Long-term evolution of antibiotic tolerance in Pseudomonas aeruginosa lung infections

Pathogenic bacteria respond to antibiotic pressure with the evolution of resistance but survival can also depend on their ability to tolerate antibiotic treatment, known as tolerance. While a variety of resistance mechanisms and underlying genetics are well characterized in vitro and in vivo, an understanding of the evolution of tolerance, and how it interacts with resistance in situ is lacking. We assayed for tolerance and resistance in isolates of Pseudomonas aeruginosa from chronic cystic fibrosis lung infections spanning up to 40 years of evolution, with 3 clinically relevant antibiotics: meropenem, ciprofloxacin, and tobramycin. We present evidence that tolerance is under positive selection in the lung and that it can act as an evolutionary stepping stone to resistance. However, by examining evolutionary patterns across multiple patients in different clone types, a key result is that the potential for an association between the evolution of resistance and tolerance is not inevitable, and difficult to predict. Antibiotic resistance in bacteria is a major challenge to our ability to treat infections. Understanding how bacteria become resistant is important, but experiments in the lab are not always representative of what actually happens within patients. Studying isolates collected over time from patients may allow us to infer retrospectively how pathogens evolve. We investigated characteristics of bacteria that make them difficult to treat in a unique collection of bacterial isolates spanning 40 years, from Danish individuals with the genetic disease cystic fibrosis. Cystic fibrosis causes the build-up of mucus in the lungs that make bacterial infections difficult to eradicate, despite intensive treatment with antibiotics. We show that the bacteria can evolve "tolerance" to antibiotics even when they are still genetically susceptible by switching their behavior temporarily to a dormant state. Our results suggest that this can allow the bacteria to subsequently evolve genetic resistance, where they are capable of actively growing despite the presence of drugs. In summary, the picture from "real life infections" is more complex than a straightforward expectation of antibiotic treatment leads to selection for resistance, leads to the persistence of infection. Once again, nature proves to be more complex and unpredictable than controlled lab experiments would lead us to expect. But despite the challenges, more studies like this are needed to understand the strategies bacterial cells adopt, and why some infections are hard to treat.