Identification of antibiotic resistance conferring mutations in E.coli from evolution in a continuous culturing device.

Here we have used MinION Nanopore sequencing to sequence the whole genomes of E.coli MG1655 derivatives from experimental evolution in a continuous culturing device called a turbidostat. We have isolated resistant allels after treatment with three different antibiotics: rifampicin, ciprofloxacin and streptomycin. The resistant alleles were selected for in two different ways after growth in the turbidostat culture on LB without the antibiotic. Some resistant clones were selected for in the turbidostat, i.e. the antibiotic was added and maintained at the same level in the turbidostat culture throughout the remainder of the experiment and the resistant alleles were isolated after growth on the antibiotic in the turbidostat. The other clones were selected for on agar plates, after the entire turbidostat cultures were spun down and plated for selection on LB agar plate containing the antibiotic (at the same concentrations that were added in the turbidostat.