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. Author Summary Resistance to antibiotics is a major cause of treatment failure in modern medicine. In addition to genetic resistance, bacterial cells can sustain periods of bactericidal application in a so-called tolerant state. Previously tolerant cells were characterized by growth arrest prior and during exposure to antibiotics. Here, we show a distinctive type of tolerance that arises out of normally growing cells, where during antibiotic exposure, cell growth is slowed but does not go into growth arrest. Cells with an intermediate growth have the best survival, which is contrary to the assumptions of exposure to a β-lactam antibiotic where selection is assumed to act against the fastest growing cells and the least against non-growing cells. The novel characteristics of tolerance that we have uncovered provides bacteria with another route to evade antibiotics and that could be a considerable threat to the efficiency of antibiotic treatment.