Whole Genome Sequencing of Ciprofloxacin-Resistant Isolates

Among the FQR isolates from the phenotypic testing, 42 isolates with ciprofloxacin levels ≥ 0.5 µg/ml were randomly selected for whole genome sequencing (WGS). WGS was performed by MicrobesNG (MicrobesNG, Birmingham, UK.) using Illumina HiSeq technology [22 ]. DNA for sequencing was extracted using the MagNA Pure 96 DNA and Viral NA Large Volume kit (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacturer’s instructions and genomic libraries were prepared using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA). A 150-bp paired-end sequencing was performed using the HiSeq × 10 system (Illumina). Long and short read sequences were assembled using Unicycler (v.0.4.8.0), and genome annotation was done with Prokka (v.1.14.6). Sequences were analyzed for multisequence typing (MLST), and plasmid replicon types using MLST 1.8, ResFinder [23 (link)] and Plasmidfinder software [24 (link)].