Intermittent treatment of Escherichia coli biofilms leads to antibiotic resistance in vitro and in a pre-clinical in vivo model of catheter-related infection

Antibiotic lock therapy (ALT) to protect catheters from infection remains a topic of debate due to its variable efficacy and the unassessed risks of promoting antibiotic resistance. Using in vitro approaches and an in vivo and clinically relevant rat model of pediatric venous access ports commonly used in clinical settings, we demonstrated that a continuous 10-day therapy eradicates Escherichia coli biofilms in vitro without emergence of antibiotic resistance. In contrast, a 8-hour intermittent therapy that is used in infected parenteral nutrition patients rapidly selected amikacin-resistant mutants (MICs of 24–32 µg/mL in vitro and 24–96 µg/mL in vivo, compared to 16 µg/mL in the ancestor strains) via fusA, sbmA, and cpxA mutations. We showed that compensatory fusA adaptation maintained resistance fitness within biofilms in our rat model of catheter biofilm infections. Our findings therefore indicate that intermittent dosing generates pulsed selective pressure, favoring the development of resistance mutants within spatially structured biofilm communities. This suggests that biofilms may act as evolutionary incubators, in which medical interventions could unintentionally influence adaptation outcomes. Furthermore, the low-level resistance developing in treated biofilms may be overlooked in clinical settings and contribute to the selection of high-level resistant mutants. Our study, therefore, underscore that, in addition to dosing, optimizing the timing of antimicrobial treatment could mitigate the emergence of resistance. These principles are applicable beyond catheters to any biofilm-related infections where short-term antibiotic exposure may impact microbial community adaptation.