Many antibiotics rapidly kill growing populations of bacteria but struggle to kill non-growing populations.
Even for drugs that can kill the majority of growth-inhibited bacteria, such as fluoroquinolones (FQs), the
presence of persisters can lead to treatment failure. While current paradigms suggest that persisters survive
due to limited antibiotic-induced damage, for FQs this is not the case. In non-growing populations, FQ
persisters experience the same amount of antibiotic-induced DNA damage as their genetically identical kin and
require the homologous recombination repair machinery during the post-antibiotic recovery period in order to
survive. Currently, the mechanism underlying why persisters can survive FQ-induced damage while their clonal
kin cannot remains ill-defined. We hypothesize that, i) chromosome number, and ii) the relative timing of DNA
synthesis and repair during the post-antibiotic period, are phenotypic variables that govern the likelihood a
bacterium will be an FQ persister. Since our first hypothesis is based on the importance of homologous
recombination to FQ persistence in growth-inhibited populations, we will use fluorescence-activated cell sorting
(FACS) to sort live wild-type and mutant populations of Escherichia coli based on chromosome number as
determined by staining with cell-permeant nucleic acid dyes, and will subject the isolated populations to
tolerance assays and quantitative PCR for chromosome number verification. To complement these assays, we
will use time-lapse microscopy of an FQ-treated E. coli strain that harbors an origin of replication reporter in
order to visualize the chromosome content of persisters and nonpersisters during the post-FQ recovery period.
Our second hypothesis is based on a recent study from our group that showed that starvation following FQ
treatment increased persister levels in non-growing populations in a RecA- and time-dependent manner. To
test whether the timing of DNA replication vs. DNA repair during recovery impacts FQ persistence, we will
conduct time-lapse fluorescence microscopy of single cells harboring reporters for DNA repair or DNA
replication both in the presence and absence of nutrients. We will then conduct bulk culture experiments by
employing temperature sensitive mutants and inducible systems of the DNA replication and DNA repair
machinery. We will first investigate levofloxacin, a representative FQ, and stationary-phase E. coli cultures,
because non-growing infections are the most difficult to eradicate, before establishing the generality of any
findings by using other FQs (e.g., moxifloxacin) and bacterial species (e.g., Pseudomonas aeruginosa). Data
from these experiments will assess whether chromosome number and the relative timing of DNA synthesis vs.
DNA repair during recovery from FQ treatment are phenotypic variables important for FQ persistence.
Increased understanding of persister survival tactics will open the door for the development of anti-persister
strategies, which would reduce the burden of chronic and relapsing infections.