Pathogen Detection Using Metagenomic Next Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda

Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma samples using metagenomic sequencing in a previously well characterized cohort of 254 predominantly HIV infected patients with sepsis in Uganda. We used Illumina RNA 150 base pair (bp) paired-end read sequencing and the Chan Zuckerberg ID cloud-based metagenomic bioinformatics platform to sequence and identify pathogens. A broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda. An unexpectedly high rate of hepatitis B and EBV viremia was found. Whether these viral infections in HIV patients with sepsis are clinically important requires further study.