Vinchhi, R. | Search bioRxiv

bioRxiv2026

Divergent genotype-phenotype maps determine the capacity for adaptation to antibiotics among Enterobacteria

What dictates the extent to which a bacterial strain can evolve under antibiotic pressure remains poorly defined, despite its implications for the effectiveness of antibiotics in clinical practice. In this study, we compare the evolution of Escherichia coli and Klebsiella aerogenes, two medically relevant members of Enterobacteriaceae, under colistin and trimethoprim selection. We discover that the mere presence of effector genes of resistance, as well as conserved gene regulatory architecture, do not necessarily translate to similar evolvabilities during antibiotic challenge. Instead genotype-phenotype maps of adaptive mutations, which can diverge at different biological levels, govern how effectively a strain evolves resistance. Both, E. coli and K. aerogenes, demonstrated strikingly parallel capacities for adaptation to trimethoprim, as a result of conserved mechanisms of resistance, including drug target modification and efflux. On the other hand, E. coli was driven to extinction by colistin, while K. aerogenes was able to evolve a high level of colistin resistance. Like the better studied K. pneumoniae, K. aerogenes acquired mutations in the BasSR (also called PmrAB) and PhoQP two-component signalling pathways under colistin selection. These mutations increased the expression of chromosomally-encoded lipopolysaccharide (LPS) modifiers, EptA and Arn. Similar mutations in E. coli were unable to confer protection against colistin, despite successfully up-regulating homologous effectors genes. However, expression of MCR-1, a horizontally acquired EptA-homolog found in clinical strains, conferred high level colistin resistance to E. coli. This difference in the intrinsic capacity to adapt to colistin was reflected in frequencies of resistance among clinical isolates from around the world. It also altered the dependency of Escherichia and Klebsiella species on horizontal gene acquisition for colistin resistance. Our study highlights the importance of understanding pathogen-specific genotype-phenotype maps of drug resistance to better predict long-term effectiveness of antibiotic therapies and define resistance-proof treatment strategies.

microbiology↗

bioRxiv2023

Adaptive and maladaptive consequences of deregulation in a bacterial gene regulatory network

The archetypal PhoQP two-component system from Enterobacteria regulates crucial pathways like magnesium homeostasis in Escherichia coli and virulence factor expression in Salmonella enterica. Previously we had reported that a laboratory strain of E. coli rapidly accumulated loss-of-function mutations in the mgrB gene, a negative feedback regulator of PhoQP, when evolved in the presence of the antibiotic trimethoprim. Hyperactive PhoQP enhanced the expression of dihydrofolate reductase (folA), target of trimethoprim, resulting in antibiotic tolerance. Here we ask, firstly, how important are mutations in mgrB for trimethoprim resistance? Using laboratory evolution, we show that trimethoprim resistance evolves by different mutational trajectories under condition of high and low PhoQP activity. Mutations in mgrB are only fixed when PhoQP is active. Importantly, loss of functional MgrB, though itself only mildly beneficial, enhances the fixation probability of trimethoprim-resistant bacteria under selection and this can be explained by epistasis between mgrB and folA loci. As a result, the activation status of PhoQP directly impacts how fast resistance is acquired by evolving populations of E. coli. Secondly, we investigate why negative feedback may be needed in the PhoQP system. We show that under drug-free conditions MgrB is required to mitigate the fitness costs of pervasive gene dysregulation by hyperactive PhoQP. Using RNA-seq transcriptomics and genetic analyses, we demonstrate that PhoQP-hyperactivation perturbs the balance of RpoS and RpoD-regulated transcriptional programs, and spontaneous mutations in rpoS rectify this imbalance. We propose that deregulation can be adaptive or maladaptive depending on the environmental context and this explain the evolution of negative feedback in bacterial gene regulatory networks.

microbiology↗