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Bacterial persisters in long-term infection: Emergence and fitness in a complex host environment
Jennifer A Bartell1, David R Cameron2,3, Biljana Mojsoska4
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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, we have determined the prevalence of persisters in a large patient cohort using 460 longitudinal isolates of P. aeruginosa from 39 CF patients. Isolates were classed as high persister variants (Hip) if they regrew following antibiotic treatment in at least 75% of the experimental replicates. Strain genomic data, isolate phenotyping, and patient treatment records were integrated in a lineage-based analysis of persister formation and clinical impact. In total, 19% of the isolates were classified as Hip and Hip emergence increased over lineage colonization time within 22 Hip+ patients. Most Hip+ lineages produced multiple Hip isolates, but few Hip+ lineages were dominated by Hip. While we observed no strong signal of adaptive genetic convergence within Hip isolates, they generally emerged in parallel or following the development of ciprofloxacin resistance and slowed growth. Transient lineages were majority Hip-, while strains that persisted over a clinically diagnosed 'eradication' period were majority Hip+. Patients received indistinguishable treatment regimens before Hip emergence, but Hip+ patients overall were treated significantly more than Hip- patients, signaling repeated treatment failure. When subjected to in vivo-similar antibiotic dosing, a Hip isolate survived better than a non-Hip in a structured biofilm environment. In sum, the Hip phenotype appears to substantially contribute to long-term establishment of a lineage in the CF lung environment. Our results 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 and treatment failure in CF airways.
Insights
High persister variants (Hip) of Pseudomonas aeruginosa are common in cystic fibrosis lungs and contribute to treatment failure. Many pathways, not just genetic resistance, enable bacterial persistence and survival in patients.
Area of Science:
- Microbiology and Infectious Diseases
- Cystic Fibrosis Research
- Bacterial Persistence Mechanisms
Background:
- Pseudomonas aeruginosa is a persistent pathogen in cystic fibrosis (CF) airways, often evading antibiotic treatment.
- Bacterial persister cells, tolerant to antibiotics without genetic resistance, are implicated in treatment failure.
- Understanding the prevalence and impact of persister variants in CF is crucial for developing effective therapies.
Purpose of the Study:
- To determine the prevalence of high persister (Hip) variants of P. aeruginosa in a large cohort of CF patients.
- To investigate the emergence, genetic characteristics, and clinical impact of Hip variants during chronic lung infection.
- To explore the role of the Hip phenotype in P. aeruginosa survival and treatment failure in the CF lung environment.
Main Methods:
- High-throughput screening assays to identify Hip variants based on regrowth after high-concentration ciprofloxacin treatment.
- Analysis of 460 longitudinal P. aeruginosa isolates from 39 CF patients, integrating genomic data, phenotypic data, and clinical records.
- Lineage-based analysis to track Hip emergence and its correlation with colonization time, antibiotic resistance, and patient treatment history.
Main Results:
- 19% of P. aeruginosa isolates were classified as Hip variants.
- Hip emergence increased with colonization time in Hip-positive (Hip+) patients; Hip+ patients received significantly more antibiotic treatment, indicating treatment failure.
- Hip variants demonstrated enhanced survival in structured biofilms under antibiotic pressure and were more prevalent in strains persisting through eradication attempts.
Conclusions:
- The Hip phenotype significantly contributes to the long-term establishment and persistence of P. aeruginosa lineages in CF airways.
- Bacterial antibiotic persistence in CF is multifactorial, involving diverse phenotypic and genetic routes rather than a single dominant mechanism.
- Targeting persister formation pathways may be essential for improving treatment outcomes in cystic fibrosis patients with P. aeruginosa infections.
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