Nanopore sequencing for detection of carbapenem-resistant and extended-spectrum betalactamase-producing Enterobacteriaceae in urine samples
DNA was extracted from bacterial pellets in spun urine using the QIAamp PowerFecal Pro DNA kit (Qiagen). The purified DNA was sequenced in native form by a Nanopore sequencer (MinION, R9 Flow Cell) using a Rapid Barcoding kit (SQK-RBK004, Oxford Nanopore) to identify the organisms and beta-lactamase genes.