Developing Metagenomic Approaches to Identify the Causes of Neonatal Sepsis and Acquisition of Antimicrobial Resistance in The Gambia

Thushan de Silva, Abdul Karim Sesay, Helen Brotherton, and Beate Kampmann of the Medical Research Council in the United Kingdom will locally implement equipment and methods for next generation sequencing of a range of clinical sample types to detect infectious pathogens in hospitalized neonates in low-resource settings. Almost three million children under five years old die each year in sub-Saharan Africa, which is the highest rate globally. A substantial proportion is likely to be caused by pathogenic infections, including multi-drug resistant organisms. However, defining the etiology of neonatal infections, which is crucial for timely and effective treatment and to block disease spread, remains challenging in countries with limited resources. They will test the potential for next generation sequencing to overcome this challenge by conducting a pilot study using clinical samples from around 30 hospitalized neonates within an ongoing clinical trial in a low-resource setting in West Africa. They will optimize protocols on site for detecting pathogens from a range of sample types and develop methods to specifically detect relevant anti-microbial resistant strains. They plan to use the study to install a network of sites across the region that can perform next generation sequencing and share the resulting large datasets with other sites.