There is limited data on the epidemiology of sepsis in low-and middle-income countries (LMICs), where most cases of sepsis occur. Understanding the pathogenic etiology of sepsis can inform systems-level approaches for improving care for pediatric sepsis patients, as well as strategies for addressing the growing challenge of antibiotic resistance. The etiology of sepsis may also be predictive of long-term outcomes for those who survive, which could inform approaches to identifying and improving follow-up care of vulnerable children.
Blood cultures are the current gold standard for bacterial pathogen identification in clinical and research settings but are often not available within LMICs. This has hampered sepsis research in all but highly selected facilities. The collection and storage of blood samples is relatively inexpensive, and readily available in most global settings. However, techniques to identify pathogens from stored clinical blood isolates collected from young infants remain under-developed. Next generation sequencing approaches have been used to identify pathogenic bacteria in blood collected from pediatric sepsis patients. This study aim to validate an approach that combines 16S rRNA amplification with nanopore sequencing in a subset of blood samples previously collected from infants with sepsis (0-6 months of age) at health facilities in East Africa. If successful, we will leverage our finding to support future studies to validate this approach in larger cohorts and multiple countries to better characterize the epidemiology of pediatric sepsis, within East Africa and globally.