Escherichia coli Genome sequencing and assembly

In this study, we retrospectively analyzed 234 E. coli isolates from positive blood cultures with WGS and microdilution for 11 clinical relevant antibiotics. The sequenced data were analyzed for acquired resistance using BioNumerics v.8.1 (Applied Maths, Biomerieux, Belgium). DNA-purification was done with a Maxwell RSC Instrument (Promega, US) and WGS was performed on a NovaSeq 6000 (Illumina, US) by Brussels Interuniversity Genomics High Throughput core (BRIGHTcore). Minimal inhibitory concentration (MIC) was performed for amoxicillin, cefepime, cefotaxime, ceftazidime, meropenem, amoxicillin/clavulanic acid, piperacillin/tazobactam, amikacin, gentamicin, tobramycin and ciprofloxacin by using the ISO 20776-1 standard broth microdilution method, referred by the EUCAST. Sensititre Custom Plates according to EUCAST-guidelines were used.