Illumina HiSeq 4000 paired end sequencing; Whole-genome sequencing of clincal nitrofurantoin-resistant E. coli isolate IN05
Genomic DNA was extracted using a phenol/chloroform method and checked for integrity using gel electrophoresis. The DNA library was prepared in a paired-end layout with NEBNext Ultra II FS DNA Library Prep Kit (New England BioLabs, UK) and was sequenced under a 150-bp read length using an Illumina HiSeq 4000 system and HiSeq SBS Kit v4 reagents (Illumina, USA). Mean and standard deviation of insert sizes are based on information from TapeStation used for pre-sequencing quality control.