BackgroundThe enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial.Methodology/principal findingsFecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1–4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well.ConclusionsWe describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.

BackgroundThe frequent occurrence of bacterial gastroenteritis among HIV-infected individuals together with increased antimicrobial drug resistance pose a significant public health challenge in developing countries. This study aimed to determine the prevalence of enteric bacterial pathogens and their antimicrobial susceptibility pattern among HIV-infected patients in a tertiary hospital in southern Ethiopia.MethodsA hospital-based cross-sectional study was conducted at Hawassa University Comprehensive Specialized Hospital from February to May, 2016. A consecutive 215 HIV-infected patients, with complaints of gastrointestinal tract disease, were enrolled. Data on socio-demography and related factors was collected using a structured questionnaire. A stool sample was collected from each study participant and cultured to isolate enteric bacterial pathogens; isolates were characterized using biochemical tests. Antimicrobial susceptibility was determined using the Kirby- Bauer disk diffusion technique.ResultsOut of 215 patients, 27(12.6%) were culture positive for various bacterial pathogens. Campylobacter species was the most common bacterial isolate (6.04%), followed by Salmonella species (5.1%). The majority of isolates was sensitive to norfloxacin, nalidixic acid, gentamicin, ceftriaxone and ciprofloxacin and showed resistance to trimethoprim sulfamethoxazole (SXT) and chloramphenicol. Consumption of raw food was the only risk factor found to be significantly associated with enteric bacterial infection (crude odds ratio 3.41 95% CI 1.13–10.3).ConclusionsThe observed rate of enteric bacterial pathogens and their antimicrobial resistance pattern to the commonly prescribed antibiotics highlights the need to strengthen intervention efforts and promote rational use of antimicrobials. In this regard, the need to strengthen antimicrobial stewardship efforts should be emphasized to slow grown antimicrobial resistance among this population group.

Abstract. Intestinal parasites are important contributors to global morbidity and mortality and are the second most common cause of outpatient morbidity in Ethiopia. This cross-sectional survey describes the prevalence of soil-transmitted helminths and intestinal protozoa in preschool children 0-5 years of age in seven communities in the Amhara region of Ethiopia, and investigates associations between infection, household water and sanitation characteristics, and child growth. Stool samples were collected from children 0-5 years of age, 1 g of sample was preserved in sodium acetate-acetic acid-formalin, and examined for intestinal helminth eggs and protozoa cysts ether-concentration method. A total of 212 samples were collected from 255 randomly selected children. The prevalence of Ascaris lumbricoides, Trichuris trichiura, and hookworm were 10.8% (95% confidence interval [CI] 6.6-15.1), 1.4% (95% CI = 0-3.0), and 0% (95% CI = 0-1.7), respectively. The prevalence of the pathogenic intestinal protozoa Giardia lamblia and Entamoeba histolytica/dispar were 10.4% (95% CI = 6.2-14.6) and 3.3% (95% CI = 0.09-5.7), respectively. Children with A. lumbricoides infections had lower height-for-age z-scores compared with those without, but were not more likely to have stunting. Compared with those without G. lamblia, children with G. lamblia infections had lower weight-for-age and weight-for-height z-scores and were more than five times as likely to meet the z-score definition for wasting (prevalence ratio = 5.42, 95% CI = 2.97-9.89). This article adds to a growing body of research on child growth and intestinal parasitic infections and has implications for their treatment and prevention in preschool-aged children.

BackgroundStool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.MethodsWe examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.ResultsOf 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman’s r = − 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).ConclusionsIn conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.Electronic supplementary materialThe online version of this article (10.1186/s12879-019-3674-3) contains supplementary material, which is available to authorized users.

IntroductionFacial hygiene promotion and environmental improvements are central components of the global trachoma elimination strategy despite a lack of experimental evidence supporting the effectiveness of water, sanitation and hygiene (WASH) measures for reducing trachoma transmission. The objective of the WUHA (WASH Upgrades for Health in Amhara) trial is to evaluate if a comprehensive water improvement and hygiene education programme reduces the prevalence of ocular chlamydia infection in rural Africa.Methods and analysisForty study clusters, each of which had received at least annual mass azithromycin distributions for the 7 years prior to the start of the study, are randomised in a 1:1 ratio to the WASH intervention arm or a delayed WASH arm. The WASH package includes a community water point, community-based hygiene promotion workers, household wash stations, household WASH education books, household soap distribution and a primary school hygiene curriculum. Educational activities emphasise face-washing and latrine use. Mass antibiotic distributions are not provided during the first 3 years but are provided annually over the final 4 years of the trial. Annual monitoring visits are conducted in each community. The primary outcome is PCR evidence of ocular chlamydia infection among children aged 0–5 years, measured in a separate random sample of children annually over 7 years. A secondary outcome is improvement of the clinical signs of trachoma between the baseline and final study visits as assessed by conjunctival photography. Laboratory workers and photo-graders are masked to treatment allocation.Ethics and disseminationStudy protocols have been approved by human subjects review boards at the University of California, San Francisco, Emory University, the Ethiopian Food and Drug Authority, and the Ethiopian Ministry of Innovation and Technology. A data safety and monitoring committee oversees the trial. Results will be disseminated through peer-reviewed publications and presentations.Trial registration number(http://www.clinicaltrials.gov): NCT02754583; Pre-results.