Ultrafast detection of -lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing

Aim: This study aimed to assess the ultra-fast method using MinION (TM) sequencing for rapid identification of beta-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures.Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for beta-lactamase resistance genes. Multilocus sequence typing and beta-lactamase variant characterization were performed after assembly.Results: The ultra-fast method identified clinically relevant beta-lactamase resistance genes in less than 1 h. Multilocus sequence typing and beta-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration.Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.