Data from: Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence

Bacterial persistence is a phenomenon in which a small fraction of
isogenic bacterial cells survives a lethal dose of antibiotics. Although
the refractoriness of persistent cell populations has classically been
attributed to the presence of growth-inactive cells generated prior to
drug exposure, evidence is accumulating that actively growing cell
fractions can also produce persister cells, depending on bacterial
species, antibiotics, and culture conditions. However, the direct
elucidation of survival modes, drug response diversity, and growth history
dependence by single-cell observation is limited due to the extremely low
frequencies of persisters. Here, we visualize the responses of more than
106 individual cells of wildtype Escherichia coli to lethal doses of
antibiotics, sampling cells from different growth phases and culture media
into a microfluidic device. We show that when cells sampled from
exponentially growing cell populations in batch cultures were treated with
ampicillin or ciprofloxacin, all persisters for which we identified their
single-cell histories were growing prior to antibiotic treatment. We
detected pre-existing growth-arrested non-growing persisters to ampicillin
for an E. coli strain expressing a defective general stress response
regulator, but these constituted minor fractions of persister cells.
Growing persisters exhibit heterogeneous survival dynamics in response to
drug exposure, including continuous growth and fission with L-form-like
morphologies, responsive growth arrest, or post-exposure filamentation.
Incubating cells under stationary phase conditions increases both the
frequency and the probability of survival of non-growing persisters to
ampicillin. However, no non-growing persisters were identified for
ciprofloxacin treatment, even in post-stationary phase cell populations.
These results demonstrate diverse persistence dynamics at the single-cell
level depending on antibiotic types and the pre-exposure cultivation
history.