Applying nanopore sequencing and real-time antimicrobial resistance gene analysis to address the threat of carbapenem-resistant gram-negative organisms

More than 700,000 people around the world die from antibiotic-resistant infections annually, translating to 1,900 deaths per day. One of the most significant antibiotic resistance threats is carbapenem-resistant Gram-negative organisms (CRO). This presentation will review methods for which Nanopore sequencing and real-time antimicrobial resistance gene analysis can help to address the threat of CRO as a diagnostic tool in the Medical Microbiology Laboratory. Applications reviewed will include detection of gastrointestinal colonization with CRO using metagenomics next-generation sequencing and real-time resistance gene analysis of whole genome sequencing data from carbapenem-resistant organisms to predict therapy. These applications of nanopore sequencing in the hospital setting has the potential to impact infection control and antimicrobial stewardship initiatives.