Recent Advances in Antimicrobial Resistance: Insights from Escherichia coli as a Model Organism

Abstract

Antimicrobial resistance (AMR) represents a critical global health threat, and a thorough understanding of resistance mechanisms in Escherichia coli is needed to guide effective treatment interventions. This review explores recent advances for investigating AMR in E. coli, including machine learning for resistance pattern analysis, laboratory evolution to generate resistant mutants, mutant library construction, and genome sequencing for in-depth characterization. Key resistance mechanisms are discussed, including drug inactivation, target modification, altered transport, and metabolic adaptation. Additionally, we highlight strategies to mitigate the spread of AMR, such as dynamic resistance monitoring, innovative therapies like phage therapy and CRISPR-Cas technology, and tighter regulation of antibiotic use in animal production systems. This review provides actionable insights into E. coli resistance mechanisms and identifies promising directions for future antibiotic development and AMR management.

Keywords: AMR prevention; Escherichia coli; antimicrobial resistance; machine learning; synthetic biology.

Figure 1

Illustration of research methods for studying E. coli antibiotic resistance. (A) Exploration of resistance mechanisms using machine learning. (B) Investigation of resistant strains obtained through laboratory evolution. (C) Analysis of resistance genes and mechanisms through the construction of mutant libraries. (D) Analysis of resistance genes using whole-genome sequencing. (E) Traditional disk diffusion and MIC methods for antibiotic resistance testing. (F) Detection of β-lactamase-producing bacteria using MALDI-TOF MS.

Figure 2

Common Mechanisms of AMR in E. coli. (A) Resistant strains arise through inactivation or modification of antibiotics. (B) Resistance also occurs by modifying the target’s structure or blocking antibiotic binding, allowing the target to function properly. (C) Efflux pumps enhance resistance by actively expelling antibiotics from the cell. (D) Persistence is achieved by forming dormant cells that can tolerate and survive antibiotic treatment.