Tonight I watched Madjid Morsli from the Mediterranean Infection Foundation and & Aix-Marselle University in France present at London Calling 2022 on “Point-of-care, real-time, metagenomics-based pathogen genome detection of life-threatening community-acquired meningitis.” They spoke about infectious bacterial meningitis and how the genotype of the pathogen affects prognosis. Morsli noted that at least 200 pathogens have been identified in cerebrospinal fluid! They conducted a retrospective investigation from December 2014- December 2019. They proposed real-time whole genome sequencing of direct pathogens as a point-of-care system. Morsli shared two publications ini which they use rapid sequencing to detect the pathogen. In one Case Report they identified Streptococcus pneumoniae in two hours! Morsli and colleagues implemented real-time metagenomic workflows with Oxford Nanopore Technologies, DNA extraction, and custom bioinformatics. They used a barcoding library prep and used known samples to confirm their workflow. Out of 52, they obtained two discorant classifications. As part of the workflow, they did antibiotic resistance profiling in silico. Morsli concluded that this workflow allows for direct detection, genotyping, and antibiotic resistance of meningitis directly from cerebrospinal fluid samples. I wonder what their extraction process is and how “custom” their bioinformatics workflows are. I could not find the DNA extraction process on their slides, but did see EPI2ME was used maybe initially. Nevertheless, the examples and work done to confirm the approach were informative. It is impressive that in twenty minutes of sequencing they detected most of their test samples!
