The antimicrobial resistance (AMR) crisis threatens to endanger modern medicine within the next 20-30 years. A key part of the problem is the emergence of AMR within patients themselves, during courses of antibiotic therapy. Whilst within-patient AMR emergence is increasingly receiving attention in the literature, investigations commonly involve a small number of patients and study single-patient cases which may poorly represent the more general patient population. Here we report finding on the evolution of ciprofloxacin resistance by Pseudomonas aeruginosa across a large-scale clinical trial. This trial utilised inhaled liposomal ciprofloxacin as therapy for patients with the lung condition bronchiectasis, who suffered with P. aeruginosa infection. We isolated a total of ~25,000 independent bacterial colonies, prior to treatment and during the year-long the trial, measured the ciprofloxacin MIC and growth rates in KB broth for all isolates, and performed whole genome sequencing of ~4069 isolates. Across the trial, ciprofloxacin MICs increased during periods of treatment and decreased during treatment withdrawal, in a pattern suggestive of resistance fitness trade-offs operating within patients. We also find that distinct phenotypic adaptive trajectories are followed in different patient cases, indicating diverse evolutionary dynamics driving resistance emergence. We also characterise the genetic mechanisms driving the within-patient evolution of resistance and highlight that this occurs through at least 3 distinct mechanisms for P. aeruginosa. These findings allow us to start characterising the mechanisms through with AMR can emerge within-patients during treatment, and to ask questions on how best we could predict resistance emergence in the future.

Manchester