Nanopore-based Amplicon Sequencing on Rapid Detection of Pathogens and AMR genes from Low-biomass Samples in the Hospital Environment
)
Legionella pneumophila and Pseudomonas aeruginosa are the most common bacterium associated with ventilator-associated pneumonia and nosocomial infections. Investigation of pathogens by genome sequencing has been established as an important tool for outbreak management. Genome sequencing directly from samples (i.e. without isolation and culture) with low biomass remains challenging due to low numbers of genome copies in typical water samples. The portable MinION sequencer (Oxford Nanopore Technologies) has potential for rapid genome sequencing and offline bioinformatic analysis, making it suitable for on-site and real-time detection and lineage assignment and resistance identification of L. pneumophila and P. aeruginosa directly from environmental samples.