Bacterial persisters in long-term infection: emergence and fitness in a complex host environment

Abstract

Despite intensive antibiotic treatment, Pseudomonas aeruginosa often persists in the airways of cystic fibrosis (CF) patients for decades, and can do so without antibiotic resistance development. Using high-throughput screening assays of bacterial survival after treatment with high concentrations of ciprofloxacin and tobramycin, we have determined the prevalence of persisters in a large patient cohort consisting of 460 longitudinal isolates of P. aeruginosa from 39 CF patients. Thirty patients exhibited high persister variants (Hip, defined by survival of at least 75% of replicates) in at least one of the two antibiotic screens (25% of isolates in total). Few bacterial lineages were dominated by Hip, but Hip emergence increased over lineage colonization time. Furthermore, transient lineages were significantly less likely to exhibit Hips than non-transient lineages, suggesting that the Hip phenotype is decisive for long-term establishment of a lineage. While we observed no strong signal of adaptive genetic convergence across all lineages with Hip emergence, Hip+ lineages were significantly correlated with lineages with slow growing isolates. Finally, we evaluated Hips in a model CF structured environment by testing the fitness properties of otherwise genotypically and phenotypically similar low-persister (Lop) and Hip isolates in co-culture using a flow-cell biofilm system with antibiotic dosing modelled on in vivo dynamics. Hip survived ciprofloxacin treatment better than Lop. Our results strongly argue against the existence of a single dominant molecular mechanism underlying bacterial antibiotic persistence. We instead show that many routes, both phenotypic and genetic, are available for persister formation and consequent increases in strain fitness in CF airways. BIOLOGICAL SCIENCES Microbiology