Implementation of innovative cell-free DNA-based sepsis diagnostics in resource-limited Ethiopian settings | LC26

Abstract
Traditional sepsis diagnostics face significant limitations, especially in resource-limited settings such as the Asella Referral and Teaching Hospital in Ethiopia. Extensive requirements for consumables and infrastructure, prolonged time-to-result, and low diagnostic yield restrict gold-standard diagnostics to few patients. Sequencing-based diagnostics offer an innovative alternative. A cell-free DNA (cfDNA) sequencing pilot study was initiated at two Ethiopian sites (Asella and Jimma), targeting vulnerable populations: children under five years and patients with advanced HIV disease (ISAVE project, funded by Gesellschaft für Internationale Zusammenarbeit (GIZ), Hospital Partnerships Program). Blood samples were collected in blood culture bottles and Streck Cell-Free DNA BCT tubes. cfDNA was extracted using QIAamp MinElute ccfDNA kits (Qiagen). Multiplex ligation sequencing libraries were prepared for MinION sequencing. A comprehensive workshop trained Ethiopian researchers in the complete cfDNA workflow, from sample processing to bioinformatics analysis. Local computational infrastructure was established for on-site analysis and sustainable capacity building. Initial sequencing of six pilot samples generated high-quality nanopore data suitable for metagenomic analysis. Microbial DNA was detected in four of six suspected sepsis cases, including Streptococcus pneumoniae, Streptococcus spp., and Cytomegalovirus in an HIV-positive patient with negative blood culture. Ongoing validation comparing cfDNA sequencing with traditional blood culture will establish diagnostic sensitivity, specificity, and clinical benefit. Preliminary evidence indicates successful pathogen detection when conventional methods yielded negative or delayed results. This pilot demonstrates that cfDNA sequencing for sepsis diagnostics can be effectively implemented in resource-limited healthcare facilities through integrated capacity-building and infrastructure development, offering a promising alternative for vulnerable populations requiring rapid, accurate pathogen identification.

Biography
Anna Rommerskirchen is a microbiologist and bioinformatician at Heinrich-Heine-University Düsseldorf, specializing in bacterial genomics and antimicrobial resistance. Her research focuses on Oxford Nanopore sequencing applications, including pathogen characterization, analysis of mobile genetic elements, and innovative diagnostic approaches such as cell-free DNA for sepsis detection. Through international collaborations, particularly with the Ethiopian Public Health Institute and the Hirsch Institute for Tropical Medicine (Asella, Ethiopia), they advance genomic surveillance capacity in resource-limited settings, combining wet-lab expertise with computational analysis to advance One Health approaches.