Tracking Acquisition of Pathogens In Real-Time using Metagenomics

The aim of the study was to determine the emergence, dis-semination and population dynamics of health care-associated bacterial pathogens at single ward level by implementing real-time genome surveillance by metagenomics sequencing directly from screening swabs using Oxford Nanopore Technology MinION. We also compared it with classical microbiology and pure colony short read sequencing using Illumina. We surveyed the neonatal intensive care unit for a year as a model since clustering of isolates is routinely observed but our ability to track early transmission events is hampered by the time it takes for culturing and subsequent typing. The detection of clustering of isolates has impact on infection control, as either cohorting of patients or even closure of the ward needs to be considered. Hence, it is imperative to identify transmission events, and identify them early for timely intervention. This study contains the Illumina sequencing samples, including the control samples for water and swab. Metagenomic sequences can be found in study PRJEB82667.