Dominant resistance and negative epistasis can limit the co-selection of de novo resistance mutations and antibiotic resistance genes

Andreas Porse,Morten O A Sommer,Mostafa M H Ellabaan,Leonie J Jahn

doi:10.1038/s41467-020-15080-8

Andreas Porse, Morten O A Sommer + Show 2 more

Open Access

https://doi.org/10.1038/s41467-020-15080-8

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Abstract

To tackle the global antibiotic resistance crisis, antibiotic resistance acquired either vertically by chromosomal mutations or horizontally through antibiotic resistance genes (ARGs) have been studied. Yet, little is known about the interactions between the two, which may impact the evolution of antibiotic resistance. Here, we develop a multiplexed barcoded approach to assess the fitness of 144 mutant-ARG combinations in Escherichia coli subjected to eight different antibiotics at 11 different concentrations. While most interactions are neutral, we identify significant interactions for 12% of the mutant-ARG combinations. The ability of most ARGs to confer high-level resistance at a low fitness cost shields the selective dynamics of mutants at low drug concentrations. Therefore, high-fitness mutants are often selected regardless of their resistance level. Finally, we identify strong negative epistasis between two unrelated resistance mechanisms: the tetA tetracycline resistance gene and loss-of-function nuo mutations involved in aminoglycoside tolerance. Our study highlights important constraints that may allow better prediction and control of antibiotic resistance evolution.

Highlights

To tackle the global antibiotic resistance crisis, antibiotic resistance acquired either vertically by chromosomal mutations or horizontally through antibiotic resistance genes (ARGs) have been studied
While ARGs have evolved to function in a broad range of genomic contexts, and genomic mutations leading to resistance are host-specific, the resulting resistance mechanisms often overlap[13]
Mutations associated with aminoglycoside resistance confer sensitivity towards multiple antibiotic drug classes, including beta-lactams, quinolones, and tetracyclines[17,18,19], and this sensitivity is thought to arise from a reduction in the proton motive force (PMF) that reduces the uptake of aminoglycoside, while simultaneously decreasing multidrug efflux[18]

Summary

Introduction

To tackle the global antibiotic resistance crisis, antibiotic resistance acquired either vertically by chromosomal mutations or horizontally through antibiotic resistance genes (ARGs) have been studied. Bacterial evolution is driven by two main mechanisms: selection of genomic mutations (vertical evolution) and the acquisition of foreign DNA through horizontal gene transfer (HGT) These two modes of evolution provide the genetic plasticity that allows bacteria to inhabit virtually all ecological niches on the planet and underlines the emergence of antibiotic-resistant pathogenic bacteria increasingly compromising our ability to treat infections[1,2]. A protein targeted by an antibiotic may be altered via mutation(s) to avoid inhibition; or by horizontal acquisition of effectors that modify or replace the protein target, thereby rendering the cell resistant[14] Taken together, these observations suggest that chromosomal mutations and HGT events could interact to contribute to the development of antibiotic resistance. It is unclear to what extent the observed epistatic effects are caused by the plasmid-encoded ARGs or other components of the large plasmid backbones and whether these interactions are maintained during antibiotic selection

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