Prognostic factors and outcomes of COVID-19 cases in Ethiopia: multi-center cohort study protocol.

BACKGROUND: The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) and became pandemic after emerging in Wuhan, China, in December 2019. Several studies have been conducted to understand the key features of COVID-19 and its public health impact. However, the prognostic factors of COVID-19 are not well studied in the African setting. In this study, we aim to determine the epidemiological and clinical features of COVID-19 cases, immunological and virological courses, interaction with nutritional status, and response to treatment for COVID-19 patients in Ethiopia. METHODS: A multi-center cohort study design will be performed. Patients with confirmed COVID-19 infection admitted to selected treatment centers will be enrolled irrespective of their symptoms and followed-up for 12 months. Baseline epidemiological, clinical, laboratory and imaging data will be collected from treatment records, interviews, physical measurements, and biological samples. Follow-up data collection involves treatment and prognostic outcomes to be measured using different biomarkers and clinical parameters. Data collection will be done electronically using the Open Data Kit (ODK) software package and then exported to STATA/SPSS for analysis. Both descriptive and multivariable analyses will be performed to assess the independent determinants of the treatment outcome and prognosis to generate relevant information for informed prevention and case management. The primary outcomes of this study are death/survival and viral shedding. Secondary outcomes include epidemiological characteristics, clinical features, genetic frequency shifts (genotypic variations), and nutritional status. DISCUSSION: This is the first large prospective cohort study of patients in hospitals with COVID-19 in Ethiopia. The results will enable us to better understand the epidemiology of SARS-CoV-2 in Africa. This study will also provide useful information for effective public health measures and future pandemic preparedness and in response to outbreaks. It will also support policymakers in managing the epidemic based on scientific evidence. TRIAL REGISTRATION: The Protocol prospectively registered in ClinicalTrials.gov (NCT04584424) on 30 October, 2020.

Standardizing clinical culture specimen collection in Ethiopia: a training-of-trainers.

BACKGROUND: Proper specimen collection is central to improving patient care by ensuring optimal yield of diagnostic tests, guiding appropriate management, and targeting treatment. The purpose of this article is to describe the development and implementation of a training-of-trainers educational program designed to improve clinical culture specimen collection among healthcare personnel (HCP) in Ethiopia. METHODS: A Clinical Specimen Collection training package was created consisting of a Trainer's Manual, Reference Manual, Assessment Tools, Step-by-Step Instruction Guides (i.e., job aides), and Core Module PowerPoint Slides. RESULTS: A two-day course was used in training 16 master trainers and 47 facility-based trainers responsible for cascading trainings on clinical specimen collection to HCP at the pre-service, in-service, or national-levels. The Clinical Specimen Collection Package is offered online via The Ohio State University's CANVAS online platform. CONCLUSIONS: The training-of-trainers approach may be an effective model for development of enhanced specimen collection practices in low-resource countries.

Correction: Multidrug resistance pattern of Acinetobacter species isolated from clinical specimens referred to the Ethiopian Public Health Institute: 2014 to 2018 trend anaylsis.

[This corrects the article DOI: 10.1371/journal.pone.0250896.].

Prevalence of respiratory syncytial virus infection and associated factors in children aged under five years with severe acute respiratory illness and influenza-like illness in Ethiopia.

Objectives: Acute respiratory infections because of respiratory syncytial viruses (RSVs) are among the major leading causes of morbidity and mortality in children worldwide. RSV prevalence and its contributing factors among children aged under 5 years in Ethiopia are not well studied. To assess the prevalence and associated factors of RSV infection in children aged under 5 years using influenza sentinel surveillance sites in Ethiopia. Methods: A cross-sectional study design was used utilizing influenza-like illness/sever acute respiratory illness surveillance data from January 2021 to December 2022 at the Ethiopian Public Health Institute. Results: In total, 2234 cases were included, with an overall RSV positivity rate of 16.2%. The RSV positivity rate was high in children aged under 1 year (22.8%) and during fall season (24.8%). The RSV positivity rate was significantly associated with ages under 1 year (adjusted odds ratio [AOR] 2.8, 95% confidence interval [CI]: 1.89-4.15) and 1-2 years (AOR 1.9, 95% CI: 1.26-2.73) and the fall season (AOR 1.67, 95% CI: 1.17-2.38). Conclusion: The study revealed that a considerably high RSV positivity rate was detected in children aged under 5 years. The age of children and season have a significant association with RSV positivity rate. Further studies of RSV viral genotype, clinical characteristics, and disease outcome need to be conducted for a better understanding of the virus and disease outcome.

SARS-CoV-2 co-detection with influenza and human respiratory syncytial virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022.

SARS-CoV-2 co-infection with the influenza virus or human respiratory syncytial virus (RSV) may complicate its progress and clinical outcomes. However, data on the co-detection of SARS-CoV-2 with other respiratory viruses are limited in Ethiopia and other parts of Africa to inform evidence-based response and decision-making. We analyzed 4,989 patients' data captured from the national severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance sites over 18 months period from January 01, 2021, to June 30, 2022. Laboratory specimens were collected from the patients and tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR) at the national influenza center. The median age of the patients was 14 years (IQR: 1-35 years), with a slight preponderance of them being at the age of 15 to less than 50 years. SARS-CoV-2 was detected among 459 (9.2%, 95% CI: 8.4-10.0) patients, and 64 (1.3%, 95% CI: 1.0-1.6) of SARS-CoV-2 were co-detected either with Influenza virus (54.7%) or RSV (32.8%) and 12.5% were detected with both of the viruses. A substantial proportion (54.7%) of SARS-CoV-2 co-detection with other respiratory viruses was identified among patients in the age group from 15 to less than 50 years. The multivariable analysis found that the odds of SARS-CoV-2 co-detection was higher among individuals with the age category of 20 to 39 years as compared to those less than 20 years old (AOR: 1.98, 95%CI:1.15-3.42) while the odds of SARS-CoV-2 co-detection was lower among cases from other regions of the country as compared to those from Addis Ababa (AOR:0.16 95%CI:0.07-0.34). Although the SARS-CoV-2 co-detection with other respiratory viral pathogens was minimal, the findings of this study underscore that it is critical to continuously monitor the co-infections to reduce transmission and improve patient outcomes, particularly among the youth and patients with ILI.

Regional and temporal variations in COVID-19 cases and deaths in Ethiopia: Lessons learned from the COVID-19 enhanced surveillance and response.

BACKGROUND: The COVID-19 pandemic is one of the most devastating public health emergencies of international concern to have occurred in the past century. To ensure a safe, scalable, and sustainable response, it is imperative to understand the burden of disease, epidemiological trends, and responses to activities that have already been implemented. We aimed to analyze how COVID-19 tests, cases, and deaths varied by time and region in the general population and healthcare workers (HCWs) in Ethiopia. METHODS: COVID-19 data were captured between October 01, 2021, and September 30, 2022, in 64 systematically selected health facilities throughout Ethiopia. The number of health facilities included in the study was proportionally allocated to the regional states of Ethiopia. Data were captured by standardized tools and formats. Analysis of COVID-19 testing performed, cases detected, and deaths registered by region and time was carried out. RESULTS: We analyzed 215,024 individuals' data that were captured through COVID-19 surveillance in Ethiopia. Of the 215,024 total tests, 18,964 COVID-19 cases (8.8%, 95% CI: 8.7%- 9.0%) were identified and 534 (2.8%, 95% CI: 2.6%- 3.1%) were deceased. The positivity rate ranged from 1% in the Afar region to 15% in the Sidama region. Eight (1.2%, 95% CI: 0.4%- 2.0%) HCWs died out of 664 infected HCWs, of which 81.5% were from Addis Ababa. Three waves of outbreaks were detected during the analysis period, with the highest positivity rate of 35% during the Omicron period and the highest rate of ICU beds and mechanical ventilators (38%) occupied by COVID-19 patients during the Delta period. CONCLUSIONS: The temporal and regional variations in COVID-19 cases and deaths in Ethiopia underscore the need for concerted efforts to address the disparities in the COVID-19 surveillance and response system. These lessons should be critically considered during the integration of the COVID-19 surveillance system into the routine surveillance system.

Prevalence of Staphylococcus aureus, Methicillin-Resistant Staphylococcus aureus and Potential Risk Factors in Selected Dairy Farms at the Interface of Animal and Human in Bishoftu, Ethiopia.

BACKGROUND: Staphylococcus aureus (S. aureus) has been reported as the most commonly isolated highly contagious pathogen from human, animals and animal products. Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a significant pathogen with zoonotic potential that could have devastating consequence for the health and well-being of animals and human. METHODS: A cross-sectional study was conducted from July 2020 to January 2021. A total of 233 samples from cow milk, udder swabs and milkers' hand swabs were collected for culture and identification based on the standard protocol. Antimicrobial susceptibility tests were performed for all isolates by using Kirby Bauer's disk diffusion test. MRSA was detected by cefoxitin disk diffusion test. RESULTS: S. aureus was isolated from 50 (21.46%) of 233 samples and the prevalence of MRSA was 4%. The highest prevalence was found in cow milk 36 (25.53%) followed by hand swabs 10 (19.23%) and udder swabs 4 (10%). S. aureus prevalence was 58.33%, 30.0%, 21.43%, 17.92%, 15.79% in farm D, C, E, A, B respectively. A large percentage (58.33% and 30%) were from farm D and C. S. aureus isolation rate showed statistically significant association with farm types (p = 0.011) and with previous mastitis exposure (p = 0.001). High level of resistance was observed to penicillin (94%) and ampicillin (92%), but low level resistance to gentamicin (0%), amikacin (0%), ceftriaxone (0%), chloramphenicol (4%), ciprofloxacin and cefoxitin (4%). The overall prevalence of multidrug resistance (MDR) was 10.42%. CONCLUSION: Prevalence of S. aureus in milk showed statistically significant association with respect to previous mastitis exposure and farm types (p = 0.011). High level of resistant to penicillin and ampicillin was observed. Therefore, effective mastitis control programs, best veterinary practice among all farms and use of antibiotics in the farm should be strictly controlled.

Multidrug resistance pattern of Acinetobacter species isolated from clinical specimens referred to the Ethiopian Public Health Institute: 2014 to 2018 trend anaylsis.

BACKGROUND: Acinetobacter species have been a leading cause of nosocomial infections, causing significant morbidity and mortality over the entire world including Ethiopia. The most important features of A. baumannii are its ability to persist in the hospital environment and rapidly develop resistance to a wide variety of antibiotics. This study aimed to determine trend of antimicrobial resistance in Acinetobacter species over a five years period. METHOD: A retrospective data regarding occurrence and antimicrobial resistance of Acinetobacter species recovered from clinical specimens referred to the national reference laboratory was extracted from microbiology laboratory data source covering a time range from 2014 to 2018. Socio-demographic characteristics and laboratory record data was analyzed using SPSS 20. RESULTS: A total of 102 strains of Acinetobacter species were analyzed from various clinical specimens. Majority of them were from pus (33.3%) followed by blood (23.5%), urine (15.6%) and body fluid (11.7%). Significant ascending trends of antimicrobial resistance was shown for meropenem (12.5% to 60.7%), ceftazidime (82.1% to 100%), ciprofloxacin (59.4% to 74.4%), ceftriaxone (87.1% to 98.6%), cefepime (80.0% to 93.3%) and pipracillin- tazobactam (67.8% to 96.3%). However, there was descending trend of antimicrobial resistance for tobramycin (56.5% to 42.8%), amikacin (42.1% to 31.4%) and trimethoprim-sulfamethoxazole (79.0 to 68.2%). The overall rate of carbapenem non-susceptible and multidrug resistance rates in Acinetobacter species were 56.7% and 71.6%.respectively. CONCLUSION: A five year antimicrobial resistance trend analysis of Acinetobacter species showed increasing MDR and resistance to high potent antimicrobial agents posing therapeutic challenge in our Hospitals and health care settings. Continuous surveillance and appropriate infection prevention and control strategies need to be strengthened to circumvent the spread of multidrug resistant pathogens in health care facilities.

Phenotypic characterization of carbapenem non-susceptible gram-negative bacilli isolated from clinical specimens.

BACKGROUND: Multidrug resistant, extremely drug-resistant, pan-drug resistant, carbapenem-resistant, and carbapenemase-producing gram-negative bacteria are becoming more common in health care settings and are posing a growing threat to public health. OBJECTIVE: The study was aimed to detect and phenotypically characterize carbapenem no- susceptible gram-negative bacilli at the Ethiopian Public Health Institute. MATERIALS AND METHODS: A prospective cross-sectional study was conducted from June 30, 2019, to May 30, 2020, at the national reference laboratory of the Ethiopian Public Health Institute. Clinical samples were collected, inoculated, and incubated for each sample in accordance with standard protocol. Antimicrobial susceptibility testing was conducted using Kirby-Bauer disk diffusion method. Identification was done using the traditional biochemical method. Multidrug-resistant and extensively drug-resistant isolates were classified using a standardized definition established by the European Centre for Disease Prevention and Control and the United States Centers for Disease Prevention and Control. Gram-negative organisms with reduced susceptibility to carbapenem antibiotics were considered candidate carbapenemase producers and subjected to modified carbapenem inactivation and simplified carbapenem inactivation methods. Meropenem with EDTA was used to differentiate metallo-ß-lactamase (MBL) from serine carbapenemase. Meropenem (MRP)/meropenem + phenylboronic acid (MBO) were used to differentiate Klebsiella pneumoniae carbapenemase (KPC) from other serine carbapenemase producing gram-negative organisms. RESULTS: A total of 1,337 clinical specimens were analyzed, of which 429 gram-negative bacterial isolates were recovered. Out of 429 isolates, 319, 74, and 36 were Enterobacterales, Acinetobacter species, and Pseudomonas aeruginosa respectively. In our study, the prevalence of multidrug-resistant, extensively drug-resistant, carbapenemase-producing, and carbapenem nonsusceptible gram-negative bacilli were 45.2%, 7.7%, 5.4%, and 15.4% respectively. Out of 429 isolates, 66 demonstrated reduced susceptibility to the antibiotics meropenem and imipenem. These isolates were tested for carbapenemase production of which 34.8% (23/66) were carbapenemase producers. Out of 23 carbapenemase positive gram-negative bacteria, ten (10) and thirteen (13) were metallo-beta-lactamase and serine carbapenemase respectively. Three of 13 serine carbapenemase positive organisms were Klebsiella pneumoniae carbapenemase. CONCLUSION: This study revealed an alarming level of antimicrobial resistance (AMR), with a high prevalence of multidrug-resistant (MDR) and extremely drug-resistant, carbapenemase-producing gram-negative bacteria, particularly among intensive care unit patients at the health facility level. These findings point to a scenario in which clinical management of infected patients becomes increasingly difficult and necessitates the use of "last-resort" antimicrobials likely exacerbating the magnitude of the global AMR crisis. This mandates robust AMR monitoring and an infection prevention and control program.

Knowledge, practice and associated factors towards the prevention of COVID-19 among high-risk groups: A cross-sectional study in Addis Ababa, Ethiopia.

BACKGROUND: Coronavirus disease (COVID-19) is a highly transmittable virus that continues to disrupt livelihoods, particularly those of low-income segments of society, around the world. In Ethiopia, more specifically in the capital city of Addis Ababa, a sudden increase in the number of confirmed positive cases in high-risk groups of the community has been observed over the last few weeks of the first case. Therefore, this study aims to assess knowledge, practice and associated factors that can contribute to the prevention of COVID-19 among high-risk groups in Addis Ababa. METHODS: A cross-sectional in person survey (n = 6007) was conducted from 14-30 April, 2020 following a prioritization within high-risk groups in Addis Ababa. The study area targeted bus stations, public transport drivers, air transport infrastructure, health facilities, public and private pharmacies, hotels, government-owned and private banks, telecom centers, trade centers, orphanages, elderly centers, prison, prisons and selected slum areas where the people live in a crowded areas. A questionnaire comprised of four sections (demographics, knowledge, practice and reported symptoms) was used for data collection. The outcomes (knowledge on the transmission and prevention of COVID-19 and practice) were measured using four items. A multi variable logistic regression was applied with adjustment for potential confounding. RESULTS: About half (48%, 95% CI: 46-49) of the study participants had poor knowledge on the transmission mode of COVID-19 whereas six out of ten (60%, 95% CI: 58-61) had good knowledge on prevention methods for COVID-19. The practice of preventive measures towards COVID-19 was found to be low (49%, 95% CI: 48-50). Factors that influence knowledge on COVID-19 transmission mechanisms were female gender, older age, occupation (health care and grocery worker), lower income and the use of the 8335 free call centre. Older age, occupation (being a health worker), middle income, experience of respiratory illness and religion were significantly associated with being knowledgeable about the prevention methods for COVID-19. The study found that occupation, religion, income, knowledge on the transmission and prevention of COVID-19 were associated with the practice of precautionary measures towards COVID-19. CONCLUSION: The study highlighted that there was moderate knowledge about transmission modes and prevention mechanisms. Similarly, there was moderate practice of measures that contribute towards the prevention of COVID-19 among these priority and high-risk communities of Addis Ababa. There is an urgent need to fill the knowledge gap in terms of transmission mode and prevention methods of COVID-19 to improve prevention practices and control the spread of COVID-19. Use of female public figures and religious leaders could support the effort towards the increase in awareness.

Antimicrobial susceptibility profile of Gonococcal isolates obtained from men presenting with urethral discharge in Addis Ababa, Ethiopia: Implications for national syndromic treatment guideline.

BACKGROUND: Neisseria gonorrhoeae (gonococcus) is the etiologic agent for the sexually transmitted Infection gonorrhea, a disease with a significant global public health impact. The treatment regimen for gonorrhea has been changed frequently over the past few decades due to the organism's propensity for developing antibiotic resistance. This study investigated antimicrobial susceptibility patterns of quinolones, third-generation cephalosporin, and other relevant antimicrobials found in N. gonorrhoeae isolated from men presenting with urethral discharge at selected healthcare facilities in Addis Ababa, Ethiopia, with the aim of revising the national treatment regimen based on the information generated from this study. METHODS: A total of 599 male patients presenting with urethral discharge were included in the current study. Urethral discharge specimens were cultured on Modified Thayer Martín media and suspected gonococcal colonies were confirmed using Oxidase and Superoxol tests followed by identification through a commercial kit (API-NHR). Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method using ciprofloxacin (5µg), ceftriaxone (30µg), cefixime (5µg), cefoxitin (30 µg), penicillin (10µg) and spectinomycin (100 µg) on enriched GC agar. Minimum Inhibitory Concentration (MIC) was also carried out using concentration gradient strips (E-tests) of the same antimicrobial agents. RESULTS: The prevalence of gonococcal isolates in the current study was 69%. Out of the 361 gonococcal isolates, close to 68% were fluoroquinolone non-susceptible, with 60% resistant and 7% having an intermediate status. However, all tested isolates were susceptible to ceftriaxone. In addition, all of the isolates have shown reduced non-susceptibility to spectinomycin and cefoxitin. CONCLUSION: The prevalence of gonococcal isolates in men presenting with urethral discharge at selected healthcare facilities in Addis Ababa, Ethiopia was found to be high. The high level of fluoroquinolone resistance observed in gonococcal isolates recovered in this study necessitates revision of the national syndromic treatment guideline.