The authors thank É. Kondorosi for providing the cationic antimicrobial peptide NCR335, and M.O.A. Sommer for the clinical isolates. The authors also acknowledge the following financial support: the Hungarian Academy of Sciences Postdoctoral Fellowship Programme (V.L.), the Hungarian Scientific Research Fund NKFI PD 116222 (A.M.), NKFI 120220 (B.K.), OTKA PD 109572 (B.C.) and NKFI FK 124254 (O.M.), the ‘Lendület’ Programme of the Hungarian Academy of Sciences and The Wellcome Trust (B.P. and C.P.), the European Research Council H2020-ERC-2014-CoG 648364 - Resistance Evolution (C.P.), GINOP-2.3.2-15-2016-00014 (EVOMER), GINOP-2.3.2-15-2016-00020 (MolMedEx TUMORDNS) and GINOP-2.3.3-15-2016-00001. I.N. and B.K. were supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and Á.N. by the Ph.D. fellowship of the Boehringer Ingelheim Fonds.

Author contributions

C.P. and B.P. conceived and supervised the project. V.L. and A.M. designed the experiments and developed data analysis procedures. C.P., B.P., V.L., A.M. and R.S. wrote the paper. R.S., A.K., A.D., F.W. and M.D. performed the zeta potential measurements. G.O., Z.H. and T.A.M. synthetized the peptides magainin 2 and anginex. R.S. and O.M. purified RNA for transcriptomic analysis. B.B. and I.N. performed RNA-Seq experiments. P.K.J., G.F., M.S. and B.K. generated and analysed the chemogenomic data. E.U. isolated and identified E. coli clinical isolates. B.C. and A.N. prepared the mutant strains. V.L., L.D., A.M., R.S. and B.C. contributed to all other experiments. V.L., A.M., G.G., G.F. and A.G. analysed and interpreted the data.