Experimental Evolution of Copper Resistance in Escherichia coli Produces Evolutionary Trade-Offs in the Antibiotics Chloramphenicol, Bacitracin, and Sulfonamide

Abstract

The rise in antimicrobial resistant bacteria have prompted the need for antibiotic alternatives. To address this problem, significant attention has been given to the antimicrobial use and novel applications of copper. As novel applications of antimicrobial copper increase, it is important to investigate how bacteria may adapt to copper over time. Here, we used experimental evolution with re-sequencing (EER-seq) and RNA-sequencing to study the evolution of copper resistance in Escherichia coli. Subsequently, we tested whether copper resistance led to rifampicin, chloramphenicol, bacitracin, and/or sulfonamide resistance. Our results demonstrate that E. coli is capable of rapidly evolving resistance to CuSO4 after 37 days of selection. We also identified multiple de novo mutations and differential gene expression patterns associated with copper, most notably those mutations identified in the cpx gene. Furthermore, we found that the copper resistant bacteria had decreased sensitivity when compared to the ancestors in the presence of chloramphenicol, bacitracin, and sulfonamide. Our data suggest that the selection of copper resistance may inhibit growth in the antimicrobials tested, resulting in evolutionary trade-offs. The results of our study may have important implications as we consider the antimicrobial use of copper and how bacteria may respond to increased use over time.

Copper Resistance Mechanism and Copper Response Genes in Corynebacterium crenatum

“…E. coli, P. aeruginosa, Bacillus cereus, and B. subtilis showed apparent reductions in growth rates with 0.1 mM copper [20]. E. coli K-12 MG1655 demonstrated growth retardation with 0.78 mM copper [21]. Corynebacterium glutamicum is a close relative of C. crenatum, and its growth rate tested with 0.5 mM copper decreased by 40% compared with that tested without copper [22].…”

The role of the universal sugar transport system components PtsI (EI) and PtsH (HPr) in Enterococcus faecium

“…Copper accumulates at sites of infection, including the gastrointestinal and respiratory tracts, blood, and urine, and its antibacterial toxicity is directly leveraged by phagocytic cells to kill pathogens (Focarelli et al 2022 ). Several studies have shown significant changes in carbon source acquisition, central metabolism, and PTS gene expression in the presence of copper, as well as the fixation of mutants in PTS genes during experimental evolutionary studies on copper resistance (Quesille-Villalobos et al 2019 , Boyd et al 2022 , Dao et al 2023 ). Copper signaling has also been demonstrated to regulate the DNA-binding activity of CcpA in Staphylococcus aureus (Liao et al 2022 ), and excess copper in the environment has been shown to increase the catabolic diversity of Gram-positive bacteria (Yang et al 2022 ).…”

Dark Fermentation in the Dark Biosphere: The Case of Citrobacter sp. T1.2D-12

“…We found multiple genes associated with resistance to these types of compounds, such as cusRS and cusCFBA, the former being a response system that induces the expression of the latter, which functions as a pump that retires the excess of Cu (I) from the periplasmic space of E. coli. We also identified the transcriptional regulator cueR, which enhances the expression of the also present copA, whose function is to transport Cu (I) from the cytosol to the periplasm, where it is reduced to Cu (II) (a less toxic form) by CueO [75]. We also identified nikABCDE operon, which encodes an Ni import system [76], and rcnA, which is translated into a membrane-associated protein whose presence has been related to an increase in resistance to Co and Ni.…”