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An investigation of gene dosage reveals that increased sensitivity to D-cycloserine divergently impacts the transience of heteroresistance in Escherichia coli

Sniezek KJ, Brynildsen MP

mBio, 2025

Abstract

Heteroresistance describes the phenomenon where seemingly isogenic bacterial populations contain subpopulations with elevated resistance compared to the susceptible majority that are often missed in routine susceptibility testing. The enhanced resistance of those subpopulations can either be maintained (stable) or quickly lost (unstable/transient) after treatment, where transient cases return susceptibility results identical to those of original cultures. Recent work has implicated increased gene dosage of resistance determinants as a major cause of unstable heteroresistance in clinical isolates. Inspired by that work, we sought to systematically evaluate how gene dosage of an antibiotic's target network components impacted heteroresistance and its stability. To accomplish that, we used Escherichia coli MG1655 as a model organism, and D-cycloserine (DCS), a cell-wall synthesis inhibitor that enters through a transporter (CycA) and inhibits multiple enzymes (DdlA, DdlB, DadX, and Alr), as a model antibiotic. To measure heteroresistance, we used population analysis profiling, and to quantify stability, we used a population-level model to define a heteroresistance stability index ([Formula: see text]), which quantifies the proportion of heteroresistant subpopulation j that maintained elevated resistance over t generations. We found that increased sensitivity to DCS through gene dosage variation of cycA and ddlB divergently impacted heteroresistance stability, with ddlB…

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