In some cases, antibiotic therapy is not sufficient to clear bacterial infections. The reason for this is often a reduced sensitivity of the pathogens to the administered antibiotic. This sensitivity is largely determined by genetically encoded antibiotic resistance. In addition, bacterial populations also harbor a small fraction of phenotypic variants that are temporarily insensitive to the lethal effects of antibiotics. These so-called persister cells are formed by phenotypic transition from an antibiotic-sensitive 'normal' cell to an antibiotic-tolerant dormant state. On the other hand, persister cells can also return to the 'normal' state and resume growth, giving rise to the formation of a new population. Persistors represent an important but poorly understood clinical problem. For example, they play an underappreciated role in the failure of antimicrobial therapy in chronic infections. In addition, persisters contribute to the development of antibiotic resistance.
Little is known about how persistence evolves when bacteria are confronted with continuous or repeated antibiotic pressure. In silico predictions and previous in vitro work have shown that persister levels increase with frequent antibiotic exposure and that the period in the tolerant state is determined by the duration of treatment. We hypothesize that a similar evolutionary strategy occurs in vivo and that this contributes to the chronic nature of many infections. To support this hypothesis, we propose to collect longitudinal isolates from patients with recurrent or chronic UTIs. Since these patients visit the hospital at irregular and unpredictable time intervals, we will also collect isolates from patients with a suprapubic catheter. These patients do not necessarily suffer from chronic infections, but suprapubic catheters are usually colonized by microbial biofilms. We will also collect isolates from patients with a nephrostomy catheter. Similar to patients with suprapubic catheters, these patients visit the hospital regularly (± 6 weeks interval) for routine catheter changes and during these consultations, urine samples and catheter tips are easily collected. Furthermore, many of these patients are exposed to multiple antibiotic regimens (including, in the case of nephrostomy patients, high-dose cefazolin or ceftriaxone at the time of catheter change), creating a unique opportunity to study the evolution of antibiotic tolerance in a clinical setting.
