Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing

Abstract

Antibiotics can kill or stop the growth of bacteria, and their effectiveness depends on many factors. It is important to understand the relation between bacterial physiology, the environment and antibiotic action. While many of the mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. Death rate in antibiotics has often been shown to rise linearly with growth rate; however, it remains unclear how environmental factors, in concert with whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated bacterial death. We found that death rate is linear in growth rate only under certain conditions and deviates significantly from linearity in stressful growth environments: stressors lower the death rate compared to a non-stressed environment with the same growth rate. To understand the role of stress, we developed a mathematical model of bacterial death based on resource allocation that takes into account a newly defined stress-response sector; we identify this sector using RNAseq. Our model accurately predicts the death rate and minimal inhibitory concentration of antibiotics across a wide range of conditions, including a previously unknown increase in the stress response and protection from death at very low levels of cAMP. The present death-growth model suggests conditions that may improve antibiotic efficacy.

Gene expression tradeoffs determine bacterial survival and adaptation to antibiotic stress

“…Experimental data are from from Ref. [17] and are of E. coli NCM3722 cells grown in different sugars or exposed to different amounts of the bactericidal antibiotic TMP, before the MIC of nalidixic acid was measured. Model behavior is robust to parameter choice (see Fig.…”

“…where translation becomes significantly attenuated for amino acid concentrations below a t , and the amino acid supply flux becomes significantly attenuated by feedback inhibition for a above a n . Steady-state transcriptomic analysis reveals that ribosomal sector expression is reduced to allow for stress sector expression [17]. As such, the fraction of total synthesis capacity devoted to ribosomes, f R , is now a function of both a and U, specifically,…”

“…Previous work has shown that death rate increases approximately linearly with growth rate, but that the sensitivity of death rate to changes in growth rate depends significantly on environment and metabolic state [17, 23–25] Many mathematical models have been developed to link antibiotic dose to growth rate [13, 26–28] but little has been done to connect growth physiology mechanistically to cell survival outcome. A recent work [17] identified a general stress-response sector in E. coli , whose expression reduces death rate. However, many questions remain unanswered: how is resource allocation to stress protein production mechanistically linked to the environment, and what specific effects does it have on cell physiology to mitigate antibiotic-induced death?…”

“…(A) Minimum Inhibitory Concentration (MIC) as a function of pre-shift growth rate under nutrient limitation (blue), and growth inhibition via low levels of pre-shift antibiotic (green), as computed from(5). Experimental data are from from Ref [17]. and are of E. coli NCM3722 cells grown in different sugars or exposed to different amounts of the bactericidal antibiotic TMP, before the MIC of nalidixic acid was measured.…”

“…Solid lines indicate our proposed model, dashed line indicates growth-optimal resource allocation model. Data from Ref [17]. .…”