MinION sequencing
DNA from pure E. coli cultures was extracted using the NZYMicrobial gDNA Isolation Kit (NZYtech) according to the manufacturer's instructions. DNA purity and concentration were assessed with a Nanodrop ND1000 v2.5.3 spectrophotometer (ThermoFisher Scientific) and a Qubit 2.0 fluorometer (Invitrogen). Libraries were prepared using Rapid Barcoding kit (SQK-RBK004) and sequenced on the flow cell FLO-MIN106D (R9.4.1). Sequencing was run on a MinION MK1C device (ONT) and raw sequencing data were subjected to high accuracy basecalling (HAC) and filtered by quality (Qscore> 9). 
Rapid Barcoding kit (SQK-RBK004) and sequenced on the flow cell FLO-MIN106D (R9.4.1) 