliser rate. The study has demonstrated that the use of grain legumes, particularly dolichos in rotation with maize, is a viable and preferable option to weedy fallows and maize-maize sequences. RÉSUMÉ Les coûts très élevés des engrais et le déclin de la fertilité du sol sont parmi les facteurs clés qui contribuent au faible rendement des cultures au Kenya. La contribution de cinq légumineuses cultivées durant la petite saison de pluie au status de l'azote du sol et la performance du maïs suivant (Zea mays L.) a été étudiée dans un essai à Njoro et Rongai dans les hautes Terres du Rift Valley du Kenya, de 1997 à 1999. Les traitements comprenaient une jachère sarclée, cinq légumineuses à graines et le maïs (H513) cultivés pendant la petite saison de pluie suivie par le maïs durant la grande saison pluvieuse d' avril-Août .Les légumineuses étaient le pois chiche (Cicer arietinum L.), le haricot (Phaseolus vulgaris L.), le soya {Glycine max (L.), Merril}, le petit pois (Pisum sativum L.), le lablab {Lablab purpureus (L.) Sweet}. Des residues des cultures et la végétation de la jachère étaient incorporées au sol pendant la préparation du semis pour de longues saisons pluvieuses. Le maïs test a été fourni avec trois niveaux d'azote, 0, 30 et 60 kg ha-1 comme facteur principal alors que les options de gestions de la jachère étaient des sous-facteurs dans un arrangement de traitement en split-plot des blocks complètement rendomisés avec trois répétitions. Des résultats ont montré le status de l'azote amélioré après des légumineuses, avec le lablab donnant de l'azote disponible très élevé. Le rendement grain du maïs suivant les légumineuses était 24-68% plus élevé que le maïs suivant la jachère sarclée. En l'absence des intrants d'engrais azoté, le maïs suivant le lablab a donné 20-40% de rendement supérieur à celui du maïs après la jachère sarclée traités avec le taux recommandé de 60 kg N ha-1. L'étude a montré que l'utilisation des légumineuses, en particulier le lablab en rotation avec le maïs, est une option viable et préferable à la jachère sarclée et à la séquence maïs- maïs. (Af Crop Science and Production: 2001 9(4): 667-676

Morphological and Molecular Identification of the Causal Agent of Anthracnose Disease of Avocado in Kenya

Anthracnose disease of avocado contributes to a huge loss of avocado fruits due to postharvest rot in Kenya. The causal agent of this disease has not been clear but presumed to be Colletotrichum gloeosporioides as reported in other regions where avocado is grown. The fungus mainly infects fruits causing symptoms such as small blackish spots, “pepper spots,” and black spots with raised margin which coalesce as infection progresses. Due to economic losses associated with the disease and emerging information of other species of fungi as causal agents of the disease, this study was aimed at identifying causal agent(s) of the disease. A total of 80 fungal isolates were collected from diseased avocado fruits in Murang’a County, the main avocado growing region in Kenya. Forty-six isolates were morphologically identified as Colletotrichum spp. based on their cultural characteristics, mainly whitish, greyish, and creamish colour and cottony/velvety mycelia on the top side of the culture and greyish cream with concentric zonation on the reverse side. Their spores were straight with rounded end and nonseptate. Thirty-four isolates were identified as Pestalotiopsis spp. based on their cultural characteristics: whitish grey mycelium with black fruiting structure on the upper side and greyish black one on the lower side and septate spores with 3-4 septa and 2 or 3 appendages at one end. Further molecular studies using ITS indicated Colletotrichum gloeosporioides, Colletotrichum boninense, and Pestalotiopsis microspora as the causal agents of anthracnose disease in avocado. However, with this being the first report, there is a need to conduct further studies to establish whether there is coinfection or any interaction thereof

Prevalence and risk factors of Schistosoma mansoni infection among children under two years of age in Mbita, Western Kenya.

Despite growing evidence that infants and very young children can be infected with schistosomes, the epidemiological features and risk factors are not well described in this age group. We aimed to assess the prevalence of S. mansoni infection in children under two years of age from a population with a known high burden of infection in school-aged children and adults and thus inform the need for interventions in this potentially vulnerable age group. In a cross-sectional study in Mbita Sub-county, along the east coast of Lake Victoria, Western Kenya, we enrolled 361 children aged 6-23 months. The prevalence of S. mansoni infection was detected using the Kato-Katz stool examination and a point-of-care test for urinary circulating cathodic antigen (POC-CCA) (Rapid Medical Diagnostics, Pretoria, South Africa). Three-hundred and five (305) children had complete data of whom 276 (90.5%, 95%CI: 86.6-93.5) children were positive for S. mansoni by the POC-CCA test, while 11 (3.6%, 95%CI: 1.8-6.4) were positive by the Kato-Katz method. All Kato-Katz positive cases were also positive by the POC-CCA test. In multivariable analysis, only geographical area, Rusinga West (AOR = 7.1, 95%CI: 1.4-35.2, P = 0.02), was associated with S. mansoni infection using Kato-Katz test. Independent associations for POC-CCA positivity included age, (12-17 months vs 6-11 months; AOR = 7.8, 95%CI: 1.8-32.6, P = 0.002) and breastfeeding in the previous 24 hours (AOR = 3.4, 95%CI: 1.3-9.0, P = 0.009). We found a potentially very high prevalence of S. mansoni infection among children under two years of age based on POC-CCA test results in Mbita Sub-county, Kenya, which if confirmed strongly supports the need to include infants in public health strategies providing universal prophylactic treatment in high burden settings. Further research is required to determine the accuracy of diagnostic tools to detect light infection among very young children and possible long-term health impacts

Performance of marker assisted backcross breeding (MABC) elite chickpea lines under drought conditions in Kenya

Drought is the most important constraint affecting production of chickpea and other crops as well. Quantitative traits like drought tolerance are multigenic and their inheritance is difficult to predict hence the need to explore more precise breeding techniques like maker assisted selection. The aim of this study was to introgress the identified root trait QTLs into Kenyan adapted cultivar to enhance drought tolerance through marker assisted backcrossing. Four varieties Chania Desi 1 (ICCV 97105), ICCV10, ICCV 92318, and Saina K1 (ICCV 95423) were selected as a recurrent parents for improvement among ten agronomically superior elite cultivars after exhibiting high polymorphism with SSR markers. Five molecular markers (CaM1903, CaM1502, TAA 170, NCPGR21 and GA11) were validated for use in MABC deployed in this study. Crosses were made between the four parents and ICC 4958 followed by marker screening of the F1 seedling progenies for the QTL of interest. Identified true heterozygotes were used as donors and backcrossed to the recurrent parent to obtain BC1F1 seeds. The process was repeated to obtain BC2F1 and finally BC3F1 with molecular marker identification of seedlings carrying the QTL region at each step. Results of evaluation in one trial site in Kenya semi-arid area (Koibatek ATC) of MABC lines for the four parents ICCV10 (24 lines), ICCV 92318 (8lines), ICCV 97105 (12 lines) and Saina K1-ICCV 95423 (10 lines) showed that the best progenies with higher levels of drought resistance and yield were ICCMABCD-21, 9, 20, 23, 15, 22, 5, 14, 16, 19 and 6 with yields > 2.5 tons/ha. The results indicated that it is possible to transfer QTL that confers drought tolerance using MABC. The best progenies are undergoing further evaluation to validate the contribution of the introgressed QTL in improving drought tolerance and yield

Flowering margins support natural enemies between cropping seasons

IntroductionPopulations of natural enemies of insect pests are declining owing to agricultural intensification and indiscriminate use of pesticides, and this may be exacerbated in agricultural systems that clear all margin plants after the cropping season for other uses such as fodder. Retaining a diversity of non-crop flowering vegetation outside the cropping season may support more resilient and effective natural pest regulation.MethodsWe tested the potential for non-crop vegetation to support natural enemies in fields across two locations after harvesting the primary crops of lablab and maize.ResultsA total of 54 plant species were recorded across the sites in Kenya with 59% of them being annuals and 41% perennials. There was a significant seasonal variation in plant species richness (ANOVA: F1, 16 = 33. 45; P< 0.0001) and diversity (ANOVA: F1, 16 = 7.20; P = 0.0511). While time since harvesting was a significant factor influencing the overall abundance of natural enemies (ANOVA: F2, 1,133 = 8.11; P< 0.0001), they were generally higher in abundance in locations with margin plants or where a diversity of margin plants was observed.DiscussionThese findings demonstrate that flowering plants in agricultural systems offer refuge and alternative food for natural enemies and potentially other beneficial insects between cropping seasons. The conservation of natural enemies between crops may lead to more effective natural pest regulation early in the following crop, thus reducing reliance on insecticides application

Lablab purpureus—A Crop Lost for Africa?

In recent years, so-called ‘lost crops’ have been appraised in a number of reviews, among them Lablab purpureus in the context of African vegetable species. This crop cannot truly be considered ‘lost’ because worldwide more than 150 common names are applied to it. Based on a comprehensive literature review, this paper aims to put forward four theses, (i) Lablab is one of the most diverse domesticated legume species and has multiple uses. Although its largest agro-morphological diversity occurs in South Asia, its origin appears to be Africa. (ii) Crop improvement in South Asia is based on limited genetic diversity. (iii) The restricted research and development performed in Africa focuses either on improving forage or soil properties mostly through one popular cultivar, Rongai, while the available diversity of lablab in Africa might be under threat of genetic erosion. (iv) Lablab is better adapted to drought than common beans (Phaseolus vulgaris) or cowpea (Vigna unguiculata), both of which have been preferred to lablab in African agricultural production systems. Lablab might offer comparable opportunities for African agriculture in the view of global change. Its wide potential for adaptation throughout eastern and southern Africa is shown with a GIS (geographic information systems) approach

Spatial distribution and risk factors of Schistosoma haematobium and hookworm infections among schoolchildren in Kwale, Kenya

Background: Large-scale schistosomiasis control programs are implemented in regions with diverse social and economic environments. A key epidemiological feature of schistosomiasis is its small-scale heterogeneity. Locally profiling disease dynamics including risk factors associated with its transmission is essential for designing appropriate control programs. To determine spatial distribution of schistosomiasis and its drivers, we examined schoolchildren in Kwale, Kenya. Methodology/Principal findings: We conducted a cross-sectional study of 368 schoolchildren from six primary schools. Soil-transmitted helminths and Schistosoma mansoni eggs in stool were evaluated by the Kato-Katz method. We measured the intensity of Schistosoma haematobium infection by urine filtration. The geometrical mean intensity of S. haematobium was 3.1 eggs/10 ml urine (school range, 1.4?9.2). The hookworm geometric mean intensity was 3.2 eggs/g feces (school range, 0?17.4). Heterogeneity in the intensity of S. haematobium and hookworm infections was evident in the study area. To identify factors associated with the intensity of helminth infections, we utilized negative binomial generalized linear mixed models. The intensity of S. haematobium infection was associated with religion and socioeconomic status (SES), while that of hookworm infection was related to SES, sex, distance to river and history of anthelmintic treatment. Conclusions/Significance: Both S. haematobium and hookworm infections showed micro-geographical heterogeneities in this Kwale community. To confirm and explain our observation of high S. haematobium risk among Muslims, further extensive investigations are necessary. The observed small scale clustering of the S. haematobium and hookworm infections might imply less uniform strategies even at finer scale for efficient utilization of limited resources

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

Mapping the medical outcomes study HIV health survey (MOS-HIV) to the EuroQoL 5 Dimension (EQ-5D-3L) utility index

10.1186/s12955-019-1135-8Health and Quality of Life Outcomes1718