Single-cell phenotypic characteristics of tolerance under recurring antibiotic exposure in Escherichia coli

Non-heritable drug resistance, such as tolerance and persistence towards antibiotics, is little characterized compared to genetic resistance. Tolerance and persistence allow cells to survive application of antibiotics that are bactericidal to non-tolerant cells. Non-heritable drug resistance challenges antibiotic treatment, particularly of recurrent infections, and have implications towards heritable resistance evolution. Tolerant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we explore characteristic of tolerant and susceptible E. coli single bacteria cells to different levels of recurrent antibiotic exposure and quantify their occurrence. In using a high throughput single-cell microfluidic device, we find that tolerant cells reduce their growth rate by about 50%, but contrary to previous findings do not go into growth arrest or near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as previously described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and selection did not primarily act on fast growing cells, as expected for a β-lactam antibiotic. Control experiments on population cultures confirmed and challenged scaling of single cell findings to population level processes. Our findings suggest a prevalent type of tolerance that differs from previously described tolerance and persister characteristics. Our described characteristics and its high frequency of occurrence supports acclaims of an underappreciated role of tolerant cells towards resistance evolution.

Methods
Single-cell bacteria data on survival, size, growth/cell elongation, division, under recurring exposure to eight different concentrations of ampicillin. Data was collected using a mircofluidic device, a mother machine. Original images were processed using a custom software for cell segmentation and tracking.

A parallel experiment at the cell culture level with recurent exposure of antibiotics at different concentrations has been performed counting colony forming units, as well as a control experiment under constant antibiotic concentrations measuring optical density (OD_600).