Whole-Genome Sequencing of A. baumannii

DNA was extracted on a QIAsymphony SP system with the QIAsymphony DSP virus/pathogen kit (Qiagen) according to the manufacturer’s instructions. The DNA concentration was quantified using the Quant-IT double-stranded DNA (dsDNA) high-sensitivity kit (Thermo Fisher Scientific).
Sequencing libraries were prepared from the pure A. baumannii DNA extract samples using the Nextera XT library preparation kit (Illumina Inc.) with slight modifications. One-half of the volume was used for tagmentation reagents, amplification reagents, and input DNA. Library cleanup was performed using the AxyPrep MAG PCR cleanup kit (Corning Inc., NY, USA), and libraries were pooled manually and sequenced on a NextSeq 550 platform with the NextSeq 500/550 midoutput kit v2.5 (300 cycles) (Illumina Inc.). Genome mutations were identified using breseq (39 (link)).