Combating Antimicrobial Resistance Through a Data-Driven Approach to Optimize Antibiotic Use and Improve Patient Outcomes: Protocol for a Mixed Methods Study (Preprint)

BACKGROUND It is projected that drug-resistant infections will lead to 10 million deaths annually by 2050 if left unabated. Despite this threat, surveillance data from resource-limited settings are scarce and often lack antimicrobial resistance (AMR)–related clinical outcomes and economic burden. We aim to build an AMR and antimicrobial use (AMU) data warehouse, describe the trends of resistance and antibiotic use, determine the economic burden of AMR in Uganda, and develop a machine learning algorithm to predict AMR-related clinical outcomes. OBJECTIVE The overall objective of the study is to use data-driven approaches to optimize antibiotic use and combat antimicrobial-resistant infections in Uganda. We aim to (1) build a dynamic AMR and antimicrobial use and consumption (AMUC) data warehouse to support research in AMR and AMUC to inform AMR-related interventions and public health policy, (2) evaluate the trends in AMR and antibiotic use based on annual antibiotic and point prevalence survey data collected at 9 regional referral hospitals over a 5-year period, (3) develop a machine learning model to predict the clinical outcomes of patients with bacterial infectious syndromes due to drug-resistant pathogens, and (4) estimate the annual economic burden of AMR in Uganda using the cost-of-illness approach. METHODS We will conduct a study involving data curation, machine learning–based modeling, and cost-of-illness analysis using AMR and AMU data abstracted from procurement, human resources, and clinical records of patients with bacterial infectious syndromes at 9 regional referral hospitals in Uganda collected between 2018 and 2026. We will use data curation procedures, FLAIR (Findable, Linkable, Accessible, Interactable and Repeatable) principles, and role-based access control to build a robust and dynamic AMR and AMU data warehouse. We will also apply machine learning algorithms to model AMR-related clinical outcomes, advanced statistical analysis to study AMR and AMU trends, and cost-of-illness analysis to determine the AMR-related economic burden. RESULTS The study received funding from the Wellcome Trust through the Centers for Antimicrobial Optimisation Network (CAMO-Net) in April 2023. As of October 28, 2024, we completed data warehouse development, which is now under testing; completed data curation of the historical Fleming Fund surveillance data (2020-2023); and collected retrospective AMR records for 599 patients that contained clinical outcomes and cost-of-illness economic burden data across 9 surveillance sites for objectives 3 and 4, respectively. CONCLUSIONS The data warehouse will promote access to rich and interlinked AMR and AMU data sets to answer AMR program and research questions using a wide evidence base. The AMR-related clinical outcomes model and cost data will facilitate improvement in the clinical management of AMR patients and guide resource allocation to support AMR surveillance and interventions. INTERNATIONAL REGISTERED REPORT PRR1-10.2196/58116