The 21st century witnesses increased incidence of epidemics (Zika, dengue, Ebola, SARS), with as latest highlight the recent COVID-19. Following the outbreak of several infectious diseases during the last few decade, the need for generating real-time pathogen genomic data for public health action has become more important than ever. In the African context, infrastructure, human resource capability, data analysis, including bioinformatics, lack of linkage between clinical, epidemiological, and pathogen genomic data as well the interaction between clinicians, researchers and decision makers are some of the major challenges. The aim of the EpiGen project is to build a capacity for integrated pathogen genomic surveillance for informed public health decision process. The overarching specific objectives include strengthening collection and analysis of clinical and epidemiological data, enhancing the capacity and capability for pathogen genomic sequencing, including strengthening the laboratory infrastructure, human work force, pathogen genomic data analysis, and the integration of metadata with genomic data, developing and implementing innovative digital diagnostic platforms, creating semi-real time mobile phone applications for policy decisions, and promoting communities of practice and knowledge exchange through fostering African collaboration and networking in the domain of pathogen genomic surveillance for infectious diseases. EpiGen project’s multi-disciplinary consortium is drawn from several institutions from Ethiopia engaged in National Public Health Programs, and EU partners (The Netherlands, Spain and Germany). Overall, the model approach proposed by EpiGen will enhance Ethiopia’s national effort in mitigating the threat of infectious diseases. The implementation of a national genomic-informed surveillance for infectious diseases will play significant public health role towards contributing to disease prevention and control programmes in Ethiopia and beyond.

African hospitals are increasingly providing microbiological diagnostics, hygiene and antimicrobial stewardship (AMS) procedures in response to multidrug-resistant (MDR) bacterial diseases. However implementation within integrated, multidisciplinary hospital services is often poorly established. We first aim to assess the impact of an enhanced hospital hygiene intervention on the incidence of healthcare-associated infections (HAI) in hospitalized patients, using a stepped-wedge cluster randomised trial (SW-CRT) design. Clusters (surgical, medical wards, ICUs) in four tertiary level hospitals in Ethiopia and Ghana will be transitioned to interventions focusing on hand and instrument hygiene procedures, hygiene procedures for visitors and standardized room surface cleaning. Microbiological assessments and AMR of patients and hospital environments will be conducted, with an expected 10-15% reduction in HAI incidence. Nested within the SW-CRT, we further focus on therapeutic drug monitoring (TDM) and predicted pharmacodynamic target attainment (PTA) to optimize beta-lactam antibiotic regimens as part of AMS procedures. Patients (N=400) with severe bacterial infections (e.g. sepsis) will receive standard versus standard plus TDM/PTA based AMS assessment, with dose optimization expected in up to 50% of cases. By integrating TDM/PTA into an AMS eHealth system, we aim to generate generalizable population-based PTA support, linked with cost-effectiveness analysis to promote sustainability within routine care procedures. By shifting antibiotic treatment from an empirical to a more individualized patient management strategy, we aim to introduce optimized and affordable AMS interventions, expecting an impact on improved clinical response and reduction of AMR within hospitals. Our study consortium is built on multidisciplinary expertise. Partners have been linked for years through African-European hospital partnerships implementing high quality microbiological diagnostics.

BACKGROUND There are few research ethics committees (RECs) with capacity to review and provide oversight for clinical trials in Sub-Saharan Africa (SSA), and hardly any national accreditation systems used to evaluate the quality of review by these RECs. Although digital protocol submission systems improve RECs efficiency, up to 48% RECs in SSA still use paper-based systems. Additionally, many (single country) clinical trials in SSA are not registered with any internationally recognized clinical trials registry. The SECRET project seeks to address these challenges in Uganda and Ethiopia, by establishing national RECs accreditation systems, building capacity of RECs to review clinical trials (including during outbreaks and emergencies), establishing national clinical trials registries linked to the Pan African Clinical trial registry (PACTR), and developing digital protocol submission systems. METHODOLOGY The SECRET project includes partners that have worked together in other EDCTP-funded projects, to address the identified gaps through four objectives and six work packages. We will leverage the experience of the Uganda National accreditation system to establish a national accreditation system for Ethiopia and accredit at least two RECs in Ethiopia and two in Uganda. We will also leverage the expertise of the PACTR to set up the Uganda National Clinical Trial Registry. Nuvoteq that have experience in digital solutions for health care services will support Ethiopia to set-up the digital protocol submission systems. We shall also leverage the expertise of Makerere University bioethics training unit and the National Drug Authority of Uganda to build capacity for clinical trial review and oversight for the RECs to be accredited. The Uganda National Health Research Organisation and Institute of Tropical Medicine in Antwerp, which are the coordination institutes, have worked together on ALERRT, an epidemics preparedness consortium funded by EDCTP.