The genomic DNA of J53_W61C2-1_HD10 (one of three biological replicates of the C2 transconjugant, serial passaged for 10 days under antibiotic-high conditions) was extracted using the TIANamp Bacterial DNA Kit (Tiangen). Long-read sequencing libraries were generated using SQK-LSK109 connection kit (Oxford Nanopore Technologies, UK).