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Daniel Mekonnen,1,2 Abaineh Munshea,2,3 Endalkachew Nibret,2,3 Bethlehem Adnew,4 Hailu Getachew,5 Amiro Kebede,5 Ananya Gebrewahid,5 Silvia Herrera-Leon,6 Aranzazu Amor Aramendia,7 Agustín Benito,8 Estefanía Abascal,6 Camille Jacqueline,6,9 Abraham Aseffa,4 Laura Herrera-Leon6,10 1Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; 2Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia; 3Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia; 4Armauer Hansen Research Institute, Addis Ababa, Ethiopia; 5Amhara Public Health Institute, Bahir Dar, Ethiopia; 6National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain; 7Fundación Mundo Sano, Madrid, Spain; 8National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain; 9European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden; 10CIBER Epidemiologia y Salud Publica, Madrid, SpainCorrespondence: Daniel Mekonnen, Email nigusdaniel@gmail.comIntroduction: Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs).Methods: A facility-based cross-sectional study was conducted in 2020– 2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares.Results: Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance.Conclusion: The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.Keywords: Mycobacterium tuberculosis, L.4.2.2, SIT149, drug resistance, Ethiopia

Yayehyirad Tassachew,1– 3 Tamrat Abebe,1 Yeshambel Belyhun,4 Tezazu Teffera,5 Abate Bane Shewaye,6,7 Hailemichael Desalegn,8 Henok Andualem,9 Abiy Kinfu,10 Andargachew Mulu,2 Adane Mihret,1,2 Rawleigh Howe,2 Abraham Aseffa2 1Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; 2Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia; 3School of Medical Laboratory Sciences, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia; 4School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia; 5Department of Surgery, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia; 6Department of Internal Medicine, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; 7Adera Medical Center PLC, Addis Ababa, Ethiopia; 8Department of Internal Medicine, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia; 9Department of Medical Laboratory Science, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia; 10Ethiopian National Blood Bank Service, Addis Ababa, EthiopiaCorrespondence: Yayehyirad Tassachew, Department of Microbiology, Immunology & Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia, Tel +251-916829464, Email seamyah@gmail.com; tassachewy@gmail.comBackground: The efficient use of antiretroviral drugs has significantly reduced AIDS-related morbidities and mortalities; however, mortality due to non-AIDS-related end-stage liver diseases is escalating in those living with HIV.Objective: The study was designed to determine the prevalence of HIV and its co-infection with HBV and HCV among chronic liver disease (CLD) patients in Ethiopia.Methods: Three hundred and forty-five CLD patients were included in this study in two groups: Hepatocellular carcinoma (HCC) (n=128) and non-HCC (n=217) patients. The non-HCC group comprised patients with advanced liver disease (n=98) and chronic hepatitis (n=119). Enzyme immunoassays were used to determine HBV and HCV infection markers. In addition, a serial rapid HIV testing algorithm was employed to screen HIV infection.Results: Regardless of the stage of liver disease, the overall frequency of HIV was 4.3% (15/345), with a 2% (7/345) and 0.3% (1/345) of HIV/HBV and HIV/HCV co-infection rate. Of all HIV-infected patients (n=15), 46.7% (7/15) and 6.7% (1/15) were co-infected with HBV (HBsAg+HBcAb+) and HCV (anti-HCV+ HCV-RNA+), respectively, and 86.7% (13/15) exhibited a marker of HBV exposure (total HBcAb+). Overall, the frequency of HIV and its co-infection with HBV was more noticeable among HCC than non-HCC patients [8.6% (11/128) vs 1.8 (4/217), p=0.005 and 3.9% (5/128) vs 0.9% (2/217), p=0.1]. The rate of HIV mono-infection was 3.9% (5/128) vs 0.9% (2/217) among HCC and non-HCC patients.Conclusion: The frequency of HIV and its co-infections with HBV/HCV exhibited an increasing pattern with the severity of the liver disease. Thus, screening all HIV-positive patients for HBV and HCV infection and all CLD patients for HIV infection and taking necessary preventive measures would be an essential strategy to prevent the progression of CLD and death related to liver disease in people living with HIV.Keywords: HIV, HBV, HCV, HCC, non-AIDS liver diseases

Aminu Seman,1,2 Adane Mihret,1,2 Shemse Sebre,1,2 Tewachew Awoke,3 Biruk Yeshitela,2 Berhanu Yitayew,4 Abraham Aseffa,2 Daniel Asrat,1 Tamrat Abebe1 1Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; 2Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia; 3Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; 4Department of Medical Laboratory Science, College of Medicine and Health Sciences, Debre Berhan University, Debre Berhan, EthiopiaCorrespondence: Aminu Seman, Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia, Tel +251 920 747 176, Email aminu.seman@aau.edu.et; aminumifta54@gmail.comBackground: Production of Extended spectrum beta-lactamase (ESBL) and Carbapenemase is the most common strategy for drug resistance in clinical isolates of Enterobacteriaceae. This study was conducted to determine the magnitude of ESBL and Carbapenemase production (CPE) among clinical isolates of Enterobacteriaceae causing bloodstream infections (BSI) in Ethiopia.Methods: A cross-sectional study was performed from September 2018 to January 2019 in Ethiopia. A total of 2397 BSI suspected patients were enrolled and blood culture was performed using a BacT/Alert instrument in combination with conventional methods for identification. After antimicrobial susceptibility test, phenotypic confirmation of ESBLs was done by combined disc-diffusion. Meanwhile carbapenemase production was done by modified carbapenem inactivation method. Multiplex PCR was conducted to detect the presence of blaCTX-M,blaSHV, blaTEM, blaKPC and blaNDM genes.Results: A total of 104 (4.3%) Enterobacteriaceae were isolated from 2397 BSI suspected patients. Klebsiella pneumoniae (55/104, 52%) was the predominant isolate followed by E. coli, (19.2%, 20/104) and K.oxytoca (17.3%, 18/104). ESBL and carbapenemase production were observed from 70 (67.3%, 57.4 − 76.2% at 95% CI) and 8 (7.7%, 3.4– 14.6% at 95% CI) isolates respectively. The highest frequency of ESBL and carbapenemase production was observed in K. pneumoniae 78.2% (43/55) and 9.1% (5/55), respectively. All the 70 isolates confirmed as ESBL producers harbored at least one of the ESBL genes and the majority of them carried multiple beta-lactamase genes (84.3%), where blaCTX-M, type was the most predominant (67.3%). Similarly, the entire eight isolates positive for carbapenemase carried blaNDM but none of them carried blaKPC.Conclusion: In our study, the rate of ESBL production among BSI-causing Enterobacteriaceae was alarming and most of the isolates carried multiple types of ESBL genes. A significant magnitude of CPE isolates causing BSI was recorded.Keywords: CTX-M, TEM, SHV, NDM, KPC, Ethiopia

Abel Abera Negash,1,2 Daniel Asrat,2 Workeabeba Abebe,3 Abraham Aseffa,1 Mario Vaneechoutte4 1Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia; 2Department of Microbiology, Immunology and Parasitology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia; 3Department of Pediatrics and Child Health, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia; 4Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine & Health Sciences, Ghent University, Ghent, BelgiumCorrespondence: Abel Abera NegashArmauer Hansen Research Institute (AHRI), P.O. Box 1005, Addis Ababa, EthiopiaEmail abelaberan@gmail.comBackground: In several countries, introduction of the pneumococcal conjugate vaccine (PCV) has led to a decline in antimicrobial-resistant pneumococcal disease but has also resulted in a concomitant increase in antimicrobial-resistant, non-vaccine serotypes of Streptococcus pneumoniae. We sought to determine the magnitude of penicillin and macrolide resistance among pneumococcal serotypes and the mechanisms of macrolide resistance in Ethiopia, 5 years after the introduction of PCV10 in the country.Methods: Susceptibility to penicillin and erythromycin of 119 pneumococcal isolates collected from pediatric patients aged 0– 15 years in Addis Ababa, Ethiopia, was tested using disc diffusion, and minimum inhibitory concentration (MIC) was also determined by Etest. Pneumococcal serotypes were determined by sequencing the cpsB gene and using Quellung reaction. Polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism analysis were used to detect and differentiate the macrolide resistance genes erm(B), mef(A), and mef(B).Results: Among the 119 isolates, 2.5% (3/119) were resistant to penicillin, while 58% (69/119) were intermediate. Resistance to erythromycin was observed in 33.6% (40/119) of the isolates with the highest level of resistance among isolates from middle ear discharge, i.e., 53.3% (8/15). Half (19/40) of the erythromycin resistant isolates were serotype 19A and among serotype 19A isolates, the majority i.e., 54.3% (19/35) were resistant to erythromycin. The most common macrolide resistance determinant was mef(E) with a prevalence of 50% (20/40).Conclusion: Five years after introduction of PCV10 in Ethiopia, we observed that the prevalence of penicillin-resistant S. pneumoniae was low. However, there was a high level of macrolide resistance which was mostly in serotype 19A, and the resistance was mainly mediated by efflux pumps. Introduction of PCV13 (which covers serotype 19A) would significantly improve coverage of the macrolide-resistant serotypes. Continued surveillance of pneumococcal serotype distribution and their antibiotic resistance pattern in Ethiopia is warranted.Keywords: efflux pump, erythromycin, mef(E), PCV10, penicillin, serotype 19A, Streptococcus pneumoniae

Kedir Urgesa,1 Kidist Bobosha,2 Berhanu Seyoum,2 Biftu Geda,3 Fitsum Weldegebreal,3 Adane Mihret,2 Rawleigh Howe,2 Mirgissa Kaba,4 Abraham Aseffa2 1Department of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia; 2Armauer Hansen Research Institute, Addis Ababa, Ethiopia; 3College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia; 4School of Public Health, Addis Ababa University, Addis Ababa, EthiopiaCorrespondence: Kedir Urgesa P.O Box 235, Harar, EthiopiaTel +251940635596Email kedirbofe@gmail.comIntroduction: Leprosy or Hansen’s disease is a potentially disabling disease that results in discrimination and self-stigma. A delay in case detection among leprosy patients is one of the factors resulting in disability. Although poor insights of the community toward leprosy lead to delays in case detection, studies on such matters are neglected in Ethiopia.Objective: To assess the level of community knowledge and attitudes toward leprosy in Fedis District, Eastern Ethiopia.Methods: A community-based cross-sectional study was carried out among 728 randomly selected households from July to August 2019. Each participant was interviewed using a pretested structured questionnaire consisting of participants’ socio-demographic background, questions related to knowledge of and attitudes toward leprosy. The collected data were entered using EpiData 3.1 and analyzed using STATA version 13. Chi-squared test, binary, and multivariable logistic regressions were applied as appropriate to assess the association between outcome and independent variables.Results: Among 728 study participants, 608 (83.52%) of them had heard about leprosy. Among the study participants who had heard of leprosy, 346 (56.91%) of them had high knowledge of leprosy. Multivariable logistic regression revealed that study participants who completed grade 1– 8 (AOR=1.68, 95% CI=1.09– 2.58, P=0.017) and government employees (AOR=7.56, 95% CI=2.23– 25.63, P=0.001) were significantly associated with high level of knowledge of leprosy. Out of 608 study participants who had heard of leprosy, only 248 (40.79%) had a favorable attitude toward leprosy. Study participants who completed grade 1– 8 (AOR= 2.72, 95% CI=1.76– 4.19, P= 0.000) and urban inhabitants (AOR=0.49, 95% CI=0.31– 0.75, P= 0.032) were significantly associated with favorable attitude toward leprosy. Having high knowledge of leprosy was significantly associated with favorable attitudes toward leprosy.Conclusion: This study revealed unfavorable attitudes toward leprosy among the community. Having a high overall knowledge level on leprosy has been shown to support a favorable attitude toward leprosy.Keywords: leprosy, knowledge, attitude, endemic, Ethiopia

Abstract Background The burden of sepsis worsens due to the continuation of emerging pathogens such as multidrug-resistant Pantoea species. Methods A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central, southern, and northern parts of Ethiopia. A total of 1416 sepsis patients were recruited and blood cultures were performed. At each study site, positive cultures were characterized by their colony characteristics, gram stain, and conventional biochemical tests. All Pantoea species were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF) and subjected to whole genome sequencing (WGS) using Illumina HiSeq 2500. The phylogeny structure of Pantoea isolates was calculated using IQ-TREE v1.6.12 from single-nucleotide polymorphisms detected by Snippy v.4.6.0 and filtered by Gubbins v.2.3.4. Average nucleotide identity was estimated by using OrthoANI v.0.93.1 on Shovill v.1.1.0 assemblies. Antimicrobial resistance genes and plasmid replicons were detected using ARIBA v.2.14.6. Phylogenetic trees were visualized using iTOLv.6.5.2. Results Multiple Pantoea species include: P. dispersa (n = 19), P. septica (n = 1), and a novel Pantoea spp. (n = 1), were identified among sepsis patients. All P. dispersa isolates and the novel Pantoea species were isolated at Dessie Referral Hospital and displayed phylogenetic clonality, including the ubiquity of an IncM1 plasmid and identical antimicrobial resistance (AMR) gene profiles, encoding bla CTX−M−15, bla TEM−1D, bla SCO−1, and aac(3)-lla. The novel Pantoea spp. isolate harboured bla CTX−M−9 and bla TEM−1D and carried an IncN3 plasmid replicon. The P. septica was isolated at Tikur Anbessa Specialized Hospital in Addis Ababa and carried no detectable acquired AMR genes. Conclusion The emerging Pantoea spp. carrying multiple AMR genes were identified from sepsis patients. Implementation of strong infection prevention strategies and building surveillance capacity with advanced bacteriology laboratories capable of identifying multidrug-resistant emerging pathogens is strongly recommended.

Issues concerning household livelihood strategies and households' reliance on forest goods around Ethiopia's protected areas have not been adequately addressed. Thus, the purpose of this study is to quantify and determine the influence of livelihood assets on the choice of livelihood strategy, as well as the contribution of forest goods to rural livelihood and its effect on park conservation. The data was collected in 2020 through a survey of 384 households. To discover livelihood strategies, cluster analysis was employed. According to the study's findings, the livelihood asset indicators that significantly affected the likelihood of the household being in one of the identified livelihood strategies were forest income, labor, education level, number of livestock in TLU, agricultural income, off-farm income, non-farm income, access to credit, membership in a cooperative, and ethnicity. The study also discovered that forest income accounted for 17 % of the total income of the sample households, which varies across livelihood strategies (10 %–24 %) and ethnic backgrounds (43 % for Kunama). Households in low-income livelihood strategies (small-business and mixed-activity operators) generate more total and relative forest income than households in high-income livelihood strategies (large-scale and small-scale). There was no safe livelihood strategy for conserving park resources, as households in the entire livelihood strategy were involved in unlawful exploitation of park resources, which resulted in the deterioration of the park's ecological resources over time. Policy on agricultural intensification and encouraging livelihood choices less dependent on natural resources through creating opportunities (credit access, skill and knowledge development, and technology) should be applied, and the use of natural resources should be regulated and evaluated regularly.

Background : Smear-negative tuberculosis occurs more frequently in human immunodeficiency virus (HIV)-infected patients than in non-HIV-infected patients. Besides, there are substantial numbers of patients who cannot produce sputum, making the diagnosis of pulmonary tuberculosis (PTB) difficult. Aims : To evaluate the relative yield of pre- and post-bronchoscopy sputum and bronchoalveolar lavage (BAL) in ′sputum smear′-negative, HIV-positive patients. Settings : A tertiary care referral hospital in Addis Ababa. Materials and Methods : Acid-fast stain (AFS) using the concentration technique was done on 85 pre-bronchoscopy sputum and 120 BAL samples. Direct AFS was done on all BAL and 117 post-bronchoscopy sputum samples. Culture for Mycobacterium tuberculosis (MTB) was done for all sputa and BAL. Results : MTB was isolated from 26 (21.7%), 23 (19.7%) and 13 (15.3%) of BAL, post- and pre-bronchoscopy sputum cultures respectively. AFS on pre-bronchoscopy sputum using concentration technique and direct AFS on BAL together detected 11 (41%) of the 27 culture-positive cases. In patients who could produce sputum, the sensitivity of pre-bronchoscopy sputum culture (13/85, 15.3%) was comparable to BAL (12/85, 14%) and post-bronchoscopy sputum (12/85, 14%). In patients who could not produce sputum, however, both BAL (12/35, 40%) and post-bronchoscopy sputum (12/32, 31.4%) detected significantly more patients than those who could produce sputum ( P =0.002, P =0.028 respectively). Conclusion: In HIV-infected patients, AFS by concentration method on pre-bronchoscopy sputum and direct AFS on BAL in patients who cannot produce sputum are the preferred methods of making a rapid diagnosis. BAL culture seems to add little value in patients who can produce sputum; therefore, bronchoscopy should be deferred under such circumstances.

The importance of strong coordination for research on public health and social measures was highlighted at the Seventy-fourth World Health Assembly in 2021. This article describes efforts undertaken by the World Health Organization (WHO) to develop a global research agenda on the use of public health and social measures during health emergencies. This work includes a multistep process that started with a global technical consultation convened by WHO in September 2021. The consultation included experts from around the world and from a wide range of disciplines, such as public health, education, tourism, finance and social sciences, and aimed to identify research and implementation approaches based on lessons learnt during the coronavirus disease 2019 pandemic. To prepare for future epidemics and pandemics, it is essential to adopt a more robust, comparable and systematic research approach to public health and social measures. Such comprehensive approach will better inform agile, balanced and context-specific implementation decisions during future emergencies. This article describes the methods used to develop global research priorities for public health and social measures and the next steps needed. La soixante-quatorzieme Assemblee mondiale de la Sante en 2021 a souligne l'importance d'une coordination solide pour la recherche sur la sante publique et les mesures sociales. Le present article decrit les efforts entrepris par ('Organisation mondiale de la sante (OMS) pour elaborer un programme de recherche mondial sur l'utilisation des mesures de sante publique et des mesures sociales lors de situations d'urgence sanitaire. Ce travail comprend un processus en plusieurs etapes qui a commence par une consultation technique mondiale organisee par l'OMS en septembre 2021. La consultation a reuni des experts du monde entier issus d'un large eventail de disciplines telles que la sante publique, l'education, le tourisme, la finance et les sciences sociales. Elle visait a identifier des approches de recherche et de mise en reuvre fondees sur les enseignements tires de la pandemie de maladie a coronavirus de 2019. Pour se preparer aux futures epidemies et pandemies, il est essentiel d'adopter une approche de recherche plus solide, comparable et systematique en matiere de sante publique et de mesures sociales. Cette approche globale permettra de mieux eclairer les decisions de mise en reuvre agiles, equilibrees et adaptees au contexte lors des futures situations d'urgence. Le present article decrit les methodes appliquees pour definir les priorites mondiales de recherche en matiere de sante publique et de mesures sociales, ainsi que les prochaines etapes a franchir. En la 74.a Asamblea Mundial de la Salud, celebrada en 2021, se destaco la importancia de una solida coordinacion en la investigacion sobre salud publica y medidas sociales. Este articulo describe los esfuerzos que ha emprendido la Organizacion Mundial de la Salud (OMS) para desarrollar un programa mundial de investigacion sobre el uso de medidas sociales y de salud publica durante las emergencias sanitarias. Este trabajo incluye un proceso de varios pasos que comenzo con una consulta tecnica mundial que convoco la OMS en septiembre de 2021. La consulta incluyo a expertos de todo el mundo y de una gran variedad de disciplinas, como la salud publica, la educacion, el turismo, las finanzas y las ciencias sociales, y tuvo como objetivo identificar enfoques de investigacion y aplicacion basados en las lecciones aprendidas durante la pandemia de la enfermedad por coronavirus de 2019. Para prepararse ante futuras epidemias y pandemias, es esencial adoptar un enfoque de investigacion mas solido, comparable y sistematico en materia de salud publica y medidas sociales. Este enfoque integral informara mejor las decisiones de aplicacion agiles, equilibradas y adaptadas al contexto durante futuras emergencias. En este articulo se describen los metodos utilizados para elaborar las prioridades mundiales de investigacion sobre salud publica y medidas sociales, asi como los proximos pasos necesarios. [phrase omitted], Introduction Public health and social measures refer to non-pharmaceutical interventions implemented by individuals, communities and governments at all levels. Public health and social measures are a key strategy to offer [...]

Abstract The World Health Organization [WHO] recommends a genotype-specific human papillomavirus [HPV] vaccination as a primary prevention strategy to control the burden of cervical cancer globally. In Ethiopia, where the non-vaccine-targeted HPV genotypes have not been adequately studied, a vaccination initiative was launched in 2018 targeting HPV-6,-11, -16, and -18 for girls aged 14–18 years. The co-existence of both vaccine-targeted and non-targeted genotypes is a serious concern, as it can accelerate cancer progression. Therefore, this study was conducted to determine the prevalence of non-vaccine-targeted HPV genotypes and assess the level of multiple infections with other genotypes in eastern Ethiopia. A health facility-based cross-sectional study including 110 women with positive HPV DNA results was conducted from April to August 2021. A structured questionnaire to collect demographic and clinical data was used. Cervical swabs were collected using L-shaped FLOQSwabs. Women's cytological profile was determined based on Pap smear test results. An automated nucleic acid extraction system using STARMag 96 ProPrep Universal Extraction Kit was utilized following the manufacturer's protocol. An amplification assay in real-time was employed to amplify and identify the HPV Late 1 [L1] gene, which is utilized for genotyping purposes. Following this, the collected data was entered into Epi data version 3.1 software, and the analysis was performed using STATA version 14. A total of 110 women [age range 30–60 years, mean age = 36.5 years and SD ± 6.9] had positive HPV DNA results and were included in the study. Among these, 108 women had valid co-testing [Pap test and HPV DNA test] results for further analysis, and the results of the remaining 2 women were rejected. Overall, the prevalence of non-vaccine-targeted HPV was 56 (51.8%, 95%CI [0.42, 0.61]), of which 28 women (25.4%, 95%CI [0.18, 0.34]) had a single non-vaccine HPV genotype infection. The remaining 29 women (26.4%, 95% CI: 0.190–0.355) experienced multiple infections. The non-vaccine-targeted genotypes of HPV-35 accounted for 11 cases (10%, 95%CI [0.06, 0.17]), HPV-68 was detected in 9 women (8.2%, 95%CI [0.04, 0.15]), HPV-56 and HPV-66 were both found in 8 cases each (7.3%, 95%CI [0.04, 0.14]) of the total. In addition, out of these 108 women, 93 (86.1%, 95%CI [0.78, 0.91]) had low-grade squamous intraepithelial lesions, 13 (12%, 95%CI [0.07, 0.20]) no intraepithelial lesion or malignancy, and two (1.9%, 95%CI [0.01, 0.07]) high-grade squamous intraepithelial lesions. Furthermore, there was no statistical difference [p = 0.755] between vaccine-targeted and non-vaccine-targeted genotypes as the primary cause of cervical lesions. In conclusion, the findings of the present study highlight the existence of a notable prevalence of multiple infections caused by non-vaccine-targeted HPV genotypes. Therefore, it is recommended that both the Federal and regional health bureaus to evaluate the range of hr HPV genotypes protected by the current HPV vaccine and explore the option of transitioning from the quadrivalent HPV vaccine to a novavalent vaccine that includes seven high-risk HPV genotypes.

Abstract Ethiopia has the greatest burden of Plasmodium vivax in Africa, but little is known about the epidemiological landscape of parasites across the country. We analysed the genomic diversity of 137 P. vivax isolates collected nine Ethiopian districts from 2012 to 2016. Signatures of selection were detected by cross-country comparisons with isolates from Thailand (n = 104) and Indonesia (n = 111), representing regions with low and high chloroquine resistance respectively. 26% (35/137) of Ethiopian infections were polyclonal, and 48.5% (17/35) of these comprised highly related clones (within-host identity-by-descent > 25%), indicating frequent co-transmission and superinfection. Parasite gene flow between districts could not be explained entirely by geographic distance, with economic and cultural factors hypothesised to have an impact on connectivity. Amplification of the duffy binding protein gene (pvdbp1) was prevalent across all districts (16–75%). Cross-population haplotype homozygosity revealed positive selection in a region proximal to the putative chloroquine resistance transporter gene (pvcrt-o). An S25P variant in amino acid transporter 1 (pvaat1), whose homologue has recently been implicated in P. falciparum chloroquine resistance evolution, was prevalent in Ethiopia (96%) but not Thailand or Indonesia (35–53%). The genomic architecture in Ethiopia highlights circulating variants of potential public health concern in an endemic setting with evidence of stable transmission.

BackgroundImmune control of Mycobacterium tuberculosis (Mtb) infection is largely influenced by the extensive disease heterogeneity that is typical for tuberculosis (TB). In this study, the peripheral inflammatory immune profile of different sub-groups of pulmonary TB patients was explored based on clinical disease severity, anemia of chronic disease, or the radiological extent of lung disease.MethodsPlasma samples were obtained from n=107 patients with active pulmonary TB at the time of diagnosis and after start of standard chemotherapy. A composite clinical TB symptoms score, blood hemoglobin status and chest X-ray imaging were used to sub-group TB patients into 1.) mild and moderate-severe clinical TB, 2.) anemic and non-anemic TB, or 3.) limited and extensive lung involvement. Plasma levels of biomarkers associated with inflammation pathways were assessed using a Bio-Plex Magpix 37-multiplex assay. In parallel, Th1/Th2 cytokines were quantified with a 27-multiplex in matched plasma and cell culture supernatants from whole blood stimulated with M. tuberculosis-antigens using the QuantiFERON-TB Gold assay.ResultsClinical TB disease severity correlated with low blood hemoglobin levels and anemia but not with radiological findings in this study cohort. Multiplex protein analyses revealed that distinct clusters of inflammation markers and cytokines separated the different TB disease sub-groups with variable efficacy. Several top-ranked markers overlapped, while other markers were unique with regards to their importance to differentiate the TB disease severity groups. A distinct immune response profile defined by elevated levels of BAFF, LIGHT, sTNF-R1 and 2, IP-10, osteopontin, chitinase-3-like protein 1, and IFNα2 and IL-8, were most effective in separating TB patients with different clinical disease severity and were also promising candidates for treatment monitoring. TB patients with mild disease displayed immune polarization towards mixed Th1/Th2 responses, while pro-inflammatory and B cell stimulating cytokines as well as immunomodulatory mediators predominated in moderate-severe TB disease and anemia of TB.ConclusionsOur data demonstrated that clinical disease severity in TB is associated with anemia and distinct inflammatory immune profiles. These results contribute to the understanding of immunopathology in pulmonary TB and define top-ranked inflammatory mediators as biomarkers of disease severity and treatment prognosis.

Abstract Background Neglected tropical diseases (NTDs) are a group of chronic parasitic diseases and related conditions that are the most common diseases among the 2·7 billion people globally living on less than US$2 per day. In response to the growing challenge of NTDs, Ethiopia is preparing to launch a NTD Master Plan. The purpose of this review is to underscore the burden of NTDs in Ethiopia, highlight the state of current interventions, and suggest ways forward. Results This review indicates that NTDs are significant public health problems in Ethiopia. From the analysis reported here, Ethiopia stands out for having the largest number of NTD cases following Nigeria and the Democratic Republic of Congo. Ethiopia is estimated to have the highest burden of trachoma, podoconiosis and cutaneous leishmaniasis in sub-Saharan Africa (SSA), the second highest burden in terms of ascariasis, leprosy and visceral leishmaniasis, and the third highest burden of hookworm. Infections such as schistosomiasis, trichuriasis, lymphatic filariasis and rabies are also common. A third of Ethiopians are infected with ascariasis, one quarter is infected with trichuriasis and one in eight Ethiopians lives with hookworm or is infected with trachoma. However, despite these high burdens of infection, the control of most NTDs in Ethiopia is in its infancy. In terms of NTD control achievements, Ethiopia reached the leprosy elimination target of 1 case/10,000 population in 1999. No cases of human African trypanosomiasis have been reported since 1984. Guinea worm eradication is in its final phase. The Onchocerciasis Control Program has been making steady progress since 2001. A national blindness survey was conducted in 2006 and the trachoma program has kicked off in some regions. Lymphatic Filariasis, podoconiosis and rabies mapping are underway. Conclusion Ethiopia bears a significant burden of NTDs compared to other SSA countries. To achieve success in integrated control of NTDs, integrated mapping, rapid scale up of interventions and operational research into co implementation of intervention packages will be crucial.

Abstract Background One third of the world’s population is thought to have latent tuberculosis infection (LTBI) with the potential for subsequent reactivation of disease. To better characterize this important population, studies comparing Tuberculin Skin Test (TST) and the new interferon-γ release assays including QuantiFERON®-TB Gold In-Tube (QFT-GIT) have been conducted in different parts of the world, but most of these have been in countries with a low incidence of tuberculosis (TB). The aim of this study was therefore to evaluate the use of QFT-GIT assay as compared with TST in the diagnosis of LTBI in Ethiopia, a country with a high burden of TB and routine BCG vaccination at birth. Methods Healthy medical and paramedical male students at the Faculty of Medicine, Addis Ababa University, Ethiopia were enrolled into the study from December 2008 to February 2009. The TST and QFTG-IT assay were performed using standard methods. Results The mean age of the study participants was 20.9 years. From a total of 107 study participants, 46.7% (95%CI: 37.0% to 56.6%) had a positive TST result (TST≥10 mm), 43.9% (95%CI: 34.3% to 53.9%) had a positive QFT-GIT assay result and 44.9% (95%CI: 35.2% to 54.8%) had BCG scar. There was strong agreement between TST (TST ≥10mm) and QFT-GIT assay (Kappa = 0.83, p value = 0.000). Conclusion The TST and QFT-GIT assay show similar efficacy for the diagnosis of LTBI in healthy young adults residing in Ethiopia, a country with high TB incidence.

Abstract Background Monitoring the outcome of tuberculosis treatment and understanding the specific reasons for unsuccessful treatment outcome are important in evaluating the effectiveness of tuberculosis control program. This study investigated tuberculosis treatment outcomes and predictors for unsuccessful treatment outcome in the Tigray region of Ethiopia. Methods Medical records of smear-positive pulmonary tuberculosis (PTB) patients registered from September 2009 to June 2011 in 15 districts of Tigray region, Northern Ethiopia, were reviewed. Additional data were collected using a structured questionnaire administered through house-to-house visits by trained nurses. Tuberculosis treatment outcomes were assessed according to WHO guidelines. The association of unsuccessful treatment outcome with socio-demographic and clinical factors was analyzed using logistic regression model. Results Out of the 407 PTB patients (221 males and 186 females) aged 15 years and above, 89.2% had successful and 10.8% had unsuccessful treatment outcome. In the final multivariate logistic model, the odds of unsuccessful treatment outcome was higher among patients older than 40 years of age (adj. OR = 2.50, 95% CI: 1.12-5.59), family size greater than 5 persons (adj. OR = 3.26, 95% CI: 1.43-7.44), unemployed (adj. OR = 3.10, 95% CI: 1.33-7.24) and among retreatment cases (adj. OR = 2.00, 95% CI: 1.37-2.92) as compared to their respective comparison groups. Conclusions Treatment outcome among smear-positive PTB patients was satisfactory in the Tigray region of Ethiopia. Nonetheless, those patients at high risk of an unfavorable treatment outcome should be identified early and given additional follow-up and social support.

Abstract Background In Ethiopia where there is no strong surveillance system and diagnostic facilities are limited, the real burden of tuberculosis (TB) lymphadenitis is not well known. Therefore, we conducted a study to estimate the prevalence of TB lymphadenitis in Southwest Ethiopia. Methods A community based cross-sectional study was conducted from February to March 2009 in the Gilgel Gibe field research area. A total of 30,040 individuals 15 years or older in 10,882 households were screened for TB lymphadenitis. Any individual 15 years or older with lumps in the neck, armpits or groin up on interview were considered TB lymphadenitis suspect. The diagnosis of TB lymphadenitis was established when acid fast bacilli (AFB) smear microscopy of fine needle aspiration (FNA) sample, culture or cytology suggested TB. HIV counseling and testing was offered to all TB lymphadenitis suspects. Descriptive and bivariate analysis was done using SPSS version 15. Results Complete data were available for 27,597 individuals. A total of 87 TB lymphadenitis suspects were identified. Most of the TB lymphadenitis suspects were females (72.4%). Sixteen cases of TB lymphadenitis were confirmed. The prevalence of TB lymphadenitis was thus 58.0 per 100,000 people (16/27,597) (95% CI 35.7-94.2). Individuals who had a contact history with chronic coughers (OR 5.58, 95% CI 1.23-25.43) were more likely to have TB lymphadenitis. Lymph nodes with caseous FNA were more likely to be positive for TB lymphadenitis (OR 5.46, 95% CI 1.69-17.61). Conclusion The prevalence of TB lymphadenitis in Gilgel Gibe is similar with the WHO estimates for Ethiopia. Screening of TB lymphadenitis particularly for family members who have contact with chronic coughers is recommended. Health extension workers could be trained to screen and refer TB lymphadenitis suspects using simple methods.

Abstract Background In Ethiopia where there is no strong surveillance system and state of the art diagnostic facilities are limited, the real burden of tuberculosis (TB) is not well known. We conducted a community based survey to estimate the prevalence of pulmonary TB and spoligotype pattern of the Mycobacterium tuberculosis isolates in Southwest Ethiopia. Methods A total of 30040 adults in 10882 households were screened for pulmonary TB in Gilgel Gibe field research centre in Southwest Ethiopia. A total of 482 TB suspects were identified and smear microscopy and culture was done for 428 TB suspects. Counseling and testing for HIV/AIDS was done for all TB suspects. Spoligotyping was done to characterize the Mycobacterium tuberculosis isolates. Results Majority of the TB suspects were females (60.7%) and non-literates (83.6%). Using smear microscopy, a total of 5 new and 4 old cases of pulmonary TB cases were identified making the prevalence of TB 30 per 100,000. However, using the culture method, we identified 17 new cases with a prevalence of 76.1 per 100,000. There were 4.3 undiagnosed pulmonary TB cases for every TB case who was diagnosed through the passive case detection mechanism in the health facility. Eleven isolates (64.7%) belonged to the six previously known spoligotypes: T, Haarlem and Central-Asian (CAS). Six new spoligotype patterns of Mycobacterium tuberculosis, not present in the international database (SpolDB4) were identified. None of the rural residents was HIV infected and only 5 (5.5%) of the urban TB suspects were positive for HIV. Conclusion The prevalence of TB in the rural community of Southwest Ethiopia is low. There are large numbers of undiagnosed TB cases in the community. However, the number of sputum smear-positive cases was very low and therefore the risk of transmitting the infection to others may be limited. Active case finding through health extension workers in the community can improve the low case detection rate in Ethiopia. A large scale study on the genotyping of Mycobacterium tuberculosis in Ethiopia is crucial to understand transmission dynamics, identification of drug resistant strains and design preventive strategies.

Abstract Background Ethiopia has had mechanisms for TB/HIV collaborative activities since 2002. However, no published account has defined the role of these collaborative efforts in strengthening linkages between HIV and TB management units at the point-of-care level. Our objective was to assess the extent of linkages between the two programs at the patient management level at Zewditu Memorial Hospital in Addis Ababa, Ethiopia. Between January and December 2008, the registers of 241 TB patients were reviewed to determine the HIV testing rate, the treatment charts of 238 randomly selected patients were reviewed for providers' compliance with evaluation criteria, and exit interviews were conducted with 309 TB/HIV co-infected clients to validate providers' compliance. Results From register review, it was determined that the HIV testing acceptance rate was 95%, and that 70% of patients received post-test counseling. A review of the patient chart revealed that of 51 patients with a complaint of cough, duration for cough was recorded in 35 (68.6%) cases and cough > 2 weeks was recorded in 25 (49.0%) cases. Seventy two percent (18 of 25) were linked for sputum microscopy. Linkage to cotrimoxazole prophylactic treatment was 81%, but only 47% of eligible patients were linked to isoniazid preventive therapy (IPT). Correct diagnosis was accomplished at a rate of 100% for smear positive pulmonary TB, 23% for smear negative pulmonary TB and 88% for extra pulmonary TB patients. Both chart review and exit interviews indicated that history of TB contact and cough > 2 weeks predicted TB disease. Conclusion The rates of HIV testing and linkage to cotrimoxazole prophylactic therapy were high. Improvement is needed in the areas of recording patient information, screening HIV positives for TB, initiation of IPT, referral, linkages, and TB diagnostic capacity.

Abstract Background Bovine tuberculosis (BTB) is endemic in Ethiopian cattle. The aim of this study was to assess BTB prevalence at an intensive contact interface in Meskan Woreda (district) in cattle, small ruminants and suspected TB-lymphadenitis (TBLN) human patients. Methods The comparative intradermal test (CIDT) was carried out for all animals involved in the cross-sectional study and results interpreted using a > 4 mm and a > 2 mm cut-off. One PPD positive goat was slaughtered and lymph nodes subjected to culture and molecular typing. In the same villages, people with lymphadenitis were subjected to clinical examination. Fine needle aspirates (FNA) were taken from suspected TBLN and analyzed by smear microscopy and molecular typing. Results A total of 1214 cattle and 406 small ruminants were tested for BTB. In cattle, overall individual prevalence (> 2 mm cut-off) was 6.8% (CI: 5.4-8.5%) with 100% herd prevalence. Only three small ruminants (2 sheep and 1 goat) were reactors. The overall individual prevalence in small ruminants (> 2 mm cut-off) was 0.4% (CI: 0.03-5.1%) with 25% herd prevalence. Cattle from owners with PPD positive small ruminants were all PPD negative. 83% of the owners kept their sheep and goats inside their house at night and 5% drank regularly goat milk. FNAs were taken from 33 TBLN suspected cases out of a total of 127 screened individuals with lymph node swellings. Based on cytology results, 12 were confirmed TBLN cases. Nine out of 33 cultures were AFB positive. Culture positive samples were subjected to molecular typing and they all yielded M. tuberculosis. M. tuberculosis was also isolated from the goat that was slaughtered. Conclusions This study highlighted a low BTB prevalence in sheep and goats despite intensive contact with cattle reactors. TBLN in humans was caused entirely by M. tuberculosis, the human pathogen. M. tuberculosis seems to circulate also in livestock but their role at the interface is unknown.

Abstract Background In Ethiopia, where HIV and tuberculosis (TB) are very common, little is known about the prejudice and misconceptions of rural communities towards People living with HIV/AIDS (PLHA) and TB. Methods We conducted a cross sectional study in Gilgel Gibe Field Research area (GGFRA) in southwest Ethiopia to assess the prejudice and misconceptions of rural and urban communities towards PLHA and TB. The study population consisted of 862 randomly selected adults in GGFRA. Data were collected by trained personnel using a pretested structured questionnaire. To triangulate the findings, 8 focus group discussions among women and men were done. Results Of the 862 selected study participants, 750(87%) accepted to be interviewed. The mean age of the respondents was 31.2 (SD ± 11.0). Of the total interviewed individuals, 58% of them were females. More than half of the respondents did not know the possibility of transmission of HIV from a mother to a child or by breast feeding. For fear of contagion of HIV, most people do not want to eat, drink, and share utensils or clothes with a person living with HIV/AIDS. A higher proportion of females [OR = 1.5, (95% CI: 1.0, 2.2)], non-literate individuals [OR = 2.3, (95%CI: 1.4, 3.6)], rural residents [OR = 3.8, (95%CI: 2.2, 6.6)], and individuals who had poor knowledge of HIV/AIDS [OR = 2.8, (95%CI: 1.8, 2.2)] were more likely to have high prejudice towards PLHA than respectively males, literates, urban residents and individuals with good knowledge. Exposure to cold air was implicated as a major cause of TB. Literates had a much better knowledge about the cause and methods of transmission and prevention of TB than non-literates. More than half of the individuals (56%) had high prejudice towards a patient with TB. A larger proportion of females [OR = 1.3, (95% CI: 1.0, 1.9)] and non-literate individuals [OR = 1.4, (95% CI: 1.1, 2.0)] had high prejudice towards patients with TB than males and literate individuals. Conclusion TB/HIV control programs in collaboration with other partners should invest more in social mobilization and education of the communities to rectify the widespread prejudice and misconceptions.

Abstract Background Anopheles arabiensis is the major vector of malaria in Ethiopia. Malaria vector control in Ethiopia is based on selective indoor residual spraying using DDT, distribution of long lasting insecticide treated nets and environmental management of larval breeding habitats. DDT and pyrethroid insecticides are neurotoxins and have a similar mode of action on the sodium ion channel of insects. It was therefore necessary to verify the insecticide susceptibility status of An. arabiensis, to better understand the status of cross-resistance between DDT and the pyrethroids in this species as well as to detect a resistant gene. Methods Standard WHO insecticide susceptibility tests were conducted on adults reared from larval and pupal collections from breeding sites at three villages namely: Sodere in the Rift Valley, Gorgora in the north and Ghibe River Valley in the south west of Ethiopia. The occurrence of cross-resistance between pyrethroids and DDT was determined using a DDT selected laboratory colony originally collected from Gorgora. Phenotypically characterized mosquitoes were tested for the presence of knockdown resistance (kdr) alleles using the standard polymerase chain reaction assay. Results All An. gambiae s.l. specimens assayed by PCR were identified as An. arabiensis. The knockdown and mortality results showed An. arabiensis resistance to DDT in all villages, resistance to deltamethrin and permethrin in the Ghibe River Valley and permethrin resistance in Gorgora. Bioassay susceptibility tests also indicated the presence of cross-resistance between DDT and permethrin, but not between DDT and deltamethrin. The knockdown resistance (kdr) mutation of leucine to phenylalanine in the sodium ion channel gene was detected in populations from Gorgora and the Ghibe River Valley. Conclusion Since An. arabiensis shows high levels of resistance to DDT in all villages tested and varying pyrethroid resistance in Gorgora and the Ghibe River valley, precautionary measures should be taken in future vector control operations. Moreover, the status of resistance in other locations in Ethiopia and the spread of resistant gene (s) should be investigated.

Abstract Background Plasmodium vivax accounts for about 40% of all malaria infection in Ethiopia. Chloroquine (CQ) is the first line treatment for confirmed P. vivax malaria in the country. The first report of CQ treatment failure in P. vivax was from Debre Zeit, which suggested the presence of chloroquine resistance. Methods An in vivo drug efficacy study was conducted in Debre Zeit from June to August 2006. Eighty-seven patients with microscopically confirmed P. vivax malaria, aged between 8 months and 52 years, were recruited and treated under supervision with CQ (25 mg/kg over three days). Clinical and parasitological parameters were assessed during the 28 day follow-up period. CQ and desethylchloroquine (DCQ) blood and serum concentrations were determined with high performance liquid chromatography (HPLC) in patients who showed recurrent parasitaemia. Results Of the 87 patients recruited in the study, one was lost to follow-up and three were excluded due to P. falciparum infection during follow-up. A total of 83 (95%) of the study participants completed the follow-up. On enrolment, 39.8% had documented fever and 60.2% had a history of fever. The geometric mean parasite density of the patients was 7045 parasites/μl. Among these, four patients had recurrent parasitaemia on Day 28. The blood CQ plus DCQ concentrations of these four patients were all above the minimal effective concentration (> 100 ng/ml). Conclusion Chloroquine-resistant P. vivax parasites are emerging in Debre Zeit, Ethiopia. A multi-centre national survey is needed to better understand the extent of P. vivax resistance to CQ in Ethiopia.