Evaluation of the performance of Abbott Panbio™ COVID-19 antigen rapid diagnostic test for the detection of severe acute respiratory syndrome coronavirus 2 at Harar, Eastern Ethiopia.

Background: Rapid antigen tests can help in the effective isolation of symptomatic cases and the systematic tracing of close contacts. However, their reliability must be validated before implementing them widely. Methods: A cross-sectional study was conducted on 236 COVID-19-suspected patients visiting four different health institutions in Harari Regional State, Harar, Eastern Ethiopia, from June to July 2021. Two nasopharyngeal samples were collected and processed by the Panbio™ Ag-RDT kit and qRT-PCR. The collected data were analyzed using SPSS version 25.0. Results: The Panbio tests had a sensitivity of 77.5% (95% CI: 61.6-89.2%) and a specificity of 98.5% (95% CI: 95.6-99.7%). It also had a positive predictive value of 91.2% (95% CI: 76.9-96.9%), a negative predictive value of 95.5% (95% CI: 92.3-97.4%), and a kappa of 0.81 (95% CI: 0.7-0.9). The test had a sensitivity of 94.4%, 100%, 100%, and 90% in the samples collected from patients within the 1-5 days post-onset of COVID-19 signs and symptoms, of age group ≤18 years old, with cycle threshold values of <20, and with household contact, respectively. Conclusion: This test can be used as point-of-care testing for the diagnosis of symptomatic patients with short clinical courses and contact with patients in households.

Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project.

In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.

Unravelling the reservoirs for colonisation of infants with Campylobacter spp. in rural Ethiopia: protocol for a longitudinal study during a global pandemic and political tensions.

INTRODUCTION: Undernutrition is an underlying cause of mortality in children under five (CU5) years of age. Animal-source foods have been shown to decrease malnutrition in CU5. Livestock are important reservoirs for Campylobacter bacteria, which are recognised as risk factors for child malnutrition. Increasing livestock production may be beneficial for improving nutrition of children but these benefits may be negated by increased exposure to Campylobacter and research is needed to evaluate the complex pathways of Campylobacter exposure and infection applicable to low-income and middle-income countries. We aim to identify reservoirs of infection with Campylobacter spp. of infants in rural Eastern Ethiopia and evaluate interactions with child health (environmental enteric dysfunction and stunting) in the context of their sociodemographic environment. METHODS AND ANALYSIS: This longitudinal study involves 115 infants who are followed from birth to 12 months of age and are selected randomly from 10 kebeles of Haramaya woreda, East Hararghe zone, Oromia region, Ethiopia. Questionnaire-based information is obtained on demographics, livelihoods, wealth, health, nutrition and women empowerment; animal ownership/management and diseases; and water, sanitation and hygiene. Faecal samples are collected from infants, mothers, siblings and livestock, drinking water and soil. These samples are analysed by a range of phenotypic and genotypic microbiological methods to characterise the genetic structure of the Campylobacter population in each of these reservoirs, which will support inference about the main sources of exposure for infants. ETHICS AND DISSEMINATION: Ethical approval was obtained from the University of Florida Internal Review Board (IRB201903141), the Haramaya University Institutional Health Research Ethics Committee (COHMS/1010/3796/20) and the Ethiopia National Research Ethics Review Committee (SM/14.1/1059/20). Written informed consent is obtained from all participating households. Research findings will be disseminated to stakeholders through conferences and peer-reviewed journals and through the Feed the Future Innovation Lab for Livestock Systems.

COVID-19 Testing Experience in a Resource-Limited Setting: The Use of Existing Facilities in Public Health Emergency Management.

Introduction: Coronavirus disease 2019 (COVID-19) is a public health emergency with little testing and treatment experiences at its occurrence. Diagnostic and treatment rapidly changed in the world including Ethiopia. Haramaya University has strived to change its diagnostic capacity using existing facilities in response to the national call to the pandemic. Objective: This summary aims to detail experiences of setting up COVID-19 testing in Haramaya University laboratories, Eastern Ethiopia. Methods: Desktop exercise was conducted to understand the start-up and implementations of COVID-19 testing in two Haramaya University laboratories, Hararghe Health Research Partnership and Campylobacter Genomics and Environmental Enteric Dysfunction laboratories. Communication, formats, guidelines, and standards were reviewed and summarized. Discussion with those involved in the start-up and implementation of the testing were also held. Ideas were summarized to learn the experiences the COVID-19 testing exercises. Lesson Learned: This is a huge experience for Haramaya University to participate in the national call to increase the testing platform in the management of COVID19. Close work relationship with the public health authorities at all levels demonstrated the university's commitment to public service. The university has used the opportunity to advance its molecular testing capability by training its staff and students. The University has also contributed to the capacity development for laboratories in the surrounding areas of Harar, Somali, Oromia, and Dire Dawa. The pandemic has been an opportunity in harnessing existing resource for the benefit of the public during such times of dire needs to provide critical public health laboratory interventions.

Molecular detection of multidrug-resistant tuberculosis among smear-positive pulmonary tuberculosis patients in Jigjiga town, Ethiopia.

BACKGROUND: Molecular methods that target drug resistance mutations are suitable approaches for rapid drug susceptibility testing to detect multidrug-resistant tuberculosis (MDR-TB). The aim of the study was to determine MDR-TB cases and to analyze the frequency of gene mutations associated with rifampicin (RIF) and/or isoniazid (INH) resistance of Mycobacterium tuberculosis among smear-positive pulmonary tuberculosis patients. METHODS: Institution-based cross-sectional study design was employed. Sputum specimens were collected, and using a pretested questionnaire, data for associated risk factors for drug resistance were collected from 105 consecutive smear-positive pulmonary tuberculosis patients in Karamara General Hospital. Specimens were transported to Harar Health Research and Regional Laboratory, Harar, where molecular drug susceptibility testing was performed using GenoType® MTBDRplus assay. RESULTS: Of the total 105 sputum specimens, 98 (93.3%) gave interpretable results, in which 67 (68.4%) were new cases and 31 (31.6%) were previously treated cases. Of these, 80 (81.6%) were sensitive to both drugs and 18 (18.4%) were resistant to RIF and/or INH. The prevalences of MDR-TB in total cases, new, and previously treated cases were 10 (10.2%), 3 (4.5%), and 7 (22.6%), respectively. Among the ten total RIF-resistant specimens, eight (80%) had resulted because of absence of rpoB WT8 and presence of MUT3 and in all specimens, the amino acids changed were Ser531Lue. Of the 18 total INH-resistant specimens, 15 (83.3%) had mutations in the katG gene (katG MUT1, Ser315Thr1), indicating high-level resistance, while 3 (14.7%) had mutations in the inhA promoter gene (Cys15Thr), indicating low-level resistance. CONCLUSION: Among the mutations associated with resistance to RIF and INH, the majority were in codon 531 of the rpoB gene and codon 315 of the katG gene. Relatively high prevalence of MDR-TB was observed in the study.