Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse

The vast majority of a bacterial population is killed within a time scale comparable to their generation time when treated with a lethal concentration of antibiotics. However, a small subpopulation typically survives for an extended period. To investigate the long-term killing dynamics of bacterial cells we constructed a week-long killing assay and followed the survival fraction of an E. coli K12 strain exposed to a high concentration of ciprofloxacin. We found that long-term survivors were formed during exponential growth in both a wildtype and a relA deletion strain, with some cells surviving at least 7 days. The killing dynamics showed at least three time-scales, in contrast to the commonly assumed biphasic killing. Furthermore, we observed a surprisingly long memory effect of a brief starvation pulse, which was dependent on relA . Specifically, one hour of carbon starvation increased the surviving fraction by nearly 100-fold even after 4 days of antibiotics exposure.