Selected abstract: Metagenomic Shotgun Sequencing in the Microbiology laboratory: Routine Implementation for complex cases

christophe-rodriguez-iccmg-

Selected abstract: Metagenomic Shotgun Sequencing in the Microbiology laboratory: Routine Implementation for complex cases

Next generation sequencing (NGS) is changing the field of diagnosis in Infectious Diseases. However, because of the challenge associated with the complex data analysis and the bioinformatic tools it requires, NGS is not included in the routine processes. Here, we report the routine implementation of NGS methods for microbiological diagnosis purposes in the Microbiology Department of our university hospital, which carries out the medical analysis for 3000 beds, including 1000 acute patients.

As a whole, CMg improved the diagnosis of 35% (7/20) of the tested patients. The two false negative of CMg corresponded to respiratory colonization by Candida sp.. However, CMg failed to identify Mycobacterium tuberculosis in one peritoneal sample, probably due to both its polymicrobial presentation and the poor performances associated with the nucleic acids extraction of mycobacteria.