Use of Oxford Nanopore sequencing to evaluate potential transmission of hospital infections

Abstract Whole-genome sequencing (WGS) has the potential to detect cryptic transmission of pathogens causing healthcare-associated infections (HAIs). We sought to establish an Oxford Nanopore Technologies pipeline capable of providing accurate, WGS-based comparisons of healthcare pathogens within a time frame that would allow for infection control interventions. Between August 2023 and March 2024, we used daily review of the electronic health record to identify potential healthcare-acquired, antimicrobial resistant bacterial infections. Genomic DNA was sequenced using the MinION sequencer with R10.4.1 Flow Cells, and basecalling was performed using Dorado. Genetic-relatedness was assessed using core genome multilocus sequence typing and single nucleotide polymorphism analysis. Our Oxford Nanopore pipeline accuracy was validated against Illumina WGS data. Using the work of a single graduate student, we performed nanopore sequencing on 245 unique strains with a workflow averaging 2.2 days from genomic DNA isolation to complete data analysis. Relative to Illumina, our Oxford Nanopore pipeline achieved a Q score of 60 for the assembled genomes. We identified five genetically related clusters comprising 21 isolates (8.6% of all sequenced strains). Combining Oxford Nanopore WGS data with epidemiological data, we found that >70% (15/21) of the isolates originated from patients who either stayed in the same hospital unit simultaneously for >24 hours or were admitted to the same unit within 60 days from one another. Our low-personnel Oxford Nanopore pipeline rapidly and accurately classified HAI pathogens as potentially transmitted. Our approach may assist in the efficient detection and deployment of preventative measures against HAI transmission. Biography Dr. Shelburne is a Professor in the Department of Infectious Diseases at MD Anderson, Houston, Texas, whose laboratory studies the genetic basis of infectious diseases in humans