Poster: 51Evolution of Staphylococcus aureus during chronic infection in people with cystic fibrosis

Abstract

Background

Cystic fibrosis (CF) affects over 105,000 individuals and is characterized by chronic pulmonary infections driving morbidity and mortality [1]. Staphylococcus aureus is the most frequently isolated respiratory pathogen in CF patients [2]. Early colonization is associated with chronic infection, airway inflammation and lung function decline [3]. However, mechanisms of long-term S. aureus persistence and adaptation remain poorly understood. Prior studies show genetic and phenotypic adaptation during chronic infection, including antibiotic resistance and small colony variants [4], but comprehensive genomic analyses remain limited. Whole-genome sequencing enables investigation of persistence, transmission, and adaptive evolution.

Cystic fibrosis (CF) affects over 105,000 individuals and is characterized by chronic pulmonary infections driving morbidity and mortality [1]. Staphylococcus aureus is the most frequently isolated respiratory pathogen in CF patients [2]. Early colonization is associated with chronic infection, airway inflammation and lung function decline [3]. However, mechanisms of long-term S. aureus persistence and adaptation remain poorly understood. Prior studies show genetic and phenotypic adaptation during chronic infection, including antibiotic resistance and small colony variants [4], but comprehensive genomic analyses remain limited. Whole-genome sequencing enables investigation of persistence, transmission, and adaptive evolution.

Methods

We analyzed 105 S. aureus genomes from 42 people with CF (2009–2011). Phylogenomics defined clonal relationships, persistence, and transmission. Within-host evolution was assessed using core genome alignments and ancestral reconstruction to identify single nucleotide polymorphisms (SNPs).

We analyzed 105 S. aureus genomes from 42 people with CF (2009–2011). Phylogenomics defined clonal relationships, persistence, and transmission. Within-host evolution was assessed using core genome alignments and ancestral reconstruction to identify single nucleotide polymorphisms (SNPs).

Results

In several individuals, a single clonal lineage persisted over extended periods, while others were infected by multiple strains. We identified 23 strain-sharing events suggesting potential transmission. Clonal complex 5 (CC5) predominated, contrasting with CC8 dominance in non-CF populations. A high burden of antibiotic resistance was observed, including widespread β-lactam resistance and frequent fluoroquinolone resistance; 34% of isolates carried dual gyrA/grlA mutations associated with high-level resistance, and 33% were methicillin-resistant. Longitudinal analyses showed within-host evolution consistent with substitution rates (∼10^-6 substitutions/site/year). Adaptive mutations were identified in genes involved in metabolism, stress response, protein secretion, and antibiotic resistance. Mutations linked to rifampin (rpoB) and tigecycline (rpsJ) resistance and small colony variant phenotypes were observed. Convergent and parallel evolution further supported adaptation to the CF airway environment.

In several individuals, a single clonal lineage persisted over extended periods, while others were infected by multiple strains. We identified 23 strain-sharing events suggesting potential transmission. Clonal complex 5 (CC5) predominated, contrasting with CC8 dominance in non-CF populations. A high burden of antibiotic resistance was observed, including widespread β-lactam resistance and frequent fluoroquinolone resistance; 34% of isolates carried dual gyrA/grlA mutations associated with high-level resistance, and 33% were methicillin-resistant. Longitudinal analyses showed within-host evolution consistent with substitution rates (∼10^-6 substitutions/site/year). Adaptive mutations were identified in genes involved in metabolism, stress response, protein secretion, and antibiotic resistance. Mutations linked to rifampin (rpoB) and tigecycline (rpsJ) resistance and small colony variant phenotypes were observed. Convergent and parallel evolution further supported adaptation to the CF airway environment.

Conclusions

This study provides a high-resolution genomic characterization of S. aureus population structure, persistence, and adaptation in CF airways. Findings demonstrate frequent chronic infection by single strains, interpatient transmission, and ongoing within-host evolution driven by antibiotic and host selective pressures. The dominance of CC5 and high antimicrobial resistance burden highlight therapeutic challenges. These results underscore the importance of longitudinal genomic surveillance to inform infection control and optimize treatment strategies for S. aureus in CF.

This study provides a high-resolution genomic characterization of S. aureus population structure, persistence, and adaptation in CF airways. Findings demonstrate frequent chronic infection by single strains, interpatient transmission, and ongoing within-host evolution driven by antibiotic and host selective pressures. The dominance of CC5 and high antimicrobial resistance burden highlight therapeutic challenges. These results underscore the importance of longitudinal genomic surveillance to inform infection control and optimize treatment strategies for S. aureus in CF.