Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks

Paul Lubrano; Fabian Smollich; Thorben Schramm; Elisabeth Lorenz; Alejandra Alvarado; Seraina Carmen Eigenmann; Amelie Stadelmann; Sevvalli Thavapalan; Nils Waffenschmidt; Timo Glatter; Nadine Hoffmann; Jennifer Müller; Silke Peter; Knut Drescher; Hannes Link

doi:10.1038/s44320-024-00084-z

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks

Mol Syst Biol. 2025 Jan 2. doi: 10.1038/s44320-024-00084-z. Online ahead of print.

Authors

Paul Lubrano^#^{1

2

3}, Fabian Smollich^#^{1

2

3}, Thorben Schramm^{1

4}, Elisabeth Lorenz¹, Alejandra Alvarado^{1

2}, Seraina Carmen Eigenmann⁵, Amelie Stadelmann^{1

2

3}, Sevvalli Thavapalan^{1

2

3}, Nils Waffenschmidt¹, Timo Glatter⁶, Nadine Hoffmann^{2

7}, Jennifer Müller^{7

8}, Silke Peter^{2

7

8}, Knut Drescher⁵, Hannes Link^{9

10

11}

Affiliations

¹ Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076, Tübingen, Germany.
² Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, 72076, Tübingen, Germany.
³ M3 Research Center, Otfried-Müller-Straße 37, University of Tübingen, 72076, Tübingen, Germany.
⁴ Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland.
⁵ Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
⁶ Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.
⁷ Institute of Medical Microbiology and Hygiene, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076, Tübingen, Germany.
⁸ NGS Competence Center Tübingen (NCCT), 72076, Tübingen, Germany.
⁹ Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076, Tübingen, Germany. [email protected].
¹⁰ Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, 72076, Tübingen, Germany. [email protected].
¹¹ M3 Research Center, Otfried-Müller-Straße 37, University of Tübingen, 72076, Tübingen, Germany. [email protected].

^# Contributed equally.

PMID: 39748127
DOI: 10.1038/s44320-024-00084-z

Abstract

Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.

Keywords: Escherichia coli; Antibiotic Resistance; CRISPR; Metabolism; Mutations.

Grants and funding

EXC2124/Deutsche Forschungsgemeinschaft (DFG)