Metagenomics for universal pathogens identification

My goal is to accelerate the transition of genomic and bioinformatics innovations for the identification and surveillance of infectious agents by academic laboratories to clinical tests available to the community. One of the most ambitious projects is the development of a universal metagenomic test for the identification of any pathogen (virus, bacterium, fungus and parasite) directly from clinical samples. Applied in the event of diagnostic failure on normally sterile specimens, this method is often the last chance to save the life of patients in critical situations. In the field of environmental genomics, this tool would prove useful for routine surveillance (e.g. avian flu) or identification of emerging pathogens. Collaboration with researchers in artificial intelligence to develop methods for the analysis of complex results from these metagenomics experiments. By adapting classical tools used for microbiome analysis to clinical diagnostic and environmental investigations, we aim to improve genomic-based pathogen identification and surveillance.

Development of the genomic capacities of the Quebec Public Health Laboratory

Development of an operational genomic and bioinformatics service platform for pathogen identification and surveillance. In an ISO environment, implementation of tools and automated infrastructure for routine and on-demand sequencing services. Restructuring of laboratory spaces (workflow optimization), acquisition of specialized equipment for quality control (TapeStation) and automation (EpMotion), increasing sequencing capacities (NextSeq), development of the IT infrastructure (storage, servers), defining new analysis workflows (LIMS>Workflow>Quality monitoring) and development of pipelines for sample traceability, bioinformatics analysis and result reporting. Genomic and bioinformatics training of the technical team and of clinical professionals. These changes have enabled a rapid shift from manual occasional sequencing to weekly routine automated sequencing with genomic and bioinformatic analyses under ISO certification.