Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing

The gold standard for bloodstream infection (BSI) diagnostics involves culturing positive blood cultures (BC) using phenotypic methods for organism identification and antimicrobial resistance (AMR) testing, which can take up to five days. However, it is crucial to optimize antimicrobial therapy as soon as possible to reduce morbidity and mortality. We present a novel laboratory and bioinformatic workflow to rapidly identify bacterial and fungal organisms and AMR determinants from positive BCs using Oxford Nanopore Technologies long-read sequencing. This repository contains the Illumina sequencing data from matching pure isolates.