Targeted Deep Sequencing of E. coli
Genomic DNA from each sample was homogenized after quantification using a Qubit dsDNA HS Kit (Thermo Fisher). A 260-bp region of rpoB, containing the 10 sites where mutations were introduced, was then amplified by PCR using 59- and 60-bp primers Each primer included a 20-bp sequence homologous to the flanks of the rpoB target region, a 6-bp degenerate region to aid clustering on Illumina sequencing platforms, and a 33- or 34-bp sequence compatible with the Nextera XT DNA Library Prep Kit (Illumina)