Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE
Lisa Teichmann, Marcus Wenne, Sam Luitwieler, Gaurav Dugar, Johan Bengtsson-Palme, Benno ter Kuile
Abstract
Bacteria can quickly adapt to sub-lethal concentrations of antibiotics. Several stress and DNA repair genes contribute to this adaptation process. However, the pathways leading to adaptation by acquisition of de novo mutations remain poorly understood. This study explored the roles of DNA polymerase IV (dinB) and catalase HP2 (katE) in E. coli’s adaptation to amoxicillin. These genes are thought to play essential roles in beta-lactam resistance—dinB in increasing mutation rates and katE in managing oxidative stress.
Introduction
Since bacterial resistance mechanisms were first described, considerable efforts have been devoted to revealing the underlying molecular machinery involved in developing antimicrobial resistance. Understanding the cellular pathways involved is essential for addressing the growing threat looming over modern medicine–an era where previously effective antibiotics are increasingly unable to treat resistant infections (https://www.who.int/publications/i/item/no-time-to-wait-securing-the-future-from-drug-resistant-infections).
Materials and method
Strains, growth conditions, and antimicrobial agents
The Escherichia coli strain MG1655 was utilized as the wild-type strain. Single gene knockout mutants JW0221 (ΔdinB749::kan) and JW1721 (ΔkatE731::kan) were obtained from the KEIO collection, supplied by Horizon Discovery Ltd. These knockout mutants contained kanamycin-resistant cassettes flanked by FLP recognition target (FRT) sites, which were removed using the pCP20 method prior to the experiments [32,33].
Results
Deletion of katE or dinB does not alter antibiotic adaptation rates
We investigated the adaptation rate of the wild-type compared to the dinB and katE knockout strains and found no significant differences (Fig 1). Despite their limitations in stress responses considered crucial for beta-lactam resistance, their adaptation dynamics closely reflected that of the wild-type E. coli. Indeed, the biological and technical variations between replicates were comparable to the differences observed between the strains, suggesting that knocking out dinB and katE did not confer any notable disadvantage in adaptation to amoxicillin. All strains exhibited a uniform adaptation rate until the clinical resistance threshold of 8 μg/mL (https://mic.eucast.org) and above.
Discussion
The generally assumed roles of dinB and katE in beta-lactam resistance mechanisms in E. coli need to be reconsidered. Contrary to previous assumptions, the adaptation rates to amoxicillin in the absence of dinB and katE, were similar to those observed in wild-type E. coli. The uniformity observed in the adaptation rates of both wild-type and knockout strains indicates shared adaptation mechanisms or the activation of compensatory pathways within the bacterial genome. This collective adaptation hypothesis gains support from the limited set of mutations shared across strains and the consistent pattern of gene amplifications observed in a region previously identified as a ‘pre-plasmid’ [49].
Acknowledgments
The authors thank Stanley Brul and Meike Wortel for stimulating discussions.
Citation: Teichmann L, Wenne M, Luitwieler S, Dugar G, Bengtsson-Palme J, ter Kuile B (2025) Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE. PLoS ONE 20(2): e0312223. https://doi.org/10.1371/journal.pone.0312223
Editor: Bashir Sajo Mienda, Federal University Dutse, NIGERIA
Received: October 3, 2024; Accepted: December 27, 2024; Published: February 19, 2025
Copyright: © 2025 Teichmann et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data can be found in the following GitHub link: https://github.com/mnyt-aqw/Teichmann_2024_Amoxicillin.
Funding: This study was financed by The Netherlands Food and Consumer Product Safety Authority.
Competing interests: The authors have declared that no competing interests exist.
