ArticleNature communications2022
Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review on the Occurrence of Antimicrobial-ResistantBioMed research international · 2023Pooled it
- Mapping the genomic landscape of antibiotic susceptiblity in Escherichia coli.npj antimicrobials and resistance · 2026Article
- Rapid Adaptive Evolution under Combination Therapy inACS infectious diseases · 2026Article
- PhoP-regulated VirK acts as an accessory factor to maintain virulence in polymyxin-resistant Klebsiella pneumoniae.Nucleic acids research · 2026Article
- Induction of colistin resistance and environmental toxicity assessment in Escherichia coli.PloS one · 2026Article
- Advances in adaptive laboratory evolution applications forSynthetic and systems biotechnology · 2025Review
- Improving health and productivity in laying hens with the phage cocktail SalmoFree®.Poultry science · 2025Article
- Impeding pathways of intrinsic resistance in Escherichia coli confers antibiotic sensitization and resistance proofing.PLoS biology · 2025Article
- Reviewing the complexities of bacterial biocide susceptibility and in vitro biocide adaptation methodologies.npj antimicrobials and resistance · 2025Review
- Targeting efflux pumps prevents the multi-step evolution of high-level resistance to fluoroquinolone inMicrobiology spectrum · 2025Article
- Quantitative analysis of relationship between mutation rate and speed of adaptation under antibiotic exposure in Escherichia coli.PLoS genetics · 2025Article
- A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.Nucleic acids research · 2025Article
- Genomic Pipeline for Analysis of Mutational Events in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Impact of untreated tannery wastewater in the evolution of multidrug-resistant bacteria in Bangladesh.Scientific reports · 2024Article
- Evolutionary Action-Machine Learning Model Identifies Candidate Genes Associated With Early-Onset Coronary Artery Disease.Journal of the American Heart Association · 2023Article
- Multidrug Resistance Profiles and Resistance Mechanisms to β-Lactams and Fluoroquinolones in Bacterial Isolates from Hospital Wastewater in Bangladesh.Current issues in molecular biology · 2023Article
- ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis.Bioinformatics (Oxford, England) · 2023Article
- Artificial Intelligence for Antimicrobial Resistance Prediction: Challenges and Opportunities towards Practical Implementation.Antibiotics (Basel, Switzerland) · 2023Review
- Adaptive laboratory evolution ofFrontiers in microbiology · 2023Article
- Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli.Nature communications · 2022Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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