Pan-pathogen diagnosis of "undiagnosed" infections by means of clinical metagenomics (CMg) in clinical routine.

Clinical metagenomics (CMg) is a high-throughput sequencing technique dedicated to the etiological diagnosis of infectious diseases, regardless of the nature of the pathogen involved (bacteria, viruses, fungi, parasites). This technique has been implemented in 2018 at the Henri Mondor University hospital as part of routine diagnosis for "undiagnosed" suspected infections and accredited according to the ISO15189 standard in 2019.All of the CMg prescriptions prospectively received in the laboratory and validated by the biologists have been included in this retrospective analysis. The clinical indications and type of sample were collected. Samples have been processed by our in-house MetaMIC protocol including pre-extraction by bead-beating, QiaSymphony extraction, DNA and RNA library preparation (Illumina), NextSeq500 sequencing (Illumina) and MetaMIC software analysis. Results were interpreted in the light of the clinical context by a multidisciplinary microbiologist and clinician group.