Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission

There have been numerous investigations, both retrospective and prospective, in the past several years demonstrating the potential impact that whole genome sequencing (WGS) can have in infection prevention and control (IPC) efforts. However, even studies using extensive sequencing infrastructure have not been able to provide data in the timely fashion necessary for effective IPC interventions given the demands of the current gold-standard, Illumina based sequencing. Thus, we aimed to establish an ONT-only sequencing pipeline capable of rapidly and accurately producing WGS data to classify the genetic relatedness among potentially transmitted antimicrobial-resistant (AMR) pathogens in a tertiary care cancer hospital.