Point-of-care, real-time, metagenomics-based pathogen genome detection of life-threatening community- acquired meningitis

Abstract

Community-acquired meningitis (CAM) is a life-threatening condition whose prognosis partially depends on the causative pathogen genotype. Current point-of-care (POC) diagnosis of CAM is based on multiplex RT-PCR assays targeting the 14 pathogens mostly identified in the cerebrospinal fluid (CSF). This required additional in vitro investigations for pathogen genotyping and antibiotic susceptibility testing. Herein, we proposed the real-time metagenomics (RTM) sequencing for one-shot identification, genotyping, and in silico antibiotic resistance directly from CSF samples. Furthermore, RTM allowed us to detect pathogen genomes in a leftover CSF sample from a patient with meningitis of unknown etiology. This could potentially be implemented as routine POC diagnostic of CAM in the future