Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance

Bacterial evolution of antibiotic resistance frequently has deleterious side effects on microbial growth, virulence, and susceptibility to other antimicrobial agents. However, it is unclear how these trade-offs could be utilized for manipulating antibiotic resistance in the clinic, not least because the underlying molecular mechanisms are poorly understood. Using laboratory evolution, we demonstrate that clinically relevant resistance mutations in Escherichia coli constitutively rewire a large fraction of the transcriptome in a repeatable and stereotypic manner. Strikingly, lineages adapted to functionally distinct antibiotics and having no resistance mutations in common show a wide range of parallel gene expression changes that alter oxidative stress response, iron homeostasis, and the composition of the bacterial outer membrane and cell surface. These common physiological alterations are associated with changes in cell morphology and enhanced sensitivity to antimicrobial peptides. Finally, the constitutive transcriptomic changes induced by resistance mutations are largely distinct from those induced by antibiotic stresses in the wild-type. This indicates a limited role for genetic assimilation of the induced antibiotic stress response during resistance evolution. Our work suggests that diverse resistance mutations converge on similar global transcriptomic states that shape genetic susceptibility to antimicrobial compounds. E. coli BW 25113 single mutant lines carrying one of the following resistance mutations: (envZ[Ala396Thr], marR[Val84Glu], trkH[Thr350Lys], gyrA[Asp87Gly], phoQ[Gly384Cys], rpoC[Ala784Val], soxR[Leu139*]) were established using a highly precise allele replacement protocol (Toprak et al. 2012; Lázár et al. 2013; Nyerges et al. 2016). In addition, 3 ancestor lines were treated with lethal concentration of ciprofloxacin (50 ng/ml) for 120 minutes (CC*_120). Untreated samles were collacted immediatly after antibiotic treatment (0 minutes; CC*_0). Sample groups contain 3 biological replicates.