Challenges for Food Security in Eritrea -- A Descriptive and Qualitative Analysis

Food security is about ensuring that all people at all times have both physical and economic access to the basic food they need. In a number of African countries chronic malnutrition and transitory food insecurity are pervasive. Like most African countries, Eritrea is also a victim of the problem of food insecurity. Based on this historical and recurrent food insecurity in Eritrea, an attempt is made in this paper to assess the possible causes of food insecurity in the country. Furthermore, the paper captures the available food security policy proposals of Eritrea and eventually draws conclusions and extends possible recommendations and policy remedies suited to the country

Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations

Supporting Pharmacovigilance Signal Validation and Prioritization with Analyses of Routinely Collected Health Data: Lessons Learned from an EHDEN Network Study

Introduction: Individual case reports are the main asset in pharmacovigilance signal management. Signal validation is the first stage after signal detection and aims to determine if there is sufficient evidence to justify further assessment. Throughout signal management, a prioritization of signals is continually made. Routinely collected health data can provide relevant contextual information but are primarily used at a later stage in pharmacoepidemiological studies to assess communicated signals. Objective: The aim of this study was to examine the feasibility and utility of analysing routine health data from a multinational distributed network to support signal validation and prioritization and to reflect on key user requirements for these analyses to become an integral part of this process. Methods: Statistical signal detection was performed in VigiBase, the WHO global database of individual case safety reports, targeting generic manufacturer drugs and 16 prespecified adverse events. During a 5-day study-a-thon, signal validation and prioritization were performed using information from VigiBase, regulatory documents and the scientific literature alongside descriptive analyses of routine health data from 10 partners of the European Health Data and Evidence Network (EHDEN). Databases included in the study were from the UK, Spain, Norway, the Netherlands and Serbia, capturing records from primary care and/or hospitals. Results: Ninety-five statistical signals were subjected to signal validation, of which eight were considered for descriptive analyses in the routine health data. Design, execution and interpretation of results from these analyses took up to a few hours for each signal (of which 15–60 minutes were for execution) and informed decisions for five out of eight signals. The impact of insights from the routine health data varied and included possible alternative explanations, potential public health and clinical impact and feasibility of follow-up pharmacoepidemiological studies. Three signals were selected for signal assessment, two of these decisions were supported by insights from the routine health data. Standardization of analytical code, availability of adverse event phenotypes including bridges between different source vocabularies, and governance around the access and use of routine health data were identified as important aspects for future development. Conclusions: Analyses of routine health data from a distributed network to support signal validation and prioritization are feasible in the given time limits and can inform decision making. The cost–benefit of integrating these analyses at this stage of signal management requires further research

Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

<p>Abstract</p> <p>Background</p> <p>Pneumonia and myocarditis are the most commonly reported diseases due to <it>Histophilus somni</it>, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in <it>H. somni </it>using traditional methods. Analyses of the genome sequences of several <it>Pasteurellaceae </it>species have provided insights into their biology and evolution. In view of the economic and ecological importance of <it>H. somni</it>, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the <it>Pasteurellaceae</it>.</p> <p>Results</p> <p>The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the <it>Pasteurellaceae</it>, several <it>H. somni </it>genes that may encode proteins involved in virulence (<it>e.g</it>., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.</p> <p>Conclusions</p> <p>Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two <it>H. somni </it>strains.</p

Utility of the loop-mediated isothermal amplification assay for the diagnosis of visceral leishmaniasis from blood samples in Ethiopia

Rapid and accurate diagnosis of visceral leishmaniasis (VL) is needed to initiate prompt treatment to reduce morbidity and mortality. Here, we evaluated the performance of loop-mediated isothermal amplification (LAMP) assay for the diagnosis of VL from blood in an endemic area in Ethiopia. LAMP was positive in 117/122 confirmed VL cases and negative in 149/152 controls, resulting in a sensitivity of 95.9% (95% CI: 90.69-98.66) and a specificity of 98.0% (95% CI: 94.34-99.59), respectively. The sensitivity of the LAMP assay was 95.0% (95% CI: 88.61-98.34) in HIV-negatives and 100% (95% CI: 85.18-100.0) in HIV-positives. Compared with microscopy, LAMP detected 82/87 (94.3%, 95% CI: 87.10-98.11) of the microscopy1 cases and was negative in 11/27 (40.7%, 95% CI: 22.39-61.20) of the microscopy2 cases. Compared with the rK39 serology, LAMP detected 113/120 (94.2%, 95% CI: 88.35-97.62) of the rK391 cases and was negative in 149/154 (96.8%, 95% CI: 92.59-98.94) of the rK392 cases. However, when compared with microscopy only, rK39 detected 83/87 (95.4%, 95% CI: 88.64-98.73) of the microscopy1 cases and negative in only 12/27 (44.4%, 95% CI: 25.48-64.67) of the microscopy- cases. There was an excellent agreement between rK39 and LAMP (Kappa 5 0.91, 95% CI: 0.86-0.96). Furthermore, an algorithm using rK39 followed by LAMP would yield a sensitivity of 99.2% (95%CI: 95.52-99.89) and a specificity of 98.0% (95% CI: 94.34-99.59). The findings demonstrate that LAMP assay is an accurate and rapid molecular assay for VL diagnosis, including in HIV-1 coinfected patients, in an endemic setting

Incidence and predictors of HIV related opportunistic infections after initiation of highly active antiretroviral therapy at Ayder Referral Hospital, Mekelle, Ethiopia: A retrospective single centered cohort study.

IntroductionEven though use of antiretroviral therapy (HAART) decreases the incidence of opportunistic infections (OIs) they are continuing to be a major cause of morbidity and mortality. Studies concerning this problem are scarce in Eastern Africa. The aim of this study was to determine the incidence and predictors of OIs after initiation of HAART in Ethiopia.MethodsA health facility based single centered cohort study using structured data extraction sheet was conducted. The study population was all HIV positive ART naive adolescents and adults who started HAART between January 2009 and May 2012. Simple random sampling technique was used to select 317 patients from the record. Multivariate binary logistic regression model was used to determine factors for the occurrence of OIs after initiation of HAART.ResultsThe incidence of OIs after HAART was 7.5 cases/100person years. Tuberculosis, oral candidiasis, pneumonia and toxoplasmosis were the leading OIs after HAART. A bed ridden functional status at initiation of HAART, presence of OIs before HAART, non-adherence and low hemoglobin level were predictors for the occurrence of OIs after HAART.ConclusionThe incidence of OIs after HAART was higher than in previous studies. Patients with the identified risk factors need strict follow up to reduce the morbidity and mortality attributed to OIs. Earlier initiation of HAART before advanced immune suppression, better management of TB and extended baseline assessment could help to reduce opportunistic infections and mortality after the initiation of HAART in Ethiopian patients

ANCA-Associated Intrahepatic Duct Injury Associated with Levamisole-Adulterated Cocaine

Damage to the liver or kidney can occur through direct toxic effects; however, damage can also be drug-induced immune-mediated. Levamisole-adulterated cocaine (LAC) is known to cause antineutrophil cytoplasmic antibody- (ANCA-) associated vasculitis and glomerulonephritis leading to acute kidney injury and end-stage renal disease. It remains unclear whether LAC is associated with hepatic duct damage. Here, we report a case with biopsy-proven evidence of intrahepatic duct damage months after being diagnosed with ANCA-associated crescentic and sclerosing glomerulonephritis caused by LAC use. This case represents the first report of LAC-induced ANCA-associated hepatic duct cholestasis in the setting of previous LAC-induced ANCA-positive glomerulonephritis